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Commonwealth war cemeteries commemorate the fallen of both world wars. Every casualty is remembered with a memorial or on a headstone. However, the headstones need to be maintained extensively, as microorganisms easily colonise them, affecting legibility and the stone substrate in the longer term. In the past, pesticides and other chemicals were popular to clean headstones, but due to raised environmental concerns, new treatment strategies are necessary. Within conservation science, enzymes have emerged as a popular tool for restoration. However, studies related to the use of enzymes for stone conservation are limited. Within this preliminary study, we applied commercially available enzyme-based treatments on biofouled natural building stones in the laboratory and in situ. Photography and spectrophotometry were used to monitor the effect of the treatment. The application of enzymes resulted in rapid disintegration of biological pigments, whereas visual improvement occurred more gradually. The successful application of enzymes suggests their potential to replace pesticides as the principal cleaning agent for headstones and natural building stones in a more general fashion.

Rapid contamination of drinking water in distribution and storage systems can occur due to pressure drop, backflow, cross-connections, accidents, and bio-terrorism. Small volumes of a concentrated contaminant (e.g., wastewater) can contaminate large volumes of water in a very short time with potentially severe negative health impacts. The technical limitations of conventional, cultivation-based microbial detection methods neither allow for timely detection of such contaminations, nor for the real-time monitoring of subsequent emergency remediation measures (e.g., shock-chlorination). Here we applied a newly developed continuous, ultra high-frequency flow cytometry approach to track a rapid pollution event and subsequent disinfection of drinking water in an 80-min laboratory scale simulation. We quantified total (TCC) and intact (ICC) cell concentrations as well as flow cytometric fingerprints in parallel in real-time with two different staining methods. The ingress of wastewater was detectable almost immediately (i.e., after 0.6% volume change), significantly changing TCC, ICC, and the flow cytometric fingerprint. Shock chlorination was rapid and detected in real time, causing membrane damage in the vast majority of bacteria (i.e., drop of ICC from more than 380 cells μl-1 to less than 30 cells μl-1 within 4 min). Both of these effects as well as the final wash-in of fresh tap water followed calculated predictions well. Detailed and highly quantitative tracking of microbial dynamics at very short time scales and for different characteristics (e.g., concentration, membrane integrity) is feasible. This opens up multiple possibilities for targeted investigation of a myriad of bacterial short-term dynamics (e.g., disinfection, growth, detachment, operational changes) both in laboratory-scale research and full-scale system investigations in practice., Frontiers in Microbiology, 8, ISSN:1664-302X

Single cells can be characterized in terms of their phenotypic properties using flow cytometry. However, up to our knowledge there has not yet been a thorough survey concerning the classification of bacterial species based on flow cytometric data. This paper aims to perform a thorough investigation concerning the identification of bacterial communities of various complexities in species richness. We do this by creating so-called in silico communities, communities created by aggregating the data coming from individual cultures; moreover we show that it is possible to use in silico communities to identify in vitro created communities as well, proving the biological relevance and usability of bacterial in silico communities.

Flow cytometry is able measure up to 50.000 cells in various dimensions in seconds of time. This large amount of data gives rise to the possibility of making predictions at the single-cell level, however, applied to bacterial populations a systemic investigation lacks. In order to combat this deficiency, we cultivated twenty individual bacterial populations and measured them through flow cytometry. By creating in silico communities we are able to use supervised machine learning techniques in order to examine to what extent single-cell predictions can be made; this can be used to identify the community composition. We show that for more than half of the communities consisting out of two bacterial populations we can identify single cells with an accuracy >90%. Furthermore we prove that in silico communities can be used to identify their in vitro counterpart communities. This result leads to the conclusion that in silico communities form a viable representation for synthetic bacterial communities, opening up new opportunities for the analysis of bacterial flow cytometric data and for the experimental study of low-complexity communities.

