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Martins BR, Radl V, Treder K, Michałowska D, Pritsch K, Schloter M. The rhizosphere microbiome of 51 potato cultivars with diverse plant growth characteristics. FEMS Microbiol Ecol 2024:fiae088. [PMID: 38839598 DOI: 10.1093/femsec/fiae088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2024] Open
Abstract
Rhizosphere microbial communities play a substantial role in plant productivity. We studied the rhizosphere bacteria and fungi of 51 distinct potato cultivars grown under similar greenhouse conditions using a metabarcoding approach. As expected, individual cultivars were the most important determining factor of the rhizosphere microbial composition; however, differences were also obtained when grouping cultivars according to their growth characteristics. We demonstrated that plant growth characteristics were strongly related to deterministic and stochastic assembly processes of bacterial and fungal communities, respectively. The bacterial genera Arthrobacter and Massilia (known to produce IAA and siderophores) exhibited greater relative abundance in high- and medium performing cultivars. Bacterial co-occurrence networks were larger in the rhizosphere of these cultivars and were characterized by a distinctive combination of plant beneficial Proteobacteria and Actinobacteria along with a module of diazotrophs namely Azospira, Azoarcus, Azohydromonas. Conversely, the network within low performing cultivars revealed the lowest nodes, hub taxa, edges density, robustness and the highest average path length resulting in reduced microbial associations, which may potentially limit their effectiveness in promoting plant growth. Our findings established a clear pattern between plant productivity and the rhizosphere microbiome composition and structure for the investigated potato cultivars, offering insights for future management practices.
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Hauschild K, Orth N, Liu B, Giongo A, Gschwendtner S, Beerhues L, Schloter M, Vetterlein D, Winkelmann T, Smalla K. Rhizosphere competent inoculants modulate the apple root-associated microbiome and plant phytoalexins. Appl Microbiol Biotechnol 2024; 108:344. [PMID: 38801472 PMCID: PMC11129989 DOI: 10.1007/s00253-024-13181-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 05/03/2024] [Accepted: 05/10/2024] [Indexed: 05/29/2024]
Abstract
Modulating the soil microbiome by applying microbial inoculants has gained increasing attention as eco-friendly option to improve soil disease suppressiveness. Currently, studies unraveling the interplay of inoculants, root-associated microbiome, and plant response are lacking for apple trees. Here, we provide insights into the ability of Bacillus velezensis FZB42 or Pseudomonas sp. RU47 to colonize apple root-associated microhabitats and to modulate their microbiome. We applied the two strains to apple plants grown in soils from the same site either affected by apple replant disease (ARD) or not (grass), screened their establishment by selective plating, and measured phytoalexins in roots 3, 16, and 28 days post inoculation (dpi). Sequencing of 16S rRNA gene and ITS fragments amplified from DNA extracted 28 dpi from different microhabitat samples revealed significant inoculation effects on fungal β-diversity in root-affected soil and rhizoplane. Interestingly, only in ARD soil, most abundant bacterial amplicon sequence variants (ASVs) changed significantly in relative abundance. Relative abundances of ASVs affiliated with Enterobacteriaceae were higher in rhizoplane of apple grown in ARD soil and reduced by both inoculants. Bacterial communities in the root endosphere were not affected by the inoculants but their presence was indicated. Interestingly and previously unobserved, apple plants responded to the inoculants with increased phytoalexin content in roots, more pronounced in grass than ARD soil. Altogether, our results indicate that FZB42 and RU47 were rhizosphere competent, modulated the root-associated microbiome, and were perceived by the apple plants, which could make them interesting candidates for an eco-friendly mitigation strategy of ARD. KEY POINTS: • Rhizosphere competent inoculants modulated the microbiome (mainly fungi) • Inoculants reduced relative abundance of Enterobacteriaceae in the ARD rhizoplane • Inoculants increased phytoalexin content in roots, stronger in grass than ARD soil.
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Musiol S, Harris CP, Gschwendtner S, Burrell A, Amar Y, Schnautz B, Renisch D, Braun SC, Haak S, Schloter M, Schmidt-Weber CB, Zielinski CE, Alessandrini F. The impact of high-salt diet on asthma in humans and mice: Effect on specific T-cell signatures and microbiome. Allergy 2024. [PMID: 38798015 DOI: 10.1111/all.16148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 03/25/2024] [Accepted: 04/14/2024] [Indexed: 05/29/2024]
Abstract
BACKGROUND The rise in asthma has been linked to different environmental and lifestyle factors including dietary habits. Whether dietary salt contributes to asthma incidence, remains controversial. We aimed to investigate the impact of higher salt intake on asthma incidence in humans and to evaluate underlying mechanisms using mouse models. METHODS Epidemiological research was conducted using the UK Biobank Resource. Data were obtained from 42,976 participants with a history of allergies. 24-h sodium excretion was estimated from spot urine, and its association with asthma incidence was assessed by Cox regression, adjusting for relevant covariates. For mechanistic studies, a mouse model of mite-induced allergic airway inflammation (AAI) fed with high-salt diet (HSD) or normal-salt chow was used to characterize disease development. The microbiome of lung and feces (as proxy for gut) was analyzed via 16S rRNA gene based metabarcoding approach. RESULTS In humans, urinary sodium excretion was directly associated with asthma incidence among females but not among males. HSD-fed female mice displayed an aggravated AAI characterized by increased levels of total IgE, a TH2-TH17-biased inflammatory cell infiltration accompanied by upregulation of osmosensitive stress genes. HSD induced distinct changes in serum short chain fatty acids and in both gut and lung microbiome, with a lower Bacteroidetes to Firmicutes ratio and decreased Lactobacillus relative abundance in the gut, and enriched members of Gammaproteobacteria in the lung. CONCLUSIONS High dietary salt consumption correlates with asthma incidence in female adults with a history of allergies. Female mice revealed HSD-induced T-cell lung profiles accompanied by alterations of gut and lung microbiome.
