Biology subjects

Jehmlich, N.

Publications and source records attributed to Jehmlich, N..

18 recordsLinked to original sources

bioRxiv2026

Thermal stress disrupts microbial symbiosis and host activity in the model sponge Ianthella basta

Climate change is threatening coral reef ecosystems around the world, causing significant declines in reef organisms, including sponges. The health of sponges is intimately linked to their symbiosis with microorganisms, yet little is known about their integrated response to ocean warming. Here, we present a comprehensive view of the effect of elevated sea surface temperatures (SST) on the model sponge Ianthella basta. I. basta individuals were exposed to temperatures up to 32 {degrees}C, 2-3 {degrees}C above the mean annual maxima. Host gene expression profiles showed an initial response to heat stress after 2 days, and a decreased expression of genes involved in maintaining tissue integrity, pumping capacity, vitamin transport, and stable symbioses after 4 to 8 days. Congruently, heat stressed samples started to show tissue regression and a reduced abundance of the dominant symbionts after 4 days. A significant loss of the symbionts occurred after 8 days, together with a reduction in microbially driven nitrogen cycling and amino-acid transport and an introduction of opportunistic microbes, which could lead to nutrient imbalance and further destabilisation of the holobiont. Together, this work provides important insights into the avenues through which future SST can impact host-microbe interactions in coral reef sponges.

microbiology↗

bioRxiv2026

Coculture of Collinsella aerofaciens and Bacteroides thetaiotaomicron under bile acid stress reveals vitamin B6 exchange

Although bile acid-mediated microbiome-host interactions are known to shape gut microbial composition and function, the mechanisms by which bile acid stress influences microbial metabolic interactions remain poorly understood. Here, we investigated the interaction between two key gut microbes, Bacteroides thetaiotaomicron and Collinsella aerofaciens, under deoxycholic acid (DCA) stress. In anaerobic coculture, C. aerofaciens mitigated the inhibitory effects of DCA on B. thetaiotaomicron, primarily through DCA uptake from the medium, as confirmed by DCA quantification. Proteomic analysis showed that DCA broadly disrupted amino acid and vitamin metabolism, particularly in B. thetaiotaomicron. In contrast, coculture promoted widespread metabolic activation in C. aerofaciens, including enhanced vitamin B6 metabolism and increased production of citrulline and ornithine. These findings suggest that metabolic cooperation enhances resistance to bile acid stress and may contribute to gut microbiome resilience, with potential relevance to liver- and bile acid-related disorders.

microbiology↗

bioRxiv2025

Hypoosmolarity inhibits archaeal ammonia oxidation

Salinity strongly influences the physiology and distribution of nitrifying microorganisms, yet the effects of low salinity on them remain understudied. This study investigates the impact of hypoosmolarity on different groups of ammonia oxidizers in soil and lake environments, as well as in pure culture isolates. In soil microcosms amended with ammonium, at low salinity levels ([~]120 S/cm), comparable to values commonly found in pristine terrestrial and aquatic environments, the abundance of ammonia-oxidizing bacteria (AOB), dominated by Nitrosomonas oligotropha, significantly increased. In contrast, the growth of ammonia-oxidizing archaea (AOA), dominated by "Ca. Nitrosotenuis" of the Nitrosopumilaceae family, was stimulated by high salinity ([~]760 S/cm). In ammonium-fed lake microcosms, the abundance of AOB, dominated by N. oligotropha, significantly increased under both low ([~]170 S/cm) and high salinity ([~]850 S/cm) conditions. In the presence of allylthiourea, a bacterial nitrification inhibitor, AOA were sensitive to low salinity in both soil and lake microcosms. Consistently, pure culture studies revealed marked growth inhibition of AOA, especially members of Nitrosopumilaceae, under hypoosmolarity, unlike AOB and complete ammonia oxidizer (comammox) strains. Comparative genomic analyses with AOB and comammox, along with transcriptomic studies, suggested that the sensitivity of AOA to hypoosmolarity stress was possibly due to a lack of sophisticated osmoregulatory transport systems and their S-layer cell wall structure. Overall, this study highlights hypoosmolarity as a key factor shaping the ecological niches and distribution of ammonia oxidizers, as well as nitrification activities, in terrestrial and aquatic environments that are increasingly affected by intensified water cycles due to climate change.