Microbial single cells can be characterized by their phenotypic properties using flow cytometry. Therefore flow cytometry can be used to analyze various aspects of environmental microbial communities. In recent years, researchers have focused on fully exploiting the multivariate data that such analyses generate. As they are interested in the diversity of an environmental sample, we need a proper estimation of the number of species and their abundances. We modified a recently published algorithm to estimate the microbial diversity based on flow cytometry data. After giving a brief sketch of the problem setup, we will review this algorithm alongside its various implementations. Moreover we will present our current implementation combined with future challenges we foresee.

Marine methylotrophs play a key role in the global carbon cycle by metabolizing reduced one-carbon compounds that are found in high concentrations in marine environments. Genome, physiology and diversity studies have been greatly facilitated by the numerous model organisms brought into culture. However, the availability of marine representatives remains poor. Here, we report the isolation of four novel species from North Sea sediment enrichments closely related to the Alphaproteobacterium Methyloceanibacter caenitepidi. Each of the newly isolated Methyloceanibacter species exhibited a clear genome sequence divergence which was reflected in physiological differences. Notably one strain R-67174 was capable of oxidizing methane as sole source of carbon and energy using solely a soluble methane monooxygenase and represents the first marine Alphaproteobacterial methanotroph brought into culture. Differences in maximum cell density of >1.5 orders of magnitude were observed. Furthermore, three strains were capable of producing nitrous oxide from nitrate. Together, these findings highlight the metabolic and physiologic variability within closely related Methyloceanibacter species and provide a new understanding of the physiological basis of marine methylotrophy.

Methane-oxidizing bacteria (MOB) have a large potential as a microbial sink for the greenhouse gas methane as well as for biotechnological purposes. However, their application in biotechnology has so far been hampered, in part due to the relative slow growth rate of the available strains. To enable the availability of novel strains, this study compares the isolation of MOB by conventional dilution plating with miniaturized extinction culturing, both performed after an initial enrichment step. The extinction approach rendered 22 MOB isolates from four environmental samples, while no MOB could be isolated by plating. In most cases, extinction culturing immediately yielded MOB monocultures making laborious purification redundant. Both type I (Methylomonas spp.) and type II (Methylosinus sp.) MOB were isolated. The isolated methanotrophic diversity represented at least 11 different strains and several novel species based on 16S rRNA gene sequence dissimilarity. These strains possessed the particulate (100%) and soluble (64%) methane monooxygenase gene. Also, 73% of the strains could be linked to a highly active fast-growing mixed MOB community. In conclusion, miniaturized extinction culturing was more efficient in rapidly isolating numerous MOB requiring little effort and fewer materials, compared with the more widely applied plating procedure. This miniaturized approach allowed straightforward isolation and could be very useful for subsequent screening of desired characteristics, in view of their future biotechnological potential.

Many microbial ecologists have described the composition of microbial communities in a plenitude of environments, which has greatly improved our basic understanding of microorganisms and ecosystems. However, the factors and processes that influence the behaviour and functionality of an ecosystem largely remain black boxes when using conventional approaches. Therefore, synthetic microbial ecology has gained a lot of interest in the last few years. Because of their reduced complexity and increased controllability, synthetic communities are often preferred over complex communities to examine ecological theories. They limit the factors that influence the microbial community to a minimum, allowing their management and identifying specific community responses. However, besides their use for basic research, synthetic ecosystems also found their way towards different applications, like industrial fermentation and bioremediation. Here, we review why and how synthetic microbial communities are applied for research purposes and for which applications they have been and could be successfully used.

In this work three observations are reported leading to a reconsideration of biofilm based microbial electrosynthesis (MES). The first is that stainless steel felt cathodes are able to support MES from CO2 to volatile fatty acids. The second is that biomass is efficiently trapped as a biofilm and in flocs between the stainless steel fibres, possibly enabling higher electron conversion rates due to high hydrogen partial pressures close to the biocatalysts. A third observation is transient formate production during MES of acetate. These three key findings offer a different perspective on MES i.e. challenging the biofilm paradigm. Is a biofilm really needed to achieve profitable MES?

