Chemical characterization of soil extract as growth media for the ecophysiological study of bacteria

A comprehensive review of flue gas bio-mitigation: chemolithotrophic interactions with flue gas in bio-reactors as a sustainable possibility for technological advancements

Flue gas mitigation technologies aim to reduce the environmental impact of flue gas emissions, particularly from industrial processes and power plants. One approach to mitigate flue gas emissions involves bio-mitigation, which utilizes microorganisms to convert harmful gases into less harmful or inert substances. The review thus explores the bio-mitigation efficiency of chemolithotrophic interactions with flue gas and their potential application in bio-reactors. Chemolithotrophs are microorganisms that can derive energy from inorganic compounds, such as carbon dioxide (CO2), nitrogen oxides (NOx), and sulfur dioxide (SO2), present in the flue gas. These microorganisms utilize specialized enzymatic pathways to oxidize these compounds and produce energy. By harnessing the metabolic capabilities of chemolithotrophs, flue gas emissions can be transformed into value-added products. Bio-reactors provide controlled environments for the growth and activity of chemolithotrophic microorganisms. Depending on the specific application, these can be designed as suspended or immobilized reactor systems. The choice of bio-reactor configuration depends on process efficiency, scalability, and ease of operation. Factors influencing the bio-mitigation efficiency of chemolithotrophic interactions include the concentration and composition of the flue gas, operating conditions (such as temperature, pH, and nutrient availability), and reactor design. Chemolithotrophic interactions with flue gas in bio-reactors offer a potentially efficient approach to mitigating flue gas emissions. Continued research and development in this field are necessary to optimize reactor design, microbial consortia, and operating conditions. Advances in understanding the metabolism and physiology of chemolithotrophic microorganisms will contribute to developing robust and scalable bio-mitigation technologies for flue gas emissions.

Extractability and phytotoxicity of heavy metals and essential elements from plastics in soil solutions and root exudates

Plastic waste is increasing and is a serious environmental problem. Among the threats associated with plastics is the release of contaminants into the environment. This study aimed to evaluate the efficiency of metals release from plastics (low-density polyethylene (LDPE), polyethylene terephthalate (PET), and polypropylene (PP)) as affected by different soil solution types, artificial root exudates, and distilled water. The extent of metal release varied depending on the type of solution and plastic used. Metals were leached most effectively from plastics in soil solutions, followed by root exudates, and least effectively by distilled water. LDPE released the highest concentrations of Cu and Na into solution, PP released the greatest amount of Fe, and PET released the most Cr. The efficiencies of Mg and Zn release from the plastics (PP and PET) varied by solution type. Among the plastics studied, LDPE exhibited the strongest ability to adsorb metals, such as Fe, Cr, Mg, and Zn from soil solutions. The amount of metal released from the plastics was also dependent on pH, dissolved organic carbon (DOC) concentrations, and the electrical conductivity (EC) of the solutions. Moreover, plastic extracts were found to have negative effects on germination and growth in Lepidium sativum.

The toxicological spectrum of the Bacillus cereus toxin cereulide points towards niche-specific specialisation

Most microbes share their environmental niches with very different forms of life thereby engaging in specialised relationships to enable their persistence. The bacterium Bacillus cereus occurs ubiquitously in the environment with certain strain backgrounds causing foodborne and opportunistic infections in humans. The emetic lineage of B. cereus is capable of producing the toxin cereulide, which evokes emetic illnesses. Although food products favouring the accumulation of cereulide are known, the ecological role of cereulide and the environmental niche of emetic B. cereus remain elusive. To better understand the ecology of cereulide-producing B. cereus, we systematically assayed the toxicological spectrum of cereulide on a variety of organisms belonging to different kingdoms. As cereulide is a potassium ionophore, we further tested the effect of environmental potassium levels on the action of cereulide. We found that adverse effects of cereulide exposure are species-specific, which can be exacerbated with increased environmental potassium. Additionally, we demonstrate that cereulide is produced within an insect cadaver indicating its potential ecological function for a saprophytic lifestyle. Collectively, distinct cereulide susceptibilities of other organisms may reflect its role in enabling competitive niche specialization of emetic B. cereus.

Seed Pelleting with Gum Arabic-Encapsulated Biocontrol Bacteria for Effective Control of Clubroot Disease in Pak Choi

Clubroot is one of the most serious soil-borne diseases on crucifer crops worldwide. Seed treatment with biocontrol agents is an effective and eco-friendly way to control clubroot disease. However, there is a big challenge to inoculating the seed with bacterial cells through seed pelleting due to the harsh environment on the seed surface or in the rhizosphere. In this study, a method for microbial seed pelleting was developed to protect pak choi seedlings against clubroot disease. Typically, a biocontrol bacterium, Paenibacillus polymyxa ZF129, was encapsulated by the spray-drying method with gum arabic as wall material, and then pak choi seeds were pelleted with the microencapsulated Paenibacillus polymyxa ZF129 (ZF129m). The morphology, storage stability, and release behavior of ZF129 microcapsules were evaluated. Compared with the naked Paenibacillus polymyxa ZF129 cells, encapsulated ZF129 cells showed higher viability during ambient storage on pak choi seeds. Moreover, ZF129m-pelleted seeds showed higher control efficacy (71.23%) against clubroot disease than that of nonencapsulated ZF129-pelleted seeds (61.64%) in pak choi. Seed pelleting with microencapsulated biocontrol Paenibacillus polymyxa ZF129 proved to be an effective and eco-friendly strategy for the control of clubroot disease in pak choi.

