Léa Cabrol
email: lea.cabrol@gmail.com

Luc Malhautier

Integrating microbial ecology in bioprocess understanding: the case of gas biofiltration

Keywords: Microbial ecology, Biofiltration, Diversity, Community structure, Resilience, Stability

Biofilters are packed-bed bioreactors where contaminants, once transferred from the gas phase to the biofilm, are oxidized by diverse and complex communities of attached microorganisms. Over the last decade, more and more studies aimed at opening the back box of biofiltration by unraveling the biodiversity-ecosystem function relationship. In this review, we report the insights provided by the microbial ecology approach in biofilters and we emphasize the parallels existing with other engineered ecosystems used for wastewater treatment, as they all constitute relevant model ecosystems to explore ecological issues. We considered three characteristic ecological indicators: the density, the diversity, and the structure of the microbial community. Special attention was paid to the temporal and spatial dynamics of each indicator, insofar as it can disclose the potential relationship, or absence of relation, with any operating or functional parameter. We also focused on the impact of disturbance regime on the microbial community structure, in terms of resistance, resilience, and memory. This literature review led to mitigated conclusions in terms of biodiversity-ecosystem function relationship. Depending on the environmental system itself and the way it is investigated, the spatial and temporal dynamics of the microbial community can be either correlated (e.g., spatial stratification) or uncoupled (e.g., temporal instability) to the ecosystem function. This lack of generality shows the limits of current 16S approach in complex ecosystems, where a functional approach may be more suitable.

Introduction

Engineered ecosystems are characterized by two compo-nents: a biotic component (communities) and a process component (matter and energy flows). Even though they are the key actors of the biological processes, little is known about the microbial communities involved in bioprocesses: how are they influenced by the environmental conditions, and how do they drive the ecosystem function?Unraveling the biotic/ abiotic interactions is one of the most challenging issues for ecologists [START_REF] Briones | Diversity and dynamics of microbial communities in engineered environments and their implications for process stability[END_REF]. In addition to a fundamental purpose, this better understanding can provide control, diagnostic and prevision tools for process monitoring. The biotic component has been more and more investigated during the last decades, thanks to the rapid development of molecular tools [START_REF] Talbot | Evaluation of molecular methods used for establishing the interactions and functions of microorganisms in anaerobic bioreactors[END_REF]. Even though not exempted from potential bias (Cabrol et al. 2010;[START_REF] Von Wintzingerode | Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis[END_REF], they provide a more representa-tive image of the community, without restricting to cultivable cells. The latter only represent 4% to 30% of the total biomass in gas biofilters [START_REF] Khammar | Link between spatial structure of bacterial communities and degradation of a complex mixture of volatile organic compounds in peat biofilters[END_REF][START_REF] Tresse | Dynamics of living and dead bacterial cells within a mixed-species biofilm during toluene degradation in a biotrickling filter[END_REF], and less than 15% in activated sludge [START_REF] Amann | Phylogenetic identification and in situ detection of individual microbial cells without cultivation[END_REF]. Biofilters are packed-bed reactors used for biological purification of waste gases containing inorganic contaminants (e.g., ammonia, hydrogen sulphide) and volatile organic compounds (VOCs) such as ketones, volatile fatty acids, sulphur, and aromatic compounds. Biofiltration combines physicochemical mass transfer and microbial oxidation within the biofilm which develops at the outer surface of the packing material [START_REF] Devinny | Biofiltration for air pollution control[END_REF]. As model ecosystems where inputs and outputs are controlled and monitored, biofilters constitute relevant tools to explore ecological concerns such as the biodiversity-ecosystem function (BEF) relationship. However, the investigation of microbial communities in biofilters is still relatively scarce, compared to other engineered ecosystems such as bioreactors for wastewater treatment. Hence, rather than limiting the literature review to the field of gas biofiltration, we will emphasize the parallels between biofiltration and bioprocesses for wastewater treatment, both involving the same kind of biodegradation mechanisms and addressing similar ecological questions.

In this review, we will consider the density, the diversity, and the structure of the microbial community as the three main characteristic community indicators. We will pay special attention to the temporal and spatial dynamics of each indicator. Indeed, the investigation of potential relationships between the microbial dynamics and operating and/or functional parameters can reveal the coupling or uncoupling between macroscopic and community components (Fig. 1). Besides the intrinsic community dynamics under stationary conditions, we will report some works that stress the importance to assess how the microbial community structure is impacted by transient environmental disturbances, and how it influences, in return, the macroscopic function of the ecosystem under perturbed conditions. Considering the limited number of studies in the field of biofiltration, and the contrasted conclusions depending on experimental conditions, the difficulty of giving an overview of the topic should be noted. However, keeping in mind the specificity of each system, we report here the observation of and the rationale for the major trends of the BEF relationship in engineered ecosystems. It should be added that we will focus on the microbial community structure globally (distribution of species abundance and its evolution), rather than listing an inventory of species identification in specific (biofiltration) environments.

It was interesting to have an overview of the insights provided by microbial ecology exploration in gas biofilters, about 10 years after the first publication on this subject. However, when reviewing the bibliographic data, the conclusions appeared to be extremely variable depending upon the experimental conditions applied, as well as the methodological approach employed to study the diversity. The same kind of discrepancies (high/low diversity, dynamic/stable communities…) was observed in other ecosystems. But this variability does not mean that nothing can be learnt from these studies. On the contrary, in each individual study, the microbial ecology approach reveals important and interesting information which must be cautiously interpreted according to the specific context in which it was obtained, before comparing it to other studies. We think that, unless great information loss, such a review should not ignore the specificities of each system and look for generality at all costs, but rather emphasize the different forms of the tenuous and intricate biodiversity ecosystem function relationship in different ecosystems.

It was part of the aim of this review to show these discrepancies. Furthermore, the absence of clear conclusion for the BEF relationship was particularly observed when the total bacterial community was targeted, through unspecific 16S rDNA targeting. This observation led to another Fig. 1 Links between environmental drivers, community response (at physiological and structural levels) and ecosystem process, modified from [START_REF] Lynch | Microbial diversity in soil: ecological theories, the contribution of molecular techniques and the impact of transgenic plants and transgenic microorganisms[END_REF][START_REF] Schimel | Microbial stress-response physiology and its implications for ecosystem function[END_REF] important point we wanted to highlight, i.e., the need for a more specific approach, permitting to overstep the shortcomings of current methods, by targeting active and functional members of the community, effectively involved in contaminant degradation.

Bacterial density

The first attempt to characterize a microbial community relies on the estimation of its density. As assessed by direct microscopic counts after DAPI staining, cell densities in gas biofilters typically range from 10 9 to 10 10 cells per gram of dry material, for organic carriers such as wood chips, roots, or peat [START_REF] Friedrich | Microbial community and physicochemical analysis of an industrial waste gas biofilter and design of 16S rRNA-targeting oligonucleotide probes[END_REF][START_REF] Khammar | Link between spatial structure of bacterial communities and degradation of a complex mixture of volatile organic compounds in peat biofilters[END_REF][START_REF] Von Keitz | Characterization of microbial communities of biofilters by phospholipid fatty acid analysis and rRNA targeted oligonucleotide probes[END_REF].

From a temporal point of view, cell density is usually stable over months in wastewater and waste gas bioreactors [START_REF] Carvalho | Long-term performance and microbial dynamics of an up-flow fixed bed reactor established for the biodegradation of fluorobenzene[END_REF][START_REF] Song | Effect of vapor-phase bioreactor operation on biomass accumulation, distribution, and activity: linking biofilm properties to bioreactor performance[END_REF][START_REF] Van Der Gast | Temporal scaling of bacterial taxa is influenced by both stochastic and deterministic ecological factors[END_REF]. Most of the time, despite some fluctuations, density cannot be consistently linked with any environmental or functional parameter [START_REF] Khammar | Link between spatial structure of bacterial communities and degradation of a complex mixture of volatile organic compounds in peat biofilters[END_REF][START_REF] Gentile | Correlation of functional instability and community dynamics in denitrifying dispersed-growth reactors[END_REF][START_REF] Widenfalk | Effects of pesticides on community composition and activity of sediment microbes-responses at various levels of microbial community organization[END_REF].