microbiology↗

bioRxiv2025

Cover crop root channels promote bacterial adaptation to drought in the maize rhizosphere

BackgroundIncreasing drought frequency poses a significant threat to agricultural productivity. A promising strategy to enhance crop resilience against drought is the utilisation of root channels left by winter cover crops, which can improve access to subsoil water and nutrients for subsequent cash crops like maize (Zea mays L.). The impact of drought on bacterial communities inhabiting these root channels remains largely unknown. Here, we investigated drought-induced shifts in maize rhizosphere bacterial communities and their functional adaptation in cover crop root channels across three soil types in northern Germany (Luvisol, Podzol, and Phaeozem). ResultsUsing a multi-omics approach (16S rRNA gene amplicon sequencing, qPCR, and metaproteomics), we identified significant taxonomic and functional responses to drought. A rise in the abundance of K-strategist bacterial communities indicate a shift towards stress-tolerant populations with drought. Under drought stress, the relative abundances of Acidobacteriota, Actinomycetota, Planctomycetota, and Pseudomonadota increased, while Chloroflexota, Methylomirabilota, Ca. Patescibacteria, and Verrucomicrobiota declined. Functional analyses revealed that drought-stressed aerobic taxa among the Pseudomonadota and Verrucomicrobiota upregulated the glyoxylate cycle, potentially enhancing carbon and energy conservation, and increased antioxidant defences (catalase-glutathione peroxidase and methionine cycle-transsulfuration pathway). These drought-mitigating strategies were especially pronounced in root channels formed by Brassicaceae and Poaceae cover crops in the Luvisol and Podzol soils. ConclusionsThese findings demonstrate the functional plasticity of rhizosphere bacterial communities in reused root channels in response to drought, highlighting the potential to leverage microbiome-mediated resilience for agricultural practices. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=100 SRC="FIGDIR/small/651044v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@7c3f69org.highwire.dtl.DTLVardef@127182forg.highwire.dtl.DTLVardef@1a4bb61org.highwire.dtl.DTLVardef@9f7c4_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2025

Critical Assessment of MetaProteome Investigation 2 (CAMPI-2): Multi-laboratory assessment of sample processing methods to stabilize fecal microbiome for functional analysis

BackgroundFecal samples are widely used as a proxy for studying gut microbiome composition in both human and animal research. Fecal metaproteomics provides valuable insights by tracking changes in the relative abundance of microbial taxa and their protein functions. To ensure reliable results, it is crucial to minimize alterations in the metaproteome occurring from sample collection to protein extraction. Therefore, employing effective stabilization methods is essential to preserve the integrity of the fecal metaproteome from sample collection to laboratory analysis, particularly over long distances or when rapid freezing options are not readily available. In line with these needs, the second edition of the Critical Assessment of MetaProteome Investigation (CAMPI-2) was specifically focused on testing sample stabilization protocols to be applied before metaproteomic analysis. ResultsThis collaborative multicenter study assessed the ability of five different stabilization methods, based on two commercial devices and three specific reagents (acetone, lithium dodecyl sulfate, and an RNAlater-like buffer), respectively, to stabilize the fecal metaproteome during room-temperature storage (14 days) and shipment to mass spectrometry facilities. The five methods were tested simultaneously by eight different laboratories across Europe, using aliquots from the same fecal sample. After protein extraction and digestion, duplicate aliquots of the resulting peptides were analyzed independently by two mass spectrometry facilities at distinct international locations. Analysis of the mass spectrometric data using two different search engines revealed that the fecal metaproteome profile differed considerably depending on the stabilization method used in terms of richness, alpha and beta diversity, reproducibility, and quantitative distribution of main taxa and functions. Although each method showed unique strengths and weaknesses, a commercial swab-based device stood out for its remarkable reproducibility and ranked highest for most of the metrics measured. ConclusionsCAMPI-2 allowed a robust evaluation of five different methods for preserving fecal metaproteome samples. The present investigation provides useful data for the design of metaproteomics and multi-omics studies where fecal sampling cannot be immediately followed by long-term storage at -80{degrees}C. Further optimization of the tested protocols is necessary to improve stabilization efficiency and control bias in the taxonomic and functional profile of the gut microbiome.

