The Ecological and Physiological Significance of the Growth of Heterotrophic Microorganisms with Mixtures of Substrates

Spatiotemporal dynamics of high and low nucleic acid-content bacterial communities in Chinese coastal seawater: assembly process, co-occurrence relationship and the ecological functions

Studies of high nucleic acid-content (HNA) and low nucleic acid-content (LNA) bacterial communities are updating our view of their distributions and taxonomic composition. However, there are still large gaps in our knowledge of the composition, assembly processes, co-occurrence relationships and ecological functions of HNA and LNA bacterial communities. Here, using 16S rRNA gene amplicon sequencing, we investigated the spatiotemporal dynamics, assembly processes, co-occurrence relationships and ecological functions of HNA and LNA bacterial communities in the samples collected in summer and winter in Chinese coastal seas. The communities of HNA and LNA bacteria had clear spatiotemporal patterns and LNA bacteria was phylogenetically less diverse than HNA bacteria in both seasons. The distribution of HNA and LNA bacteria were significantly affected by the environmental factors and a significant seasonal-consistent distance-decay patterns were found in HNA and LNA bacteria. Furthermore, a quantitative assessment of ecological processes revealed that dispersal limitation, homogeneous selection exerted important roles in the community assembly of HNA and LNA bacteria. More importantly, we observed seasonality in the co-occurrence relationships: closer inter-taxa connections of HNA bacterial communities in winter than in summer and the opposite is true in the LNA bacterial communities. Some ecological functions, such as: phototrophy, photoautotrophy, oxygenic photoautotrophy, were different between HNA and LNA bacteria. These results provide a better understanding of spatiotemporal patterns, processes, and the ecological functions of HNA and LNA bacterial communities in Chinese coastal seawater.

Dynamic utilization of low-molecular-weight organic substrates across a microbial growth rate gradient

AIM

Low-molecular-weight organic substances (LMWOSs) are at the nexus between microorganisms, plant roots, detritus, and the soil mineral matrix. Nominal oxidation state of carbon (NOSC) has been suggested a potential parameter for modeling microbial uptake rates of LMWOSs and the efficiency of carbon incorporation into new biomass.

METHODS AND RESULTS

In this study, we assessed the role of compound class and oxidation state on uptake kinetics and substrate-specific carbon use efficiency (SUE) during the growth of three model soil microorganisms, a fungal isolate (Penicillium spinulosum) and two bacterial isolates (Paraburkholderia solitsugae, and Ralstonia pickettii). Isolates were chosen that spanned a growth rate gradient (0.046-0.316 h^-1 ) in media containing 34 common LMWOSs at realistically low initial concentrations (25 μM each). Clustered, co-utilization of LMWOSs occurred for all three organisms. Potential trends (p < 0.05) for early utilization of more oxidized substrates were present for the two bacterial isolates (P. solitsugae and R. pickettii), but high variability (R² < 0.15) and a small effect of NOSC indicate these relationships are not useful for prediction. The SUEs of selected substrates ranged from 0.16-0.99 and there was no observed relationship between NOSC and SUE.

CONCLUSION

Our results do not provide compelling population-level support for NOSC as a predictive tool for either uptake kinetics or the efficiency of use of LMWOS in soil solution.

SIGNIFICANCE AND IMPACT OF THE STUDY

Metabolic strategies of organisms are likely more important than chemical identity in determining LMWOS cycling in soils. Previous community-level observations may be biased towards fast-responding bacterial community members.

Linking Increased Isotope Fractionation at Low Concentrations to Enzyme Activity Regulation: 4-Cl Phenol Degradation by Arthrobacter chlorophenolicus A6

Slow microbial degradation of organic trace chemicals ("micropollutants") has been attributed to either downregulation of enzymatic turnover or rate-limiting substrate supply at low concentrations. In previous biodegradation studies, a drastic decrease in isotope fractionation of atrazine revealed a transition from rate-limiting enzyme turnover to membrane permeation as a bottleneck when concentrations fell below the Monod constant of microbial growth. With degradation of the pollutant 4-chlorophenol (4-CP) by Arthrobacter chlorophenolicus A6, this study targeted a bacterium which adapts its enzyme activity to concentrations. Unlike with atrazine degradation, isotope fractionation of 4-CP increased at lower concentrations, from ε(C) = -1.0 ± 0.5‰ in chemostats (D = 0.090 h^-1, 88 mg L^-1) and ε(C) = -2.1 ± 0.5‰ in batch (c₀ = 220 mg L^-1) to ε(C) = -4.1 ± 0.2‰ in chemostats at 90 μg L^-1. Surprisingly, fatty acid composition indicated increased cell wall permeability at high concentrations, while proteomics revealed that catabolic enzymes (CphCI and CphCII) were differentially expressed at D = 0.090 h^-1. These observations support regulation on the enzyme activity level─through either a metabolic shift between catabolic pathways or decreased enzymatic turnover at low concentrations─and, hence, reveal an alternative end-member scenario for bacterial adaptation at low concentrations. Including more degrader strains into this multidisciplinary analytical approach offers the perspective to build a knowledge base on bottlenecks of bioremediation at low concentrations that considers bacterial adaptation.

Metabolic patterns reveal enhanced anammox activity at low nitrogen conditions in the integrated I-ABR

Substrate concentrations greatly influence bacterial growth and metabolism. However, optimal nitrogen concentrations for anammox bacteria in nitrogen-limited environments remain unclear. Here, we observed enhanced nitrogen metabolism and anabolism of anammox bacteria at low nitrogen conditions. Efficient nitrogen removal was achieved at ammonium and nitrite influent concentration of 30 mg/L under HRT of 1 hr, with an average nitrogen removal rate (NRR) of 0.73 kg N/(m³ ·day) in I-ABR composed of four compartments. The highest anammox activity of 6.25 mmol N/ (gVSS·hr) was observed in the fourth compartment (C4) with the lowest substrate levels (ammonium and nitrite of 11.6 mg/L and 7 mg/L). This could be resulted from the highest expression level of genes involved in nitrogen metabolism in C4, which was 1.49-1.67 times higher than that in other compartments. Besides, the second compartment (C2) exhibited the most active anabolism at ammonium and nitrite of 17 mg/L and 13 mg/L, respectively, which contributed to the most active amino acid synthesis and thus the highest EPS (1.35 times higher) in C2. This enhanced amino acid auxotrophy between anammox bacteria with heterotrophs, and consequently, heterotrophs thrived and competed for nitrite. These results hint at the potential application of anammox process in micro-polluted water. PRACTITIONER POINTS: High nitrogen removal and efficient biomass retention at low nitrogen concentrations under short HRT was achieved in I-ABR. Optimal concentrations for anammox nitrogen removal and anabolism were discussed under low nitrogen concentrations. More active anabolism contributed to enhanced amino acid synthesis and thus higher EPS contents. Low substrate levels led to enhanced expression of genes involved in nitrogen metabolism and thus high anammox activity.