Insights into the metabolic specificities of pathogenic strains from the Ralstonia solanacearum species complex

All the strains grouped under the species Ralstonia solanacearum represent a species complex responsible for many diseases on agricultural crops throughout the world. The strains have different lifestyles and host range. Here, we investigated whether specific metabolic pathways contribute to strain diversification. To this end, we carried out systematic comparisons on 11 strains representing the diversity of the species complex. We reconstructed the metabolic network of each strain from its genome sequence and looked for the metabolic pathways differentiating the different reconstructed networks and, by extension, the different strains. Finally, we conducted an experimental validation by determining the metabolic profile of each strain with the Biolog technology. Results revealed that the metabolism is conserved between strains, with a core metabolism composed of 82% of the pan-reactome. The three species composing the species complex could be distinguished according to the presence/absence of some metabolic pathways, in particular, one involving salicylic acid degradation. Phenotypic assays revealed that the trophic preferences on organic acids and several amino acids such as glutamine, glutamate, aspartate, and asparagine are conserved between strains. Finally, we generated mutants lacking the quorum-sensing-dependent regulator PhcA in four diverse strains, and we showed that the phcA-dependent trade-off between growth and production of virulence factors is conserved across the R. solanacearum species complex. IMPORTANCE Ralstonia solanacearum is one of the most important threats to plant health worldwide, causing disease on a very large range of agricultural crops such as tomato or potato. Behind the R. solanacearum name are hundreds of strains with different host range and lifestyle, classified into three species. Studying the differences between strains allows to better apprehend the biology of the pathogens and the specificity of some strains. None of the published genomic comparative studies have focused on the metabolism of the strains so far. We developed a new bioinformatic pipeline to build high-quality metabolic networks and used a combination of metabolic modeling and high-throughput phenotypic Biolog microplates to look for the metabolic differences between 11 strains across the three species. Our study revealed that genes encoding enzymes are overall conserved, with few variations between strains. However, more variations were observed when considering substrate usage. These variations probably result from regulation rather than the presence or absence of enzymes in the genome.

Escherichia coli Strains Display Varying Susceptibility to Grazing by the Soil Amoeba Dictyostelium discoideum

Recent studies have shown that Escherichia coli can survive in different environments, including soils, and they can maintain populations in sterile soil for a long period of time. This indicates that growth-supporting nutrients are available; however, when grown in non-sterile soils, populations decline, suggesting that other biological factors play a role in controlling E. coli populations in soil. Free-living protozoa can affect the bacterial population by grazing. We hypothesized that E. coli strains capable of surviving in non-sterile soil possess mechanisms to protect themselves from amoeba predation. We determined the grazing rate of E. coli pasture isolates by using Dictyostelium discoideum. Bacterial suspensions applied to lactose agar as lines were allowed to grow for 24 h, when 4 μL of D. discoideum culture was inoculated in the center of each bacterial line. Grazing distances were measured after 4 days. The genomes of five grazing-susceptible and five grazing-resistant isolates were sequenced and compared. Grazing distance varied among isolates, which indicated that some E. coli are more susceptible to grazing by protozoa than others. When presented with a choice between grazing-susceptible and grazing-resistant isolates, D. discoideum grazed only on the susceptible strain. Grazing susceptibility phenotype did not align with the phylogroup, with both B1 and E strains found in both grazing groups. They also did not align by core genome phylogeny. Whole genome comparisons revealed that the five most highly grazed strains had 389 shared genes not found in the five least grazed strains. Conversely, the five least grazed strains shared 130 unique genes. The results indicate that long-term persistence of E. coli in soil is due at least in part to resistance to grazing by soil amoeba.

Bradyrhizobium diazoefficiens USDA 110 displays plasticity in the attachment phenotype when grown in different soybean root exudate compounds

Introduction

Bradyrhizobium diazoefficiens, a symbiotic nitrogen fixer for soybean, forms nodules after developing a symbiotic association with the root. For this association, bacteria need to move toward and attach to the root. These steps are mediated by the surface and phenotypic cell properties of bacteria and secreted root exudate compounds. Immense work has been carried out on nodule formation and nitrogen fixation, but little is known about the phenotype of these microorganisms under the influence of different root exudate chemical compounds (RECCs) or how this phenotype impacts the root attachment ability.