microbiology↗

bioRxiv2024

Integrated multi-omics highlights alterations of gut microbiome functions in prodromal and idiopathic Parkinson's disease

Parkinsons disease (PD) is associated with gut microbiome shifts, but the functional consequences remain unclear. Here, we use an integrated multi-omics approach to compare the gut microbiomes of individuals with PD and prodromal PD as well as healthy individuals. After analyzing each omics, meta-metabolomic was selected to inform the analysis as it represents the most discriminatory and robust ome. We identified 11 metabolites that were differentially abundant between the groups, amongst which {beta}-glutamate was increased in PD and prodromal PD, and correlated with the transcriptional activities of Methanobrevibacter smithii and Clostridium spp. We identified decreases in transcripts, but not in gene abundances, related to glutamate metabolism, bile acids, chemotaxis and flagellar assembly in PD, particularly in keystone genera such as Roseburia, Agathobacter and Blautia. Our findings, integrated into the Expobiome map, reveal multifactorial microbiome alterations which converge with PD pathways. Our study highlights the importance of investigating the gut microbiomes functional dimensions to better resolve microbiome-host interactions in health and disease.

systems biology↗

bioRxiv2024

Land use effects on soil microbiome composition and traits with consequences for its ecosystem carbon use efficiency

The soil microbiome determines the fate of belowground inputs of plant fixed carbon. The shifts in soil properties caused by changes in land use leads to modifications in microbiome structure and function, resulting in either loss or gain of soil organic carbon (SOC). Soil pH is the primary factor regulating microbiome characteristics leading to distinct pathways of microbial carbon cycling, but the underlying mechanisms remain understudied. Here, the taxa-trait relationships behind the variable fate of SOC were investigated across two temperate paired land use intensity contrasts with differing soil pH using metaproteomics, metabarcoding and a 13C labelled litter decomposition experiment. 13C incorporation into microbial biomass increased with land use intensification in low pH soils but decreased in high pH soils, impacting ecosystem carbon use efficiency (CUE) in opposing directions. Reduction in biosynthesis traits across land use intensity contrasts was due to increased abundance of proteins linked to resource acquisition and stress tolerance. These community-level trait trade-offs were underpinned by land use intensification-induced changes in dominant taxa with distinct traits. These trait changes alter the balance of decomposition and stabilisation of carbon in soil through divergent pH-controlled pathways. In low pH soils, land use intensification alleviates microbial abiotic stress resulting in increased CUE but promotes decomposition and SOC loss. In contrast, in high pH soils, land use intensification increases microbial physiological constraints and decreases CUE, leading to reduced necromass build-up and SOC stabilisation. We demonstrate how microbial CUE can be decoupled from SOC highlighting the need for its careful consideration in predicting or managing SOC storage for soil health and climate change mitigation.

ecology↗

bioRxiv2023

High-Throughput Screening of the Effects of 90 Xenobiotics on the Simplified Human Gut Microbiota Model (SIHUMIx): A Metaproteomic and Metabolomic Study