From a spatial point of view, if a vertical stratification of cell densities is reported in the bioreactor, it mostly follows the concentration gradient [START_REF] Carvalho | Long-term performance and microbial dynamics of an up-flow fixed bed reactor established for the biodegradation of fluorobenzene[END_REF][START_REF] Kim | Spatial distribution and physiological state of bacteria in a sand column experiment during the biodegradation of toluene[END_REF][START_REF] Kim | Role of biological activity and biomass distribution in air biofilter performance[END_REF], but it can also be reversed [START_REF] Khammar | Link between spatial structure of bacterial communities and degradation of a complex mixture of volatile organic compounds in peat biofilters[END_REF]). In the case of easily degradable compounds, the high contaminant concentration favors the growth of copiotrophic organisms [START_REF] Borin | Microbial succession in a compost-packed biofilter treating benzene-contaminated air[END_REF][START_REF] Hekmat | Biofilm population dynamics in a trickle-bed bioreactor used for the biodegradation of aromatic hydrocarbons from waste gas under transient conditions[END_REF]) resulting in higher cell density in the inlet section [START_REF] Pineda | Microbial characterization of organic carrier colonization during a model biofiltration experiment[END_REF][START_REF] Sundh | Effects of glucose overloading on microbial community structure and biogas production in a laboratory-scale anaerobic digester[END_REF], while the progressive substrate and/or nutrient limitation leads to a decrease of cell density along the biofilter height [START_REF] Acuña | Microbiological and kinetic aspects of a biofilter for the removal of toluene from waste gases[END_REF][START_REF] Kim | Role of biological activity and biomass distribution in air biofilter performance[END_REF]. On the contrary, for recalcitrant compounds, the lower biomass density at the inlet may be attributed to more drastic conditions in terms of moisture content and contaminant toxicity [START_REF] García-Peña | Correlation of biological activity and reactor performance in biofiltration of toluene with the fungus Paecilomyces variotii CBS115145[END_REF][START_REF] Khammar | Link between spatial structure of bacterial communities and degradation of a complex mixture of volatile organic compounds in peat biofilters[END_REF][START_REF] Song | Microbial response and elimination capacity in biofilters subjected to high toluene loadings[END_REF]. On a long term, despite an initial stratification, the density of bacterial colonization tends to homogenize along the biofilter height [START_REF] Grove | Assessment of changes in the microorganism community in a biofilter[END_REF][START_REF] Juteau | Analysis of the relative abundance of different types of bacteria capable of toluene degradation in a compost biofilter[END_REF].

Eventually, as it is hardly correlated to functional parameters, in terms of both temporal and spatial variability, the total bacterial density is not a sufficient indicator to reveal the potential links between microbial and functional components.

Bacterial diversity

Diversity estimators (richness, evenness, or Shannon indices) are computed from multivariate data provided by fingerprinting or clone library sequencing.

Spatial and temporal variability

From a temporal point of view, bacterial diversity is usually stable over time in wastewater and waste gas bioreactors, under constant [START_REF] Ayarza | Nonrandom assembly of bacterial populations in activated sludge flocs[END_REF][START_REF] Falk | Microbial community dynamics in replicate membrane bioreactors-natural reproducible fluctuations[END_REF][START_REF] Van Der Gast | Temporal scaling of bacterial taxa is influenced by both stochastic and deterministic ecological factors[END_REF] or disturbed [START_REF] Nadarajah | Effects of transient temperature conditions on the divergence of activated sludge bacterial community structure and function[END_REF][START_REF] Smith | Stability of the bacterial community in a pulp mill effluent treatment system during normal operation and a system shutdown[END_REF] operating conditions. From a spatial point of view, several works highlighted the higher diversity of bacterial communities within the inlet section of the reactors [START_REF] Calvo-Bado | Spatial and temporal analysis of the microbial community in slow sand filters used for treating horticultural irrigation water[END_REF][START_REF] Roy | Bacterial community dynamics in an anaerobic plug-flow type bioreactor treating swine manure[END_REF][START_REF] Sakano | Spatial distribution of total, ammonia-oxidizing, and denitrifying bacteria in biological wastewater treatment reactors for bioregenearuve life support[END_REF]. The development of highly diverse communities seems to be enhanced by high resource availability [START_REF] Borin | Microbial succession in a compost-packed biofilter treating benzene-contaminated air[END_REF], especially for easily biodegradable substrates [START_REF] Fernandez | Flexible community structure correlates with stable community function in methanogenic bioreactor communities perturbed by glucose[END_REF][START_REF] Lozada | Replicability of dominant bacterial populations after long-term surfactantenrichment in lab-scale activated sludge[END_REF]) at non-toxic concentrations [START_REF] Li | Dynamic changes in microbial activity and community structure during biodegradation of petroleum compounds: a laboratory experiment[END_REF][START_REF] Sei | Monitoring behaviour of catabolic genes and change of microbial community structures in seawater microcosms Turing aromatic compound degradation[END_REF]), while recalcitrant and/or toxic compounds induce more specific (less diverse) populations [START_REF] Bayle | Structural and functional responses of sewage microbial communities used for the treatment of a complex mixture of volatile organic compounds (VOCs)[END_REF][START_REF] Eichner | Thermal gradient gel electrophoresis analysis of bioprotection from pollutant shocks in the activated sludge microbial community[END_REF][START_REF] Van Der Gast | Temporal scaling of bacterial taxa is influenced by both stochastic and deterministic ecological factors[END_REF].

High diversity in biofilter communities

Insofar as we consider gas biofilters packed with organic material and treating relatively low concentrations of odorous compounds (as it is mostly the case at full scale), the biofiltration communities are usually characterized by high diversity levels (e.g., [START_REF] Friedrich | Microbial community and physicochemical analysis of an industrial waste gas biofilter and design of 16S rRNA-targeting oligonucleotide probes[END_REF]. Apart from the primary degraders, this high diversity may result from the proliferation of microorganisms growing on by-products, as well as saprophytes consuming products from the cell lysis, the extracellular polymeric substances (EPS) matrix, or the packing material [START_REF] Borin | Microbial succession in a compost-packed biofilter treating benzene-contaminated air[END_REF][START_REF] Stoffels | Bacterial community dynamics during start-up of a trickle-bed bioreactor degrading aromatic compounds[END_REF]. The active primary degraders can represent as little as 4% of the community [START_REF] Møller | Activity and three-dimensional distribution of toluene-degrading Pseudomonas putida in a multispecies biofilm assessed by quantitative in situ hybridization and scanning confocal laser microscopy[END_REF], while saprophytes are dominant [START_REF] Hekmat | Biofilm population dynamics in a trickle-bed bioreactor used for the biodegradation of aromatic hydrocarbons from waste gas under transient conditions[END_REF][START_REF] Juteau | Analysis of the relative abundance of different types of bacteria capable of toluene degradation in a compost biofilter[END_REF][START_REF] Song | Effect of vapor-phase bioreactor operation on biomass accumulation, distribution, and activity: linking biofilm properties to bioreactor performance[END_REF]. Moreover, the high diversity can be interpreted as the expression of species coexistence. Coexistence may arise (a) through niche differentiation, especially in biofilm structures characterized by a variety of microhabitats [START_REF] Fernandez | How stable is stable? Function versus community composition[END_REF][START_REF] Massol-Deyá | Succession and convergence of biofilm communities in fixed-film reactors treating aromatic hydrocarbons in groundwater[END_REF], and (b) from functional complementarity, through resource partitioning or positive interactions among different species [START_REF] Loreau | Biodiversity and ecosystem functioning: current knowledge and future challenges[END_REF][START_REF] Tilman | Causes, consequences and ethics of biodiversity[END_REF].

Relation between diversity and function

It is now well-established that the bacterial community diversity is influenced by environmental conditions (Fig. 1), principally the contaminant concentration [START_REF] Briones | Microbial diversity and dynamics in multiand single-compartment anaerobic bioreactors processing sulfaterich waste streams[END_REF][START_REF] Pholchan | Systematic study of the effect of operating variables on reactor performance and microbial diversity in laboratory-scale activated sludge reactors[END_REF]. The reverse (i.e., to what extent the diversity drives the macroscopic function in terms of biodegradation performance or stability) is still a critical question for ecologists (Fig. 1).

In the context of gas biofiltration, the effect of diversity on removal efficiency has not been explored in a systematic way. High purification performances have been reported in biofilters exhibiting either high [START_REF] Ding | Correlation of reactor performance and bacterial community composition during the removal of trimethylamine in three-stage biofilters[END_REF] or low [START_REF] Steele | Structure of microbial communities in ethanol biofilters[END_REF]) microbial diversity. There are still challenges in designing experiments to conclusively discern the contribution of diversity to function, being careful of the meaning given to the overused and confusing word "diversity" (e.g., precising where in the community the diversity happens).