Manganese (II) and manganese-oxidizing bacteria were used as an efficient biological system for the degradation of the xenoestrogen 17 alpha-ethinylestradiol (EE2) at trace concentrations. Mn(2+)-derived higher oxidation states of Mn (Mn(3+), Mn(4+)) by Mn(2+)-oxidizing bacteria mediate the oxidative cleavage of the polycyclic target compound EE2. The presence of manganese (II) was found to be essential for the degradation of EE2 by Leptothrix discophora, Pseudomonas putida MB1, P. putida MB6 and P. putida MB29. Mn(2+)-dependent degradation of EE2 was found to be a slow process, which requires multi-fold excess of Mn(2+) and occurs in the late stationary phase of growth, implying a chemical process taking place. EE2-derived degradation products were shown to no longer exhibit undesirable estrogenic activity.

The suitability of hydrogen-oxidizing bacteria (HOB) as microbial protein producers was the focus of the earliest studies on these organisms and, in the current scenario of climate change, remains a relevant topic. Their ability to use hydrogen as a single electron donor translates into the possibility of developing new technologies based on renewable energy. Secondly, in contrast to processes based on heterotrophic organisms which result in the production of carbon dioxide, HOB can capture it from industrial point sources. Lastly, nutrients such as nitrogen and phosphorus can be upgraded into biomass. These features are clearly relevant in the context of microbial protein production but can also be of interest in the field of bioremediation. The main purpose of this doctoral dissertation is to explore the potential of HOB in the context of nutrient remediation and nutrient recovery. Specifically, we evaluated the practical use of an HOB enriched biofilm to remove orthophosphate from surface water, as a strategy to avoid algae blooms (nutrient remediation). In parallel, we investigated the added value of using conditions such as salt and temperature to steer HOB communities to lower diversities, whilst maintaining a high protein content and a high quality amino acid profile (nutrient recovery). In a nutshell, we show HOB are able to remove orthophosphate from different water sources to ultra-low concentrations, without the addition of any chemicals or nutrients. In addition, we also show the use of salt and temperature provides an alternative to stabilize microbial communities and achieve a more defined composition.

Natural and managed freshwater ecosystems are hotspots of biodiversity, biogeochemical cycling, and provide numerous societal services (e.g., drinking water production, wastewater treatment). The microbial communities that inhabit these systems form complex assemblages of interacting microbial taxa, for which the community structure and function are not yet fully understood. This research presents new insights into the microbial community ecology of both natural and managed freshwater systems by developing and validating new technologies to study them and by investigating the genomic adaptations to their freshwater habitat. A first line of hypotheses focused on the development and application of novel flow cytometry tools to monitor the structure of aquatic microbial communities in a fast and non-invasive manner. These tools were then applied to both natural (Lake Michigan) and managed (cooling and drinking water) freshwater ecosystems. In parallel, a second line of hypotheses delved into the genomic properties that some of the abundant populations in these communities have evolved to their freshwater environment.

The production of vegetables in growing media is an efficient way to produce vegetables in soilless culture systems. The management of the microbial community associated with growing media may serve as potential sustainable pathway to increase eco-efficiency. Consequently, it is important to find out how biotic and abiotic factors affect the composition and diversity of microbial communities associated with growing media. The aim of this PhD thesis was to study the ecology of the microbial community in soilless culture systems. First, the microbial community of a mineral and an organic growing medium was examined and it was found that both growing media have a distinct, microbial community structure. Second, key functionalities of growing media and their individual constituents were quantified. Particularly, the nitrogen dynamics were studied in relation to the microbial community associated with plant and growing medium. Third, the valorization of recycled nutrients as a high-value microalgae fertilizer and struvite was investigated. In addition, an adapted fertigation strategy in combination with organic fertilizers was developed to narrow the yield gap with a pure mineral growing medium when cultivating tomatoes. Afterwards, the microbial community structure of four contrasting soil and soilless tomato cultivating systems were studied. Finally, the effect of fertilizers and plant type on the microbial community structure of the rhizosphere and the bulk zone were investigated. Overall, organic growing media show a potential for developing novel cultivating systems fitting into a more sustainable horticulture.