Ecophysiological Study of Paraburkholderia sp. Strain 1N under Soil Solution Conditions: Dynamic Substrate Preferences and Characterization of Carbon Use Efficiency

We used time-resolved metabolic footprinting, an important technical approach used to monitor changes in extracellular compound concentrations during microbial growth, to study the order of substrate utilization (i.e., substrate preferences) and kinetics of a fast-growing soil isolate, Paraburkholderia sp. strain 1N. The growth of Paraburkholderia sp. 1N was monitored under aerobic conditions in a soil-extracted solubilized organic matter medium, representing a realistic diversity of available substrates and gradient of initial concentrations. We combined multiple analytical approaches to track over 150 compounds in the medium and complemented this with bulk carbon and nitrogen measurements, allowing estimates of carbon use efficiency throughout the growth curve. Targeted methods allowed the quantification of common low-molecular-weight substrates: glucose, 20 amino acids, and 9 organic acids. All targeted compounds were depleted from the medium, and depletion followed a sigmoidal curve where sufficient data were available. Substrates were utilized in at least three distinct temporal clusters as Paraburkholderia sp. 1N produced biomass at a cumulative carbon use efficiency of 0.43. The two substrates with highest initial concentrations, glucose and valine, exhibited longer usage windows, at higher biomass-normalized rates, and later in the growth curve. Contrary to hypotheses based on previous studies, we found no clear relationship between substrate nominal oxidation state of carbon (NOSC) or maximal growth rate and the order of substrate depletion. Under soil solution conditions, the growth of Paraburkholderia sp. 1N induced multiauxic substrate depletion patterns that could not be explained by the traditional paradigm of catabolite repression.IMPORTANCE Exometabolomic footprinting methods have the capability to provide time-resolved observations of the uptake and release of hundreds of compounds during microbial growth. Of particular interest is microbial phenotyping under environmentally relevant soil conditions, consisting of relatively low concentrations and modeling pulse input events. Here, we show that growth of a bacterial soil isolate, Paraburkholderia sp. 1N, on a dilute soil extract resulted in a multiauxic metabolic response, characterized by discrete temporal clusters of substrate depletion and metabolite production. Our data did not support the hypothesis that compounds with lower energy content are used preferentially, as each cluster contained compounds with a range of nominal oxidation states of carbon. These new findings with Paraburkholderia sp. 1N, which belongs to a metabolically diverse genus, provide insights on ecological strategies employed by aerobic heterotrophs competing for low-molecular-weight substrates in soil solution.

Improving Biodegradation of Clofibric Acid by Trametes pubescens through the Design of Experimental Tools

Clofibric acid (CLF) is the main pharmacologically active metabolite in composition of the pharmaceutical products used for controlling blood lipid content. This xenobiotic compound is highly persistent in the aquatic environment and passes unchanged or poorly transformed in wastewater treatment plants. A white-rot fungal strain of Trametes pubescens was previously selected, for its ability for clofibric acid biodegradation (up to 30%) during cultivation in submerged system under aerobic conditions at an initial CLF concentration of 15 mg L⁻¹. Plackett-Burman design (PBD) and response surface methodology (RSM) were used for experimental planning, mathematical modelling and statistical analysis of data of the biotechnological process of CLF biotransformation by Trametes pubescens fungal strain. After optimization, the capacity of the selected Trametes pubescens strain to degrade CLF was increased by cultivation in a liquid medium containing 3 g·L⁻¹ yeast extract, 15 g·L⁻¹ peptone, 5 g·L⁻¹ glucose and mineral salts, inoculated at 2% (v/v) vegetative inoculum and cultivated at pH 5.5, during 14 days at 25 °C and 135 rpm. In these optimized biotechnological conditions, the CLF biotransformation yield was 60%.

The ecology of heterogeneity: soil bacterial communities and C dynamics

Heterogeneity is a fundamental property of soil that is often overlooked in microbial ecology. Although it is generally accepted that the heterogeneity of soil underpins the emergence and maintenance of microbial diversity, the profound and far-reaching consequences that heterogeneity can have on many aspects of microbial ecology and activity have yet to be fully apprehended and have not been fully integrated into our understanding of microbial functioning. In this contribution we first discuss how the heterogeneity of the soil microbial environment, and the consequent uncertainty associated with acquiring resources, may have affected how microbial metabolism, motility and interactions evolved and, ultimately, the overall microbial activity that is represented in ecosystem models, such as heterotrophic decomposition or respiration. We then present an analysis of predicted metabolic pathways for soil bacteria, obtained from the MetaCyc pathway/genome database collection (https://metacyc.org/). The analysis suggests that while there is a relationship between phylogenic affiliation and the catabolic range of soil bacterial taxa, there does not appear to be a trade-off between the 16S rRNA gene copy number, taken as a proxy of potential growth rate, of bacterial strains and the range of substrates that can be used. Finally, we present a simple, spatially explicit model that can be used to understand how the interactions between decomposers and environmental heterogeneity affect the bacterial decomposition of organic matter, suggesting that environmental heterogeneity might have important consequences on the variability of this process. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.

Phototrophic Lactate Utilization by Rhodopseudomonas palustris Is Stimulated by Coutilization with Additional Substrates

The phototrophic purple nonsulfur bacterium Rhodopseudomonas palustris is known for its metabolic versatility and is of interest for various industrial and environmental applications. Despite decades of research on R. palustris growth under diverse conditions, patterns of R. palustris growth and carbon utilization with mixtures of carbon substrates remain largely unknown. R. palustris readily utilizes most short-chain organic acids but cannot readily use lactate as a sole carbon source. Here we investigated the influence of mixed-substrate utilization on phototrophic lactate consumption by R. palustris We found that lactate was simultaneously utilized with a variety of other organic acids and glycerol in time frames that were insufficient for R. palustris growth on lactate alone. Thus, lactate utilization by R. palustris was expedited by its coutilization with additional substrates. Separately, experiments using carbon pairs that did not contain lactate revealed acetate-mediated inhibition of glycerol utilization in R. palustris This inhibition was specific to the acetate-glycerol pair, as R. palustris simultaneously utilized acetate or glycerol when either was paired with succinate or lactate. Overall, our results demonstrate that (i) R. palustris commonly employs simultaneous mixed-substrate utilization, (ii) mixed-substrate utilization expands the spectrum of readily utilized organic acids in this species, and (iii) R. palustris has the capacity to exert carbon catabolite control in a substrate-specific manner.IMPORTANCE Bacterial carbon source utilization is frequently assessed using cultures provided single carbon sources. However, the utilization of carbon mixtures by bacteria (i.e., mixed-substrate utilization) is of both fundamental and practical importance; it is central to bacterial physiology and ecology, and it influences the utility of bacteria as biotechnology. Here we investigated mixed-substrate utilization by the model organism Rhodopseudomonas palustris Using mixtures of organic acids and glycerol, we show that R. palustris exhibits an expanded range of usable carbon substrates when provided substrates in mixtures. Specifically, coutilization enabled the prompt consumption of lactate, a substrate that is otherwise not readily used by R. palustris Additionally, we found that R. palustris utilizes acetate and glycerol sequentially, revealing that this species has the capacity to use some substrates in a preferential order. These results provide insights into R. palustris physiology that will aid the use of R. palustris for industrial and commercial applications.

Application of unstructured kinetic models to predict microcystin biodegradation: Towards a practical approach for drinking water treatment

Biological drinking water treatment technologies offer a cost-effective and sustainable approach to mitigate microcystin (MC) toxins from harmful algal blooms. To effectively engineer these systems, an improved predictive understanding of the bacteria degrading these toxins is required. This study reports an initial comparison of several unstructured kinetic models to describe MC microbial metabolism by isolated degrading populations. Experimental data was acquired from the literature describing both MC removal and cell growth kinetics when MC was utilized as the primary carbon and energy source. A novel model-data calibration approach melding global single-objective, multi-objective, and Bayesian optimization in addition to a fully Bayesian approach to model selection and hypothesis testing were applied to identify and compare parameter and predictive uncertainties associated with each model structure. The results indicated that models incorporating mechanisms of enzyme-MC saturation, affinity, and cooperative binding interactions of a theoretical single, rate limiting reaction accurately and reliably predicted MC degradation and bacterial growth kinetics. Diverse growth characteristics were observed among MC degraders, including moderate to high maximum specific growth rates, very low to substantial affinities for MC, high yield of new biomass, and varying degrees of cooperative enzyme-MC binding. Model predictions suggest that low specific growth rates and MC removal rates of degraders are expected in practice, as MC concentrations in the environment are well below saturating levels for optimal growth. Overall, this study represents an initial step towards the development of a practical and comprehensive kinetic model to describe MC biodegradation in the environment.

