Lukas Y Wick

• Dr. phil., dipl.Chem.; Malik Master of Management
• Deputy Head of Department at Helmholtz Centre for Environmental Research UFZ

Draft genomes of two phenanthrene-degrading bacterial isolates from oil sands process-affected water (OSPW) in Alberta, Canada were sequenced. Both isolates grew in close association on agar plates and were difficult to obtain axenically. They represent novel Pseudomonas chengduensis and Sphingobium sp. strains with genomes of 5.5 and 4.1 Mbases le...

Biofiltration is a simple and low-cost method for the cleanup of contaminated water. However, the reduced availability of dissolved chemicals to surface-attached degrader bacteria may limit its efficient use at certain hydraulic loadings. When a direct current (DC) electric field is applied to an immersed packed bed, it invokes electrokinetic proce...

It is recognized that compost application incorporates a high diversity of microorganisms in soils, promoting the sustainable agriculture. However, bacterial–fungal interactions (BFI) in compost application remain insufficiently explored. Here, we determined and compared the composition of bacterial community in samples of commercial compost (C), c...

Bacteriophages play a crucial role in shaping bacterial communities, yet the mechanisms by which nonmotile bacteriophages interact with their hosts remain poorly understood. This knowledge gap is especially pronounced in structured environments like soil, where spatial constraints and air-filled zones hinder aqueous diffusion. In soil, hyphae of fi...

Endophytes isolated from extremophile plants are interesting microbes for improving the stress tolerance of agricultural plants. Here, we isolated and characterized endophytic bacteria showing plant growth-promoting (PGP) traits from plants in two extreme Chilean biomes (Atacama Desert and Chilean Patagonia). Forty-two isolates were characterized a...

Bioaugmentation constitutes a viable approach for the bioremediation of soils polluted by organic chemicals, but limitations may arise due to the poor in situ performance of the inoculated microorganisms. This chapter examines these – poorly understood – drawbacks in the light of the latest advances in microbial ecology and bioremediation strategie...

Mycelial networks allow fungi to spread efficiently and traverse air-filled pores. By transporting nutrients from nutrient-rich and to nutrient-poor areas, they also promote bacterial growth and cometabolic degradation of contaminants. Mycelia likewise connect microhabitats and act as dispersal vectors (fungal highways) for aerobic and anaerobic ba...

This study presents an inexpensive approach for the macro- and microscopic observation of fungal mycelial growth. The “fungal drops” method allows to investigate the development of a mycelial network in filamentous microorganisms at the colony and hyphal scales. A heterogeneous environment is created by depositing 15-20 µL drops on a hydrophobic su...

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 cumbers...

The study provides advances for understanding fungal-bacterial relationships, particularly on the selection and dispersion of bacterial communities by fungi, which are crucial for the organization of microbial communities and their functioning in coastal PAH-contaminated sediments. The transportation of bacteria via fungal hyphae (fungal highway) r...

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. W...

Increased drought intensity and frequency exposes soil bacteria to prolonged water stress. While numerous studies reported on behavioral and physiological mechanisms of bacterial adaptation to water stress, changes in bacterial cell surface properties during adaptation are not well researched. We studied adaptive changes in cell surface hydropho-bi...

Bile acids are crucial for the uptake of dietary lipids and can shape the gut-microbiome composition. This latter function is associated with the toxicity of bile acids and can be modulated by bile acid modifying bacteria such as Eggerthella lenta, but the molecular details of the interaction of bacteria depending on bile acid modifications are not...

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. W...

Background To disperse in water-unsaturated environments, such as the soil, bacteria rely on the availability and structure of water films forming on biotic and abiotic surfaces, and, especially, along fungal mycelia. Dispersal along such “fungal highways” may be driven both by mycelial physical properties and by interactions between bacteria and f...

Trifluoroacetic acid (TFA) is a very persistent, very mobile substance (vPvM) with potential toxicity, and causes increasing environmental concerns worldwide. Conventional wastewater treatment strategies are inefficient for selective TFA removal in the presence of inorganic anions. Here we show that surface defunctionalized activated carbon felt (D...