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Benning S, Pritsch K, Radl V, Siani R, Wang Z, Schloter M. (Pan)genomic analysis of two Rhodococcus isolates and their role in phenolic compound degradation. Microbiol Spectr 2024; 12:e0378323. [PMID: 38376357 PMCID: PMC10986565 DOI: 10.1128/spectrum.03783-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 01/25/2024] [Indexed: 02/21/2024] Open
Abstract
The genus Rhodococcus is recognized for its potential to degrade a large range of aromatic substances, including plant-derived phenolic compounds. We used comparative genomics in the context of the broader Rhodococcus pan-genome to study genomic traits of two newly described Rhodococcus strains (type-strain Rhodococcus pseudokoreensis R79T and Rhodococcus koreensis R85) isolated from apple rhizosphere. Of particular interest was their ability to degrade phenolic compounds as part of an integrated approach to treat apple replant disease (ARD) syndrome. The pan-genome of the genus Rhodococcus based on 109 high-quality genomes was open with a small core (1.3%) consisting of genes assigned to basic cell functioning. The range of genome sizes in Rhodococcus was high, from 3.7 to 10.9 Mbp. Genomes from host-associated strains were generally smaller compared to environmental isolates which were characterized by exceptionally large genome sizes. Due to large genomic differences, we propose the reclassification of distinct groups of rhodococci like the Rhodococcus equi cluster to new genera. Taxonomic species affiliation was the most important factor in predicting genetic content and clustering of the genomes. Additionally, we found genes that discriminated between the strains based on habitat. All members of the genus Rhodococcus had at least one gene involved in the pathway for the degradation of benzoate, while biphenyl degradation was mainly restricted to strains in close phylogenetic relationships with our isolates. The ~40% of genes still unclassified in larger Rhodococcus genomes, particularly those of environmental isolates, need more research to explore the metabolic potential of this genus.IMPORTANCERhodococcus is a diverse, metabolically powerful genus, with high potential to adapt to different habitats due to the linear plasmids and large genome sizes. The analysis of its pan-genome allowed us to separate host-associated from environmental strains, supporting taxonomic reclassification. It was shown which genes contribute to the differentiation of the genomes based on habitat, which can possibly be used for targeted isolation and screening for desired traits. With respect to apple replant disease (ARD), our isolates showed genome traits that suggest potential for application in reducing plant-derived phenolic substances in soil, which makes them good candidates for further testing against ARD.
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Broadbent AAD, Newbold LK, Pritchard WJ, Michas A, Goodall T, Cordero I, Giunta A, Snell HSK, Pepper VVLH, Grant HK, Soto DX, Kaufmann R, Schloter M, Griffiths RI, Bahn M, Bardgett RD. Climate change disrupts the seasonal coupling of plant and soil microbial nutrient cycling in an alpine ecosystem. GLOBAL CHANGE BIOLOGY 2024; 30:e17245. [PMID: 38511487 DOI: 10.1111/gcb.17245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 03/04/2024] [Indexed: 03/22/2024]
Abstract
The seasonal coupling of plant and soil microbial nutrient demands is crucial for efficient ecosystem nutrient cycling and plant production, especially in strongly seasonal alpine ecosystems. Yet, how these seasonal nutrient cycling processes are modified by climate change and what the consequences are for nutrient loss and retention in alpine ecosystems remain unclear. Here, we explored how two pervasive climate change factors, reduced snow cover and shrub expansion, interactively modify the seasonal coupling of plant and soil microbial nitrogen (N) cycling in alpine grasslands, which are warming at double the rate of the global average. We found that the combination of reduced snow cover and shrub expansion disrupted the seasonal coupling of plant and soil N-cycling, with pronounced effects in spring (shortly after snow melt) and autumn (at the onset of plant senescence). In combination, both climate change factors decreased plant organic N-uptake by 70% and 82%, soil microbial biomass N by 19% and 38% and increased soil denitrifier abundances by 253% and 136% in spring and autumn, respectively. Shrub expansion also individually modified the seasonality of soil microbial community composition and stoichiometry towards more N-limited conditions and slower nutrient cycling in spring and autumn. In winter, snow removal markedly reduced the fungal:bacterial biomass ratio, soil N pools and shifted bacterial community composition. Taken together, our findings suggest that interactions between climate change factors can disrupt the temporal coupling of plant and soil microbial N-cycling processes in alpine grasslands. This could diminish the capacity of these globally widespread alpine ecosystems to retain N and support plant productivity under future climate change.
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Neyret M, Le Provost G, Boesing AL, Schneider FD, Baulechner D, Bergmann J, de Vries FT, Fiore-Donno AM, Geisen S, Goldmann K, Merges A, Saifutdinov RA, Simons NK, Tobias JA, Zaitsev AS, Gossner MM, Jung K, Kandeler E, Krauss J, Penone C, Schloter M, Schulz S, Staab M, Wolters V, Apostolakis A, Birkhofer K, Boch S, Boeddinghaus RS, Bolliger R, Bonkowski M, Buscot F, Dumack K, Fischer M, Gan HY, Heinze J, Hölzel N, John K, Klaus VH, Kleinebecker T, Marhan S, Müller J, Renner SC, Rillig MC, Schenk NV, Schöning I, Schrumpf M, Seibold S, Socher SA, Solly EF, Teuscher M, van Kleunen M, Wubet T, Manning P. A slow-fast trait continuum at the whole community level in relation to land-use intensification. Nat Commun 2024; 15:1251. [PMID: 38341437 PMCID: PMC10858939 DOI: 10.1038/s41467-024-45113-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 01/16/2024] [Indexed: 02/12/2024] Open
Abstract
Organismal functional strategies form a continuum from slow- to fast-growing organisms, in response to common drivers such as resource availability and disturbance. However, whether there is synchronisation of these strategies at the entire community level is unclear. Here, we combine trait data for >2800 above- and belowground taxa from 14 trophic guilds spanning a disturbance and resource availability gradient in German grasslands. The results indicate that most guilds consistently respond to these drivers through both direct and trophically mediated effects, resulting in a 'slow-fast' axis at the level of the entire community. Using 15 indicators of carbon and nutrient fluxes, biomass production and decomposition, we also show that fast trait communities are associated with faster rates of ecosystem functioning. These findings demonstrate that 'slow' and 'fast' strategies can be manifested at the level of whole communities, opening new avenues of ecosystem-level functional classification.