This discrepancy reflects the highly controversial debate on diversity function which arose in other ecosystems. Indeed, since the key works of Naeem [START_REF] Naeem | Declining biodiversity can alter the performance of ecosystems[END_REF] and Tilman [START_REF] Tilman | Biodiversity and stability in grasslands[END_REF] on plant communities, the positive effect of diversity on ecosystem function and stability has been evidenced in various environments, at different scales, for widespread or specialized functions: microbial nitrification [START_REF] Rowan | Composition and diversity of ammonia-oxidising bacterial communities in wastewater treatment reactors of different design treating identical wastewater[END_REF]Wittebolle et al. 2009c), microbial respiration [START_REF] Bell | The contribution of species richness and composition to bacterial services[END_REF], mercury reduction [START_REF] Von Canstein | Species diversity improves the efficiency of mercury-reducing biofilms under changing environmental conditions[END_REF], carbon assimilation [START_REF] Ptacnik | Diversity predicts stability and resource use efficiency in natural phytoplankton communities[END_REF], and decomposition and mineralization of organic matter in soil [START_REF] Girvan | Bacterial diversity promotes community stability and functional resilience after perturbation[END_REF][START_REF] Griffiths | Ecosystem response of pasture soil communities to fumigation-induced microbial diversity reductions: an examination of the biodiversity-ecosystem function relationship[END_REF]. On the basis of theoretical ecology and modeling, the stabilizing effect of diversity may rely on statistical averaging (known as "portfolio effect"), while the contribution of diversity to improve productivity has been mainly attributed to complementarity between differentiated niches [START_REF] Lehman | Biodiversity, stability, and productivity in competitive communities[END_REF].

Other community factors driving the ecosystem function However, high efficiency and stability have been reported independently of the diversity level in wastewater reactors [START_REF] Cook | Effect of microbial species richness on community stability and community function in a model plant-based wastewater processing system[END_REF][START_REF] Fernandez | Flexible community structure correlates with stable community function in methanogenic bioreactor communities perturbed by glucose[END_REF][START_REF] Mota | Effects of aeration cycles on nitrifying bacterial populations and nitrogen removal in intermittently aerated reactors[END_REF], aquatic mesocosms [START_REF] Engelhardt | Species traits, species richness and the resilience of wetlands after disturbance[END_REF], and soil [START_REF] Wertz | Maintenance of soil functioning following erosion of microbial diversity[END_REF]. Beyond the potential artifacts of the experimental design (sampling effect, hidden treatment) [START_REF] Huston | Hidden treatments in ecological experiments: reevaluating the ecosystem function of biodiversity[END_REF][START_REF] Wardle | Biodiversity and ecosystem function: an issue in ecology[END_REF], various authors showed that, rather than by the diversity itself, the ecosystem function was influenced by components of the diversity [START_REF] Giller | Biodiversity effects on ecosystem functioning: emerging issues and their experimental test in aquatic environments[END_REF][START_REF] Schläpfer | Ecosystem effects of biodiversity: a classification of hypotheses and exploration of empirical results[END_REF]. Among these components are the evenness of the species distribution [START_REF] Hillebrand | Consequences of dominance: a review of evenness effects on local and regional ecosystem processes[END_REF]Wittebolle et al. 2009b), the species composition with the presence of particular traits [START_REF] Cook | Effect of microbial species richness on community stability and community function in a model plant-based wastewater processing system[END_REF], the positive species interactions, such as synergism, facilitation, and cometabolism [START_REF] Hooper | Effects of biodiversity on ecosystem functioning: a consensus of current knowledge[END_REF][START_REF] Møller | In situ gene expression in mixedculture biofilms: evidence of metabolic interactions between community members[END_REF][START_REF] Shim | Biofiltration and inhibitory interactions of gaseous benzene, toluene, xylene, and methyl tert-butyl ether[END_REF], and the functional redundancy [START_REF] Loreau | Biodiversity and ecosystem functioning: current knowledge and future challenges[END_REF]). In the latter case, among a large reservoir of organisms conducting the same function, the loss of any species will have little effect on process since other species will fill the gap (this is obviously not valid for specialistic function) [START_REF] Lynch | Microbial diversity in soil: ecological theories, the contribution of molecular techniques and the impact of transgenic plants and transgenic microorganisms[END_REF]). Moreover, under environmental changes, the redun-dant species are no more redundant; their wide range of stress response enhances the chance for a minor but resistant species to emerge, thus increasing the system stability according to the insurance hypothesis [START_REF] Elmqvist | Response diversity, ecosystem change, and resilience[END_REF][START_REF] Franklin | Structural and functional responses of a sewage microbial community to dilution-induced reductions in diversity[END_REF][START_REF] Loreau | Biodiversity and ecosystem functioning: current knowledge and future challenges[END_REF].

The divergence of empirical evidence for diversityfunction relationship is no longer surprising if we consider that contrasting predictions can play a role in this relation. First, processes carried out by a limited range of microorganisms (e.g., nitrification, methane oxidation), are more sensitive to a loss of diversity than processes sustained by a wide range of microorganisms (respiration, denitrification, and organic matter decomposition) for which there is more functional redundancy [START_REF] Griffiths | Ecosystem response of pasture soil communities to fumigation-induced microbial diversity reductions: an examination of the biodiversity-ecosystem function relationship[END_REF]. Secondly, according to the driving force of the ecosystem processselection or complementarity-the productivity will be favored by, respectively, dominance of a particular trait or evenness distribution of a diverse community [START_REF] Hillebrand | Consequences of dominance: a review of evenness effects on local and regional ecosystem processes[END_REF]). To finish, in a stable environment, the highest process rate is sustained by a particular optimal trait, from which any deviance (by increasing the diversity) will be functionally unfavorable. On the contrary, when the process undergoes environmental fluctuations, its productivity and stability are enhanced by higher trait variance, which provides faster adaptation capacity to new constraints [START_REF] Hillebrand | Consequences of dominance: a review of evenness effects on local and regional ecosystem processes[END_REF].

To conclude, even if dominant species are sufficient in mono-contaminant ecosystems, a consensus seems to accept the existence of a positive diversity effect in complex ecosystems-despite unclear mechanisms implying various diversity components. This effect may be stronger in variable than in stable environments [START_REF] Hillebrand | Consequences of dominance: a review of evenness effects on local and regional ecosystem processes[END_REF][START_REF] Loreau | Biodiversity and ecosystem functioning: current knowledge and future challenges[END_REF]) and when the biodegradation involves metabolic pathways scattered across different species [START_REF] Griffiths | Ecosystem response of pasture soil communities to fumigation-induced microbial diversity reductions: an examination of the biodiversity-ecosystem function relationship[END_REF].

Microbial community structure

The community structure is an image, at a given time and place, of the assemblage and organization of the community. It represents how the community members are distributed among species of different relative abundance, exhibiting different functional properties and contributions, and able to interact. Investigating the spatial and temporal dynamics of both ecosystem components (microscopic and macroscopic) provides clues to disentangle the potential relationship between ecosystem function and community structure.

Spatial variability

As attached biomass systems, biofilters exhibit physicochemical gradients through the bed height (decrease of pollutant and increase of by-product concentrations), leading to heterogeneous environmental microhabitats. Most biofiltration studies highlighted a longitudinal distribution of biodegradation activities characterized by higher removal efficiency near the gas inlet [START_REF] Cabrol | Evaluation de la robustesse d'un système de biofiltration d'effluent de compostage: Approche structurelle et fonctionnelle[END_REF]. Are these concentration and activity profiles correlated to the microbial distribution?

Stratification

The microbial community composition is generally heterogeneous along the bed height of attached biomass bioreactors, as observed in waste gas [START_REF] Hayes | Linking performance to microbiology in biofilters treating dimethyl sulphide in the presence and absence of methanol[END_REF][START_REF] Khammar | Link between spatial structure of bacterial communities and degradation of a complex mixture of volatile organic compounds in peat biofilters[END_REF][START_REF] Li | Assessment of microbial populations in methyl ethyl ketone degrading biofilters by denaturing gradient gel electrophoresis[END_REF][START_REF] Maestre | Bacterial community analysis of a gas-phase biotrickling filter for biogas mimics desulfurization through the rRNA approach[END_REF]) and wastewater [START_REF] Roy | Bacterial community dynamics in an anaerobic plug-flow type bioreactor treating swine manure[END_REF][START_REF] Sakano | Spatial distribution of total, ammonia-oxidizing, and denitrifying bacteria in biological wastewater treatment reactors for bioregenearuve life support[END_REF] treatment. The variability of the community structures along the bed height is usually correlated with macroscopic parameters, at two possible levels.