The human gut microbiota is a complex microbial community with critical functions for the host, including the transformation of various chemicals. While effects on microorganisms has been evaluated using single-species models, their functional effects within more complex microbial communities remain unclear. In this study, we investigated the response of a simplified human gut microbiota model (SIHUMIx) cultivated in an in vitro bioreactor system in combination with 96 deep-well plates after exposure to 90 different xenobiotics, comprising 54 plant protection products and 36 food additives and dyes, at environmentally relevant concentrations. We employed metaproteomics and metabolomics to evaluate changes in bacterial abundances, the production of Short Chain Fatty Acids (SCFAs), and the regulation of metabolic pathways. Our findings unveiled significant changes induced by 23 out of 54 plant protection products and 28 out of 36 food additives across all three categories assessed. Notable highlights include azoxystrobin, fluroxypyr, and ethoxyquin causing a substantial reduction (log2FC <-0.5) in the concentrations of the primary SCFAs: acetate, butyrate, and propionate. Several food additives had significant effects on the relative abundances of bacterial species; for example, acid orange 7 and saccharin led to a 75% decrease in Clostridium butyricum, with saccharin causing an additional 2.5-fold increase in E. coli compared to the control. Furthermore, both groups exhibited up- and down-regulation of various pathways, including those related to the metabolism of amino acids such as histidine, valine, leucine, and isoleucine, as well as bacterial secretion systems and energy pathways like starch, sucrose, butanoate, and pyruvate metabolism. This research introduces an efficient in vitro technique that enables high-throughput screening of the structure and function of a simplified and well-defined human gut microbiota model against 90 chemicals using metaproteomics and metabolomics. We believe this approach will be instrumental in characterizing chemical-microbiota interactions especially important for regulatory chemical risk assessments.

molecular biology↗

bioRxiv2023

Differential contribution of nitrifying prokaryotes to nitrification in groundwater

The ecophysiology of complete ammonia-oxidizing bacteria (CMX) of the genus Nitrospira and their widespread occurrence in groundwater suggests that CMX bacteria have a competitive advantage over ammonia-oxidizing bacteria (AOB) and archaea (AOA) in these environments. However, the specific contribution of their activity to nitrification processes has remained unclear. We aimed to disentangle the contribution of CMX, AOA and AOB to nitrification and to identify the environmental drivers of their niche differentiation at different levels of ammonium and oxygen in oligotrophic carbonate rock aquifers. CMX amoA genes accounted on average for 16 to 75% of the total groundwater amoA genes detected. Nitrification rates were positively correlated to CMX clade A associated phylotypes and AOB affiliated with Nitrosomonas ureae. Short-term incubations amended with the nitrification inhibitors allylthiourea and chlorate suggested that AOB contributed a large fraction to overall ammonia oxidation, while metaproteomics analysis confirmed an active role of CMX in both ammonia and nitrite oxidation. Ecophysiological niche differentiation of CMX clades A and B, AOB and AOA was linked to their requirements for ammonium, oxygen tolerance, and metabolic versatility. Our results demonstrate that despite numerical predominance of CMX, the first step of nitrification in oligotrophic groundwater appears to be primarily governed by AOB. Higher growth yields at lower ammonia turnover rates and energy derived from nitrite oxidation most likely enable CMX to maintain consistently high populations.

microbiology↗

bioRxiv2022

Mycelial nutrient transfer promotes bacterial co-metabolic organochlorine pesticide degradation in nutrient-deprived environments.