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de Souza YPA, Schloter M, Weisser W, Huang Y, Schulz S. The seeds of Plantago lanceolata comprise a stable core microbiome along a plant richness gradient. ENVIRONMENTAL MICROBIOME 2024; 19:11. [PMID: 38308354 PMCID: PMC10835927 DOI: 10.1186/s40793-024-00552-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 01/19/2024] [Indexed: 02/04/2024]
Abstract
BACKGROUND Seed endophytic bacteria are beneficial to plants. They improve seedling growth by enhancing plant nutrient uptake, modulating stress-related phytohormone production, and targeting pests and pathogens with antibiotics. Seed endophyte composition can be influenced by pollination, plant cultivar, and soil physicochemical conditions. However, the effects of plant community richness on seed endophytes are unknown. To investigate the effects of increasing plant species richness on the diversity and composition of the seed microbiome, we made use of a well-established long-term biodiversity experiment in Germany (The Jena Experiment). We sampled seeds from different Plantago lanceolata blossoms in a plant diversity gradient ranging from monoculture to 16 species mixtures. The seeds were surface sterilized to remove seed surface-associated bacteria and subjected to a metabarcoding approach to assess bacterial community structure. RESULTS Our data indicate a very stable core microbiome, which accounted for more than 90% of the reads and was present in all seeds independent of the plant richness level the seeds originated from. It consisted mainly of reads linked to Pseudomonas rhizosphaerae, Sphingomonas faeni and Pirellulla spp. 9% of the obtained reads were not part of the core microbiome and were only present in plots of specific diversity levels. The number of unique ASVs was positively correlated with plant richness. Interestingly, most reads described as non-core members belonged to the same genera described as the core microbiome, indicating the presence of different strains or species with possibly different functional properties important for seed performance. CONCLUSION Our data indicate that Plantago lanceolata maintains a large seeds core microbiome across the plant richness gradient. However, the number of unique ASVs increases alongside the plant community richness, indicating that ecosystem biodiversity also mitigates diversity loss in seed endophytes.
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Ishola OA, Kublik S, Durai Raj AC, Ohnmacht C, Schulz S, Foesel BU, Schloter M. Comparative Metagenomic Analysis of Bacteriophages and Prophages in Gnotobiotic Mouse Models. Microorganisms 2024; 12:255. [PMID: 38399658 PMCID: PMC10892684 DOI: 10.3390/microorganisms12020255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/19/2024] [Accepted: 01/23/2024] [Indexed: 02/25/2024] Open
Abstract
Gnotobiotic murine models are important to understand microbiota-host interactions. Despite the role of bacteriophages as drivers for microbiome structure and function, there is no information about the structure and function of the gut virome in gnotobiotic models and the link between bacterial and bacteriophage/prophage diversity. We studied the virome of gnotobiotic murine Oligo-MM12 (12 bacterial species) and reduced Altered Schaedler Flora (ASF, three bacterial species). As reference, the virome of Specific Pathogen-Free (SPF) mice was investigated. A metagenomic approach was used to assess prophages and bacteriophages in the guts of 6-week-old female mice. We identified a positive correlation between bacteria diversity, and bacteriophages and prophages. Caudoviricetes (82.4%) were the most prominent class of phages in all samples with differing relative abundance. However, the host specificity of bacteriophages belonging to class Caudoviricetes differed depending on model bacterial diversity. We further studied the role of bacteriophages in horizontal gene transfer and microbial adaptation to the host's environment. Analysis of mobile genetic elements showed the contribution of bacteriophages to the adaptation of bacterial amino acid metabolism. Overall, our results implicate virome "dark matter" and interactions with the host system as factors for microbial community structure and function which determine host health. Taking the importance of the virome in the microbiome diversity and horizontal gene transfer, reductions in the virome might be an important factor driving losses of microbial biodiversity and the subsequent dysbiosis of the gut microbiome.
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Behr JH, Kuhl-Nagel T, Sommermann L, Moradtalab N, Chowdhury SP, Schloter M, Windisch S, Schellenberg I, Maccario L, Sørensen SJ, Rothballer M, Geistlinger J, Smalla K, Ludewig U, Neumann G, Grosch R, Babin D. Long-term conservation tillage with reduced nitrogen fertilization intensity can improve winter wheat health via positive plant-microorganism feedback in the rhizosphere. FEMS Microbiol Ecol 2024; 100:fiae003. [PMID: 38224956 PMCID: PMC10847717 DOI: 10.1093/femsec/fiae003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/21/2023] [Accepted: 01/12/2024] [Indexed: 01/17/2024] Open
Abstract
Microbiome-based solutions are regarded key for sustainable agroecosystems. However, it is unclear how agricultural practices affect the rhizosphere microbiome, plant-microorganism interactions and crop performance under field conditions. Therefore, we installed root observation windows in a winter wheat field cultivated either under long-term mouldboard plough (MP) or cultivator tillage (CT). Each tillage practice was also compared at two nitrogen (N) fertilization intensities, intensive (recommended N-supply with pesticides/growth regulators) or extensive (reduced N-supply, no fungicides/growth regulators). Shoot biomass, root exudates and rhizosphere metabolites, physiological stress indicators, and gene expression were analyzed together with the rhizosphere microbiome (bacterial/archaeal 16S rRNA gene, fungal ITS amplicon, and shotgun metagenome sequencing) shortly before flowering. Compared to MP, the rhizosphere of CT winter wheat contained more primary and secondary metabolites, especially benzoxazinoid derivatives. Potential copiotrophic and plant-beneficial taxa (e.g. Bacillus, Devosia, and Trichoderma) as well as functional genes (e.g. siderophore production, trehalose synthase, and ACC deaminase) were enriched in the CT rhizosphere, suggesting that tillage affected belowground plant-microorganism interactions. In addition, physiological stress markers were suppressed in CT winter wheat compared to MP. In summary, tillage practice was a major driver of crop performance, root deposits, and rhizosphere microbiome interactions, while the N-fertilization intensity was also relevant, but less important.