First, the structural stratification can be seen as the result of the physicochemical stratification through the differential selective pressure imposed by distinct concentration levels. Secondly, the structural stratification can in return influence the functions which are realized at the different levels. A first example of this correlation between microbial distribution and functional stratification is the spatial partition of mixed biofilm communities of heterotrophic and nitrifying bacteria in gas biofilter. The restriction of ammoniaoxidizing bacteria to the outlet section of the filter was explained by both outcompetition of heterotrophic bacteria for oxygen consumption and inhibition by HNO 2 [START_REF] Juhler | Distribution and rate of microbial processes in an ammonia-loaded air filter biofilm[END_REF]. Another example of structure/function correlation has been revealed in a plug-flow type anaerobic reactor consisting of eight sequential compartments, where different functions (volatile fatty acids and methane production) were performed by bacterial communities with different structures [START_REF] Roy | Bacterial community dynamics in an anaerobic plug-flow type bioreactor treating swine manure[END_REF].

Not only the concentration, but also the composition of the gas to be treated plays a role in shaping the community structure along the reactor. In biofilters treating a mixture of gaseous compounds, the readily degradable compounds are removed near the gas inlet, while the more recalcitrant ones are degraded in lower sections. This functional stratification is correlated to different community structures along the biofilter depth, suggesting that different populations are involved in different compound removal (Cabrol 2010).

Homogenization

Nevertheless, the spatial change of the community structure is not always correlated with the distribution of the degradation activity [START_REF] Friedrich | Microbial community and physicochemical analysis of an industrial waste gas biofilter and design of 16S rRNA-targeting oligonucleotide probes[END_REF]. Despite the functional stratification, the microbial community composition sometimes exhibits a surprising longitudinal homogeneity in gas biofilters [START_REF] Hekmat | Biofilm population dynamics in a trickle-bed bioreactor used for the biodegradation of aromatic hydrocarbons from waste gas under transient conditions[END_REF][START_REF] Sercu | H 2 S degradation is reflected by both the activity and composition of the microbial community in a compost biofilter[END_REF][START_REF] Tresse | Population dynamics of freefloating and attached bacteria in a styrene-degrading biotrickling filter analyzed by denaturing gradient gel electrophoresis[END_REF] and wastewater bioreactors [START_REF] Carvalho | Long-term performance and microbial dynamics of an up-flow fixed bed reactor established for the biodegradation of fluorobenzene[END_REF][START_REF] Massol-Deyá | Succession and convergence of biofilm communities in fixed-film reactors treating aromatic hydrocarbons in groundwater[END_REF][START_REF] Mcguinness | Replicability of bacterial communities in denitrifying bioreactors as measured by PCR/T-RFLP analysis[END_REF].

The absence of correlation between the physicochemical and microbial spatial distributions might be linked to experimental biases linked to the lack of sensitivity of the community profiling method or the persistence of dead cell DNA [START_REF] Lynch | Microbial diversity in soil: ecological theories, the contribution of molecular techniques and the impact of transgenic plants and transgenic microorganisms[END_REF]). Besides, the longitudinal microbial homogeneity can be explained by the growth of ubiquist and generalist populations [START_REF] Curtis | Prokaryotic diversity and its limits: microbial community structure in nature and implications for microbial ecology[END_REF] which are not influenced by the gradient environmental conditions and/or not involved in primary substrate degradation. It can be also due to the environmental standardization along the bed height, arising from (a) the supply of carbon and energy source by the packing material [START_REF] Friedrich | Microbial community and physicochemical analysis of an industrial waste gas biofilter and design of 16S rRNA-targeting oligonucleotide probes[END_REF], or (b) the percolation of water and nutrients through the packing material in biofilters, a fortiori in biotrickling filters [START_REF] Tresse | Population dynamics of freefloating and attached bacteria in a styrene-degrading biotrickling filter analyzed by denaturing gradient gel electrophoresis[END_REF] and wastewater bioreactors.

Temporal variability

Acclimatization phase

The biofilter start-up is generally the most structurally dynamic period (Sercu et al. 2005a;[START_REF] Stoffels | Bacterial community dynamics during start-up of a trickle-bed bioreactor degrading aromatic compounds[END_REF], as also reported for wastewater treatment bioreactors (Ayaladel-Río et al. 2004;[START_REF] Miura | Bacterial community structure in MBRs treating municipal wastewater: relationship between community stability and reactor performance[END_REF]Wittebolle et al. 2009a). When the system has been inoculated-as frequently done-by sludge from full-scale WWTP, the structure of the microbial community which develops after the acclimatization is dramatically divergent from the inoculum one [START_REF] Steele | Structure of microbial communities in ethanol biofilters[END_REF], even if the inoculum had been previously adapted to the contaminants [START_REF] Falk | Microbial community dynamics in replicate membrane bioreactors-natural reproducible fluctuations[END_REF]). This divergence is mostly attributed to drastic changes between full-scale and pilot-scale environment [START_REF] Eichner | Thermal gradient gel electrophoresis analysis of bioprotection from pollutant shocks in the activated sludge microbial community[END_REF][START_REF] Kaewpipat | Microbial population dynamics in laboratory-scale activated sludge reactors[END_REF], mainly in terms of growth conditions (attached biofilm vs planktonic biomass) and substrate availability (food to microorganism ratio) [START_REF] Miura | Bacterial community structure in MBRs treating municipal wastewater: relationship between community stability and reactor performance[END_REF][START_REF] Tresse | Population dynamics of freefloating and attached bacteria in a styrene-degrading biotrickling filter analyzed by denaturing gradient gel electrophoresis[END_REF]. In the case of organic packing material (i.e., already colonized by an endogenous microflora), both the inoculation and the operating conditions are sufficient to induce substantial modifications of the endogenous community structure [START_REF] Ding | Correlation of reactor performance and bacterial community composition during the removal of trimethylamine in three-stage biofilters[END_REF], even despite the absence of contaminants [START_REF] Pineda | Microbial characterization of organic carrier colonization during a model biofiltration experiment[END_REF][START_REF] Sei | Monitoring behaviour of catabolic genes and change of microbial community structures in seawater microcosms Turing aromatic compound degradation[END_REF].

The acclimatization period is generally characterized by a significant decrease of the tremendous inoculum diversity in biological filters for waste gas treatment [START_REF] Ding | Correlation of reactor performance and bacterial community composition during the removal of trimethylamine in three-stage biofilters[END_REF][START_REF] Maestre | Bacterial community analysis of a gas-phase biotrickling filter for biogas mimics desulfurization through the rRNA approach[END_REF][START_REF] Stoffels | Bacterial community dynamics during start-up of a trickle-bed bioreactor degrading aromatic compounds[END_REF]) and wastewater treatment reactors [START_REF] Sakano | Spatial distribution of total, ammonia-oxidizing, and denitrifying bacteria in biological wastewater treatment reactors for bioregenearuve life support[END_REF]. The diversity loss can be interpreted as community specialization, through various mechanisms: selection of the fittest species [START_REF] Eichner | Thermal gradient gel electrophoresis analysis of bioprotection from pollutant shocks in the activated sludge microbial community[END_REF][START_REF] Sakano | Assessment of changes in microbiol community structure Turing operation of an ammonia biofilter with molecular tools[END_REF]; competitive exclusion [START_REF] Steele | Structure of microbial communities in ethanol biofilters[END_REF]; toxic effect of the contaminants; and reduction of resource variety [START_REF] Konopka | Community dynamics and heterogeneities in mixed bacterial communities subjected to nutrient periodicities[END_REF]). More globally, the enrichment and dominance of a specific population, favored by specific operating conditions, is due to its competitive advantages in terms of growth and substrate affinity, as highlighted by kinetic studies [START_REF] Baptista | Evidence of species succession during chlorobenzene biodegradation[END_REF][START_REF] Massol-Deyá | Succession and convergence of biofilm communities in fixed-film reactors treating aromatic hydrocarbons in groundwater[END_REF].

Several works revealed the emergence of species which were not detected in the inoculum [START_REF] Sakano | Spatial distribution of total, ammonia-oxidizing, and denitrifying bacteria in biological wastewater treatment reactors for bioregenearuve life support[END_REF]. They proceed from (a) the inoculum wherein their abundance was below the detection limit of the analytical method, (b) the endogenous diversity reservoir constituted by the packing material itself, and (c) the polluted gaseous effluent or aerosols through immigration mechanisms [START_REF] Ho | Microbial populations analysis and field application of biofilter for the removal of volatile-sulfur compounds from swine wastewater treatment system[END_REF].

