Tillmann Lueders

University of Bayreuth · Chair of Ecological Microbiology

Bacterial protoplasts are known to reproduce independently of canonical molecular biological processes. Although their reproduction is thought to be influenced by environmental conditions, the growth of protoplasts in their natural habitat has never been empirically studied. Here, we studied the life cycle of protoplasts in their native environment...

Microbial biofilms occur in many shapes and different dimensions. In natural and semi‐artificial caves they are forming pendulous structures of 10 cm and more. In this study a methane driven microbial community of a former medicinal spring was investigated. The habitat was completely covered by massive biofilms and snottites with a wobbly, gelatino...

Plastic input to the terrestrial environment is of global concern and the still increasing production and release worldwide reinforces this problem. It has been shown that microplastics (MPs) can affect soil structure and soil organisms, possibly leading to an increase in soil carbon turnover, microbial activity and resulting CO2 emissions. Yet, th...

Background and Aim Stomatal regulation allows plants to promptly respond to water stress. However, our understanding of the impact of above and belowground hydraulic traits on stomatal regulation remains incomplete. The objective of this study was to investigate how key plant hydraulic traits impact transpiration of maize during soil drying. We hyp...

The increasing accumulation of microplastics (MP) in the environment is considered one of the most important environmental challenges of our times. Reliable extraction and detection methods for MP in environmental samples are essential for determining the extent of pollution and assessing ecological risks. However, extraction of MP from complex env...

Impact statement Methane oxidizing microbes play a key role in reducing the emission of this potent greenhouse gas to the atmosphere. The known versatility of the recently discovered anaerobic Methylomirabilota methanotrophs is limited. Here, we report a novel uncultured Methylomirabilis species, Candidatus Methylomirabilis iodofontis, with the gen...

The most primitive cells or protocells were thought to be devoid of all complex molecular biological processes. They are believed to have mediated cellular processes like reproduction entirely by biophysical properties of cell constituents and fluctuating environmental conditions. Despite these propositions, a complex biological process like reprod...

Cable bacteria (CB) perform electrogenic sulphur oxidation (e-SOX) by spatially separating redox-half-reactions over cm-distances. For freshwater systems, the ecology of CB is not yet well understood, partly because they proved difficult to cultivate. This study introduces a new “agar pillar” approach to selectively enrich and investigate CB-popula...

The input of nitrate and other agricultural pollutants in higher-order streams largely derives from first-order streams. The streambed as the transition zone between groundwater and stream water has a decisive impact on the attenuation of such pollutants. This reactivity is not yet well understood for lower-order agricultural streams, which are oft...

Protocells are thought to have existed on early Earth before the origin of prokaryotes. These primitive cells are believed to have carried out processes like replication solely based on the physicochemical properties of their cell constituents. Despite considerable efforts, replication of a living cell-driven entirely by laws of physics and chemist...

Oldest known microfossils were known to have the most complex of morphologies among prokaryotes. Given the morphology of an organism is governed by information encoded in its genome, it was proposed that these primitive organisms most likely possessed complex molecular biological processes. Here we worked with bacterial protoplasts under environmen...

Complex microbial communities in environmental systems play a key role in the detoxification of chemical contaminants by transforming them into less active metabolites or by complete mineralization. Biotransformation, i.e., transformation by microbes, is well understood for a number of priority pollutants, but a similar level of understanding is la...

Nitrate removal in oligotrophic environments is often limited by the availability of suitable organic electron donors. Chemolithoautotrophic bacteria may play a key role in denitrification in aquifers depleted in organic carbon. Under anoxic and circumneutral pH conditions, iron(II) was hypothesized to serve as an electron donor for microbially med...

Groundwater systems are key for the provisioning of water for human use, but at the same time impacted by a massive and constantly increasing footprint of anthropogenic pollutants. Fortunately, aquifers are also inhabited by a plethora of microbes, which safeguard water quality with their biogeochemical activities. Here, we discuss microbial contam...

Plastics entering the environment can not only undergo physical degradation and fragmentation processes, but they also tend to be colonized by microorganisms. Microbial colonization and the subsequent biofilm formation on plastics can alter their palatability to organisms and result in a higher ingestion as compared to pristine plastics. To date, t...

Sulfate-reducing microorganisms (SRMs) often compete with methanogens for common substrates. Due to thermodynamic reasons, SRMs should outcompete methanogens in the presence of sulfate. However, many studies have documented coexistence of these microbial groups in natural environments, suggesting that thermodynamics alone cannot explain the interac...