Stable isotope fractionation of toluene under dynamic phase exchange was studied aiming at ascertaining the effects of gas-liquid partitioning and biodegradation of toluene stable isotope composition in liquid-air phase exchange reactors (Laper). The liquid phase consisted of a mixture of aqueous minimal media, a known amount of a mixture of deuter...

Creating unique microenvironments, hyphal surfaces and their surroundings allow for spatially distinct microbial interactions and functions at the microscale. Using a microfluidic system and pH-sensitive whole-cell bioreporters (Synechocystis sp. PCC6803) attached to hyphae, we spatially resolved the pH along surfaces of growing hyphae of the basid...

Anoxic microsites arising in fungal biofilms may foster the presence of obligate anaerobes. Here, we analyzed whether and to which degree hyphae of Coprinopsis cinerea thriving in oxic habitats enable the germination, growth, and dispersal of the obligate anaerobic soil bacterium Clostridium acetobutylicum. Time-resolved optical oxygen mapping, mic...

To disseminate in water-unsaturated environments, such as the soil, bacteria rely on the availability and structure of water films forming on biotic and abiotic surfaces, and, especially, along fungal mycelia. Dispersal along such “fungal highways” is driven both by mycelial physical properties and by interactions between bacteria and fungi. To und...

Anoxic microsites arising in fungal biofilms may foster the presence of obligate anaerobes even in well-areated environments. Here, we analyzed whether and to which degree fractal hyphae of Coprinopsis cinerea thriving in oxic habitats enable the germination, growth, and dispersal of obligate anaerobic soil bacterium Clostridium acetobutylicum. Tim...

The draft genome sequences of two Sphingobium strains that are hexachlorocyclohexane (HCH) degraders are presented. The strains were isolated from HCH-contaminated soil in Kitengela, Kenya. Both genomes possess the lin genes responsible for HCH degradation and gene clusters for degradation of other xenobiotic compounds.

Recent studies have demonstrated that phages can be co-transported with motile non-host bacteria, thereby enabling their invasion of biofilms and control of biofilm composition. Here, we developed a novel approach to isolate non-host bacteria able to co-transport phages from soil. It is based on the capability of phage-carrying non-host bacteria to...

Nonmotile microorganisms often enter new habitats by co-transport with motile microorganisms. Here, we report that also lytic phages can co-transport with hyphal-riding bacteria and facilitate bacterial colonization of a new habitat. This is comparable to the concept of biological invasions in macroecology. In analogy to invasion frameworks in plan...

The pH of an environment is both a driver and the result of diversity and functioning of microbial habitats such as the area affected by fungal hyphae (mycosphere). Here we used a novel pH-sensitive bioreporter, Synechocystis sp. PCC6803_peripHlu, and ratiometric fluorescence microscopy, to spatially and temporally resolve the mycosphere pH at the...

Marine phages have been applied to trace ground- and surface water flows. Yet, information on their transport in soil and related particle intactness is limited. Here we compared the breakthrough of two lytic marine tracer phages (Pseudoalteromonas phages PSA-HM1 and PSA-HS2) with the commonly used Escherichia virus T4 in soil- and sand-filled labo...

We present the draft genome sequence of Fusarium equiseti strain K3, a fungus isolated from a hexachlorocyclohexane (HCH)-contaminated soil (Kitengela, Kenya). The 37.88-Mb draft genome sequence consists of 206 contigs, 12,311 predicted protein-coding sequences, and 261 tRNA sequences.

Microbial populations often display different degrees of heterogeneity in their substrate assimilation, that is, anabolic heterogeneity. It has been shown that nutrient limitations are a relevant trigger for this behavior. Here we explore the dynamics of anabolic heterogeneity under nutrient replete conditions. We applied time‐resolved stable isoto...

Use of compost is a common agricultural practice. It improves soil fertility by adding nutrients and plant growth promoting (PGP) microorganisms. The role of bacterial-fungal interactions for compost-driven fertilization, however, is still poorly understood. In this study, we investigated whether putative PGP bacteria associate to and disperse alon...