Oscillatory behaviour control in a continuous culture under double-substrate limitation

The paper discusses the possibility of using a mixture of two growth limiting substrates to induce or eliminate self-sustained oscillations in a continuous culture process. The proportion of both substrates in the mixture is treated as a new control variable. The presented approach is based on the assumption that the oscillatory behaviour occurs for selected substrates in some range of dilution rates. Because a double-substrate limitation may occur, the analysis is performed for two fundamental substrate utilization patterns: simultaneous consumption and diauxic growth. By using model simulations and bifurcation analysis, we show that an appropriate proportion of two substrates in the mixture allows for the control of the oscillatory behaviour.

The Effect of Organic Carbon Addition on the Community Structure and Kinetics of Microcystin-Degrading Bacterial Consortia

Microcystin (MC), a hepatotoxin that is associated with cyanobacterial blooms in freshwater lakes, threatens the quality of drinking water resources. Biodegradation of MC using biofiltration is emerging as a cost-effective solution for drinking water treatment. This study reports isolation of five MC-degrading microbial consortia and investigation of their community structure and kinetics in the presence or absence of a readily-bioavailable organic carbon source. The results indicated that the presence of a bioavailable organic carbon source caused: (1) the proliferation of community members previously unobserved in each consortium cultured without ethanol; (2) a shift in abundance of representative taxa; (3) a fluctuation in genera affiliated with MC-biodegradation; and, (4) a unique response in simulated diversity among consortia. These changes to each microbial consortium were paralleled by a significant decline in MC degradation kinetics. Overall, this study highlights the importance of integrating environmental conditions into the design and operation of biofiltration systems for MC biodegradation.

A metabolomic view of how low nitrogen strength favors anammox biomass yield and nitrogen removal capability

The low yield of anaerobic ammonium oxidation (anammox) biomass has attracted great attention because of its difficulty to be abundantly enriched. Patterns of substrate supply greatly influence microbial metabolism and behavior. The present study proposed that low nitrogen strength was beneficial to anammox biomass yield and nitrogen removal when comparing a membrane bioreactor (MBR) operated at low nitrogen strength with short hydraulic retention time (HRT) (R-low; influent: fixed at 100 mg-N L^-1) and one operated at high nitrogen strength with long HRT (R-stepwise; influent: 100-700 mg-N L^-1). Different nitrite concentrations in the two MBRs would indicate discrepant environments, and inevitably resulted in the discrepant microbial responses for anammox community. In particular, we found that at low nitrogen strength, increased activities of purine and pyrimidine metabolism pathways provided more abundant nucleic acids for bacterial proliferation. More active reaction of lipid and protein synthesis favored the synthesis of cellular structure. Importantly, the metabolism of cheaper amino acids was more active under low nitrogen strength, which was coupled with higher metabolic flux and potentially more active exchange of costly amino acids as public goods. In this way, more energy could be saved and applied to biomass yield. Higher active bacterial diversity and more positive interactions among bacterial species in R-low further favored biomass yield and nitrogen removal. The present study highlighted the significant effect of substrate supply patterns on anammox, which is meaningful to overcome the current bottleneck of deficient anammox biomass for application in wastewater treatment.

Exometabolite niche partitioning among sympatric soil bacteria

Soils are arguably the most microbially diverse ecosystems. Physicochemical properties have been associated with the maintenance of this diversity. Yet, the role of microbial substrate specialization is largely unexplored since substrate utilization studies have focused on simple substrates, not the complex mixtures representative of the soil environment. Here we examine the exometabolite composition of desert biological soil crusts (biocrusts) and the substrate preferences of seven biocrust isolates. The biocrust's main primary producer releases a diverse array of metabolites, and isolates of physically associated taxa use unique subsets of the complex metabolite pool. Individual isolates use only 13−26% of available metabolites, with only 2 out of 470 used by all and 40% not used by any. An extension of this approach to a mesophilic soil environment also reveals high levels of microbial substrate specialization. These results suggest that exometabolite niche partitioning may be an important factor in the maintenance of microbial diversity.

Production and consumption of metabolites by soil microorganisms are important for nutrient cycling and maintenance of microbial diversity. Here, Baran et al. study metabolite uptake and release by desert soil microorganisms, showing that coexisting microbes can have divergent substrate preferences.

Effect of Global Regulators RpoS and Cyclic-AMP/CRP on the Catabolome and Transcriptome of Escherichia coli K12 during Carbon- and Energy-Limited Growth

For heterotrophic microbes, limited availability of carbon and energy sources is one of the major nutritional factors restricting the rate of growth in most ecosystems. Physiological adaptation to this hunger state requires metabolic versatility which usually involves expression of a wide range of different catabolic pathways and of high-affinity carbon transporters; together, this allows for simultaneous utilization of mixtures of carbonaceous compounds at low concentrations. In Escherichia coli the stationary phase sigma factor RpoS and the signal molecule cAMP are the major players in the regulation of transcription under such conditions; however, their interaction is still not fully understood. Therefore, during growth of E. coli in carbon-limited chemostat culture at different dilution rates, the transcriptomes, expression of periplasmic proteins and catabolomes of strains lacking one of these global regulators, either rpoS or adenylate cyclase (cya), were compared to those of the wild-type strain. The inability to synthesize cAMP exerted a strong negative influence on the expression of alternative carbon source uptake and degradation systems. In contrast, absence of RpoS increased the transcription of genes belonging to high-affinity uptake systems and central metabolism, presumably due to reduced competition of σ^D with σ^S. Phenotypical analysis confirmed this observation: The ability to respire alternative carbon substrates and to express periplasmic high-affinity binding proteins was eliminated in cya and crp mutants, while these properties were not affected in the rpoS mutant. As expected, transcription of numerous stress defence genes was negatively affected by the rpoS knock-out mutation. Interestingly, several genes of the RpoS stress response regulon were also down-regulated in the cAMP-negative strain indicating a coordinated global regulation. The results demonstrate that cAMP is crucial for catabolic flexibility during slow, carbon-limited growth, whereas RpoS is primarily involved in the regulation of stress response systems necessary for the survival of this bacterium under hunger conditions.

Biodegradation: Updating the concepts of control for microbial cleanup in contaminated aquifers

Biodegradation is one of the most favored and sustainable means of removing organic pollutants from contaminated aquifers but the major steering factors are still surprisingly poorly understood. Growing evidence questions some of the established concepts for control of biodegradation. Here, we critically discuss classical concepts such as the thermodynamic redox zonation, or the use of steady state transport scenarios for assessing biodegradation rates. Furthermore, we discuss if the absence of specific degrader populations can explain poor biodegradation. We propose updated perspectives on the controls of biodegradation in contaminant plumes. These include the plume fringe concept, transport limitations, and transient conditions as currently underestimated processes affecting biodegradation.

Life under extreme energy limitation: a synthesis of laboratory- and field-based investigations

The ability of microorganisms to withstand long periods with extremely low energy input has gained increasing scientific attention in recent years. Starvation experiments in the laboratory have shown that a phylogenetically wide range of microorganisms evolve fitness-enhancing genetic traits within weeks of incubation under low-energy stress. Studies on natural environments that are cut off from new energy supplies over geologic time scales, such as deeply buried sediments, suggest that similar adaptations might mediate survival under energy limitation in the environment. Yet, the extent to which laboratory-based evidence of starvation survival in pure or mixed cultures can be extrapolated to sustained microbial ecosystems in nature remains unclear. In this review, we discuss past investigations on microbial energy requirements and adaptations to energy limitation, identify gaps in our current knowledge, and outline possible future foci of research on life under extreme energy limitation.