Methods

To address this knowledge gap, we studied the impact of 12 different RECCs, one commonly used carbon source, and soil-extracted solubilized organic matter (SESOM) on attachment and attachment-related properties of B. diazoefficiens USDA110. We measured motility-related properties (swimming, swarming, chemotaxis, and flagellar expression), attachment-related properties (surface hydrophobicity, biofilm formation, and attachment to cellulose and soybean roots), and surface polysaccharide properties (colony morphology, exopolysaccharide quantification, lectin binding profile, and lipopolysaccharide profiling).

Results and discussion

We found that USDA 110 displays a high degree of surface phenotypic plasticity when grown on the various individual RECCs. Some of the RECCs played specific roles in modulating the motility and root attachment processes. Serine increased cell surface hydrophobicity and root and cellulose attachment, with no EPS formed. Gluconate and lactate increased EPS production and biofilm formation, while decreasing hydrophobicity and root attachment, and raffinose and gentisate promoted motility and chemotaxis. The results also indicated that the biofilm formation trait on hydrophilic surfaces (polystyrene) cannot be related to the attachment ability of Bradyrhizobium to the soybean root. Among the tested phenotypic properties, bacterial cell surface hydrophobicity was the one with a significant impact on root attachment ability. We conclude that USDA 110 displays surface plasticity properties and attachment phenotype determined by individual RECCs from the soybean. Conclusions made based on its behavior in standard carbon sources, such as arabinose or mannitol, do not hold for its behavior in soil.

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.

A Defined Medium for Cultivation and Exometabolite Profiling of Soil Bacteria

Exometabolomics is an approach to assess how microorganisms alter, or react to their environments through the depletion and production of metabolites. It allows the examination of how soil microbes transform the small molecule metabolites within their environment, which can be used to study resource competition and cross-feeding. This approach is most powerful when used with defined media that enable tracking of all metabolites. However, microbial growth media have traditionally been developed for the isolation and growth of microorganisms but not metabolite utilization profiling through Liquid Chromatography Tandem Mass Spectrometry (LC-MS/MS). Here, we describe the construction of a defined medium, the Northen Lab Defined Medium (NLDM), that not only supports the growth of diverse soil bacteria but also is defined and therefore suited for exometabolomic experiments. Metabolites included in NLDM were selected based on their presence in R2A medium and soil, elemental stoichiometry requirements, as well as knowledge of metabolite usage by different bacteria. We found that NLDM supported the growth of 108 of the 110 phylogenetically diverse (spanning 36 different families) soil bacterial isolates tested and all of its metabolites were trackable through LC–MS/MS analysis. These results demonstrate the viability and utility of the constructed NLDM medium for growing and characterizing diverse microbial isolates and communities.

Trophic preferences of the pathogen Ralstonia solanacearum and consequences on its growth in xylem sap

Ralstonia solanacearum is one of the most destructive pathogens worldwide. In the last 30 years, the molecular mechanisms at the origin of R. solanacearum pathogenicity have been studied in depth. However, the nutrition status of the pathogen once inside the plant has been poorly investigated. Yet, the pathogen needs substrates to sustain a fast-enough growth, maintain its virulence and subvert the host immunity. This study aimed to explore in-depth the xylem environment where the pathogen is abundant, and its trophic preferences. First, we determined the composition of tomato xylem sap, where fast multiplication of the pathogen occurs. Then, kinetic growth on single and mixtures of carbon sources in relation to this environment was performed to fully quantify growth. Finally, we calculated the concentration of available metabolites in the xylem sap flux to assess how much it can support bacterial growth in planta. Overall, the study underlines the adaptation of R. solanacearum to the xylem environment and the fact that the pathogen assimilates several substrates at the same time in media composed of several carbon sources. It also provides metrics on key physiological parameters governing the growth of this major pathogen, which will be instrumental in the future to better understand its metabolic behavior during infection.

The efficiency of potential food waste-degrading bacteria under harsh conditions

AIMS

Investigate the impact of highly adapted bacterial strains and their ability in waste degradation under a wide range of temperatures.

METHODS AND RESULTS

Bacteria isolated from soil and food waste were grown in various media under fluctuated temperatures. After screening for organic compound degradation, the seven strongest bacterial strains have been selected for further experiments. Their enzyme activities were expressed in terms of the size of the hydrolysis zone in a wide temperature range of 2.5-70 ºC. The enzyme production assay was carried out for each protease, cellulase, and amylase. The waste degradation was determined with a maximum 80% decrease in the volume of food waste in 21 days compared to the control in lab-scale with enriched bacterial cultures and soil bacteria as additives at room temperature around 18 ºC-20 ºC.

CONCLUSION

These seven bacteria are promising candidates for food waste biodegradation in composting especially in the winter without heating expense for maintaining ambient temperature.

SIGNIFICANCE AND IMPACT OF THE STUDY

It is necessary to coax the uncultured bacteria from the various environments into the laboratory for investigating their valuable functions. Herein, using enrichment culture of consortium and additive of soil have illustrated the significant mean in food waste degradation.