Non-motile microbes enter new habitats often by co-transport with motile microorganisms. Here, we report on the ability of hyphal-riding bacteria to co-transport lytic phages and utilize them as "weapons" during colonization of new water-unsaturated habitats. This is comparable to the concept of biological invasions in macroecology. In analogy to i...

Persistent and mobile organic compounds (PMOCs) are often detected micropollutants in the water cycle, thereby challenging the conventional wastewater and drinking water treatment techniques. Carbon-based adsorbents are often less effective or even unable to remove this class of pollutants. Understanding of PMOC adsorption mechanisms is urgently ne...

The cultivable fungal diversity from PAH-contaminated sediments was examined for the tolerance to polycyclic aromatic hydrocarbon (PAH). The 85 fungal strains, isolated in non-selective media, revealed a large diversity by ribosomal internal transcribed spacer (ITS) sequencing, even including possible new species. Most strains (64%) exhibited PAH-t...

Bacterial deposition is the first step in the formation of microbial biofilms in environmental technology, and there is high interest in controlling such deposition. Earlier work indicated that direct electric current (DC) fields could influence bacterial deposition in percolation columns. Here, a time-resolved quartz crystal microbalance with diss...

Bioavailability for contaminant degradation requires a deep understanding of the ecology of degrader microbial systems. It hence should be perceived as a microbial systems property. In this chapter we summarize recent research on microbial ecology of contaminant biodegradation in the mycosphere (i.e., the microhabitat surrounding and affected by my...

Phenotypic heterogeneity within microbial populations arises even when the cells are exposed to putatively constant and homogeneous conditions. The outcome of this phenomenon can affect the whole function of the population, resulting in, for example, new “adapted” metabolic strategies and impacting its fitness at given environmental conditions. Acc...

Phages (i.e. viruses that infect bacteria) have been considered as good tracers for the hydrological transport of colloids and (pathogenic) viruses. Little, however, is known about interactions of phages with (fungal) mycelia as the prevalent soil microbial biomass. Forming extensive and dense networks, mycelia provide significant surfaces for phag...

In recent years, research in the field of Microbial Ecology has revealed the tremendous diversity and complexity of microbial communities across different ecosystems. Microbes play a major role in ecosystem functioning and contribute to the health and fitness of higher organisms. Scientists are now facing many technological and methodological chall...

Pseudoalteromonas is a bacterial genus widely distributed in marine ecosystems. We present the genome characterization of the lytic Pseudoalteromonas virus vB_PspP-H6/1 that infects Pseudoalteromonas sp. strain H6. The virus and its host were both isolated from seawater collected from the North Sea near the island Helgoland, Germany, in the 1970s....

Pollution of ecosystems by a constantly increasing load of anthropogenic chemicals is a major driver of ecosystem service risk. This chapter summarizes relevant abiotic and biotic processes that determine the persistence, degradation, and ultimate destination of anthropogenic chemicals. It also summarizes research challenges for predicting the abil...

Botryococcus braunii is a promising microalga for the production of biofuels and other chemicals because of its high content of internal lipids and external hydrocarbons. However, due to the very thick cell wall of B. braunii, traditional chemical/physical downstream processing very often is not as effective as expected and requires high amounts of...

Bacterial deposition and transport is key to microbial ecology and biotechnological applications. We therefore tested whether electrokinetic forces (electroosmotic shear force (FEOF), electrophoretic drag force (FEP)) acting on bacteria may be used to control bacterial deposition during transport in laboratory percolation columns exposed to externa...

Chemoeffector-mediated bacterial motility and tactic swimming are major drivers for contaminant accessibility and biodegradation at submillimeter scales. In sand-filled percolated columns we tested how and to which degree chemoeffectors influenced bacterial transport and thereby promoted accessibility and degradation of distantly located 14C-naphth...

Terrestrial microbial ecosystems are exposed to many types of disturbances varying in their spatial and temporal characteristics. The ability to cope with these disturbances is crucial for maintaining microbial ecosystem functions, especially if disturbances recur regularly. Thus, understanding microbial ecosystem dynamics under recurrent disturban...