Benzoate mediates the simultaneous repression of anaerobic 4-methylbenzoate and succinate utilization in Magnetospirillum sp. strain pMbN1

Background

At high concentrations of organic substrates, microbial utilization of preferred substrates (i.e., supporting fast growth) often results in diauxic growth with hierarchical substrate depletion. Unlike the carbon catabolite repression-mediated discriminative utilization of carbohydrates, the substrate preferences of non-carbohydrate-utilizing bacteria for environmentally relevant compound classes (e.g., aliphatic or aromatic acids) are rarely investigated. The denitrifying alphaproteobacterium Magnetospirillum sp. strain pMbN1 anaerobically degrades a wide variety of aliphatic and aromatic compounds and is unique for anaerobic degradation of 4-methylbenzoate. The latter proceeds via a distinct reaction sequence analogous to the central anaerobic benzoyl-CoA pathway to intermediates of central metabolism. Considering the presence of these two different anaerobic “aromatic ring degrading” pathways, substrate preferences of Magnetospirillum sp. strain pMbN1 were investigated. Anaerobic growth and substrate consumption were monitored in binary and ternary mixtures of 4-methylbenzoate, benzoate and succinate, in conjuction with time-resolved abundance profiling of selected transcripts and/or proteins related to substrate uptake and catabolism.

Results

Diauxic growth with benzoate preference was observed for binary and ternary substrate mixtures containing 4-methylbenzoate and succinate (despite adaptation of Magnetospirillum sp. strain pMbN1 to one of the latter two substrates). On the contrary, 4-methylbenzoate and succinate were utilized simultaneously from a binary mixture, as well as after benzoate depletion from the ternary mixture. Apparently, simultaneous repression of 4-methylbenzoate and succinate utilization from the ternary substrate mixture resulted from (i) inhibition of 4-methylbenzoate uptake, and (ii) combined inhibition of succinate uptake (via the two transporters DctPQM and DctA) and succinate conversion to acetyl-CoA (via pyruvate dehydrogenase). The benzoate-mediated repression of C₄-dicarboxylate utilization in Magnetospirillum sp. strain pMbN1 differs from that recently described for “Aromatoleum aromaticum” EbN1 (involving only DctPQM).

Conclusions

The preferential or simultaneous utilization of benzoate and other aromatic acids from mixtures with aliphatic acids may represent a more common nutritional behavior among (anaerobic) degradation specialist than previously thought. Preference of Magnetospirillum sp. strain pMbN1 for benzoate from mixtures with 4-methylbenzoate, and thus temporal separation of the benzoyl-CoA (first) and 4-methylbenzoyl-CoA (second) pathway, may reflect a catabolic tuning towards metabolic efficiency and the markedly broader range of aromatic substrates feeding into the central anaerobic benzoyl-CoA pathway.

Electronic supplementary material

The online version of this article (doi:10.1186/s12866-014-0269-4) contains supplementary material, which is available to authorized users.

Gene expression analysis of E. coli strains provides insights into the role of gene regulation in diversification

Escherichia coli spans a genetic continuum from enteric strains to several phylogenetically distinct, atypical lineages that are rare in humans, but more common in extra-intestinal environments. To investigate the link between gene regulation, phylogeny and diversification in this species, we analyzed global gene expression profiles of four strains representing distinct evolutionary lineages, including a well-studied laboratory strain, a typical commensal (enteric) strain and two environmental strains. RNA-Seq was employed to compare the whole transcriptomes of strains grown under batch, chemostat and starvation conditions. Highly differentially expressed genes showed a significantly lower nucleotide sequence identity compared with other genes, indicating that gene regulation and coding sequence conservation are directly connected. Overall, distances between the strains based on gene expression profiles were largely dependent on the culture condition and did not reflect phylogenetic relatedness. Expression differences of commonly shared genes (all four strains) and E. coli core genes were consistently smaller between strains characterized by more similar primary habitats. For instance, environmental strains exhibited increased expression of stress defense genes under carbon-limited growth and entered a more pronounced survival-like phenotype during starvation compared with other strains, which stayed more alert for substrate scavenging and catabolism during no-growth conditions. Since those environmental strains show similar genetic distance to each other and to the other two strains, these findings cannot be simply attributed to genetic relatedness but suggest physiological adaptations. Our study provides new insights into ecologically relevant gene-expression and underscores the role of (differential) gene regulation for the diversification of the model bacterial species.

Molecular and metabolic adaptations of Lactococcus lactis at near-zero growth rates

This paper describes the molecular and metabolic adaptations of Lactococcus lactis during the transition from a growing to a near-zero growth state by using carbon-limited retentostat cultivation. Transcriptomic analyses revealed that metabolic patterns shifted between lactic- and mixed-acid fermentations during retentostat cultivation, which appeared to be controlled at the level of transcription of the corresponding pyruvate dissipation-encoding genes. During retentostat cultivation, cells continued to consume several amino acids but also produced specific amino acids, which may derive from the conversion of glycolytic intermediates. We identify a novel motif containing CTGTCAG in the upstream regions of several genes related to amino acid conversion, which we propose to be the target site for CodY in L. lactis KF147. Finally, under extremely low carbon availability, carbon catabolite repression was progressively relieved and alternative catabolic functions were found to be highly expressed, which was confirmed by enhanced initial acidification rates on various sugars in cells obtained from near-zero-growth cultures. The present integrated transcriptome and metabolite (amino acids and previously reported fermentation end products) study provides molecular understanding of the adaptation of L. lactis to conditions supporting low growth rates and expands our earlier analysis of the quantitative physiology of this bacterium at near-zero growth rates toward gene regulation patterns involved in zero-growth adaptation.

Column studies to assess the effects of climate variables on redox processes during riverbank filtration

Riverbank filtration is an established technique used world-wide to produce clean drinking water in a reliable and cost-efficient way. This practice is, however, facing new challenges posed by climate change, as already observed during past heat waves with the local occurrence of anoxic conditions. In this study we investigated the effect of direct (temperature) and indirect (dissolved organic matter (DOM) concentration and composition, flow rate) climate change variables on redox processes (aerobic respiration, denitrification and Mn(III/IV)/Fe(III) reduction) by means of column experiments. Natural river water, modified river water and river water mixed with treated wastewater effluent were used as feed waters for the columns filled with natural sand from a river-infiltration system in Switzerland. Biodegradable dissolved organic matter was mainly removed immediately at the column inlet and particulate organic matter (POM) associated with the natural sand was the main electron donor for aerobic respiration throughout the column. Low infiltration rates (≤0.01 m/h) enhanced the oxygen consumption leading to anoxic conditions. DOM consumption did not seem to be sensitive to temperature, although oxygen consumption (i.e., associated with POM degradation) showed a strong temperature dependence with an activation energy of ∼70 kJmol(-1). Anoxic conditions developed at 30 °C with partial denitrification and formation of nitrite and ammonium. In absence of oxygen and nitrate, Mn(II) was mobilized at 20 °C, highlighting the importance of nitrate acting as a redox buffer under anoxic conditions preventing the reductive dissolution of Mn(III/IV)(hydr)oxides. Reductive dissolution of Fe(III)(hydr)oxides was not observed under these conditions.

The functional and taxonomic richness of wastewater treatment plant microbial communities are associated with each other and with ambient nitrogen and carbon availability

The number of functional traits of a wastewater treatment plant (WWTP) microbial community (i.e. functional richness) is thought to be an important determinant of its overall functional performance, but the ecological factors that determine functional richness remain unclear. The number of taxa within a community (i.e. taxonomic richness) is one ecological factor that might be important. Communities that contain more taxa are more likely to have more functional traits, and a positive association is therefore expected between functional and taxonomic richness. Empirical tests for this positive association among WWTP communities, however, are lacking. We address this knowledge gap by measuring the functional and taxonomic richness of 10 independent WWTP communities. We demonstrate that functional and taxonomic richness are positively associated with each other. We further demonstrate that functional and taxonomic richness are negatively associated with the effluent NH4 -N and BOD5 concentrations. This led us to hypothesize that correlated variation in functional and taxonomic richness is likely related to variation in ambient nitrogen and carbon availability. We finally demonstrate that this hypothesis is consistent with the functional and taxonomic attributes of the WWTP communities. Together, our results improve our basic understanding of the ecology and functioning of WWTP communities.