Temporal stability at steady state

In biofilters run under constant operating conditions, the structure of the total bacterial community can maintain a high degree of temporal stability (Sercu et al. 2005b;[START_REF] Tresse | Population dynamics of freefloating and attached bacteria in a styrene-degrading biotrickling filter analyzed by denaturing gradient gel electrophoresis[END_REF], as also observed for various macroscopic functions in wastewater treatment reactors: anaerobic digestion [START_REF] Dollhopf | Interpreting 16S rDNA T-RFLP data: application of self-organizing maps and principal component analysis to describe community dynamics and convergence[END_REF], nitrification (Wittebolle et al. 2009a), denitrification [START_REF] Gentile | Stability in a denitrifying fluidized bed reactor[END_REF], biodegradation of organic contaminants [START_REF] Falk | Microbial community dynamics in replicate membrane bioreactors-natural reproducible fluctuations[END_REF][START_REF] Konopka | Community dynamics and heterogeneities in mixed bacterial communities subjected to nutrient periodicities[END_REF][START_REF] Lapara | Stability of the bacterial communities supported by a seven-stage biological process treating pharmaceutical wastewater as revealed by PCR-DGGE[END_REF], and aromatic hydrocarbons [START_REF] Massol-Deyá | Succession and convergence of biofilm communities in fixed-film reactors treating aromatic hydrocarbons in groundwater[END_REF]. The temporal stability of the community composition has even been reported despite changing operating conditions [START_REF] Carvalho | Long-term performance and microbial dynamics of an up-flow fixed bed reactor established for the biodegradation of fluorobenzene[END_REF][START_REF] Smith | Stability of the bacterial community in a pulp mill effluent treatment system during normal operation and a system shutdown[END_REF].

It has been suggested that the constancy of the community structure would be due to the low diversity of the community [START_REF] Curtis | Prokaryotic diversity and its limits: microbial community structure in nature and implications for microbial ecology[END_REF], when for example all of the enzymes needed for the function of interest can be packaged within one organism [START_REF] Gentile | Stability in a denitrifying fluidized bed reactor[END_REF]) and when the capacity to carry out the considered function is not easily transferred to other microorganisms [START_REF] Carvalho | Long-term performance and microbial dynamics of an up-flow fixed bed reactor established for the biodegradation of fluorobenzene[END_REF].

However, significant correlation could not be pointed out between the size and/or the function of the targeted population and its dynamics. On the contrary, it is reasonable to assume that the constancy of the community is rather connected with (a) the protective and constant environment provided by the biofilm EPS matrix (Ayaladel-Río et al. 2004;[START_REF] Massol-Deyá | Succession and convergence of biofilm communities in fixed-film reactors treating aromatic hydrocarbons in groundwater[END_REF]) and (b) the strong selective pressure imposed by the environment [START_REF] Carvalho | Long-term performance and microbial dynamics of an up-flow fixed bed reactor established for the biodegradation of fluorobenzene[END_REF][START_REF] Massol-Deyá | Succession and convergence of biofilm communities in fixed-film reactors treating aromatic hydrocarbons in groundwater[END_REF], especially by the presence of contaminant [START_REF] Lozada | Impact of non-ionic surfactant on the long-term development of lab-scale activated sludge bacterial communities[END_REF]). The temporal variability of the community is reduced by the strengthening of the environmental stringency, such as periodical substrate feed [START_REF] Carrero-Colón | Effect of nutrient periodicity on microbial community dynamics[END_REF], addition of toxic pollutant [START_REF] Ayala-Del-Río | Correspondence between community structure and function during succession in phenol-and phenol-plus-trichloroethenefed sequencing batch reactors[END_REF], or increase of contaminant concentration in an industrial effluent [START_REF] Van Der Gast | Temporal scaling of bacterial taxa is influenced by both stochastic and deterministic ecological factors[END_REF]). It should be noted that when the analytical tools are not sensitive enough to assess the community profile, the stability of the dominant species may hide the instability of minor species.

Temporal dynamics at steady state

Conversely, numerous works attested that stable function could be sustained by highly dynamic communities in ammonia and VOCs biofilters [START_REF] Friedrich | Microbial community and physicochemical analysis of an industrial waste gas biofilter and design of 16S rRNA-targeting oligonucleotide probes[END_REF][START_REF] Sakano | Assessment of changes in microbiol community structure Turing operation of an ammonia biofilter with molecular tools[END_REF][START_REF] Von Keitz | Characterization of microbial communities of biofilters by phospholipid fatty acid analysis and rRNA targeted oligonucleotide probes[END_REF]) and in bioreactors performing various functions, such as anaerobic digestion [START_REF] Fernandez | How stable is stable? Function versus community composition[END_REF], nitrification [START_REF] Graham | Experimental demonstration of chaotic instability in biological nitrification[END_REF][START_REF] Wittebolle | Quantifying community dynamics of nitrifiers in functionally stable reactors[END_REF], organic contaminant removal [START_REF] Ayarza | Nonrandom assembly of bacterial populations in activated sludge flocs[END_REF][START_REF] Miura | Bacterial community structure in MBRs treating municipal wastewater: relationship between community stability and reactor performance[END_REF], and aromatic hydrocarbon degradation [START_REF] Baptista | Evidence of species succession during chlorobenzene biodegradation[END_REF]. In these reactors, the temporal dynamics is defined by (a) short-term changes of bacterial composition, (b) no persistence of particular OTU, (c) no convergence to the same climax community (Fernandez et al. 1999), and (d) no correlation between the structural variability and any operating parameter [START_REF] Nadarajah | Effects of transient temperature conditions on the divergence of activated sludge bacterial community structure and function[END_REF].

These works suggest that a constant microbial community is not essential to sustain high functional performance and stability of the process [START_REF] Wittebolle | Quantifying community dynamics of nitrifiers in functionally stable reactors[END_REF]. Rather than the persistence of a specific population, a given arrangement among populations seems more important to achieve process stability [START_REF] Fernandez | How stable is stable? Function versus community composition[END_REF].

At first, structural oscillations can be explained by uncontrolled and unnoticed fluctuations of operating conditions which influence the community composition [START_REF] Miura | Bacterial community structure in MBRs treating municipal wastewater: relationship between community stability and reactor performance[END_REF]). Moreover, a major source of variability lies in the complex network of microbial interactions [START_REF] Graham | Experimental demonstration of chaotic instability in biological nitrification[END_REF], creating condition for non-equilibrium dynamics. The maintenance of functional stability despite continuous shifts of microbial population is an indication of functional redundancy, which is ensured by the presence of a reservoir of species able to perform the same ecological function [START_REF] Briones | Diversity and dynamics of microbial communities in engineered environments and their implications for process stability[END_REF][START_REF] Franklin | Structural and functional responses of a sewage microbial community to dilution-induced reductions in diversity[END_REF]. Beyond these deterministic approaches, microbial community dynamics could be attributed to stochastic mutations according to the neutral theory [START_REF] Curtis | Prokaryotic diversity and its limits: microbial community structure in nature and implications for microbial ecology[END_REF].

Inter-replicate variability

Apart from the spatial and temporal variability of the community, it is interesting to address the question of interreplicate variability. Despite their difficulty to implement in practice, running parallel bioreactor replicates provides key information about the deterministic or stochastic forces driving the ecosystem community. The reproducibility of the community structure (in terms of species composition, spatialization and temporal patterns of species succession) has been frequently reported in wastewater treatment systems [START_REF] Ayarza | Nonrandom assembly of bacterial populations in activated sludge flocs[END_REF]Wittebolle et al. 2009a), suggesting that the microbial community is driven by deterministic mechanisms [START_REF] Loreau | Biodiversity and ecosystem functioning: current knowledge and future challenges[END_REF]). On the contrary, highly divergent communities encountered in replicate systems [START_REF] Carrero-Colón | Effect of nutrient periodicity on microbial community dynamics[END_REF][START_REF] Konopka | Community dynamics and heterogeneities in mixed bacterial communities subjected to nutrient periodicities[END_REF]) would indicate neutral mechanisms governed by stochastic events [START_REF] Curtis | Prokaryotic diversity and its limits: microbial community structure in nature and implications for microbial ecology[END_REF]. The inter-replicate variability is mainly due to minor species while the distribution of more abundant taxa is more reproducible [START_REF] Mcguinness | Replicability of bacterial communities in denitrifying bioreactors as measured by PCR/T-RFLP analysis[END_REF]. As stated by others, we infer that the validation of reproducibility is essential for the use of model ecosystems in microbial ecology studies [START_REF] Roeselers | On the reproducibility of microcosm experiments: different community composition in parallel phototrophic biofilm microcosms[END_REF].