Compound-specific stable isotope analysis (CSIA) has become an established tool for assessing biodegradation in the subsurface. Diffusion-dominated vapor phase transport thereby is often excluded from quantitative assessments due to the problem of diffusive mixing of concentrations with different isotopic signatures for CSIA interpretation. In soil...

Bacterial degradation of organic compounds is an important ecosystem function with relevance to, e.g., the cycling of elements or the degradation of organic contaminants. It remains an open question, however, to which extent ecosystems are able to maintain such biodegradation function under recurrent disturbances (functional resistance) and how thi...

In order to cope with heterogeneous environments mycelial soil fungi have developed a unique network-based growth form. Unlike bacteria, hyphae efficiently spread in heterogeneous habitats such as soil, penetrate air-water interfaces and cross over air-filled pores. Here we discuss the prevalent role of the mycosphere (i.e. the microhabitat that su...

The low solubility and high hydrophobicity of hydrocarbons means that they sorb to various solids and nonaqueous-phase liquids (NAPLs), obliging hydrocarbon degrading microorganisms to physically interact with these phases. This has various implications for the physicochemical characteristics of these microbes, their modes of hydrocarbon uptake, an...

Phages (i.e. viruses infecting bacteria) are considered to be good indicators and tracers for fecal pollution, hydraulic flow or colloidal transport in the subsurface. They are typically quantified as total virus particles (VLP) or plaque forming units (PFU) of infectious phages. As transport may lead to phage deactivation, VLP quantification can o...

Fungi and bacteria are found living together in a wide variety of environments. Their interactions are significant drivers of many ecosystem functions and are important for the health of plants and animals. A large number of fungal and bacterial families are engaged in complex interactions that lead to critical behavioural shifts of the microorgani...

This chapter discusses how the hydrophobicity and other properties of oil hydrocarbons influence their availability for toxic exposure, microbial degradation and growth. It also describes how the hydrocarbon bioavailability can control the maximum population size of a degrading microbial community in a given habitat (carrying capacity). Bioavailabi...

Fungi and bacteria often share common microhabitats. Their co-occurrence and coevolution give rise to manifold ecological interactions in the mycosphere, here defined as the microhabitats surrounding and affected by hyphae and mycelia. The extensive structure of mycelia provides ideal “logistic networks” for transport of bacteria and matter in stru...

Pseudoalteromonas phage vB_PspS-H40/1 is a lytic phage that infects Pseudoalteromonas sp. strain H40. Both, the phage and its host were isolated in the 1970s from seawater samples collected from the North Sea near the island of Helgoland, Germany. The phage particle has an icosahedral capsid with a diameter of ~43 to 45 nm and a long non-contractil...

Alteromonas virus vB_AspP-H4/4 is a member of the Podoviridae family and was isolated from North Sea water in the 1970s. The complete double-stranded DNA genome has 47,631 bp with 49 predicted genes.

Environmental surveys on soil viruses are still rare and mostly anecdotal, i. e., they mostly report on viruses at one location or for only a few sampling dates. Detailed time-series analysis with multiple samples can reveal the spatio-temporal dynamics of viral communities and provide important input as to how viruses interact with their potential...

The fate and transport of hydrophobic organic compounds (HOCs) such as oil hydrocarbons are strongly influenced by their interactions with environmental matrices including soils and sediments. These interactions can be grouped into those of nonaqueous phase liquids (NAPLs), e.g., the spreading of oil on solid surfaces and its movement in porous med...

In order to cope with heterogeneous environments mycelial fungi have developed a unique network-based growth form. Unlike bacteria, hyphae efficiently spread in heterogeneous habitats such as soil, penetrate air-water interfaces and cross over air-filled pores. Here we discuss the prevalent role of the mycosphere (i.e. the microhabitat that surroun...

The low solubility and high hydrophobicity of hydrocarbons means that they sorb to various solids and nonaqueous-phase liquids (NAPLs), obliging hydrocarbon-degrading microorganisms to physically interact with these phases. This has various implications for the physicochemical characteristics of these microbes, their modes of hydrocarbon uptake, an...