Towards habitat-oriented systems biology of "Aromatoleum aromaticum" EbN1: chemical sensing, catabolic network modulation and growth control in anaerobic aromatic compound degradation

The denitrifying betaproteobacterium "Aromatoleum aromaticum" EbN1 is a well-studied model organism for anaerobic degradation of aromatic compounds. Following publication of its genome in 2005, comprehensive physiological-proteomic studies were conducted to deduce functional understanding from the genomic blueprint. A catabolic network (85 predicted, 65 identified proteins) for anaerobic degradation of 24 aromatic growth substrates (including 11 newly recognized) was established. Newly elucidated pathways include those for 4-ethylphenol and plant-derived 3-phenylpropanoids, involving functional assignment of several paralogous genes. The substrate-specific regulation of individual peripheral degradation pathways is probably initiated by highly specific chemical sensing via dedicated sensory/regulatory proteins, e.g. three different σ⁵⁴-dependent one-component sensory/regulatory proteins are predicted to discriminate between three phenolic substrates (phenol, p-cresol and 4-ethylphenol) and two different two-component systems are assumed to differentiate between two alkylbenzenes (toluene, ethylbenzene). Investigations under in situ relevant growth conditions revealed (a) preferred utilization of benzoate from a mixture with succinate results from repressed synthesis of a C₄-dicarboxylate TRAP transporter; (b) response to alkylbenzene-induced solvent stress comprises metabolic re-routing of acetyl-CoA and reducing equivalents to poly(3-hydroxybutyrate) synthesis, alteration of cellular membrane composition and formation of putative solvent efflux systems; and (c) multifaceted adaptation to slow growth includes adjustment of energy demand for maintenance and preparedness for future nutritional opportunities, i.e. provision of uptake systems and catabolic enzymes for multiple aromatic substrates despite their absence. This broad knowledge base taken together with the recent development of a genetic system will facilitate future functional, biotechnological (stereospecific dehydrogenases) and habitat re-enacting ("eco-"systems biology) studies with "A. aromaticum" EbN1.

NOM degradation during river infiltration: effects of the climate variables temperature and discharge

Most peri-alpine shallow aquifers fed by rivers are oxic and the drinking water derived by riverbank filtration is generally of excellent quality. However, observations during past heat waves suggest that water quality may be affected by climate change due to effects on redox processes such as aerobic respiration, denitrification, reductive dissolution of manganese(III/IV)- and iron(III)(hydr)oxides that occur during river infiltration. To assess the dependence of these redox processes on the climate-related variables temperature and discharge, we performed periodic and targeted (summer and winter) field sampling campaigns at the Thur River, Switzerland, and laboratory column experiments simulating the field conditions. Typical summer and winter field conditions could be successfully simulated by the column experiments. Dissolved organic matter (DOM) was found not to be a major electron donor for aerobic respiration in summer and the DOM consumption did not reveal a significant correlation with temperature and discharge. It is hypothesized that under summer conditions, organic matter associated with the aquifer material (particulate organic matter, POM) is responsible for most of the consumption of dissolved oxygen (DO), which was the most important electron acceptor in both the field and the column system. For typical summer conditions at temperatures >20 °C, complete depletion of DO was observed in the column system and in a piezometer located only a few metres from the river. Both in the field system and the column experiments, nitrate acted as a redox buffer preventing the release of manganese(II) and iron(II). For periodic field observations over five years, DO consumption showed a pronounced temperature dependence (correlation coefficient r = 0.74) and therefore a seasonal pattern, which seemed to be mostly explained by the temperature dependence of the calculated POM consumption (r = 0.7). The river discharge was found to be highly and positively correlated with DO consumption (r = 0.85), suggesting an enhanced POM input during flood events. This high correlation could only be observed for the low-temperature range (T < 15 °C). For temperatures >15 °C, DO consumption was already high (almost complete) and the impact of discharge could not be resolved. Based on our results, we estimate the risk for similar river-infiltration systems to release manganese(II) and iron(II) to be low during future average summer conditions. However, long-lasting heat waves might lead to a consumption of the nitrate buffer, inducing a mobilization of manganese and iron.

High and stable substrate specificities of microorganisms in enhanced biological phosphorus removal plants

Microbial communities are typically characterized by conditions of nutrient limitation so the availability of the resources is likely a key factor in the niche differentiation across all species and in the regulation of the community structure. In this study we have investigated whether four species exhibit any in situ short-term changes in substrate uptake pattern when exposed to variations in substrate and growth conditions. Microautoradiography was combined with fluorescence in situ hybridization to investigate in situ cell-specific substrate uptake profiles of four probe-defined coexisting species in a wastewater treatment plant with enhanced biological phosphorus removal. These were the filamentous 'Candidatus Microthrix' and Caldilinea (type 0803), the polyphosphate-accumulating organism 'Candidatus Accumulibacter', and the denitrifying Azoarcus. The experimental conditions mimicked the conditions potentially encountered in the respective environment (starvation, high/low substrate concentration, induction with specific substrates, and single/multiple substrates). The results showed that each probe-defined species exhibited very distinct and constant substrate uptake profile in time and space, which hardly changed under any of the conditions tested. Such niche partitioning implies that a significant change in substrate composition will be reflected in a changed community structure rather than the substrate uptake response from the different species.

Competition of Escherichia coli O157 with a drinking water bacterial community at low nutrient concentrations

In contrast to studies on (long-term) survival of enteric pathogens in the environment, investigations on the principles of their growth and competition with autochthonous aquatic bacteria are rare and unexplored. Hence, improved basic knowledge is crucial for an adequate risk assessment and for understanding (and avoiding) the spreading of waterborne diseases. Therefore, the pathogen Escherichia coli O157 was grown in competition with a drinking water bacterial community on natural assimilable organic carbon (AOC) originating from diluted wastewater, in both batch and continuous culture. Growth was monitored by flow cytometry enabling enumeration of total cell concentration as well as specific E. coli O157 detection using fluorescently-labelled antibodies. An enhanced competitive fitness of E. coli O157 with higher AOC concentrations, higher temperatures and increased dilution rates (continuous culture) was observed. A classical "opportunist" versus "gleaner" relationship, where E. coli O157 is the "opportunist", specialised for growth at high nutrient concentrations (μ(max): 0.87 h(-1) and K(s): 489 μg consumed DOC L(-1)), and the bacterial community is the "gleaner" adapted to nutrient-poor environments (μ(max): 0.33 h(-1) and K(s): 7.4 μg consumed DOC L(-1)) was found. The obtained competition results can be explained by the growth properties of the two competitors determined in pure cultures and it was possible to model many of the observed dynamics based on Monod kinetics. The study provides new insights into the principles governing competition of an enteric pathogen with autochthonous aquatic bacteria.