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Heinen R, Sanchez-Mahecha O, Martijn Bezemer T, Dominoni DM, Knappe C, Kollmann J, Kopatsch A, Pfeiffer ZA, Schloter M, Sturm S, Schnitzler JP, Corina Vlot A, Weisser WW. Part-night exposure to artificial light at night has more detrimental effects on aphid colonies than fully lit nights. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220357. [PMID: 37899021 PMCID: PMC10613545 DOI: 10.1098/rstb.2022.0357] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 02/23/2023] [Indexed: 10/31/2023] Open
Abstract
Artificial light at night (ALAN) threatens natural ecosystems globally. While ALAN research is increasing, little is known about how ALAN affects plants and interactions with other organisms. We explored the effects of ALAN on plant defence and plant-insect interactions using barley (Hordeum vulgare) and the English grain aphid (Sitobion avenae). Plants were exposed to 'full' or 'part' nights of 15-20 lux ALAN, or no ALAN 'control' nights, to test the effects of ALAN on plant growth and defence. Although plant growth was only minimally affected by ALAN, aphid colony growth and aphid maturation were reduced significantly by ALAN treatments. Importantly, we found strong differences between full-night and part-night ALAN treatments. Contrary to our expectations, part ALAN had stronger negative effects on aphid colony growth than full ALAN. Defence-associated gene expression was affected in some cases by ALAN, but also positively correlated with aphid colony size, suggesting that the effects of ALAN on plant defences are indirect, and regulated via direct disruption of aphid colonies rather than via ALAN-induced upregulation of defences. Mitigating ecological side effects of ALAN is a complex problem, as reducing exposure to ALAN increased its negative impact on insect herbivores. This article is part of the theme issue 'Light pollution in complex ecological systems'.
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Bender SF, Schulz S, Martínez-Cuesta R, Laughlin RJ, Kublik S, Pfeiffer-Zakharova K, Vestergaard G, Hartman K, Parladé E, Römbke J, Watson CJ, Schloter M, van der Heijden MGA. Simplification of soil biota communities impairs nutrient recycling and enhances above- and belowground nitrogen losses. THE NEW PHYTOLOGIST 2023; 240:2020-2034. [PMID: 37700504 DOI: 10.1111/nph.19252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 08/18/2023] [Indexed: 09/14/2023]
Abstract
Agriculture is a major source of nutrient pollution, posing a threat to the earth system functioning. Factors determining the nutrient use efficiency of plant-soil systems need to be identified to develop strategies to reduce nutrient losses while ensuring crop productivity. The potential of soil biota to tighten nutrient cycles by improving plant nutrition and reducing soil nutrient losses is still poorly understood. We manipulated soil biota communities in outdoor lysimeters, planted maize, continuously collected leachates, and measured N2 O- and N2 -gas emissions after a fertilization pulse to test whether differences in soil biota communities affected nutrient recycling and N losses. Lysimeters with strongly simplified soil biota communities showed reduced crop N (-20%) and P (-58%) uptake, strongly increased N leaching losses (+65%), and gaseous emissions (+97%) of N2 O and N2 . Soil metagenomic analyses revealed differences in the abundance of genes responsible for nutrient uptake, nitrate reduction, and denitrification that helped explain the observed nutrient losses. Soil biota are major drivers of nutrient cycling and reductions in the diversity or abundance of certain groups (e.g. through land-use intensification) can disrupt nutrient cycling, reduce agricultural productivity and nutrient use efficiency, and exacerbate environmental pollution and global warming.
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Shintani M, Vestergaard G, Milaković M, Kublik S, Smalla K, Schloter M, Udiković-Kolić N. Integrons, transposons and IS elements promote diversification of multidrug resistance plasmids and adaptation of their hosts to antibiotic pollutants from pharmaceutical companies. Environ Microbiol 2023; 25:3035-3051. [PMID: 37655671 DOI: 10.1111/1462-2920.16481] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 08/01/2023] [Indexed: 09/02/2023]
Abstract
Plasmids are important vehicles for the dissemination of antibiotic resistance genes (ARGs) among bacteria by conjugation. Here, we determined the complete nucleotide sequences of nine different plasmids previously obtained by exogenous plasmid isolation from river and creek sediments and wastewater from a pharmaceutical company. We identified six IncP/P-1ε plasmids and single members of IncL, IncN and IncFII-like plasmids. Genetic structures of the accessory regions of the IncP/P-1ε plasmids obtained implied that multiple insertions and deletions had occurred, mediated by different transposons and Class 1 integrons with various ARGs. Our study provides compelling evidence that Class 1 integrons, Tn402-like transposons, Tn3-like transposons and/or IS26 played important roles in the acquisition of ARGs across all investigated plasmids. Our plasmid sequencing data provide new insights into how these mobile genetic elements could mediate the acquisition and spread of ARGs in environmental bacteria.