Microbial ecology under transient regimes

As a result of fluctuating industrial activity, full-scale biofilters are usually operated under changing conditions in terms of gas stream composition, concentration, and flow rate, which can impair their functional performance [START_REF] Kraakman | Robustness of a full-scale biological system treating industrial CS 2 emissions[END_REF]. It is thus of prime importance to identify the factors and magnitude of changing conditions that can alter the functioning and biological composition of the biofilters.

Substrate pulses as a transient regime

Apart from perturbations of operating parameters (e.g., moisture, temperature), different kinds of load perturbations have been applied at lab-scale to study the biofilter transient response, such as starvation and step increase of contaminant load. However, we believe that abrupt and transient increases of load during short periods ("shock loads") are more likely to mimic the feed fluctuations observed at industrial facilities.

As ephemeral events of resource superabundance [START_REF] Holt | Theoretical perspectives on resource pulses[END_REF], resource pulses induce microbial responses in terms of growth and decay rates or enzymatic activity [START_REF] Carrero-Colón | Effect of nutrient periodicity on microbial community dynamics[END_REF][START_REF] Ergon | Life-history traits of voles in fluctuating population respond to the immediate environment[END_REF], leading to potential shifts in biofilter microbial community structure [START_REF] Yang | What can we learn from resource pulses?[END_REF]. However, whether the responses of the biological component to resource pulses reflect genetic or physiologic adaptation is still unclear [START_REF] Carrero-Colón | Effect of nutrient periodicity on microbial community dynamics[END_REF][START_REF] Holt | Theoretical perspectives on resource pulses[END_REF]. The physiological effects may regulate the short-term stress response, whereas shifts in community composition are more likely to regulate the response over longer periods [START_REF] Schimel | Microbial stress-response physiology and its implications for ecosystem function[END_REF].

From an ecological perspective, we report here the response of biofiltration communities undergoing a disturbance regime according to an integrated three-level framework, in terms of resistance, resilience, and memory.

Resistance

The resistance capacity is defined as the degree to which the microbial composition remains unchanged in the face of a disturbance [START_REF] Allison | Resistance, resilience, and redundancy in microbial communities[END_REF]. Most studies highlight that the composition of biofiltration communities is sensitive to changes of gas concentration [START_REF] Borin | Microbial succession in a compost-packed biofilter treating benzene-contaminated air[END_REF] or composition [START_REF] Hayes | Linking performance to microbiology in biofilters treating dimethyl sulphide in the presence and absence of methanol[END_REF][START_REF] Shim | Biofiltration and inhibitory interactions of gaseous benzene, toluene, xylene, and methyl tert-butyl ether[END_REF]. This poor structural resistance capacity in the face of environment disturbance is also reported in wastewater ecosystems [START_REF] Dollhopf | Interpreting 16S rDNA T-RFLP data: application of self-organizing maps and principal component analysis to describe community dynamics and convergence[END_REF][START_REF] Nadarajah | Effects of transient temperature conditions on the divergence of activated sludge bacterial community structure and function[END_REF][START_REF] Sundh | Effects of glucose overloading on microbial community structure and biogas production in a laboratory-scale anaerobic digester[END_REF] and soils [START_REF] Li | Dynamic changes in microbial activity and community structure during biodegradation of petroleum compounds: a laboratory experiment[END_REF][START_REF] Widenfalk | Effects of pesticides on community composition and activity of sediment microbes-responses at various levels of microbial community organization[END_REF]).

These composition changes can be interpreted as the differential effects of the disturbance on the different populations within the community. The stress-associated cost falls differently on different organisms, depending on their inherent tolerance and acclimation capacities [START_REF] Schimel | Microbial stress-response physiology and its implications for ecosystem function[END_REF]). Indeed, the potential toxic effect of contaminants is species-selective [START_REF] Song | Microbial response and elimination capacity in biofilters subjected to high toluene loadings[END_REF][START_REF] Szabó | Importance of rare and abundant populations for the structure and functional potential of freshwater bacterial communities[END_REF]), while the growth-benefit effect of resource increase during shock loads depends on the species kinetic strategy. It favors the growth of r-strategists at the expense of K-strategists [START_REF] Chesson | Resource pulses, species interactions, and diversity maintenance in arid and semi-arid environments[END_REF].

The lack of ecological resistance is generally not correlated to a poor functional resistance. On the contrary, the composition changes reflect the plasticity and flexibility of the community, i.e., its ability to maintain stable functional traits via rapid adaptations to environmental fluctuations [START_REF] Fernandez | Flexible community structure correlates with stable community function in methanogenic bioreactor communities perturbed by glucose[END_REF][START_REF] Loreau | Biodiversity and ecosystem functioning: current knowledge and future challenges[END_REF]. It is well-documented that communities displaying distinct species composition (before and after the disturbance) can yet fulfill the same global macroscopic function, thus supporting the concept of functional redundancy [START_REF] Botton | Resilience of microbial systems towards disturbances[END_REF][START_REF] Briones | Diversity and dynamics of microbial communities in engineered environments and their implications for process stability[END_REF].

The effect of diversity on resistance is less predictable. The lower the diversity, the more the system resistance will depend on the stress sensitivity or tolerance of the dominant species. [START_REF] Hillebrand | Consequences of dominance: a review of evenness effects on local and regional ecosystem processes[END_REF]. In other words, the ecosystem function is affected by the extinction order of its species following a disturbance. In absence of compensation, if the most extinction prone species are the most functionally efficient, then the ecosystem function will be disrupted more rapidly than predicted by random species loss [START_REF] Larsen | Extinction order and altered community structure rapidly disrupt ecosystem functioning[END_REF].

On another hand, communities considered as ecologically resistant (composition-stable) can actually respond to substrate pulses by physiological modifications implying variations of enzymatic activity [START_REF] Carreiro | Microbial enzyme shifts explain litter decay responses to simulated nitrogen deposition[END_REF] or gene expression rate [START_REF] Callister | Relating perturbation magnitude to temporal gene expression in biological systems[END_REF][START_REF] Gunsch | Relative gene expression quantification in a fungal gas-phase biofilter[END_REF]). The physiological response to stress infers a change of resource allocation from growth to survival pathways [START_REF] Schimel | Microbial stress-response physiology and its implications for ecosystem function[END_REF]).

Resilience

The engineering resilience is the rate at which a system returns to its original state after being disturbed [START_REF] Holling | Resilience and stability of ecological systems[END_REF].

From a functional point of view, gas biofilters usually show high resilience capacity, as they are able to recover high and stable removal performance aftershocks (e.g. Cabrol 2010). However, from an ecological point of view, there is no study of structural resilience in gas biofilters to date.

After stress-induced structural changes, the microbial community can either (a) continue changing if the structural breakdown was irreversible [START_REF] Nadarajah | Effects of transient temperature conditions on the divergence of activated sludge bacterial community structure and function[END_REF]), (b) stay in a new equilibrium state, stable but different from the previous disturbance state [START_REF] Eichner | Thermal gradient gel electrophoresis analysis of bioprotection from pollutant shocks in the activated sludge microbial community[END_REF]), (c) recover a structural organization similar to the one before the disturbance [START_REF] Fernandez | Flexible community structure correlates with stable community function in methanogenic bioreactor communities perturbed by glucose[END_REF][START_REF] Gentile | Stability in a denitrifying fluidized bed reactor[END_REF].

The reversibility of the structural changes may be the sign of phenotypic or physiologic changes. Moreover, a high resilience capacity may result from several microbial features contributing to the fast adaptation capacity of the microorganisms, such as their fast growth rate, their metabolic versatility, their physiologic flexibility, and their rapid evolution through mutations or horizontal gene transfer [START_REF] Allison | Resistance, resilience, and redundancy in microbial communities[END_REF][START_REF] Loreau | Biodiversity and ecosystem functioning: current knowledge and future challenges[END_REF]. The resilience of the ecosystem function is often reported to occur faster than the resilience of the community structure [START_REF] Gentile | Stability in a denitrifying fluidized bed reactor[END_REF][START_REF] Sundh | Effects of glucose overloading on microbial community structure and biogas production in a laboratory-scale anaerobic digester[END_REF], or even without resilience of the microbial composition, which supports the concept of functional redundancy [START_REF] Girvan | Bacterial diversity promotes community stability and functional resilience after perturbation[END_REF]. Rather than to a stable and diverse initial community, the resilience capacity seems to be correlated to a flexible community, able to adapt by both metabolic and structural changes, where the minor species play a major importance [START_REF] Fernandez | Flexible community structure correlates with stable community function in methanogenic bioreactor communities perturbed by glucose[END_REF][START_REF] Gentile | Stability in a denitrifying fluidized bed reactor[END_REF]).