Microorganisms are essential in the degradation of environmental pollutants. Aromatic hydrocarbons, e.g., benzene, toluene, ethylbenzene, and xylene (BTEX), are common aquifer contaminants, whose degradation in situ is often limited by the availability of electron acceptors. It is clear that different electron acceptors such as nitrate, iron, or su...

Perennial low order streams are normally well connected to shallow groundwater and therefore, they are among the first receptors of agricultural effluents. Understanding the processes governing the water quality in agricultural areas requires identifying sources of potential pollutants (such as nitrate), hotspots of biogeochemical reactivity and de...

Microorganisms play an essential role in nitrogen cycling and greenhouse gas emissions in soils and sediments. The recently discovered oxygenic denitrifiers are proposed to reduce nitrate and nitrite via nitric oxide dismutation directly to N2 and O2. So far, the ecological role of these microbes is not well understood. The only available tool for...

Many ecological and evolutionary processes in animals depend upon microbial symbioses. In spiders, the role of the microbiome in these processes remains mostly unknown. We compared the microbiome between populations, individuals, and tissue types of a range-expanding spider, using 16S rRNA gene sequencing. Our study is one of the first to go beyond...

Background: Recognition is growing that many ecological and evolutionary processes in animals are dependent upon microbial symbioses. Although there is much known about the ecology and evolution of spiders, the role of the microbiome in these processes remains mostly unknown. We conducted an exploratory study of the microbiome of a range-expanding...

Zoogloea oleivorans, capable of using toluene as a sole source of carbon and energy, was earlier found to be an active degrader under microaerobic conditions in aquifer samples. To uncover the genetic background of the ability of microaerobic toluene degradation in Z. oleivorans, the whole-genome sequence of the type strain Buc T was revealed. Meta...

Oxygenic denitrification represents a new route in reductive nitrogen turnover which differs from canonical denitrification in how nitric oxide (NO) is transformed into dinitrogen gas. Instead of NO reduction via N2O to N2, NO is proposed to be directly disproportionated into N2 and O2 in oxygenic denitrification, catalyzed by the putative NO dismu...

Saturated acid sulfate soils with hypersulfidic material are productive wetland soils, but when they dry, they generate large amounts of sulfuric acid due to oxidation of pyrite to form sulfuric material (pH <4) and consequently sulfuric soils. After re-saturation of sulfuric soils and thus the re-establishment of reduced conditions, activity of su...

Numerous ¹³ CO 2 labeling studies have traced the flow of carbon from fresh plant exudates into rhizosphere bacterial communities. However, the succession of the uptake of carbon leaving the roots by distinct rhizosphere microbiota has rarely been resolved between microbial kingdoms. This can provide valuable insights on the niche partitioning of p...

Aquifers are typically perceived as rather stable habitats, characterized by low biogeochemical and microbial community dynamics. Upon contamination, aquifers shift to a perturbed ecological status, in which specialized populations of contaminant degraders establish and mediate aquifer restoration. However, the ecological controls of such degrader...

While most studies using RNA-stable isotope probing (SIP) to date have focused on ribosomal RNA, the detection of 13C-labeled mRNA has rarely been demonstrated. This approach could alleviate some of the major caveats of current non-target environmental “omics.” Here, we demonstrate the feasibility of total RNA-SIP in an experiment where hydrocarbon...

Substantial amounts of organic matter are mobilized from upper soil layers during extreme precipitation events. This results in considerable fluxes of carbon from plant-associated topsoil to deeper mineral soil and to groundwater. Microbes constitute an important part of this mobile organic matter (MOM) pool. Previous work has shown that specific b...

The anaerobic degradation of petroleum hydrocarbons is an important ecosystem service provided by microbes in systems impacted by pollution. Research in recent years has resulted in substantial advances in our understanding of the diversity and ecology of natural populations of anaerobic hydrocarbon degraders, both in marine and terrestrial sedimen...

The availability of oxygen is often a limiting factor for the degradation of aromatic hydrocarbons in subsurface environments. However, while both aerobic and anaerobic degraders have been intensively studied, degradation betwixt, under micro- or hypoxic conditions has rarely been addressed. It is speculated that in environments with limited, but s...

Stable isotope probing (SIP) of isotopically labelled RNA is well-established in environmental microbiology. The concept of a labelling-based detection of process-relevant microbes independent of cellular replication or growth allows for a direct handle on functionally relevant microbiome components. Although applied mostly for rRNA, RNA-SIP also h...

Microbial communities are the driving force behind the degradation of contaminants like aromatic hydrocarbons in groundwater ecosystems. However, little is known about the response of native microbial communities to contamination in pristine environments as well as their potential to recover from a contamination event. Here, we used an indoor aquif...