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Martins BR, Siani R, Treder K, Michałowska D, Radl V, Pritsch K, Schloter M. Cultivar-specific dynamics: unravelling rhizosphere microbiome responses to water deficit stress in potato cultivars. BMC Microbiol 2023; 23:377. [PMID: 38036970 PMCID: PMC10691024 DOI: 10.1186/s12866-023-03120-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 11/10/2023] [Indexed: 12/02/2023] Open
Abstract
BACKGROUND Growing evidence suggests that soil microbes can improve plant fitness under drought. However, in potato, the world's most important non-cereal crop, the role of the rhizosphere microbiome under drought has been poorly studied. Using a cultivation independent metabarcoding approach, we examined the rhizosphere microbiome of two potato cultivars with different drought tolerance as a function of water regime (continuous versus reduced watering) and manipulation of soil microbial diversity (i.e., natural (NSM), vs. disturbed (DSM) soil microbiome). RESULTS Water regime and soil pre-treatment showed a significant interaction with bacterial community composition of the sensitive (HERBST) but not the resistant cultivar (MONI). Overall, MONI had a moderate response to the treatments and its rhizosphere selected Rhizobiales under reduced watering in NSM soil, whereas Bradyrhizobium, Ammoniphilus, Symbiobacterium and unclassified Hydrogenedensaceae in DSM soil. In contrast, HERBST response to the treatments was more pronounced. Notably, in NSM soil treated with reduced watering, the root endophytic fungus Falciphora and many Actinobacteriota members (Streptomyces, Glycomyces, Marmoricola, Aeromicrobium, Mycobacterium and others) were largely represented. However, DSM soil treatment resulted in no fungal taxa and fewer enrichment of these Actinobacteriota under reduced watering. Moreover, the number of bacterial core amplicon sequence variants (core ASVs) was more consistent in MONI regardless of soil pre-treatment and water regimes as opposed to HERBST, in which a marked reduction of core ASVs was observed in DSM soil. CONCLUSIONS Besides the influence of soil conditions, our results indicate a strong cultivar-dependent relationship between the rhizosphere microbiome of potato cultivars and their capacity to respond to perturbations such as reduced soil moisture. Our study highlights the importance of integrating soil conditions and plant genetic variability as key factors in future breeding programs aiming to develop drought resistance in a major food crop like potato. Elucidating the molecular mechanisms how plants recruit microbes from soil which help to mitigate plant stress and to identify key microbial taxa, which harbour the respective traits might therefore be an important topic for future research.
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Kallies R, Hu D, Abdulkadir N, Schloter M, Rocha U. Identification of Huge Phages from Wastewater Metagenomes. Viruses 2023; 15:2330. [PMID: 38140571 PMCID: PMC10747093 DOI: 10.3390/v15122330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 11/20/2023] [Accepted: 11/22/2023] [Indexed: 12/24/2023] Open
Abstract
Huge phages have genomes larger than 200 kilobases, which are particularly interesting for their genetic inventory and evolution. We screened 165 wastewater metagenomes for the presence of viral sequences. After identifying over 600 potential huge phage genomes, we reduced the dataset using manual curation by excluding viral contigs that did not contain viral protein-coding genes or consisted of concatemers of several small phage genomes. This dataset showed seven fully annotated huge phage genomes. The phages grouped into distinct phylogenetic clades, likely forming new genera and families. A phylogenomic analysis between our huge phages and phages with smaller genomes, i.e., less than 200 kb, supported the hypothesis that huge phages have undergone convergent evolution. The genomes contained typical phage protein-coding genes, sequential gene cassettes for metabolic pathways, and complete inventories of tRNA genes covering all standard and rare amino acids. Our study showed a pipeline for huge phage analyses that may lead to new enzymes for therapeutic or biotechnological applications.
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Pinheiro Alves de Souza Y, Schloter M, Weisser W, Schulz S. Deterministic Development of Soil Microbial Communities in Disturbed Soils Depends on Microbial Biomass of the Bioinoculum. MICROBIAL ECOLOGY 2023; 86:2882-2893. [PMID: 37624441 PMCID: PMC10640511 DOI: 10.1007/s00248-023-02285-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 08/04/2023] [Indexed: 08/26/2023]
Abstract
Despite its enormous importance for ecosystem services, factors driving microbial recolonization of soils after disturbance are still poorly understood. Here, we compared the microbial recolonization patterns of a disturbed, autoclaved soil using different amounts of the original non-disturbed soil as inoculum. By using this approach, we manipulated microbial biomass, but did not change microbial diversity of the inoculum. We followed the development of a new soil microbiome after reinoculation over a period of 4 weeks using a molecular barcoding approach as well as qPCR. Focus was given on the assessment of bacteria and archaea. We could show that 1 week after inoculation in all inoculated treatments bacterial biomass exceeded the values from the original soil as a consequence of high dissolved organic carbon (DOC) concentrations in the disturbed soil resulting from the disturbance. This high biomass was persistent over the complete experimental period. In line with the high DOC concentrations, in the first 2 weeks of incubation, copiotrophic bacteria dominated the community, which derived from the inoculum used. Only in the disturbed control soils which did not receive a microbial inoculum, recolonization pattern differed. In contrast, archaeal biomass did not recover over the experimental period and recolonization was strongly triggered by amount of inoculated original soil added. Interestingly, the variability between replicates of the same inoculation density decreased with increasing biomass in the inoculum, indicating a deterministic development of soil microbiomes if higher numbers of cells are used for reinoculation.