Memory

The history of the ecosystem can shape the ecosystem response to environmental changes [START_REF] Sousa | The responses of a community to disturbance: the importance of successional age and species' life histories[END_REF][START_REF] Strickland | Testing the functional significance of microbial community composition[END_REF]. In some rare cases, previous perturbations of the system may alter the system stability face to further perturbations [START_REF] Tobor-Kapłon | Functional stability of microbial communities in contaminated soils[END_REF]. But it is generally accepted that when exposed to a new stress, the resistance and resilience capacity of an ecosystem are enhanced if it has previously experienced recurrent and small magnitude stresses, as observed in soil [START_REF] Bressan | Response of soil bacterial community structure to successive perturbations of different types and intensities[END_REF]Ranjard et al. 2008), marine chemostats [START_REF] Zemb | L'écosystème a-t-il une mémoire ? Importance de l'histoire sur la résilience fonctionnelle de communautés bactériennes hétérotrophes marines et anaérobies[END_REF]) and anaerobic digesters [START_REF] Mcmahon | Microbial population dynamics during start-up and overload conditions of anaerobic digesters treating municipal solid waste and sewage sludge[END_REF][START_REF] Zemb | L'écosystème a-t-il une mémoire ? Importance de l'histoire sur la résilience fonctionnelle de communautés bactériennes hétérotrophes marines et anaérobies[END_REF]). The community composition, density, and function (enzymatic activities) are more sensitive and less stable when the system is exposed to forcing variables outside its "lifehistory", compared to systems that have regularly experienced environmental variability [START_REF] Waldrop | Response of microbial community composition and function to soil climate change[END_REF]. However, the effect of pre-exposure to stress is complex and may depend on the relatedness of the consecutive stresses. The pre-exposure to metal has been reported to improve the community resilience only when primary and subsequent stresses were of the same nature [START_REF] Philippot | Effect of primary mild stresses on resilience and resistance of the nitrate reducer community to a subsequent severe stress[END_REF]. Apart from toxic and/or environmental stresses (e.g., pH, metals, chemicals), the alternance of feast-famine conditions is also known to increase the resistance of the ecosystem [START_REF] Irvine | Period biofilter operation for enhanced performance during unsteady-state loading conditions[END_REF][START_REF] Song | Effect of vapor-phase bioreactor operation on biomass accumulation, distribution, and activity: linking biofilm properties to bioreactor performance[END_REF][START_REF] Wright | Transient response of vapor-phase biofilters[END_REF].

The way the historical contingencies drive the ecosystem community and function relies on either physiological or structural adaptation.

Several physiological adaptations probably play a role in the memory effect, such as the increased synthesis rate of exopolysaccharides [START_REF] Ayala-Del-Río | Correspondence between community structure and function during succession in phenol-and phenol-plus-trichloroethenefed sequencing batch reactors[END_REF]) and heat shock proteins, as well as the increased storage capacity of substrates during feast periods, which can be consumed during famine periods [START_REF] Chesson | Resource pulses, species interactions, and diversity maintenance in arid and semi-arid environments[END_REF][START_REF] Holt | Theoretical perspectives on resource pulses[END_REF][START_REF] Irvine | Period biofilter operation for enhanced performance during unsteady-state loading conditions[END_REF]. These physiological adaptations appear under unspecific stress conditions. It may explain that physiological-driven memory effect is observed for various kinds of stress, either similar or completely different from the previous ones experienced by the ecosystem [START_REF] Ayala-Del-Río | Correspondence between community structure and function during succession in phenol-and phenol-plus-trichloroethenefed sequencing batch reactors[END_REF]).

The historical contingencies may also have shaped the community structure [START_REF] Waldrop | Response of microbial community composition and function to soil climate change[END_REF] and involved modifications of the community composition and abundance ratios, with selection of the most fitted species. The density and diversity of microbial communities are influenced by the historical exposure to contamination [START_REF] Bouskill | Temporal bacterial diversity associated with metalcontaminated river sediments[END_REF]. According to the intermediate disturbance hypothesis, variable environments enable to maintain a higher diversity level than under stable conditions [START_REF] Flöder | Diversity in planktonic communities: an experimental test of the intermediate disturbance hypothesis[END_REF][START_REF] Yamamoto | Pulsed nutrient supply as a factor inducing phytoplankton diversity[END_REF]. Moreover, the niche variability of fluctuating environments offers axis for differentiation, thus permitting the coexistence of species with differentiated characteristics [START_REF] Chesson | Resource pulses, species interactions, and diversity maintenance in arid and semi-arid environments[END_REF][START_REF] Stewart | Partitioning of resources and the outcome of interspecific competition: a model and some general considerations[END_REF]. This higher diversity, acquired through historical stresses, may confer higher functional and stability advantages to the ecosystem in case of subsequent stress.

Conclusion and perspectives

This literature review led to mitigated conclusions in terms of biodiversity-ecosystem function relationship. Depending on the specific case under study (both the environmental system itself and the way it is investigated), the spatial and temporal dynamics of the microbial community (in terms of density, diversity and structure) can be either correlated or uncoupled to the ecosystem function. This antagonism indicates that the conclusions found in literature must be considered with caution as they depend on several criteria: (a) the analytical tool to explore the microbial diversity; (b) the method to calculate diversity, similarity, and stability indices, according to multiple definitions [START_REF] Grimm | Babel, or the ecological stability discussions: an inventory and analysis of terminology and a guide for avoiding confusion[END_REF]), (c) the time scale [START_REF] Grove | Assessment of changes in the microorganism community in a biofilter[END_REF], and (d) the specific function and population which are targeted [START_REF] Peterson | Ecological resilience, biodiversity, and scale[END_REF]. Operating conditions such as pH, packing material, temperature, or the applied inlet load [START_REF] Ding | Correlation of reactor performance and bacterial community composition during the removal of trimethylamine in three-stage biofilters[END_REF][START_REF] Egli | Community analysis of ammonia and nitrite oxidizers during start-up of nitritation reactors[END_REF] can also influence the temporal and spatial variability. These experimental and methodological factors must be accurately defined in further studies, especially when looking for comparisons with other ecosystems.

The concept of stability must be handled cautiously because of its relativity [START_REF] Carpenter | From metaphor to measurement: resilience of what to what?[END_REF]. Indeed resistance and resilience capacities are tightly dependent upon the component considered within the ecosystem (either biological or functional), the variable chosen to describe this component (e.g., biomass density or system productivity), the kind of disturbance applied to the system, and the environmental conditions prevailing before and after the disturbance period [START_REF] Botton | Resilience of microbial systems towards disturbances[END_REF][START_REF] Hillebrand | Consequences of dominance: a review of evenness effects on local and regional ecosystem processes[END_REF]. According to the observation level (genetic, physiologic, biochemical), the community organisation and dynamics can be coupled or uncoupled to the disturbances [START_REF] Chaer | Shifts in microbial community composition and physiological profiles across a gradient of induced soil degradation[END_REF].

Finally, the lack of correlation between community dynamics and ecosystem function can effectively indicate the structure-function uncoupling, due to, e.g., functional redundancy, stochastic dynamics, or generalist populations. The potential structure-function link is even obscured and more difficult to establish by the possibility of horizontal gene transfer [START_REF] Lynch | Microbial diversity in soil: ecological theories, the contribution of molecular techniques and the impact of transgenic plants and transgenic microorganisms[END_REF]). However, it can also disclose the inadequacy between the ecosystem complexity and the resolutive power of the analytical tool used to study it. For example, specific functional populations actually involved in the degradation can be hidden by the high diversity in complex biofiltration systems with high resource availability and low selective pressure, where most of the community is not involved in primary degradation [START_REF] Møller | Activity and three-dimensional distribution of toluene-degrading Pseudomonas putida in a multispecies biofilm assessed by quantitative in situ hybridization and scanning confocal laser microscopy[END_REF][START_REF] Song | Effect of vapor-phase bioreactor operation on biomass accumulation, distribution, and activity: linking biofilm properties to bioreactor performance[END_REF]. In such systems, targeting the total bacterial community, with current 16S rDNA-based methods, may not be discriminant enough to reveal the potential link between a specific minor population and a specific function.