Methane (CH4) is an important greenhouse gas, and the majority (ca. 60%) of its emission originates from anthropogenic sources. Methane oxidizing bacteria (MOB) are characterized by their unique ability to use CH4 as a sole carbon and energy source. Recently, accumulating evidence demonstrated that methane oxidation is stimulated when MOB are interacting with non-methanotrophic microbes. These interactions can be very specific, although it is not yet entirely elucidated what the determining factors to a successful partnership are. Hence, it seems that a methanotrophic interactome is required for effective biological aerobic methane oxidation, rather than individual obligate methanotrophic bacteria. In this dissertation, we focused on bacterial interactions between MOB and non-MOB and try to assess what are the determinants for non-MOB partner selection in the methanotrophic interactome. We focus specifically on representatives of alpha- and gammaproteobacterial MOB, which are known to exhibit differential functional traits which can in turn be conceptualized as distinct life strategies. The impact of these differences in MOB life strategies on interactions with non-MOB has not been studied. An increased insight in the co-existence and the extent of co-dependence of MOB and non-MOB partners is required to fully understand the essential ecosystem service of biological methane oxidation. In PART 1 (TOP-DOWN APPROACH), we dissected a methanotrophic enrichment culture (optimal methanotrophic interactome) by means of time-resolved stable isotope probing combined with 454-pyrosequencing of the 16S rRNA genes to assess which interactome partners are most intricately involved in the assimilation of 13CH4-derived carbon. In PART 2 (BOTTOM-UP APPROACH), we artificially assembled an optimal methanotrophic interactome by piecing together multiple non-MOB strains with MOB (co-cultivation). Firstly, we supervised the selection of MOB for non-MOB partners by establishing compatibility and matching selected MOB with non-MOB partners. Microbial adaptation and abundance of all partners was investigated using q-PCR. Secondly, we allowed an unsupervised selection for non-MOB partners by the MOB and these interactions were monitored by DGGE. In PART 3 (CRYOPRESERVETION), we develop a cryopreservation protocol based on DMSO (and DMSO+TT) as a cryopretactant, which can used to adequately preserve optimal interactomes (preservation of key functional characteristics as well as composition) to allow possible biotechnological applications. In PART 1, we found that 13CH4-derived carbon is differentially distributed among interactome partners through time. We suggested that the most intricately associated non-MOB partners would be the first to assimilate 13CH4-C and could hence be considered “primary consumers” of whereas organisms labeled later in the time-course SIP experiment are more loosely associated with the MOB and may be “secondary consumers” of organic carbon derived from both the MOB and the primary consumers. In PART 2a, we could not observe adaptation of a moderately compatible partner to MOB (or vice versa) during repeated co-cultivation with a gammaproteobacterial MOB. Conversely, clear (though limited) adaptation was observed with an alphaproteobacterial MOB. Regardless of its initial compatibility with the MOB, a third partner nearly always completely obliterated the non-MOB partner in the existing MOB:non-MOB interactome. In PART 2b, we showed a clear partner selection where some of the persisting partners were “promiscuous” and could persist regardless of MOB type , whereas others were more specifically associated with either MOB type. Additionally, we observed that alpha- and gammaproteobacterial MOB differentially route CH4-derived carbon to the interactome. Finally, while repeated co-cultivation did not significantly impact the magnitude of overall methane oxidation rates (MOR), it did appear to stabilize the biological variability in MOR as compared to acenically grown MOB. In PART 3, the optimized cryopreservation protocol for storage of mixed microbial cultures adequately preserved both community structure and functionality of a methanotrophic interactome (among others) for 3 months at -80°C. These findings may be of significance for methanotrophic interactome Microbial Resource Management, if biotechnological application of non-MOB partners is the ultimate goal. Overall, unsupervised synthetic interactome assembly approaches should be preferred, as they specifically restrict only non-MOB partners that can persist with the MOB from other non-MOB partners. If specific biotechnological applications can be found for such an optimal combination of interactome partners, it is of great interest to preserve a reproducible sample of it for extended periods of time. Exploitation and engineering of these methanotrophic interactomes could lead to improved and sustainable mitigation and recovery of CH4 in the form of metabolic energy or CH4-derived carbon.