Biotransformation of soil organochlorine pesticides (OCP) is often impeded by a lack of nutrients relevant for bacterial growth and/or co-metabolic OCP biotransformation. By providing space-filling mycelia, fungi promote contaminant biodegradation by facilitating bacterial dispersal and the mobilization and release of nutrients in the mycosphere. We here tested whether mycelial nutrient transfer from nutrient-rich to nutrient-deprived areas facilitates bacterial OCP degradation in a nutrient-deficient habitat. The legacy pesticide hexachlorocyclohexane (HCH), a non-HCH-degrading fungus (Fusarium equiseti K3) and a co-metabolically HCH-degrading bacterium (Sphingomonas sp. S8) isolated from the same HCH-contaminated soil were used in spatially structured model ecosystems. Using 13C-labelled fungal biomass and protein-based stable isotope probing (protein-SIP), we traced the incorporation of 13C fungal metabolites into bacterial proteins while simultaneously determining the biotransformation of the HCH isomers. The relative isotope abundance (RIA, 7.1 - 14.2%), labeling ratio (LR, 0.13 - 0.35), and the shape of isotopic mass distribution profiles of bacterial peptides indicated the transfer of 13C-labeled fungal metabolites into bacterial proteins. Distinct 13C incorporation into the haloalkane dehalogenase (linB) and 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase (LinC), as key enzymes in metabolic HCH degradation, underpin the role of mycelial nutrient transport and fungal-bacterial interactions for co-metabolic bacterial HCH degradation in heterogeneous habitats. Nutrient uptake from mycelia increased HCH removal by twofold as compared to bacterial monocultures. Fungal-bacterial interactions hence may play an important role in the co-metabolic biotransformation of OCP or recalcitrant micropollutants (MPs).

microbiology↗

bioRxiv2022

Neonatal Peyer's patch cDC activation as a pacemaker of postnatal immune maturation

Marked differences exist between the mucosal immune system of the neonate and adult host. The pronounced influence of the enteric microbiota in adults suggests a causal relationship between postnatal colonization and immune maturation. However, using metagenomic, metaproteomic, and functional immunological analyses we demonstrate an early presence of bacteria and immunogenic microbial antigens preceding immune maturation in the small intestine, the primary inductive site of intestinal immunity. Instead, transcriptomic, flow cytometric and histological analysis indicated neonatal Peyers patch (PP) mononuclear phagocytes (MNP) as rate limiting factor of postnatal immune maturation. Despite the early presence of MNPs, conventional dendritic cells (cDC) of type 1, 2a and 2b exhibited significant age-dependent differences in tissue distribution and cellular composition. Single cell transcriptional profiling and functional assays revealed decreased antimicrobial and antigen processing/presentation capacity, an overall retarded cell maturation and reduced antigen uptake. In cDC2a this resulted in a reduced proportion of CCR7+ migratory cells and a consequent defect in CD4 T cell priming. Interestingly, transcriptional profiling of neonatal DC subsets identified reduced expression of type I interferon (IFN)-stimulated genes (ISG). Type I IFN induction by oral administration of the TLR7 agonist R848 accelerated MNP maturation and enhanced cognate antigen CD4 T cell priming. However, humoral responses to oral vaccination in the presence of R848 were significantly reduced. Together, our results identify PP MNP maturation as pacemaker of postnatal mucosal immune priming, indicate the biological role of delayed maturation and demonstrate that targeted interventional strategies allow manipulation of mucosal responses in early life.

immunology↗

bioRxiv2022

Database-independent analysis of probable post-translational modifications of soil proteins across ecosystems

The identification rate of measured peptide spectra to proteins barely scratches 1% in best-case scenarios. Hundreds of thousands of valuable spectra are lost as no viable match in the database is found. Here, we apply the delta m/z plot that was previously implemented in MSnbase as tool for quality control to 63 soil samples from three ecosystems with different vegetation (39 forests, 11 grasslands, and 13 shrublands) with the aim to extract probable post-translational modifications (PTM) without the need of a reference database. The validity of the approach was verified with amino acids proposed for their respective 1 Da mass interval and compared to their relative abundance in proteins. We found that the average probable PTM and most known PTMs proposed for the mass intervals are similar across ecosystems. Otherwise, 11 mass intervals changed significantly in relative abundance in the three ecosystems but only for one an annotation could be proposed. Our approach not only highlights the opportunity of the database-independent analysis in soil metaproteomics but paves the way for targeted analysis of the yet unknown PTMs.