In order to point out significant the BEF relationships which can find practical applications for biofilter moni-toring, it will be necessary to go beyond the shortcomings of current 16S rDNA approach, from "who is there" to "who does what" concerns. Further research should focus on active [START_REF] Boon | Bioaugmentation as a tool to protect the structure and function of an activatedsludge microbial community against a 3-chloroaniline shock load[END_REF][START_REF] Roy | Bacterial community dynamics in an anaerobic plug-flow type bioreactor treating swine manure[END_REF]) and functional populations [START_REF] Wittebolle | Quantifying community dynamics of nitrifiers in functionally stable reactors[END_REF][START_REF] Falk | Microbial community dynamics in replicate membrane bioreactors-natural reproducible fluctuations[END_REF]) actually involved in contaminant degradation. To overstep the simplified statement "one gene one protein", studies should combine functional gene targeting with proteomics approach. Stable isotope-based labelling of contaminant degraders can also provide deep insights for characterization of actively degrading microbial populations [START_REF] Alexandrino | Stable-isotope-based labeling of styrene-degrading microorganisms in biofilters[END_REF]).

Acknowledgements The work of Dr. Léa Cabrol was supported by a PhD grant CIFRE 2006/497 from Veolia Environnement Recherche et Innovation. The authors would like to thank Dr. Franck Poly from the Laboratory of Microbial Ecology, University of Lyon I, for helpful discussions.


Kévin Delcourt

Kevin Delcourt
email: kevin.delcourt@irit.fr

Towards Multi-Agent Interactive Reinforcement Learning for Opportunistic Software Composition in Ambient Environments

Keywords: Ambient Intelligence, Machine Learning, Human-AI Interaction, Multi-Agent System, Human-in-the-loop, Emergence

published or not. The documents may come   L'archive ouverte pluridisciplinaire

CONTEXT 1.Ambient Intelligence

Ambient Intelligence [START_REF] Sadri | Ambient intelligence: A survey[END_REF] aims to provide a human user with a personalized cyber-physical environment and associated software, that are tailored to their specific situation and needs. Openness, dynamism, unpredictability of ambient systems are all difficulties to overcome. Furthermore, the ever-changing needs of each user are another source of complexity.

As a result, it is extremely onerous for a designer to anticipate every possible state of the ambient environment and the user needs, then design user-adapted applications in the traditional top-down way.

Opportunistic Software Composition

My Ph. D. thesis is part of a research project that addresses those challenges by designing and developing a solution that learns from its user, to bring out tailored applications composed in a bottom-up manner from software services that are present at the time in their ubiquitous environment. This opportunistic composition model [START_REF] Younes | Agent-mediated application emergence through reinforcement learning from user feedback[END_REF] is based on continuous reinforcement learning [START_REF] Sutton | Reinforcement learning: An introduction[END_REF] from the user's feedback. Learning and decision are distributed in a multi-agent system (MAS) [START_REF] Wooldridge | An Introduction to MultiAgent Systems[END_REF] to meet requirements such as scalability in number of devices as well as distribution in the cyber-physical space.

In this model, every agent manages a basic service of the user's environment, and collaborates to decide on the composition of its service with another. Thus, due to agents' distributed interactions, applications emerge from the environment in the form of a set of service compositions. Agents' decision is built from their local view of the environment, and from the feedback provided by the user during their everyday routine, i.e. their preferred applications for any given environment.

Project Status

This project is at the crossroads of several research areas: ambient intelligence, machine learning, human-computer interaction, and MAS. We considered several research questions in past works:

• A prior work examined the problem of building composite applications with the user-in-the-loop [START_REF] Younes | Agent-mediated application emergence through reinforcement learning from user feedback[END_REF]. However, the solution takes into account the human user in a limited way, over-stressing them. • As preliminary work, I published a demonstration of our solution's prototype in a controlled ambient environment [START_REF] Delcourt | Automatic and Intelligent Composition of Pervasive Applications -Demonstration[END_REF], also available as a video 1 . • In order to present composite applications to an end-user in an understandable way, we developed a domain-specific language, and a tool allowing for a user to have access to several views of the application [START_REF] Trouilhet | Model-Driven Engineering for End-Users in the Loop in Smart Ambient Systems[END_REF].

PH.D. THESIS SCOPE 2.1 Research Questions

Human users have complex and dynamic goals that depend on their preferences and the services available in the ambient cyberphysical environment. Moreover, they are prone to make mistakes when interacting with learning systems. And so, since our past works only sporadically treated human factors, we focus on the interactions between the human user and the learning system and how best to learn from them:

• How to best build and adapt the life-long model of the human user?

1 https://www.irit.fr/%7eSylvie.Trouilhet/demo/outletSeeking.mp4

• How to decentralize this user-oriented intelligence in a MAS, in order to allow, among other things, the learning system to scale up? • How can autonomous learning agents collaborate to build useful collective knowledge? • How to do so and not burden the user with excessive solicitation? [START_REF] Bach | Adaptation of ergonomic criteria to human-virtual environments interactions[END_REF] • Is knowledge about one user transferable to another, and how? Indeed, for now, we only studied the case of a single user in an ambient environment. • Finally, how to assess any proposed solution and validate that the above issues are taken into account?

Concerning the fourth research question, I have explored in a prior work [START_REF] Delcourt | Interactive Reinforcement Learning for Software Composition via Software Product Lines -Approach and Research Questions[END_REF] the possibility of leveraging software product lines [START_REF] Metzger | Software product line engineering and variability management: achievements and challenges[END_REF] in order to decrease the amount of feedback required from the user. Working on addressing these issues led me to study the field of Interactive Machine Learning.

Interactive Machine Learning

Interactive machine learning (IML) systems regroup all systems that allow end-users, devoid of ML knowledge, to produce an ML-based solution satisfying their needs [START_REF] Amershi | Power to the people: The role of humans in interactive machine learning[END_REF]. Thus, recommendation systems [START_REF] Schnabel | The Impact of More Transparent Interfaces on Behavior in Personalized Recommendation[END_REF] and end-user programming systems of intelligent software [START_REF] Fails | Interactive machine learning[END_REF] are related to this domain. IML being at the intersection of human-computer interaction (HCI) and machine learning (ML), most studies in the field tend to lean towards one or the other. On the HCI side, work on IML tends to focus on the impact of human-AI interaction on the user experience, improving global performance by focusing on usability issues:

• Amershi et al. extracted 18 guidelines from the literature that could be used by designers to produce more user-friendly intelligent systems [START_REF] Amershi | Guidelines for human-AI interaction[END_REF]. • In [START_REF] Honeycutt | Soliciting human-in-the-loop user feedback for interactive machine learning reduces user trust and impressions of model accuracy[END_REF], Honeycutt et al. study the impact of the interaction with an automated learning system on the user's trust. It is an important factor to consider: if a user does not trust a system enough, its usage will decline. On the contrary a higher trust than necessary means the user won't be watchful for system poor decisions with potentially dire consequences.

On the ML side, studies focus on finding and tuning ML algorithms to best learn from human interaction, therefore increasing global performance:

• In [START_REF] Holzinger | Interactive machine learning: experimental evidence for the human in the algorithmic loop[END_REF], Holzinger et al. showed that an ant colony optimization system produced better results when receiving human guidance. • Christiano et al. present an interactive reinforcement learning system leveraging deep neural networks to minimize the interaction needed to learn a sequence of actions from human feedback [START_REF] Christiano | Deep reinforcement learning from human preferences[END_REF].

Research Proposal

The main objective of my thesis is to propose a non-intrusive solution taking into account human factors, based on the insights gained from IML and related domains. And later to produce a software prototype out of this model. In this contribution, the interactions between the learning system and the user would benefit the system which gets feedback on its predictions, as well as the user who gets a pertinent service offer. Finally, we would then need to study and validate this solution in an open dynamic environment, in relation to end-users, in order to affirm the quality of our proposal regarding the user experience of the system. That is a transverse issue as every contribution in this project would benefit from being thoroughly validated.

Proc. of the 21st International Conference on Autonomous Agents and Multiagent Systems (AAMAS 2022), P. Faliszewski, V. Mascardi, C. Pelachaud, M.E. Taylor (eds.), May 9-13, 2022, Online. © 2022 International Foundation for Autonomous Agents and Multiagent Systems (www.ifaamas.org). All rights reserved.

CONCLUSIONWe presented in this extended abstract the research domain and the specific questions to be addressed during my Ph.D., namely how to learn from the human user and distribute knowledge through a MAS, to bring out in an ambient environment the applications that most suit their need. To the extent of our knowledge, this is a relatively emergent field of study, and we hope to get valuable feedback and insights on our past, present, and future works during the doctoral consortium.