Inflammatory bowel diseases (IBD) are characterized by a severe chronic, relapsing intestinal inflammation. An imbalance in structural and functional properties of the gut microbiota that can disrupt host-microbe homeostasis – defined as microbial dysbiosis – is associated with the etiology of IBD. Modulation of the dysbiosed gut microbiota in IBD is gaining more attention as a novel strategy to control the disease and to support current therapy. Butyrate-producing bacteria are considered as the future probiotics for IBD because butyrate has anti-inflammatory functions and has the capacity to strengthen the intestinal barrier. Before setting up clinical trials in humans with these novel probiotic candidates, more knowledge of their behavior under gastrointestinal conditions is required. The aim of this PhD research was to characterize and evaluate the potency of butyrate-producing bacteria, and especially of Butyricicoccus pullicaecorum, to modulate the microbiome and epithelial barrier in IBD. By using an in vitro intestinal technology platform, simulating the conditions from the stomach to the colon, we provided more insights in the potential of applying B. pullicaecorum or a mix of butyrate-producing bacteria as future probiotic for IBD.

Self-healing concrete has become the main focus of several research programs that have been bringing together people from academia and industry. The remediation of the micro-cracks that are formed in the concrete structures has been the aim of these research programs. These cracks are a quite well known problem that can lead to corrosion of the steel reinforcement and, in the worst cases, to the failure of the entire concrete structure. The maintenance costs due to the repair of these cracks can be of the order of € 130 (direct costs) per m3 of concrete. Hence, a self-healing technology is of interest to the industrial partners. Scientific studies indicate that a Microbial Induced Carbonate Precipitation (MICP), using microbial spores as active agent, can be an alternative for the actual repair methods. The precipitation of this concrete compatible material allows the filling of the cracks restoring the water tightness of the concrete structure. By avoiding the water ingression one also avoids the corrosion of the reinforcement. However, the production of bacterial spores is yet imposing considerable costs. Industrial concrete producers and contractors are willing to pay extra € 15 to € 20 per m3 of concrete for a bio-based self-healing product if the increase in service life is ensured. There is an urgent need to develop the production of a bio-additive to make the biological self-healing industrial applicable. Furthermore, protective carriers or encapsulation materials have been used in microbial self-healing concrete studies due to the harsh environment of concrete, i.e. very high pH (~ 13), relatively small pore size (< 0.1 nm) and dry conditions. These protection methodologies improve the survival probability of the bacterial agents once incorporated in the concrete matrix. This study deals with the up-scaling of suitable bacterial spores for self-healing concrete applications and with the study of some protection methodologies. The first part of this work is directly related with the up-scaling of axenic bacterial spore cultures while a non-axenic bacterial culture is studied in a second part. In the third part of the study different protection methods were tested in order to evaluate concrete compatibility with industrially available materials. The fourth and last part of this study deals with the economic and ecological consequences of this technology and its industrial feasibility. Up-scaling of axenic bacterial spore cultures Both Bacillus sphaericus and Bacillus cohnii spores were first produced at lab scale in order to evaluate and select the best growth conditions. Different media formulations were used to produce the bacterial spores in order to evaluate the most optimal one. MBS (Minimal Basal Salts) and SM2 (Sporulation Medium 2) media were selected among the tested possibilities as sporulation media for Bacillus sphaericus and Bacillus cohnii respectively. Biological parameters such as microbial activity and calcium carbonate precipitation capabilities were evaluated for both Bacillus sphaericus and Bacillus cohnii vegetative cells resulting from the germination of their respective bacterial spores. Increasing the production volume showed to have no effect on either microbial activity or calcium carbonate precipitation capabilities of both axenic cultures. Despite of the good microbial activity observed, a decrease in the biomass yield from 3.5 to 2.5 g CDW/L was registered in the Bacillus sphaericus cultures while no difference was noticed in the Bacillus cohnii cultures. Nevertheless, the biomass yield of the Bacillus sphaericus was still a factor 6 higher than the one of Bacillus cohnii cultures. Moreover, the amount of calcium carbonate precipitated by the Bacillus sphaericus cells was 5 times higher than the one obtained with the Bacillus cohnii cells. Additionally, the sporulation time required for Bacillus sphaericus cultures at 5 L scale, defined as the time required to obtain 90 % of the biomass present in the form of spores, was a factor 4 lower when compared with the one for Bacillus cohnii spores. Both bacterial spores unfortunately provoked