Supplementary Figures and Supplementary Table

Fungal–bacterial interactions are highly diverse and contribute to many ecosystem processes. Their emergence under common environmental stress scenarios however, remains elusive. Here we use a synthetic microbial ecosystem based on the germination of Bacillus subtilis spores to examine whether fungal and fungal-like (oomycete) mycelia reduce bacter...

Tons of anthropogenic silver nanoparticles (AgNPs) are assumed to be released into the environment due to their use in many consumer products. AgNPs are known to be toxic toward microorganisms and thus may harm their specific functions in ecosystems. Here we explore the impact of AgNPs on functioning of single cells in microbial populations at dose...

Our understanding of the interactions between minerals, organic matter, and microorganisms at so-called biogeochemical interfaces in soil is still hampered by the inherent complexity of these systems. Artificial soil maturation experiments can help to bridge a gap in complexity between simple abiotic sorption experiments and larger-scale field expe...

This chapter discusses how the hydrophobicity and other properties of oil hydrocarbons influences their availability for toxic exposure, microbial degradation and growth. It also describes how the hydrocarbon bioavailability can control the maximum population size of a degrading microbial community in a given habitat (carrying capacity). Bioavailab...

Research into the biodegradation of soil contaminants has rarely addressed the consequences of predator-prey interactions. Here, we investigated the joint effect of predation and dispersal networks on contaminant degradation by linking spatial abundances of degrader (Pseudomonas fluorescens) and predator (Bdellovibrio bacteriovorus) bacteria to the...

Plant growth‐promoting rhizobacteria (PGPR) are studied as complements/alternatives to chemical fertilizers used in agriculture. However, poor information exists on the potential of PGPR from undisturbed ecosystems. Here, we have evaluated the plant growth‐promoting (PGP) effect of rhizobacterial consortia from undisturbed Chilean arid ecosystems (...

To cope with heterogeneous environments and resource distributions, filamentous fungi have evolved a spatially extensive growth enabling their hyphae to penetrate air-water interfaces and pass through air-filled pores. Such mycelia are also known to act as dispersal networks for the mobilisation of bacteria ('fungal highways') and connection of mic...

Horizontal gene transfer (HGT) is a main mechanism of bacterial evolution endowing bacteria with new genetic traits. The transfer of mobile genetic elements such as plasmids (conjugation) requires the close proximity of cells. HGT between genetically distinct bacteria largely depends on cell movement in water films, which are typically discontinuou...

The soil bacterium Burkholderia terrae strain BS001 can interact with varying soil fungi, using mechanisms that range from the utilization of carbon/energy sources such as glycerol to the ability to reach novel territories in soil via co-migration with growing fungal mycelia. Here, we investigate the intrinsic properties of the B. terrae BS001 inte...

Although several studies examined the transport of viruses in the terrestrial systems only few studies exist on marine phages (i.e. non-terrestrial viruses infecting marine host bacteria) as sensitively detectable microbial tracers for subsurface colloid transport and water flow. Here, we systematically quantified and compared for the first time th...

Mycolata form a group of Gram-positive bacteria with unique cell envelope structures that are known for their high tolerance against antibiotics and both aromatic and aliphatic hydrocarbons. An important part of the unique surface structure of the mycolata is the presence of long chain α-alkyl-β-hydroxy fatty acids, the mycolic acids. In order to i...

Contaminant biodegradation in soils is hampered by the heterogeneous distribution of degrading communities colonizing isolated microenvironments as a result of the soil architecture. Over the last years, soil salinization was recognized as an additional problem especially in arid and semiarid ecosystems as it drastically reduces the activity and mo...

The quantitative relationship between a compound’s availability for biological removal and eco-toxicity is a key issue for retrospective risk assessment and remediation frameworks. Here, we investigated the impact of facilitated bacterial dispersal on a model soil-atmosphere interface on the release, degradation and outgassing of a semi-volatile co...