Root exudates shape microbial communities at the plant soil interface. Here we compared bacterial communities that utilise plant-derived carbon in the rhizosphere of wheat in different soil depths, including topsoil, as well as two subsoil layers up to 1 m depth. The experiment was performed in a green house using soil monoliths with intact soil st...

Massive biofilms have been discovered in the cave of an iodine-rich former medicinal spring in southern Germany. The biofilms completely cover the walls and ceilings of the cave, giving rise to speculations about their metabolism. Here we report on first insights into the structure and function of the biofilm microbiota, combining geochemical, imag...

Predation is a fundamental mechanism of all food webs, but its drivers and organismic connectivities, especially at microbial level, are still poorly understood. Specifically, competitive carbon flows in the presence of multiple micropredators, as well as trophic links within and between microbial kingdoms have rarely been resolved. Here, using mai...

The built environment (BE) and in particular kitchen environments harbor a remarkable microbial diversity, including pathogens. We analyzed the bacterial microbiome of used kitchen sponges by 454–pyrosequencing of 16S rRNA genes and fluorescence in situ hybridization coupled with confocal laser scanning microscopy (FISH–CLSM). Pyrosequencing showed...

Importance statement: NO dismutation into N2 and O2 is a novel process, catalyzed by putative NO dismutase (Nod). To date only two bacteria, the anaerobic methane oxidizing bacterium Methylomirabilis oxyfera and the alkane-oxidizing gammaproteobacterium HdN1, are known to harbor nod genes. In this study, we report the first efficient molecular too...

The degradation of benzene, toluene, ethylbenzene and xylene (BTEX) contaminants in groundwater relies largely on anaerobic processes. While the physiology and biochemistry of selected relevant microbes have been intensively studied, research has now started to take the generated knowledge back to the field, in order to trace the populations truly...

Geothermal energy plays an increasingly important role as a renewable energy source. However, it induces temperature changes in natural thermally static groundwater ecosystems. Temperature impacts can considerably alter the groundwater chemical composition and quality, the metabolism of organisms, and, consequently, biogeochemical processes and eco...

Background and aims Forest ecosystems may act as sinks for or source of atmospheric CO2. While inorganic nitrogen (N) fertilization increases aboveground tree biomass, the effects on soil and rhizosphere microorganisms are less clear, indicating potentially unpredictable changes in nutrient cycling processes maintaining ecosystem functioning. Altho...

Stable isotope probing of RNA has enthused researchers right from its first introduction in 2002. The concept of a labelling-based detection of process-targeted microbes independent of cellular replication or growth has allowed for a much more direct handle on functionally relevant microbiota than by labelling of other biomarkers. This has led to a...

The flow of plant-derived carbon in soil is a key component of global carbon cycling. Conceptual models of trophic carbon fluxes in soil have assumed separate bacterial and fungal energy channels in the detritusphere, controlled by both substrate complexity and recalcitrance. However, detailed understanding of the key populations involved and niche...

The hyporheic interstitial provides habitat for many different organisms − from bacteria to burrowing invertebrates. Due to their burrowing and sediment reworking behaviour, these ecosystem engineers have the potential to affect hyporheic processes such as respiration and nutrient cycling. However, there is a lack of studies that characterize the i...

The biodegradation of organic pollutants in aquifers is often restricted to the fringes of contaminant plumes where steep countergradients of electron donors and acceptors are separated by limited dispersive mixing. However, long-distance electron transfer (LDET) by filamentous 'cable bacteria' has recently been discovered in marine sediments to co...

Stable isotope probing (SIP) techniques have become state-of-the-art in microbial ecology over the last 10 years, allowing for the targeted detection and identification of organisms, metabolic pathways and elemental fluxes active in specific processes within complex microbial communities. For studying anaerobic hydrocarbon-degrading microbial commu...

Anaerobic degradation is a key process in many environments either naturally or anthropogenically exposed to petroleum hydrocarbons. Considerable advances into the biochemistry and physiology of selected anaerobic degraders have been achieved over the last decades, especially for the degradation of aromatic hydrocarbons. However, researchers have o...

Hydrocarbons are abundant in anoxic environments and pose biochemical challenges to their anaerobic degradation by microorganisms. Within the framework of the Priority Program 1319, investigations funded by the Deutsche Forschungsgemeinschaft on the anaerobic microbial degradation of hydrocarbons ranged from isolation and enrichment of hitherto unk...