ecology↗

bioRxiv2021

Oxygen production by an ammonia-oxidizing archaeon

Ammonia-oxidizing archaea (AOA) are one of the most abundant groups of microbes in the worlds oceans and are key players in the nitrogen cycle. Their energy metabolism, the oxidation of ammonia to nitrite, requires oxygen. Nevertheless, AOA are abundant in environments where oxygen is undetectable. In incubation experiments, where oxygen concentrations were resolved to the nanomolar range, we show that Nitrosopumilus maritimus produces oxygen (O2) and dinitrogen (N2). The pathway is not completely resolved, but it has nitric oxide as a key intermediate. Part of the oxygen produced is directly used for ammonia oxidation, while some accumulates in the surrounding environment. N. maritimus joins a small handful of organisms known to produce oxygen in the dark, and based on this ability, we re-evaluate their role in oxygen-depleted marine environments.

microbiology↗

bioRxiv2021

Critical Assessment of Metaproteome Investigation (CAMPI): a Multi-Lab Comparison of Established Workflows

Metaproteomics has matured into a powerful tool to assess functional interactions in microbial communities. While many metaproteomic workflows are available, the impact of method choice on results remains unclear. Here, we carried out the first community-driven, multi-laboratory comparison in metaproteomics: the critical assessment of metaproteome investigation study (CAMPI). Based on well-established workflows, we evaluated the effect of sample preparation, mass spectrometry, and bioinformatic analysis using two samples: a simplified, laboratory-assembled human intestinal model and a human fecal sample. We observed that variability at the peptide level was predominantly due to sample processing workflows, with a smaller contribution of bioinformatic pipelines. These peptide-level differences largely disappeared at the protein group level. While differences were observed for predicted community composition, similar functional profiles were obtained across workflows. CAMPI demonstrates the robustness of present-day metaproteomics research, serves as a template for multi-laboratory studies in metaproteomics, and provides publicly available data sets for benchmarking future developments.

microbiology↗

bioRxiv2021

Sulfur-fueled chemolithoautotrophs replenish organic carbon inventory in groundwater

The current understanding of organic carbon inputs into ecosystems lacking photosynthetic primary production is predicated on data and inferences derived almost entirely from metagenomic analyses. The elevated abundances of putative chemolithoautotrophs in groundwaters suggest that dark CO2 fixation is an integral component of subsurface trophic webs. To understand the impact of autotrophically-fixed carbon, the flux of CO2-derived carbon through various subpopulations of subsurface microbiota must first be resolved, both quantitatively and temporally. Here, we implement novel stable isotope cluster analysis to render a time-resolved and quantitative evaluation of 13CO-derived carbon flow through a groundwater microbiome stimulated with reduced sulfur compounds. We demonstrate that mixotrophs, not obligate chemolithoautotrophs, were the most abundant active organisms in groundwater microcosms. Species of Hydrogenophaga, Polaromonas, Dechloromonas, and other metabolically versatile mixotrophs drove the recycling of organic carbon and, when chance afforded, supplemented their carbon requirements via chemolithoautotrophy and uptake of available organic compounds. Mixotrophic activity facilitated the replacement of 43 and 80% of total microbial carbon stores with 13C in just 21 and 70 days, respectively. This opportunistic "utilize whatever pathways net the greatest advantage in fitness" strategy may explain the great abundances of mixotrophs in other oligotrophic habitats, like the upper ocean and boreal lakes.

microbiology↗

bioRxiv2020

Explorative meta-analysis of 417 extant archaeal genomes to predict their contribution to the total microbiome functionality