Influence of soil microbes on Escherichia coli O157:H7 survival in soil rinse and artificial soil

AIMS

This research investigated the influence of soil microbiota on Escherichia coli O157:H7 survival in soil rinse and artificial soil. Additionally, the influence of selected soil bacteria on E. coli O157:H7 in soil environments was determined.

METHODS AND RESULTS

Escherichia coli O157:H7 counts (log CFU per ml or g^-1 ) were determined by spread plating: (i) artificial soil amended with soil rinse (filter-sterilized and unfiltered) at 30°C; (ii) unfiltered soil rinse (50 ml) treated with cycloheximide (200 μg ml^-1 ), vancomycin (40 μg ml^-1 ), heat (80°C, 15 min) and no treatment (control) for 7 days at 30°C and (iii) filtered soil rinse with selected soil bacterial isolates over 7 days. There was a significant difference (P = 0·027) in E. coli O157:H7 counts after 35 days between artificial soils amended with filtered (4·45 ± 0·29) and non-filtered (1·83 ± 0·33) soil rinse. There were significant differences (P < 0·05) in E. coli O157:H7 counts after 3 days of incubation between soil rinse treatments (heat (7·04 ± 0·03), cycloheximide (6·94 ± 0·05), vancomycin (4·26 ± 0·98) and control (5·00 ± 0·93)). Lastly, a significant difference (P < 0·05) in E. coli O157:H7 counts was observed after 3 days of incubation at 30°C in filtered soil rinse when incubated with Paenibacillus alvei versus other soil bacterial isolates evaluated.

CONCLUSIONS

Soil microbiota isolated from Florida sandy soil influenced E. coli O157:H7 survival. Specifically, P. alvei reduced E. coli O157:H7 by over 3 log CFU per ml after 3 days of incubation at 30°C in filtered soil rinse.

SIGNIFICANCE AND IMPACT OF THE STUDY

This research identified soil bacterial isolates that may reduce E. coli O157:H7 in the soil environment and be used in future biocontrol applications.

Bacterial communities associated with sugarcane under different agricultural management exhibit a diversity of plant growth-promoting traits and evidence of synergistic effect

Plant-associated microbiomes have been a target of interest for the prospection of microorganisms, which may be acting as effectors to increase agricultural productivity. For years, the search for beneficial microorganisms has been carried out from the characterization of functional traits of growth-promotion using tests with a few isolates. However, eventually, the expectations with positive results may not be realized when the evaluation is performed in association with plants. In our study, we accessed the cultivable sugarcane microbiome under two conditions of agronomic management: organic and conventional. From the use of a new customized culture medium, we recovered 944 endophytic and epiphytic bacterial communities derived from plant roots, stalks, leaves, and rhizospheric soil. This could be accomplished by using a large-scale approach, initially performing an in planta (Cynodon dactylon) screening process of inoculation to avoid early incompatibility. The inoculation was performed using the bacterial communities, considering that in this way, they could act synergistically. This process resulted in 38 candidate communities, 17 of which had higher Indole-3-acetic acid (IAA) production and phosphate solubilization activity and, were submitted to a new in planta test using Brachiaria ruziziensis and quantification of functional traits for growth-promotion and physiological tests. Enrichment analysis of selected communities has shown that they derived mainly from epiphytic populations of sugarcane stalks under conventional management. The sequencing of the V3-V4 region of the 16S rRNA gene revealed 34 genera and 24 species distributed among the phylum Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria. We also observed a network of genera in these communities where the genus Chryseobacterium stands out with a greater degree of interaction, indicating a possible direct or indirect role as a keystone taxon in communities with plant-growth promotion capacities. From the results achieved, we can conclude that the approach is useful in the recovery of a set of sugarcane bacterial communities and that there is, evidence of synergistic action providing benefits to plants, and that they are compatible with plants of the same family (Poaceae). Thus, we are reporting the beneficial bacterial communities identified as suitable candidates with rated potential to be exploited as bioinoculants for crops.

Seed coating as a delivery system for the endophyte Trichoderma koningiopsis Th003 in rice (Oryza sativa)

Seed coating is a technique to cover seeds with external agents to upgrade their performance, handling, and plant establishment. Plant beneficial microbes (PBMs), such as plant growth-promoting bacteria, mycorrhizal fungi, and other fungi (e.g., Trichoderma spp.), decrease agrochemical inputs, enhance tolerance to biotic-abiotic stresses, and increase essential plant nutrition. The demand for pre-treated seeds as delivery systems for biological agents is advancing. Here, a seed coating formulation containing Trichoderma koningiopsis is presented. The physicochemical and biological characterization of the seed coating prototypes included drying protector screening, the effect of the inoculum concentration on survival, the assessment of microbial release profiles in soil extract, and plant tissue colonization capability under semi-controlled conditions. Gelatine and pectin, two of the tested drying protectors, maintained fungus germination after 60 days at 18 °C with significantly higher values of up to 38% compared with the control. The initial concentration of 10⁶ colony-forming units (CFU) per seed undergoes a positive effect on survival over time. Regarding plant tissue colonization, the fungus establishes endophytically in rice. In conclusion, seed coating is a promising alternative for the formulation of beneficial microbial agents such as Trichoderma sp., maintaining cell survival and further promoting the establishment in rice systems.Key points• Enhancing drying survival of T. koningiopsis formulates• Seed coating formulation approach for T. koningiopsis in rice• Colonization capacity of formulated T. koningiopsis in rice tissue.