Use of 16S rRNA-targeted oligonucleotide probes to investigate function and phylogeny of sulphate-reducing bacteria and methanogenic archaea in a UK estuary

Abstract Sulphate-reducing bacteria (SRB) and methanogenic archaea (MA) are important anaerobic terminal oxidisers of organic matter. However, we have little knowledge about the distribution and types of SRB and MA in the environment or the functional role they play in situ. Here we have utilised sediment slurry microcosms amended with ecologically significant substrates, including acetate and hydrogen, and specific functional inhibitors, to identify the important SRB and MA groups in two contrasting sites on a UK estuary. Substrate and inhibitor additions had significant effects on methane production and on acetate and sulphate consumption in the slurries. By using specific 16S-targeted oligonucleotide probes we were able to link specific SRB and MA groups to the use of the added substrates. Acetate consumption in the freshwater-dominated sediments was mediated by Methanosarcinales under low-sulphate conditions and Desulfobacter under the high-sulphate conditions that simulated a tidal incursion. In the marine-dominated sediments, acetate consumption was linked to Desulfobacter. Addition of trimethylamine, a non-competitive substrate for methanogenesis, led to a large increase in Methanosarcinales signal in marine slurries. Desulfobulbus was linked to non-sulphate-dependent H(2) consumption in the freshwater sediments. The addition of sulphate to freshwater sediments inhibited methane production and reduced signal from probes targeted to Methanosarcinales and Methanomicrobiales, while the addition of molybdate to marine sediments inhibited Desulfobulbus and Desulfobacterium. These data complement our understanding of the ecophysiology of the organisms detected and make a firm connection between the capabilities of species, as observed in the laboratory, to their roles in the environment.

Groundwater biofilm dynamics grown in situ along a nutrient gradient

This paper describes the in situ response of groundwater biofilms in an alluvial gravel aquifer system on the Canterbury Plains, New Zealand. Biofilms were developed on aquifer gravel, encased in fine mesh bags and suspended in protective columns in monitoring wells for at least 20 weeks. Four sites were selected in the same groundwater system where previous analyses indicated a gradient of increasing nitrate down the hydraulic gradient from Sites 1 to 4. Measurements during the current study classified the groundwater as oligotrophic. Biofilm responses to the nutrient gradients were assessed using bioassays, with biomass determined using protein and cellular and nucleic acid staining and biofilm activity using enzyme assays for lipid, carbohydrate, phosphate metabolism, and cell viability. In general, biofilm activity decreased as nitrate levels increased from Sites 1 to 4, with the opposite relationship for carbon and phosphorus concentrations. These results showed that the groundwater system supported biofilm growth and that the upper catchment supported efficient and productive biofilms (high ratio of activity per unit biomass).

Biodegradation of volatile organic compounds from paint industries

Methyl ethyl ketone (MEK) and methyl iso-butyl ketone (MIBK) constitute significant proportion of the total VOC emissions from manufacturing and application processes of surface coatings. Biodegradation of MEK and MIBK using an acclimatized mixed culture was evaluated, under aerobic condition. Biodegradation studies were carried out using MEK and MIBK as single substrates and in combination. Mixed-pollutant studies were conducted in MEK-dominated system, MIBK-dominated system, and MEK-MIBK equi-concentration systems to understand the concentration-dependent interaction of these compounds in a biosystem. Experimental data obtained from single-pollutant system was used to estimate the biokinetic parameters, viz. μ(max), K(s), K(i), and Y(T), for these compounds. Among the several bio-kinetic models tested, Monod inhibition model was best suited for predicting the biodegradation of these two VOCs. Four multiple-substrate models, viz. no-interaction, competitive, un-competitive, and non-competitive were used to study the nature of inhibition for different combinations of these compounds. The biodegradation of MEK and MIBK mixtures was found to be best described by competitive inhibition model. However, the predictions were not very good for systems where MEK concentration was higher than MIBK concentration.

Disconnect of microbial structure and function: enzyme activities and bacterial communities in nascent stream corridors

A fundamental issue in microbial and general ecology is the question to what extent environmental conditions dictate the structure of communities and the linkages with functional properties of ecosystems (that is, ecosystem function). We approached this question by taking advantage of environmental gradients established in soil and sediments of small stream corridors in a recently created, early successional catchment. Specifically, we determined spatial and temporal patterns of bacterial community structure and their linkages with potential microbial enzyme activities along the hydrological flow paths of the catchment. Soil and sediments were sampled in a total of 15 sites on four occasions spread throughout a year. Denaturing gradient gel electrophoresis (DGGE) was used to characterize bacterial communities, and substrate analogs linked to fluorescent molecules served to track 10 different enzymes as specific measures of ecosystem function. Potential enzyme activities varied little among sites, despite contrasting environmental conditions, especially in terms of water availability. Temporal changes, in contrast, were pronounced and remarkably variable among the enzymes tested. This suggests much greater importance of temporal dynamics than spatial heterogeneity in affecting specific ecosystem functions. Most strikingly, bacterial community structure revealed neither temporal nor spatial patterns. The resulting disconnect between bacterial community structure and potential enzyme activities indicates high functional redundancy within microbial communities even in the physically and biologically simplified stream corridors of early successional landscapes.

In glucose-limited continuous culture the minimum substrate concentration for growth, Smin, is crucial in the competition between the enterobacterium Escherichia coli and Chelatobacter heintzii, an environmentally abundant bacterium

The competition for glucose between Escherichia coli ML30, a typical copiotrophic enterobacterium and Chelatobacter heintzii ATCC29600, an environmentally successful strain, was studied in a carbon-limited culture at low dilution rates. First, as a base for modelling, the kinetic parameters μ(max) and K(s) were determined for growth with glucose. For both strains, μ(max) was determined in batch culture after different precultivation conditions. In the case of C. heintzii, μ(max) was virtually independent of precultivation conditions. When inoculated into a glucose-excess batch culture medium from a glucose-limited chemostat run at a dilution rate of 0.075 h(-1) C. heintzii grew immediately with a μ(max) of 0.17 ± 0.03 h(-1). After five transfers in batch culture, μ(max) had increased only slightly to 0.18 ± 0.03 h(-1). A different pattern was observed in the case of E. coli. Inoculated from a glucose-limited chemostat at D = 0.075 h(-1) into glucose-excess batch medium E. coli grew only after an acceleration phase of ~3.5 h with a μ(max) of 0.52 h(-1). After 120 generations and several transfers into fresh medium, μ(max) had increased to 0.80 ± 0.03 h(-1). For long-term adapted chemostat-cultivated cells, a K(s) for glucose of 15 μg l(-1) for C. heintzii, and of 35 μg l(-1) for E. coli, respectively, was determined in (14)C-labelled glucose uptake experiments. In competition experiments, the population dynamics of the mixed culture was determined using specific surface antibodies against C. heintzii and a specific 16S rRNA probe for E. coli. C. heintzii outcompeted E. coli in glucose-limited continuous culture at the low dilution rates of 0.05 and 0.075 h(-1). Using the determined pure culture parameter values for K(s) and μ(max), it was only possible to simulate the population dynamics during competition with an extended form of the Monod model, which includes a finite substrate concentration at zero growth rate (s(min)). The values estimated for s(min) were dependent on growth rate; at D = 0.05 h(-1), it was 12.6 and 0 μg l(-1) for E. coli and C. heintzii, respectively. To fit the data at D=0.075 h(-1), s(min) for E. coli had to be raised to 34.9 μg l(-1) whereas s(min) for C. heintzii remained zero. The results of the mathematical simulation suggest that it is not so much the higher K(s) value, which is responsible for the unsuccessful competition of E. coli at low residual glucose concentration, but rather the existence of a significant s(min).

Effect of glucose on the fatty acid composition of Cupriavidus necator JMP134 during 2,4-dichlorophenoxyacetic acid degradation: implications for lipid-based stable isotope probing methods

Combining lipid biomarker profiling with stable isotope probing (SIP) is a powerful technique for studying specific microbial populations responsible for the degradation of organic pollutants in various natural environments. However, the presence of other easily degradable substrates may induce significant physiological changes by altering both the rate of incorporation of the target compound into the biomass and the microbial lipid profiles. In order to test this hypothesis, Cupriavidus necator JMP134, a 2,4-dichlorophenoxyacetic acid (2,4-D)-degrading bacterium, was incubated with [(13)C]2,4-D, [(13)C]glucose, or mixtures of both substrates alternatively labeled with (13)C. C. necator JMP134 exhibited a preferential use of 2,4-D over glucose. The isotopic analysis showed that glucose had only a small effect on the incorporation of the acetic chain of 2,4-D into the biomass (at days 2 and 3) and no effect on that of the benzenic ring. The addition of glucose did change the fatty acid methyl ester (FAME) composition. However, the overall FAME isotopic signature reflected that of the entire biomass. Compound-specific individual isotopic analyses of FAME composition showed that the (13)C-enriched FAME profiles were slightly or not affected when tracing the 2,4-D acetic chain or 2,4-D benzenic ring, respectively. This batch study is a necessary step for validating the use of lipid-based SIP methods in complex environments.