Unveiling the relationship between taxonomy and function in microbiomes is crucial to determine their contribution to ecosystem functioning. However, while the relationship between taxonomic and functional diversity in bacteria and fungi was reported, this is not the case for archaea. Here, we used a meta-analysis of completely annotated extant genomes of 417 taxonomically unique archaeal species to describe intergenome and intragenome redundancy of functions and to predict the extent of microbiome functionality on Earth contained within archaeal genomes using accumulation curves of all known functions from the level 3 of KEGG Orthology. We found that intergenome redundancy as functions present in multiple genomes was inversely related to intragenome redundancy as multiple copies of a gene in one genome, implying the trade of between additional copies of functionally important genes or a higher number of different genes. A logarithmic model described the relationship between functional diversity and species richness better than both the unsaturated and the saturated model, which suggests a limited total number of archaeal functions in contrast to the potential of bacteria and fungi. Using a global archaeal species richness estimate of 13,159, the logarithmic model predicts a total of 4,164.1 {+/-}2.9 KEGG level 3 functions while the non-parametric bootstrap estimate yields a lower bound of 2,994 {+/-}57 KEGG level 3 functions. Our approach not only highlights similarities in functional redundancy but also the difference in functional potential of archaea compared to other domains of life.

ecology↗

bioRxiv2019

The total fungal microbiome functionality

Unveiling the relationship between taxonomy and function of the microbiome is crucial to determine its contribution to ecosystem functioning. However, while there is a considerable amount of information on microbial taxonomic diversity, our understanding of its relationship to functional diversity is still scarce. Here we used a meta-analysis of 377 completely annotated and taxonomically different fungal genomes to predict the total fungal microbiome functionality on Earth with all known functions from level 3 of KEGG Orthology using both parametric and non-parametric estimations. The unsaturated model described the accumulation of functions with increasing species richness significantly better (P-value < 2.2e-16) than the saturated model suggesting the presence of widespread and rare functions. Consistent with the parametric approach, the non-parametric Chao-1 estimator that assumes a maximum functional richness did not reach a plateau. Based on previous estimates of fungal species richness on Earth, we propagated the unsaturated model to predict a total fungal microbiome functionality of 42.4 million. Of those, only 0.06% are known today since the vast majority belongs to yet unknown rare functions. Logically, our approach not only highlighted the presence of two types of functions but pointed towards the necessity of novel and more sophisticated methods to unveil the entirety of functions to fully understand the involvement of the fungal microbiome in ecosystem functioning.

ecology↗

bioRxiv2019

Interspecies metabolite transfer in a co-culture of Dehalococcoides and Sulfurospirillum leads to rapid and complete tetrachloroethene dechlorination

Microbial communities involving dehalogenating bacteria assist in bioremediation of areas contaminated with halocarbons. To understand molecular interactions between dehalogenating bacteria, we co-cultured Sulfurospirillum multivorans, dechlorinating tetrachloroethene (PCE) to cis-1,2-dichloroethene (cDCE), and Dehalococcoides mccartyi strains BTF08 or 195, dehalogenating PCE to ethene. The co-cultures were cultivated with lactate as electron donor. In this co-culture, the bacterial cells formed aggregates and D. mccartyi established an unusual, barrel-like morphology. An extracellular matrix surrounding bacterial cells in the aggregates enhanced cell-to-cell contact. PCE was dehalogenated to ethene at least three times faster in the co-culture. The dehalogenation was carried out via PceA of S. multivorans, and PteA (a recently described PCE dehalogenase) and VcrA of D. mccartyi BTF08, as supported by protein abundance. The co-culture was not dependent on exogenous hydrogen and acetate, suggesting a syntrophic relationship in which the obligate hydrogen consumer D. mccartyi consumes hydrogen and acetate produced by S. multivorans. The cobamide cofactor of the reductive dehalogenase - mandatory for D. mccartyi - was also produced by S. multivorans. D. mccartyi strain 195 dechlorinated cDCE in the presence of norpseudo-B12 produced by S. multivorans, but D. mccartyi strain BTF08 depended on an exogenous lower cobamide ligand. This observation is important for bioremediation, since cofactor supply in the environment might be a limiting factor for PCE dehalogenation to ethene, described for D. mccartyi exclusively. The findings from this co-culture give new insights into aggregate formation and the physiology of D. mccartyi within a bacterial community.

microbiology↗