A new strategy using nanoscale zero-valent iron to simultaneously promote remediation and safe crop production in contaminated soil

Novel versatile nanomaterials may facilitate strategies for simultaneous soil remediation and agricultural production, but a thorough and mechanistic assessment of efficacy and safety is needed. We have established a new soil remediation strategy using nanoscale zero-valent iron (nZVI) coupled with safe rice production in paddy soil contaminated with pentachlorophenol (PCP). In comparison with rice cultivation in contaminated soil with 100 mg PCP per kg soil but without nZVI, the addition of 100 mg nZVI per kg soil increased grain yield by 47.1-55.0%, decreased grain PCP content by 83.6-86.2% and increased the soil PCP removal rate from 49.9 to 83.9-89.0%. The specific role of nZVI-derived root iron plaque formation in the safe production of rice has been elucidated, and the synergistic effect of nZVI treatment and rice cultivation identified in the nZVI-facilitated rhizosphere microbial degradation of PCP. This work opens a new strategy for the application of nanomaterials in soil remediation that could simultaneously enable safe crop production in contaminated lands.

Kinetics Growth and Recovery of Valuable Nutrients from Selangor Peat Swamp and Pristine Forest Soils Using Different Extraction Methods as Potential Microalgae Growth Enhancers

Soil extracts are useful nutrients to enhance the growth of microalgae. Therefore, the present study attempts for the use of virgin soils from Peninsular Malaysia as growth enhancer. Soils collected from Raja Musa Forest Reserve (RMFR) and Ayer Hitam Forest Reserve (AHFR) were treated using different extraction methods. The total dissolved nitrogen (TDN), total dissolved phosphorus (TDP), and dissolved organic carbon (DOC) concentrations in the autoclave methods were relatively higher than natural extraction with up to 132.0 mg N/L, 10.7 mg P/L, and 2629 mg C/L, respectively for RMFR. The results of TDN, TDP, and DOC suggested that the best extraction methods are autoclaved at 121 °C twice with increasing 87%, 84%, and 95%, respectively. Chlorella vulgaris TRG 4C dominated the growth at 121 °C twice extraction method in the RMRF and AHRF samples, with increasing 54.3% and 14%, respectively. The specific growth rate (µ) of both microalgae were relatively higher, 0.23 d^-1 in the Ayer Hitam Soil. This extract served well as a microalgal growth promoter, reducing the cost and the needs for synthetic medium. Mass production of microalgae as aquatic feed will be attempted eventually. The high recovery rate of nutrients has a huge potential to serve as a growth promoter for microalgae.

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.

Isolation and screening of indigenous bacteria from phosphogypsum-contaminated soils for their potential in promoting plant growth and trace elements mobilization

Bacteria isolated from soils in the vicinity of phosphogypsum (PG) stockpiles were studied for their potential use in bioaugmentation-assisted phytoextraction. Quick, miniaturized biochemical tests were performed in the presence of metal trace elements (MTE), including rare earth elements (Cd, Sr, Ce, La, Nd and Y), corresponding to their bioavailable concentrations in PG. The intention herein was to assess the capacity of bacteria to: i) grow in PG; ii) produce indole acetic acid and ACC deaminase to promote plant growth and reduce stress; and iii) produce siderophores, including pyoverdine, to mobilize MTE. Results showed that even at maximum PG concentration (10 g/L and pH 3.40), 7 out of 32 isolates were able to grow. The biochemical tests showed differences in the presence or absence of MTE. The presence of MTE seems to promote the production of IAA by a factor of 3.25. On the contrary, it inhibits ACC deaminase and siderophore production, including pyoverdine. According to a scoring method applied, the two most efficient isolates exhibiting maximum metabolite production were identified as Bacillus sp.

Effective Soil Extraction Method for Cultivating Previously Uncultured Soil Bacteria

Here, a new medium, named intensive soil extract medium (ISEM), based on new soil extract (NSE) using 80% methanol, was used to efficiently isolate previously uncultured bacteria and new taxonomic candidates, which accounted for 49% and 55% of the total isolates examined (n = 258), respectively. The new isolates were affiliated with seven phyla (Proteobacteria, Acidobacteria, Firmicutes, Actinobacteria, Verrucomicrobia, Planctomycetes, and Bacteroidetes). The result of chemical analysis showed that NSE included more diverse components of low-molecular-weight organic substances than two conventional soil extracts made using distilled water. Cultivation of previously uncultured bacteria is expected to extend knowledge through the discovery of new phenotypic, physiological, and functional properties and even roles of unknown genes.IMPORTANCE Both metagenomics and single-cell sequencing can detect unknown genes from uncultured microbial strains in environments, and either method may find the significant potential metabolites and roles of these strains. However, such gene/genome-based techniques do not allow detailed investigations that are possible with cultures. To solve this problem, various approaches for cultivation of uncultured bacteria have been developed, but there are still difficulties in maintaining pure cultures by subculture.