Flavobacterium johnsoniae as a model organism for characterizing biopolymer utilization in oligotrophic freshwater environments

Biopolymers are important substrates for heterotrophic bacteria in oligotrophic freshwater environments, but information on bacterial growth kinetics with biopolymers is scarce. The objective of this study was to characterize bacterial biopolymer utilization in these environments by assessing the growth kinetics of Flavobacterium johnsoniae strain A3, which is specialized in utilizing biopolymers at μg liter(-1) levels. Growth of strain A3 with amylopectin, xyloglucan, gelatin, maltose, or fructose at 0 to 200 μg C liter(-1) in tap water followed Monod or Teissier kinetics, whereas growth with laminarin followed Teissier kinetics. Classification of the specific affinity of strain A3 for the tested substrates resulted in the following affinity order: laminarin (7.9 × 10(-2) liter·μg(-1) of C·h(-1)) ≫ maltose > amylopectin ≈ gelatin ≈ xyloglucan > fructose (0.69 × 10(-2) liter·μg(-1) of C·h(-1)). No specific affinity could be determined for proline, but it appeared to be high. Extracellular degradation controlled growth with amylopectin, xyloglucan, or gelatin but not with laminarin, which could explain the higher affinity for laminarin. The main degradation products were oligosaccharides or oligopeptides, because only some individual monosaccharides and amino acids promoted growth. A higher yield and a lower ATP cell(-1) level was achieved at ≤10 μg C liter(-1) than at >10 μg C liter(-1) with every substrate except gelatin. The high specific affinities of strain A3 for different biopolymers confirm that some representatives of the classes Cytophagia-Flavobacteria are highly adapted to growth with these compounds at μg liter(-1) levels and support the hypothesis that Cytophagia-Flavobacteria play an important role in biopolymer degradation in (ultra)oligotrophic freshwater environments.

Mixtures of environmental pollutants: effects on microorganisms and their activities in soils

Soil is the ultimate sink for most contaminants and rarely has only a single contaminant. More than is generally acknowledge, environmental pollutants exist as mixtures (organic-organic, inorganic-inorganic, and organic-inorganic). It is much more difficult to study chemical mixtures than individual chemicals, especially in the complex soil environment. Similarly, understanding the toxicity of a chemical mixture on different microbial species is much more complex, time consuming and expensive, because multiple testing designs are needed for an increased array of variables. Therefore, until now, scientific enquiries worldwide have extensively addressed the effects of only individual pollutants toward nontarget microorganisms. In this review, we emphasize the present status of research on (i) the environmental occurrence of pollutant mixtures; (ii) the interactions between pollutant mixtures and ecologically beneficial microorganisms; and (iii) the impact of such interactions on environmental quality. We also address the limitations of traditional cultivation based methods for monitoring the effects of pollutant mixtures on microorganisms. Long-term monitoring of the effects of pollutant mixtures on microorganisms, particularly in soil and aquatic ecosystems, has received little attention. Microbial communities that can degrade or can degrade or can develop tolerance to, or are inhibited by chemical mixtures greatly contribute to resilience and resistance in soil environments. We also stress in this review the important emerging trend associated with the employment of molecular methods for establishing the effects of pollutant mixtures on microbial communities. There is currently a lack of sufficient cogent toxicological data on chemical mixtures for making informed decision making in risk assessment by regulators. Therefore, not only more toxicology information on mixtures is needed but also there is an urgent need to generate sufficient, suitable, and long-term modeling data that have higher predictability when assessing pollutant mixture effects on microorganisms. Such data would improve risk assessment at contaminated sites and would help devise more effective bioremediation strategies.

How to live at very low substrate concentration

Availability of carbon/energy sources and temperature are the two environmental factors that severely restrict heterotrophic growth in most ecosystems. DOC concentrations in ground, drinking and surface waters are typically in the range of 0.5-5 mg/L, but most of this is present in a polymeric, inaccessible form for microbes. Concentrations of microbiologically available carbon compounds (so-called assimilable organic carbon, AOC) are usually in the range of 10-100 μg/L, those of individual sugars or amino acids are not higher than a few μg/L. Until recently microbiologists assumed that such nutrient-poor (oligotrophic) environments are "deserts" for life, and that the majority of bacterial cells seen in the microscope are dead, dormant or at least severely starved. Nevertheless, despite the low concentrations of available carbon compounds, bacterial cell numbers recorded in these environments typically are in the range of 10(5)-10(6) per mL. Over the last years, we have learnt that most of these microbes are perfectly alive, metabolizing and ready to grow when given the chance. Hence, microbes have adapted and developed strategies to cope with this situation. Laboratory studies with pure cultures suggest that bacterial cells have developed two strategies to live under such conditions. The first strategy is to perform a "multivorous" way of life by taking up and metabolizing dozens of different carbon substrates simultaneously (i.e., they are NOT specializing on a particular substrate, which they can take up with very high affinity). This "mixed substrate growth" equips the cell with a kinetic advantage and metabolic flexibility. Simultaneous utilization of a multitude of carbon substrates allows fast growth at minute concentrations of individual substrates. The second strategy is to minimize maintenance requirements (unfortunately we still know little about how this is achieved). Recently, flow cytometry has been employed to study microbial growth in very dilute, nutrient-poor environments. The technique allows fast and easy quantification of microbial growth of natural bacterial communities, including "uncultivable" members, under environmental conditions. When combined with strain-specific fluorescent immunoprobes, this technique allows investigation of the growth and competition of pathogens with the indigenous microbial flora. This method is particularly suited for studying questions concerning microbial growth and survival in drinking water systems.

Establishment and metabolic analysis of a model microbial community for understanding trophic and electron accepting interactions of subsurface anaerobic environments

Background

Communities of microorganisms control the rates of key biogeochemical cycles, and are important for biotechnology, bioremediation, and industrial microbiological processes. For this reason, we constructed a model microbial community comprised of three species dependent on trophic interactions. The three species microbial community was comprised of Clostridium cellulolyticum, Desulfovibrio vulgaris Hildenborough, and Geobacter sulfurreducens and was grown under continuous culture conditions. Cellobiose served as the carbon and energy source for C. cellulolyticum, whereas D. vulgaris and G. sulfurreducens derived carbon and energy from the metabolic products of cellobiose fermentation and were provided with sulfate and fumarate respectively as electron acceptors.

Results

qPCR monitoring of the culture revealed C. cellulolyticum to be dominant as expected and confirmed the presence of D. vulgaris and G. sulfurreducens. Proposed metabolic modeling of carbon and electron flow of the three-species community indicated that the growth of C. cellulolyticum and D. vulgaris were electron donor limited whereas G. sulfurreducens was electron acceptor limited.

Conclusions

The results demonstrate that C. cellulolyticum, D. vulgaris, and G. sulfurreducens can be grown in coculture in a continuous culture system in which D. vulgaris and G. sulfurreducens are dependent upon the metabolic byproducts of C. cellulolyticum for nutrients. This represents a step towards developing a tractable model ecosystem comprised of members representing the functional groups of a trophic network.