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Staude B, Gschwendtner S, Frodermann T, Oehmke F, Kohl T, Kublik S, Schloter M, Ehrhardt H. Microbial signatures in amniotic fluid at preterm birth and association with bronchopulmonary dysplasia. Respir Res 2023; 24:248. [PMID: 37845700 PMCID: PMC10577941 DOI: 10.1186/s12931-023-02560-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 10/09/2023] [Indexed: 10/18/2023] Open
Abstract
BACKGROUND Microbiome dysbiosis can have long-lasting effects on our health and induce the development of various diseases. Bronchopulmonary dysplasia (BPD) is a multifactorial disease with pre- and postnatal origins including intra-amniotic infection as main risk factor. Recently, postnatal pathologic lung microbiota colonization was associated with BPD. The objectives of this prospective observational cohort study were to describe differences in bacterial signatures in the amniotic fluid (AF) of intact pregnancies without clinical signs or risk of preterm delivery and AF samples obtained during preterm deliveries and their variations between different BPD disease severity stages. METHODS AF samples were collected under sterile conditions during fetal intervention from intact pregnancies (n = 17) or immediately before preterm delivery < 32 weeks (n = 126). Metabarcoding based approaches were used for the molecular assessment of bacterial 16S rRNA genes to describe bacterial community structure. RESULTS The absolute amount of 16S rRNA genes was significantly increased in AF of preterm deliveries and detailed profiling revealed a reduced alpha diversity and a significant change in beta diversity with a reduced relative abundance of 16S rRNA genes indicative for Lactobacillus and Acetobacter while Fusobacterium, Pseudomonas, Ureaplasma and Staphylococcus 16S rRNA gene prevailed. Although classification of BPD by disease severity revealed equivalent absolute 16S rRNA gene abundance and alpha and beta diversity in no, mild and moderate/severe BPD groups, for some 16S rRNA genes differences were observed in AF samples. Bacterial signatures of infants with moderate/severe BPD showed predominance of 16S rRNA genes belonging to the Escherichia-Shigella cluster while Ureaplasma and Enterococcus species were enriched in AF samples of infants with mild BPD. CONCLUSIONS Our study identified distinct and diverse intrauterine 16S rRNA gene patterns in preterm infants immediately before birth, differing from the 16S rRNA gene signature of intact pregnancies. The distinct 16S rRNA gene signatures at birth derive from bacteria with varying pathogenicity to the immature lung and are suited to identify preterm infants at risk. Our results emphasize the prenatal impact to the origins of BPD.
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Sessitsch A, Wakelin S, Schloter M, Maguin E, Cernava T, Champomier-Verges MC, Charles TC, Cotter PD, Ferrocino I, Kriaa A, Lebre P, Cowan D, Lange L, Kiran S, Markiewicz L, Meisner A, Olivares M, Sarand I, Schelkle B, Selvin J, Smidt H, van Overbeek L, Berg G, Cocolin L, Sanz Y, Fernandes WL, Liu SJ, Ryan M, Singh B, Kostic T. Microbiome Interconnectedness throughout Environments with Major Consequences for Healthy People and a Healthy Planet. Microbiol Mol Biol Rev 2023; 87:e0021222. [PMID: 37367231 PMCID: PMC10521359 DOI: 10.1128/mmbr.00212-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023] Open
Abstract
Microbiomes have highly important roles for ecosystem functioning and carry out key functions that support planetary health, including nutrient cycling, climate regulation, and water filtration. Microbiomes are also intimately associated with complex multicellular organisms such as humans, other animals, plants, and insects and perform crucial roles for the health of their hosts. Although we are starting to understand that microbiomes in different systems are interconnected, there is still a poor understanding of microbiome transfer and connectivity. In this review we show how microbiomes are connected within and transferred between different habitats and discuss the functional consequences of these connections. Microbiome transfer occurs between and within abiotic (e.g., air, soil, and water) and biotic environments, and can either be mediated through different vectors (e.g., insects or food) or direct interactions. Such transfer processes may also include the transmission of pathogens or antibiotic resistance genes. However, here, we highlight the fact that microbiome transmission can have positive effects on planetary and human health, where transmitted microorganisms potentially providing novel functions may be important for the adaptation of ecosystems.
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Amar Y, Rogner D, Silva RL, Foesel BU, Ud-Dean M, Lagkouvardos I, Steimle-Grauer SA, Niedermeier S, Kublik S, Jargosch M, Heinig M, Thomas J, Eyerich S, Wikström JD, Schloter M, Eyerich K, Biedermann T, Köberle M. Correction: Darier's disease exhibits a unique cutaneous microbial dysbiosis associated with inflammation and body malodour. MICROBIOME 2023; 11:206. [PMID: 37705089 PMCID: PMC10500857 DOI: 10.1186/s40168-023-01665-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/15/2023]
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Marques Dos Santos M, Pivniouk V, Rankl B, Walker A, Pagani G, Hertkorn N, Schmitt-Kopplin P, Müller C, Bracher F, Merl-Pham J, Hauck SM, Schloter M, Michael AN, Anderson D, Honeker L, Gozdz J, Pivniouk O, Ober C, Holbreich M, Martinez FD, Snyder SA, von Mutius E, Vercelli D. Asthma-protective agents in dust from traditional farm environments. J Allergy Clin Immunol 2023; 152:610-621. [PMID: 37271318 PMCID: PMC10680491 DOI: 10.1016/j.jaci.2023.05.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 04/05/2023] [Accepted: 05/05/2023] [Indexed: 06/06/2023]
Abstract
BACKGROUND Growing up on traditional European or US Amish dairy farms in close contact with cows and hay protects children against asthma, and airway administration of extracts from dust collected from cowsheds of those farms prevents allergic asthma in mice. OBJECTIVES This study sought to begin identifying farm-derived asthma-protective agents. METHODS Our work unfolded along 2 unbiased and independent but complementary discovery paths. Dust extracts (DEs) from protective and nonprotective farms (European and Amish cowsheds vs European sheep sheds) were analyzed by comparative nuclear magnetic resonance profiling and differential proteomics. Bioactivity-guided size fractionation focused on protective Amish cowshed DEs. Multiple in vitro and in vivo functional assays were used in both paths. Some of the proteins thus identified were characterized by in-solution and in-gel sodium dodecyl sulfate-polyacrylamide gel electrophoresis enzymatic digestion/peptide mapping followed by liquid chromatography/mass spectrometry. The cargo carried by these proteins was analyzed by untargeted liquid chromatography-high-resolution mass spectrometry. RESULTS Twelve carrier proteins of animal and plant origin, including the bovine lipocalins Bos d 2 and odorant binding protein, were enriched in DEs from protective European cowsheds. A potent asthma-protective fraction of Amish cowshed DEs (≈0.5% of the total carbon content of unfractionated extracts) contained 7 animal and plant proteins, including Bos d 2 and odorant binding protein loaded with fatty acid metabolites from plants, bacteria, and fungi. CONCLUSIONS Animals and plants from traditional farms produce proteins that transport hydrophobic microbial and plant metabolites. When delivered to mucosal surfaces, these agents might regulate airway responses.