Growth and Extended Survival of Escherichia coli O157:H7 in Soil Organic Matter

Enterohaemorrhagic Escherichia coli, such as serotype O157:H7, are a leading cause of food-associated outbreaks. While the primary reservoir is associated with cattle, plant foods have been associated as sources of human infection. E. coli is able to grow in the tissue of food plants such as spinach. While fecal contamination is the primary suspect, soil has been underestimated as a potential reservoir. Persistence of bacterial populations in open systems is the product of growth, death, predation, and competition. Here we report that E. coli O157:H7 can grow using the soluble compounds in soil, and characterize the effect of soil growth on the stationary phase proteome. E. coli 933D (stxII⁻) was cultured in Soil Extracted Soluble Organic Matter (SESOM) and the culturable count determined for 24d. The proteomes of exponential and stationary phase populations were characterized by 2D gel electrophoresis and protein spots were identified by MALDI-TOF mass spectrometry. While LB controls displayed a death phase, SESOM grown population remained culturable for 24d, indicating an altered physiological state with superior longevity. This was not due to decreased cell density on entry to stationary phase as 24 h SESOM populations concentrated 10-fold retained their longevity. Principal component analysis showed that stationary phase proteomes from SESOM and LB were different. Differences included proteins involved in stress response, motility, membrane and wall composition, nutrient uptake, translation and protein turnover, and anabolic and catabolic pathways, indicating an altered physiological state of soil-grown cells entering stationary phase. The results suggest that E. coli may be a soil commensal that, in absence of predation and competition, maintains stable populations in soil.

Microbiome analysis and bacterial isolation from Lejía Lake soil in Atacama Desert

As a consequence of the severe climatic change affecting our entire world, many lakes in the Andes Cordillera are likely to disappear within a few decades. One of these lakes is Lejía Lake, located in the central Atacama Desert. The objectives of this study were: (1) to characterize the bacterial community from Lejía Lake shore soil (LLS) using 16S rRNA sequencing and (2) to test a culture-based approach using a soil extract medium (SEM) to recover soil bacteria. This extreme ecosystem was dominated by three phyla: Bacteroidetes, Proteobacteria, and Firmicutes with 29.2, 28.2 and 28.1% of the relative abundance, respectively. Using SEM, we recovered 7.4% of the operational taxonomic units from LLS, all of which belonged to the same three dominant phyla from LLS (6.9% of Bacteroidetes, 77.6% of Proteobacteria, and 15.3% of Firmicutes). In addition, we used SEM to recover isolates from LLS and supplemented the culture medium with increasing salt concentrations to isolate microbial representatives of salt tolerance (Halomonas spp.). The results of this study complement the list of microbial taxa diversity from the Atacama Desert and assess a pipeline to isolate selective bacteria that could represent useful elements for biotechnological approaches.

Novel Method Reveals a Narrow Phylogenetic Distribution of Bacterial Dispersers in Environmental Communities Exposed to Low-Hydration Conditions

In this study, we developed a method that provides profiles of community-level surface dispersal from environmental samples under controlled hydration conditions and enables us to isolate and uncover the diversity of the fastest bacterial dispersers. The method expands on the porous surface model (PSM), previously used to monitor the dispersal of individual bacterial strains in liquid films at the surface of a porous ceramic disc. The novel procedure targets complex communities and captures the dispersed bacteria on a solid medium for growth and detection. The method was first validated by distinguishing motile Pseudomonas putida and Flavobacterium johnsoniae strains from their nonmotile mutants. Applying the method to soil and lake water bacterial communities showed that community-scale dispersal declined as conditions became drier. However, for both communities, dispersal was detected even under low-hydration conditions (matric potential, -3.1 kPa) previously proven too dry for P. putida strain KT2440 motility. We were then able to specifically recover and characterize the fastest dispersers from the inoculated communities. For both soil and lake samples, 16S rRNA gene amplicon sequencing revealed that the fastest dispersers were substantially less diverse than the total communities. The dispersing fraction of the soil microbial community was dominated by Pseudomonas species cells, which increased in abundance under low-hydration conditions, while the dispersing fraction of the lake community was dominated by Aeromonas species cells and, under wet conditions (-0.5 kPa), also by Exiguobacterium species cells. The results gained in this study bring us a step closer to assessing the dispersal ability within complex communities under environmentally relevant conditions.IMPORTANCE Dispersal is a key process of bacterial community assembly, and yet, very few attempts have been made to assess bacterial dispersal at the community level, as the focus has previously been on pure-culture studies. A crucial factor for dispersal in habitats where hydration conditions vary, such as soils, is the thickness of the liquid films surrounding solid surfaces, but little is known about how the ability to disperse in such films varies within bacterial communities. Therefore, we developed a method to profile community dispersal and identify fast dispersers on a rough surface resembling soil surfaces. Our results suggest that within the motile fraction of a bacterial community, only a minority of the bacterial types are able to disperse in the thinnest liquid films. During dry periods, these efficient dispersers can gain a significant fitness advantage through their ability to colonize new habitats ahead of the rest of the community.