New patterns of mixed-substrate utilization during batch growth of Escherichia coli K12

Microbial growth on mixtures of substrates is of considerable engineering and biological interest. Most of the work until now has dealt with microbial growth on binary mixtures of sugars or polyols. In these cases, it is often found that no matter how the inoculum is precultured, only one of the two substrates is consumed in the first growth phase, leading to the diauxic growth pattern. The goal of the experiments reported here is to investigate growth on mixtures containing at least one organic acid. These experiments show that the substrate utilization patterns in such mixtures are qualitatively different from the diauxic growth pattern. For instance, during growth of Escherichia coli K12 on certain binary mixtures of organic acids, the two substrates are utilized simultaneously, and the mixed-substrate maximum specific growth rate exceeds the single-substrate maximum specific growth rate on either one of the two constituent substrates. Furthermore, the very same mixed-substrate maximum specific growth and substrate uptake rates are observed no matter how the inoculum is precultured. On the other hand, in a mixture of glucose and pyruvate, the maximum specific growth rate seems to depend on the preculturing conditions, thus suggesting the existence of multiple physiological quasi-steady states. (c) 1997 John Wiley & Sons, Inc. Biotechnol Bioeng 55: 747-757, 1997.

Gene regulation in continuous cultures: a unified theory for bacteria and yeasts

During batch growth on mixtures of two growth-limiting substrates, microbes consume the substrates either sequentially (diauxie) or simultaneously. The ubiquity of these growth patterns suggests that they may be driven by a universal mechanism common to all microbial species. Recently, we showed that a minimal model accounting only for enzyme induction and dilution, the two processes that occur in all microbes, explains the phenotypes observed in batch cultures of various wild-type and mutant/recombinant cells (Narang and Pilyugin in J. Theor. Biol. 244:326-348, 2007). Here, we examine the extension of the minimal model to continuous cultures. We show that: (1) Several enzymatic trends, attributed entirely to cross-regulatory mechanisms, such as catabolite repression and inducer exclusion, can be quantitatively explained by enzyme dilution. (2) The bifurcation diagram of the minimal model for continuous cultures, which classifies the substrate consumption pattern at any given dilution rate and feed concentrations, provides a precise explanation for the empirically observed correlations between the growth patterns in batch and continuous cultures. (3) Numerical simulations of the model are in excellent agreement with the data. The model captures the variation of the steady state substrate concentrations, cell densities, and enzyme levels during the single- and mixed-substrate growth of bacteria and yeasts at various dilution rates and feed concentrations. This variation is well approximated by simple analytical expressions that furnish deep physical insights. (4) Since the minimal model describes the behavior of the cells in the absence of cross-regulatory mechanisms, it provides a rigorous framework for quantifying the effect of these mechanisms. We illustrate this by analyzing several data sets from the literature.

Escravos light crude oil degrading potentials of axenic and mixed bacterial cultures

We assessed the relationship between growth profile and the extent of biodegradation of Escravos light crude oil by axenic and mixed bacteria cultures in a shake flask. Eleven petroleum-degrading bacteria were isolated by enrichment from oil-contaminated soils including, Pseudomonas effusa, Pseudomonas fluorescens, Pseudomonas cruciviae, Arthrobacter tumescens, Pseudomonas species, Pseudomonas tralucida, Alcaligenes metacaligenes, Micrococcus colpogenes, Bacillus badius, Nocardia paraffinae and Bacillus species. Specific growth rates of axenic cultures of the bacteria during degradation of Escravos light crude oil ranged between 0.0037 and 0.0505 h(-1), while that of the mixed cultures varied from 0.0144 to 0.1301 h(-1). The crude oil was biodegraded by between 28.71% and 99.01% for single cultures and between 12.38% and 91.58% for the mixed cultures. Although specific growth rate and biomass were important at the initial stages of biodegradation, there was no significant correlation between growth rate and biomass and the extent of biodegradation of Escravos light crude oil.

A strategy to calculate the patterns of nutrient consumption by microorganisms applying a two-level optimisation principle to reconstructed metabolic networks

Bacterial responses to environmental changes rely on a complex network of biochemical reactions. The properties of the metabolic network determining these responses can be divided into two groups: the stoichiometric properties, given by the stoichiometry matrix, and the kinetic/thermodynamic properties, given by the rate equations of the reaction steps. The stoichiometry matrix represents the maximal metabolic capabilities of the organism, and the regulatory mechanisms based on the rate laws could be considered as being responsible for the administration of these capabilities. Post-genomic reconstruction of metabolic networks provides us with the stoichiometry matrix of particular strains of microorganisms, but the kinetic aspects of in vivo rate laws are still largely unknown. Therefore, the validity of predictions of cellular responses requiring detailed knowledge of the rate equations is difficult to assert. In this paper, we show that by applying optimisation criteria to the core stoichiometric network of the metabolism of Escherichia coli, and including information about reversibility/irreversibility only of the reaction steps, it is possible to calculate bacterial responses to growth media with different amounts of glucose and galactose. The target was the minimisation of the number of active reactions (subject to attaining a growth rate higher than a lower limit) and subsequent maximisation of the growth rate (subject to the number of active reactions being equal to the minimum previously calculated). Using this two-level target, we were able to obtain by calculation four fundamental behaviours found experimentally: inhibition of respiration at high glucose concentrations in aerobic conditions, turning on of respiration when glucose decreases, induction of galactose utilisation when the system is depleted of glucose and simultaneous use of glucose and galactose as carbon sources when both sugars are present in low concentrations. Preliminary results of the coarse pattern of sugar utilisation were also obtained with a genome-scale E. coli reconstructed network, yielding similar qualitative results.

Growth of Vibrio cholerae O1 Ogawa Eltor in freshwater

Growth of Vibrio cholerae O1 Ogawa Eltor was studied with a growth assay in which autoclaved and filtered (0.22 microm) freshwater was inoculated at low cell density (5 x 10(3) cells ml(-1)) and proliferation was followed with flow cytometry. Against the common view, V. cholerae was able to grow extensively in different kinds of freshwater. The bacterium multiplied in river water, lake water and effluent of a wastewater treatment plant up to a cell density of 1.55 x 10(6) cells ml(-1). In these samples, apparent assimilable organic carbon (AOC(app)) concentrations ranged from 52 up to 800 microg l(-1) and the results demonstrate a positive trend between the AOC(app) concentration and final cell concentration, suggesting that AOC was a key parameter governing growth of V. cholerae. No growth was observed in waters (tap and bottled drinking water) containing less than approximately 60 microg AOC(app) l(-1). When pure cultures of V. cholerae were grown on identical lake water at different temperatures (20, 25 and 30 degrees C) the maximum specific growth rates (micromax) achieved were 0.22 h(-1), 0.32 h(-1) and 0.45 h(-1), respectively. In addition, growth was characterized in lake water samples amended with different concentrations of NaCl. The highest micromax of V. cholerae was recorded at moderate salinity levels (5 g NaCl l(-1), micromax=0.84 h(-1)), whereas at 30 g NaCl l(-1) (micromax=0.30 h(-1)) or 0 g NaCl l(-1) (micromax)=0.40 h(-1)) specific growth rates were significantly reduced. In the water tested here, micro(max) of V. cholerae was always around 50 % of that exhibited by a freshwater community of indigenous bacteria enriched from the water sampling site. Direct batch competition experiments between V. cholerae and the lake water bacterial community were performed at different temperatures in which V. cholerae was enumerated in the total community using fluorescent-surface antibodies. In all cases V. cholerae was able to grow and constituted around 10 % of the final total cell concentration of the community. No significant effect of temperature was observed on the outcome of the competition. Mathematical modelling of the competition at the different temperatures based on the calculated micromax values confirmed these experimental observations. The results demonstrate that V. cholerae is not only able to survive, but also able to grow in freshwater samples. In these experiments the bacterium was able to use a large fraction (12-62 %) of the AOC(app) available to the bacterial AOC-test community, indicating that V. cholerae has the ability to gain access to the substrates present in freshwater even in competition with an autochthonous bacterial lake water consortium.