a decrease in compressive strength when incorporated in mortar cubes. Nevertheless, both bacterial cultures, produced at lab scale, were able to perform self-healing in mortar specimens when properly immobilized in diatomaceous earth. Both types of bacterial spores produced at lab scale were able to originate vegetative cells capable of closing cracks up to 0.4 mm. For the bacterial cultures produced at 5 L scale only Bacillus sphaericus was tested regarding self-healing capabilities, revealing the complete closure of cracks up to 0.4 mm. Yet, the survival capability of Bacillus cohnii spores produced at 5 L scale was tested upon incorporation in mortar specimens. These bacterial spores, when immobilized in diatomaceous earth, were able to survive the mortar incorporation maintaining their viability. Up-scaling of non-axenic bacterial spores culture In this part, the production of a non-axenic ureolytic bacterial culture able to sporulate was evaluated. A powderous material containing an efficient ureolytic microbial community (Cyclic EnRiched Ureolytic Powder or CERUP) was developed. Ureolytic activity, calcium carbonate precipitation capability and the effects in concrete were evaluated at production scales of 5 and 50 L. The non-axenic culture obtained following this new selective process, at both 5 L and 50 L scales, showed to be as good as the benchmark i.e. axenic vegetative cells resultant from the germination of Bacillus sphaericus spores, both in terms of urea hydrolysis (20 g urea/L in 24 hours) and calcium carbonate precipitation (0.5 g CaCO3/g CDW.h). Plain incorporation of CERUP in concrete was found to be efficient at levels of 0.5 and 1 % of the cement weight. The use of inexpensive materials to produce CERUP was beneficial for the concrete application since it decreases the total production cost. Protection methods and their compatibility with concrete The use of axenic cultures for self-healing concrete requires some sort of protection of the bacterial agents. On the one hand, biological compatibility is, naturally, an important characteristic that must be attained by the protection material. On the other hand, concrete compatibility and cost feasibility must also be strongly considered. In this part of the study the influence of different protection methodologies was evaluated. Commercially available possible protection approaches (diatomaceous earth, metakaolin, zeolite and air entrainment) were tested regarding their influence on mortar setting and compressive strength when plain incorporated or combined with Bacillus sphaericus spores and their respective nutrients. The influence of CERUP, salt protected/immobilized, was also investigated within the same scope. The most severe effect in setting time was observed in all samples containing nutrients for Bacillus sphaericus with a significantly undesirable increase of 340 minutes. Samples containing Bacillus sphaericus spores showed the most significant undesirable decreases in compressive strength up to 68 %. Yet, the use of the novel salt protected/immobilized CERUP had no significant effect on the setting and the compressive strength of mortar. These results indicate that the use of non-axenic and self-protected bacterial cultures must be considered as a valuable alternative for the currently proposed axenic cultures. Economical and ecological aspects of the microbial based self-healing concrete technology The last part of the present study deals with cost calculation regarding both axenic and non-axenic production of self-healing bacterial agents. Concrete is a very large market and thus, one must consider the need to produce several thousands of tons of biological agent to supply it. Therefore, an economical evaluation upon the different possibilities must be conducted. It was found that the production cost of axenic cultures is, at least, a factor 10 higher than the one of non-axenic cultures. Nevertheless, despite of the lower production cost calculated for the non-axenic cultures, these are still very expensive for concrete application. Hence, process optimization and new techniques must be further studied in order to bring the bacterial self-healing concrete technology closer to full scale application. Carbon dioxide (CO2) emissions caused by the production of the bacterial agents was also evaluated. It was found that both axenic cultures are responsible for a higher CO2 emission when compared with the non-axenic ones. However, the production of Bacillus sphaericus spores showed to be responsible for only 2.7 times more CO2 emitted when compared with CERUP while the production of Bacillus cohnii spores caused CO2 emissions 40 times higher than the ones caused by the production of CERUP. Overall, the non-axenic culture (CERUP) showed not only a more feasible production process as also a lower CO2 footprint. Therefore, the use of non-axenic bacterial cultures for self-healing concrete purposes is more industrially feasible than the use of axenic ones. Biological self-healing concrete requires further optimization in order to reach industrially feasible values. Nonetheless, the technology is of considerable potential and warrants to be further investigated. Future research must be conducted using axenic but particularly also with non-axenic bacterial cultures which can be more robust and hold the potential to be more cost effective.