Response of enzyme activities and microbial communities to soil amendment with sugar alcohols

Changes in microbial community structure are widely known to occur after soil amendment with low-molecular-weight organic compounds; however, there is little information on concurrent changes in soil microbial functional diversity and enzyme activities, especially following sorbitol and mannitol amendment. Soil microbial functional diversity and enzyme activities can be impacted by sorbitol and mannitol, which in turn can alter soil fertility and quality. The objective of this study was to investigate the effects of sorbitol and mannitol addition on microbial functional diversity and enzyme activities. The results demonstrated that sorbitol and mannitol addition altered the soil microbial community structure and improved enzyme activities. Specifically, the addition of sorbitol enhanced the community-level physiological profile (CLPP) compared with the control, whereas the CLPP was significantly inhibited by the addition of mannitol. The results of a varimax rotated component matrix demonstrated that carbohydrates, polymers, and carboxylic acids affected the soil microbial functional structure. Additionally, we found that enzyme activities were affected by both the concentration and type of inputs. In the presence of high concentrations of sorbitol, the urease, catalase, alkaline phosphatase, β-glucosidase, and N-acetyl-β-d-glucosaminidase activities were significantly increased, while invertase activity was decreased. Similarly, this increase in invertase, catalase, and alkaline phosphatase and N-acetyl-β-d-glucosaminidase activities was especially evident after mannitol addition, and urease activity was only slightly affected. In contrast, β-glucosidase activity was suppressed at the highest concentration. These results indicate that microbial community diversity and enzyme activities are significantly affected by soil amendment with sorbitol and mannitol.

Isolation and characterisation of a Sphingomonas strain able to degrade the fungicide ortho-phenylphenol

BACKGROUND

Ortho-phenylphenol (OPP) is a fungicide used in fruit packaging plants for the control of fungal infestations during storage. Its application leads to the production of large wastewater volumes which according to the European legislation should be treated on site. In spite of this, no efficient treatment systems are currently available, and the development of biological systems based on tailored-made pesticide-degrading inocula for the treatment of these wastewaters is an appealing solution.

RESULTS

Enrichment cultures from a soil collected from a wastewater disposal site resulted in the isolation of a pure Sphingomonas haloaromaticamans strain P3 able to degrade rapidly OPP and use it as an energy source. Its degrading capacity was dependent on the external supply of amino acids or on the presence of other bacteria that did not contribute to fungicide degradation. The isolated S. haloaromaticamans strain was able to metabolise up to 150 mg L(-1) of OPP within 7 days, in a wide range of pH (4.5-9) and temperatures (4-37 °C), and in the presence of other pesticides (thiabendazole and diphenylamine) co-used in the fruit packaging industry.

CONCLUSION

Overall, the OPP-degrading bacterium isolated showed high potential for use in future biodepuration treatment systems and bioremediation strategies.

A quick rhizobacterial selection tests for the remediation of copper contaminated soils

AIMS

The main objective of the study is to develop and improve quick bacterial tests to select the best candidates for the bioaugmentation of metal-contaminated soil, coupled with phytoextraction.

METHODS AND RESULTS

Bacteria isolates (181) were selected from a collection originated from a Cu-contaminated sediment, on the basis of several miniaturized biochemical tests adapted to the copper contamination. Amongst them, we used a growth soil based-medium to select metal-tolerant bacteria, and their ability to grow and mobilize metals by mean of metabolites (siderophores, organic acids) was also assessed.

CONCLUSION

The result of the bacterial selection tests showed differences in presence or absence of copper, especially for phosphate-solubilizing strains which ability decreased by 53% in the presence of copper hydroxide phosphate as compared to the standard tricalcium phosphate test. A promising Pseudomonas putida was selected from the collection.

SIGNIFICANCE AND IMPACT OF THE STUDY

The study underlined the importance of choosing significant selection tests regarding the nature of the metal occurring in the soil to be cleaned-up to assess the real potential of each bacterial strain for subsequent soil bioaugmentation purposes.