Slow sand filtration (SSF) is an effective low-tech water treatment method for pathogen and particle removal. Yet despite its application for centuries, it has been uncertain to which extent pathogenic microbes are removed by mechanical filtration or due to ecological interactions such as grazing and competition for nutrients. In this study, we qua...

Groundwater is an important resource but often polluted by aromatic hydrocarbons, such as BTEX compounds. To conceive efficient bioremediation technologies, it is crucial to better understand the ecology of degraders and ongoing biodegradation processes in situ, which mostly rely on anaerobic respiration. It is not yet well understood how the avail...

The use of colloidal iron oxide (FeOx) in the bioremediation of groundwater contamination implies its increasing release into the environment and requires an assessment of its ecotoxicological risk. Therefore, microcosm experiments were carried out to investigate the impact of ferrihydrite colloids (Fh-Col) on the bacterial and meiofaunal communiti...

Biodegradation is one of the most favored and sustainable means of removing organic pollutants from contaminated aquifers but the major steering factors are still surprisingly poorly understood. Growing evidence questions some of the established concepts for control of biodegradation. Here, we critically discuss classical concepts such as the therm...

The microbial degradation of hydrocarbons in contaminated environments can be driven by distinct aerobic and anaerobic populations. While the physiology and biochemistry of selected degraders isolated in pure culture have been intensively studied in recent decades, research has now started to take the generated knowledge back to the field, in order...

In laboratory column systems, transport and biogeochemical processes were compared at static water table and at fluctuating water table. Results show that periodic cycling of the water table led to increased mean transit times and differences in microbial communities attached to sediment compared to steadystate flow conditions. Groundwater table fl...

Coal-bearing sediments are major reservoirs of organic matter potentially available for methanogenic subsurface microbial communities. In this study the specific microbial community inside lignite-bearing sedimentary basin in Germany and its contribution to methanogenic hydrocarbon degradation processes was investigated. The stable isotope signatur...

Dissimilatory sulphate reduction (DSR) has been proven to be one of the most relevant redox reactions in the biodegradation of contaminants in groundwater. However, the possible role of sulphur species of intermediate oxidation state, as well as the role of potential re-oxidative sulphur cycling in biodegradation particularly at the groundwater tab...

The detection of anaerobic hydrocarbon degrader populations via catabolic gene markers is important for the understanding of processes at contaminated sites. The genes of fumarate-adding enzymes (FAEs; i.e., benzylsuccinate and alkylsuccinate synthases) are widely used as specific functional markers for anaerobic degraders of aliphatic and aromatic...

The microbial monitoring of drinking water production systems is essential to assure water quality and minimize possible risks. However, the comparative impact of microbes from the surrounding aquifer and of those established within drinking water wells on water parameters remains poorly understood. High pressure jetting is a routine method to impe...

Anaerobic microbial degradation of hydrocarbons, typically occurring at the oil-water transition zone, influences the quality of oil reservoirs. In Pitch Lake, Trinidad and Tobago—the world’s largest asphalt lake—we found that microorganisms are metabolically active in minuscule water droplets (1 to 3 microliters) entrapped in oil. Pyrotag sequenci...

Biogeochemical and microbiological data indicate that the anaerobic oxidation of non-methane hydrocarbons by sulfate-reducing bacteria (SRB) has an important role in carbon and sulfur cycling at marine seeps. Yet, little is known about the bacterial hydrocarbon degraders active in situ. Here, we provide the link between previous biogeochemical meas...

Three toluene-degrading microbial consortia were enriched under sulphate-reducing conditions from different zones of a benzene, toluene, ethylbenzene and xylenes (BTEX) plume of two connected contaminated aquifers. Two cultures were obtained from a weakly contaminated zone of the lower aquifer, while one culture originated from the highly contamina...

Plants introduce abundant carbon into soils, where it is mineralised and sequestered. Proportions of this fresh organic carbon introduced to top soils can be relocated to deeper soil layers and even to groundwater by event-driven transport upon heavy rainfalls or after snowmelt. It is assumed that a significant fraction of this flux involves biocol...

Hydrocarbon contaminants in groundwater can be degraded by microbes under different redox settings, forming hot spots of degradation especially at the fringes of contaminant plumes. At a tar-oil-contaminated aquifer in Germany, it was previously shown that the distribution of anaerobic toluene degraders as traced via catabolic and ribosomal marker...

DNA-based stable isotope probing (SIP) was introduced as a powerful tool to achieve a deeper insight of microbial processes through identifying relevant organisms that determine nutrient cycling and metabolize plant-derived compounds. Since its advent, it has been mainly used for studying micro-organisms in terrestrial ecosystems including the rhiz...