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Amar Y, Rogner D, Silva RL, Foesel BU, Ud-Dean M, Lagkouvardos I, Steimle-Grauer SA, Niedermeier S, Kublik S, Jargosch M, Heinig M, Thomas J, Eyerich S, Wikström JD, Schloter M, Eyerich K, Biedermann T, Köberle M. Darier's disease exhibits a unique cutaneous microbial dysbiosis associated with inflammation and body malodour. MICROBIOME 2023; 11:162. [PMID: 37496039 PMCID: PMC10369845 DOI: 10.1186/s40168-023-01587-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 06/01/2023] [Indexed: 07/28/2023]
Abstract
BACKGROUND Darier's disease (DD) is a genodermatosis caused by mutations of the ATP2A2 gene leading to disrupted keratinocyte adhesion. Recurrent episodes of skin inflammation and infections with a typical malodour in DD indicate a role for microbial dysbiosis. Here, for the first time, we investigated the DD skin microbiome using a metabarcoding approach of 115 skin swabs from 14 patients and 14 healthy volunteers. Furthermore, we analyzed its changes in the context of DD malodour and the cutaneous DD transcriptome. RESULTS We identified a disease-specific cutaneous microbiome with a loss of microbial diversity and of potentially beneficial commensals. Expansion of inflammation-associated microbes such as Staphylococcus aureus and Staphylococcus warneri strongly correlated with disease severity. DD dysbiosis was further characterized by abundant species belonging to Corynebacteria, Staphylococci and Streptococci groups displaying strong associations with malodour intensity. Transcriptome analyses showed marked upregulation of epidermal repair, inflammatory and immune defence pathways reflecting epithelial and immune response mechanisms to DD dysbiotic microbiome. In contrast, barrier genes including claudin-4 and cadherin-4 were downregulated. CONCLUSIONS These findings allow a better understanding of Darier exacerbations, highlighting the role of cutaneous dysbiosis in DD inflammation and associated malodour. Our data also suggest potential biomarkers and targets of intervention for DD. Video Abstract.
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Ohan JA, Siani R, Kurth JK, Sommer V, Glaser K, Karsten U, Schloter M, Schulz S. Microbiome convergence and deterministic community assembly along successional biocrust gradients on potash salt heaps. FEMS Microbiol Ecol 2023:fiad081. [PMID: 37463797 DOI: 10.1093/femsec/fiad081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023] Open
Abstract
Potash mining, typically performed for agricultural fertilizer production, can create piles of residual salt waste that are ecologically detrimental and difficult to revegetate. Biological soil crusts (biocrusts) have been found growing on and around these heaps, suggesting resilience to the hypersaline environment. We set out to understand the community dynamics of biocrust formation by examining two succesionary salinity gradients at historical mining sites using a high throughput amplicon sequencing. Bare heaps were distinct, with little overlap between sites, and were characterized by high salinity, low nutrient availability, and specialized, low diversity microbial communities, dominated by Halobacteria, Chloroflexia, and Deinococci. 'Initial' stages of biocrust development were dominated by site-specific Cyanobacteria, with significant overlap between sites. Established biocrusts were the most diverse, with large proportions of Alphaproteobacteria, Anaerolineae, and Planctomycetacia. Along the salinity gradient at both sites, salinity decreased, pH decreased, and nutrients and Chlorophyll a increased. Microbiomes between sites converged during succession and community assembly process analysis revealed biocrusts at both sites were dominated by deterministic, niche-based processes; indicating a high degree of phylogenetic turnover. We posit early cyanobacterial colonization is essential for biocrust initiation, and facilitates later establishment of plant and other higher-level biota.
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Kurth JK, Albrecht M, Glaser K, Karsten U, Vestergaard G, Armbruster M, Kublik S, Schmid CAO, Schloter M, Schulz S. Biological soil crusts on agricultural soils of mesic regions promote microbial cross-kingdom co-occurrences and nutrient retention. Front Microbiol 2023; 14:1169958. [PMID: 37520365 PMCID: PMC10382179 DOI: 10.3389/fmicb.2023.1169958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 06/21/2023] [Indexed: 08/01/2023] Open
Abstract
Introduction Biological soil crusts (biocrusts) are known as biological hotspots on undisturbed, nutrient-poor bare soil surfaces and until now, are mostly observed in (semi-) arid regions but are currently poorly understood in agricultural systems. This is a crucial knowledge gap because managed sites of mesic regions can quickly cover large areas. Thus, we addressed the questions (i) if biocrusts from agricultural sites of mesic regions also increase nutrients and microbial biomass as their (semi-) arid counterparts, and (ii) how microbial community assemblage in those biocrusts is influenced by disturbances like different fertilization and tillage regimes. Methods We compared phototrophic biomass, nutrient concentrations as well as the abundance, diversity and co-occurrence of Archaea, Bacteria, and Fungi in biocrusts and bare soils at a site with low agricultural soil quality. Results and Discussion Biocrusts built up significant quantities of phototrophic and microbial biomass and stored more nutrients compared to bare soils independent of the fertilizer applied and the tillage management. Surprisingly, particularly low abundant Actinobacteria were highly connected in the networks of biocrusts. In contrast, Cyanobacteria were rarely connected, which indicates reduced importance within the microbial community of the biocrusts. However, in bare soil networks, Cyanobacteria were the most connected bacterial group and, hence, might play a role in early biocrust formation due to their ability to, e.g., fix nitrogen and thus induce hotspot-like properties. The microbial community composition differed and network complexity was reduced by conventional tillage. Mineral and organic fertilizers led to networks that are more complex with a higher percentage of positive correlations favoring microbe-microbe interactions. Our study demonstrates that biocrusts represent a microbial hotspot on soil surfaces under agricultural use, which may have important implications for sustainable management of such soils in the future.