Since the industrial revolution, the average temperature on Earth has risen considerably, mainly due to the enormous emissions of greenhouse gases. This doctoral research focused on microbial mitigation strategies for methane (CH4), the second most important greenhouse gas after CO2. Therefore, methanotrophic microbiomes were used, the latter being entire microbial communities depending on CH4 for their activity. In a first phase, the effects of external growth parameters on the activity and structure of such communities were evaluated. Thereafter, research was done on the interactions taking place within the methanotrophic microbiomes, thereby proving that carbon fluxes take place between methanotrophs and associated microorganisms. Lastly, the methalgae concept was developed; by cocultivation of methanotrophs and algae, it was possible to treat CO2 and CH4 simultaneously under anoxic conditions.

Summary Microorganisms establish with their animal hosts close interactions. They are involved in many aspects of the host life, physiology and evolution, including nutrition, reproduction, immune homeostasis, defence and speciation. Thus, the manipulation and the exploitation the microbiota could result in important practical applications for the development of strategies for the management of insect‐related problems. This approach, defined as ‘Microbial Resource Management’ (MRM), has been applied successfully in various environments and ecosystems, as wastewater treatments, prebiotics in humans, anaerobic digestion and so on. MRM foresees the proper management of the microbial resource present in a given ecosystem in order to solve practical problems through the use of microorganisms. In this review we present an interesting field for application for MRM concept, i.e. the microbial communities associated with arthropods and nematodes. Several examples related to this field of applications are presented. Insect microbiota can be manipulated: (i) to control insect pests for agriculture; (ii) to control pathogens transmitted by insects to humans, animals and plants; (iii) to protect beneficial insects from diseases and stresses. Besides, we prospect further studies aimed to verify, improve and apply MRM by using the insect–symbiont ecosystem as a model.

Bioelectrochemical systems (BES) have been explored according to three main concepts: to produce energy from organic substrates, to generate products and to provide specific environmental services. In this work, by using an engineering approach, biological conversion rates are calculated for BES resp. anaerobic digestion. These rates are compared with currents produced by chemical batteries and chemical fuel cells in order to position BES in the energy-market. To evaluate the potential of generating various products, the biochemistry behind the biological conversion rates is examined in relation to terminal electron transfer molecules. By comparing kinetics rather than thermodynamics, more insight is gained in the biological bottlenecks that hamper a BES. The short-term future for BES research and its possible application is situated in smart niches in sustainable environmental development, i.e. in processes where no large currents or investment cost intensive reactors are needed to obtain the desired results. Some specific examples are identified.