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Angstmann H, Pfeiffer S, Kublik S, Ehrhardt B, Uliczka K, Rabe KF, Roeder T, Wagner C, Schloter M, Krauss-Etschmann S. The microbial composition of larval airways from Drosophila melanogaster differ between specimens from laboratory and natural habitats. ENVIRONMENTAL MICROBIOME 2023; 18:55. [PMID: 37370177 DOI: 10.1186/s40793-023-00506-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 05/19/2023] [Indexed: 06/29/2023]
Abstract
BACKGROUND The fruit fly Drosophila melanogaster lives in natural habitats and has also long been used as a model organism in biological research. In this study, we used a molecular barcoding approach to analyse the airways microbiome of larvae of D. melanogaster, which were obtained from eggs of flies of the laboratory strain w1118 and from immune deficient flies (NF-kB-K), and from wild-caught flies. To assess intergenerational transmission of microbes, all eggs were incubated under the same semi-sterile conditions. RESULTS The airway microbiome of larvae from both lab-strains was dominated by the two families Acetobacteraceae and Lactobacillaceae, while larvae from wild-caught flies were dominated by Lactobacillaceae, Anaplasmataceae and Leuconostocaceae. Barcodes linked to Anaplasmataceae could be further assigned to Wolbachia sp., which is a widespread intracellular pathogen in arthropods. For Leuconostoceae, the most abundant reads were assigned to Weissella sp. Both Wolbachia and Weissella affect the development of the insects. Finally, a relative high abundance of Serratia sp. was found in larvae from immune deficient relish-/- compared to w1118 and wild-caught fly airways. CONCLUSIONS Our results show for the first time that larvae from D. melanogaster harbor an airway microbiome, which is of low complexity and strongly influenced by the environmental conditions and to a lesser extent by the immune status. Furthermore, our data indicate an intergenerational transmission of the microbiome as shaped by the environment.
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Mahmoud FM, Kusari S, Kublik S, Benning S, Siani R, Zühlke S, Radl V, Mahnkopp-Dirks F, Schloter M. Draft Genome Sequence of the Bacterial Endophyte Priestia megaterium B1, Isolated from Roots of Apple ( Malus domestica). Microbiol Resour Announc 2023:e0117222. [PMID: 37199619 DOI: 10.1128/mra.01172-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2023] Open
Abstract
Over the past years, a number of important traits supporting plant growth have been shown for different strains of Priestia megaterium (formerly known as Bacillus megaterium). Here, we report the draft genome sequence of the endophytic bacterial strain Priestia megaterium B1, which was isolated from surface-sterilized roots of apple plants.
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Escher BI, Altenburger R, Blüher M, Colbourne JK, Ebinghaus R, Fantke P, Hein M, Köck W, Kümmerer K, Leipold S, Li X, Scheringer M, Scholz S, Schloter M, Schweizer PJ, Tal T, Tetko I, Traidl-Hoffmann C, Wick LY, Fenner K. Modernizing persistence-bioaccumulation-toxicity (PBT) assessment with high throughput animal-free methods. Arch Toxicol 2023; 97:1267-1283. [PMID: 36952002 PMCID: PMC10110678 DOI: 10.1007/s00204-023-03485-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Accepted: 03/13/2023] [Indexed: 03/24/2023]
Abstract
The assessment of persistence (P), bioaccumulation (B), and toxicity (T) of a chemical is a crucial first step at ensuring chemical safety and is a cornerstone of the European Union's chemicals regulation REACH (Registration, Evaluation, Authorization, and Restriction of Chemicals). Existing methods for PBT assessment are overly complex and cumbersome, have produced incorrect conclusions, and rely heavily on animal-intensive testing. We explore how new-approach methodologies (NAMs) can overcome the limitations of current PBT assessment. We propose two innovative hazard indicators, termed cumulative toxicity equivalents (CTE) and persistent toxicity equivalents (PTE). Together they are intended to replace existing PBT indicators and can also accommodate the emerging concept of PMT (where M stands for mobility). The proposed "toxicity equivalents" can be measured with high throughput in vitro bioassays. CTE refers to the toxic effects measured directly in any given sample, including single chemicals, substitution products, or mixtures. PTE is the equivalent measure of cumulative toxicity equivalents measured after simulated environmental degradation of the sample. With an appropriate panel of animal-free or alternative in vitro bioassays, CTE and PTE comprise key environmental and human health hazard indicators. CTE and PTE do not require analytical identification of transformation products and mixture components but instead prompt two key questions: is the chemical or mixture toxic, and is this toxicity persistent or can it be attenuated by environmental degradation? Taken together, the proposed hazard indicators CTE and PTE have the potential to integrate P, B/M and T assessment into one high-throughput experimental workflow that sidesteps the need for analytical measurements and will support the Chemicals Strategy for Sustainability of the European Union.
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