A time resolved metabolomics study: the influence of different carbon sources during growth and starvation of Bacillus subtilis

In its natural environment, the soil, the Gram-positive model bacterium Bacillus subtilis frequently encounters nutrient limitation and other stress factors. Efficient adaptation mechanisms are necessary to cope with this wide range of environmental challenges. The ability to utilize diverse carbon sources represents a key adaptation process that allows B. subtilis to thrive in its natural habitat. To gain a comprehensive insight into the metabolism of B. subtilis, global metabolite analyses were performed during growth with glucose alone or glucose with either malate, fumarate or citrate as carbon/energy sources. Furthermore, to achieve a comprehensive coverage of a wide range of chemically different metabolites, complementary GC-MS, LC-MS and (1)H-NMR analyses were applied. This study reveals that the availability of different carbon sources results in different extracellular metabolite profiles whereas a regulated intracellular metabolite equilibrium was observed. In addition, the typical energy-starvation induced activation of the general stress sigma factor σ(B) was only observed upon entry into the stationary phase with glucose or glucose and malate as carbon sources.

Cell physiology of the biotechnological relevant bacterium Bacillus pumilus-an omics-based approach

Members of the species Bacillus pumilus get more and more in focus of the biotechnological industry as potential new production strains. Based on exoproteome analysis, B. pumilus strain Jo2, possessing a high secretion capability, was chosen for an omics-based investigation. The proteome and metabolome of B. pumilus cells growing either in minimal or complex medium was analyzed. In total, 1542 proteins were identified in growing B. pumilus cells, among them 1182 cytosolic proteins, 297 membrane and lipoproteins and 63 secreted proteins. This accounts for about 43% of the 3616 proteins encoded in the B. pumilus Jo2 genome sequence. By using GC-MS, IP-LC/MS and H NMR methods numerous metabolites were analyzed and assigned to reconstructed metabolic pathways. In the genome sequence a functional secretion system including the components of the Sec- and Tat-secretion machinery was found. Analysis of the exoproteome revealed secretion of about 70 proteins with predicted secretion signals. In addition, selected production-relevant genome features such as restriction modification systems and NRPS clusters of B. pumilus Jo2 are discussed.

Specificity of plant-microbe interactions in the tree mycorrhizosphere biome and consequences for soil C cycling

Mycorrhizal associations are ubiquitous and form a substantial component of the microbial biomass in forest ecosystems and fluxes of C to these belowground organisms account for a substantial portion of carbon assimilated by forest vegetation. Climate change has been predicted to alter belowground plant-allocated C which may cause compositional shifts in soil microbial communities, and it has been hypothesized that this community change will influence C mitigation in forest ecosystems. Some 10,000 species of ectomycorrhizal fungi are currently recognized, some of which are host specific and will only associate with a single tree species, for example, Suillus grevillei with larch. Mycorrhizae are a strong sink for plant C, differences in mycorrhizal anatomy, particularly the presence and extent of emanating hyphae, can affect the amount of plant C allocated to these assemblages. Mycorrhizal morphology affects not only spatial distribution of C in forests, but also differences in the longevity of these diverse structures may have important consequences for C sequestration in soil. Mycorrhizal growth form has been used to group fungi into distinctive functional groups that vary qualitatively and spatially in their foraging and nutrient acquiring potential. Through new genomic techniques we are beginning to understand the mechanisms involved in the specificity and selection of ectomycorrhizal associations though much less is known about arbuscular mycorrhizal associations. In this review we examine evidence for tree species- mycorrhizal specificity, and the mechanisms involved (e.g., signal compounds). We also explore what is known about the effects of these associations and interactions with other soil organisms on the quality and quantity of C flow into the mycorrhizosphere (the area under the influence of mycorrhizal root tips), including spatial and seasonal variations. The enormity of the mycorrhizosphere biome in forests and its potential to sequester substantial C belowground highlights the vital importance of increasing our knowledge of the dynamics of the different mycorrhizal functional groups in diverse forests.

Methodological approaches to help unravel the intracellular metabolome of Bacillus subtilis

Background

Bacillus subtilis (B. subtilis) has become widely accepted as a model organism for studies on Gram-positive bacteria. A deeper insight into the physiology of this prokaryote requires advanced studies of its metabolism. To provide a reliable basis for metabolome investigations, a validated experimental protocol is needed since the quality of the analytical sample and the final data are strongly affected by the sampling steps. To ensure that the sample analyzed precisely reflects the biological condition of interest, outside biases have to be avoided during sample preparation.

Results

Procedures for sampling, quenching, extraction of metabolites, cell disruption, as well as metabolite leakage were tested and optimized for B. subtilis. In particular the energy status of the bacterial cell, characterized by the adenylate energy charge, was used to evaluate sampling accuracy. Moreover, the results of the present study demonstrate that the cultivation medium can affect the efficiency of the developed sampling procedure.

Conclusion

The final workflow presented here allows for the reproducible and reliable generation of physiological data. The method with the highest qualitative and quantitative metabolite yield was chosen, and when used together with complementary bioanalytical methods (i.e., GC-MS, LC-MS and ¹H-NMR) provides a solid basis to gather information on the metabolome of B. subtilis.

Role of N-terminal protein formylation in central metabolic processes in Staphylococcus aureus

Background

Bacterial protein biosynthesis usually depends on a formylated methionyl start tRNA but Staphylococcus aureus is viable in the absence of Fmt, the tRNA^Met formyl transferase. fmt mutants exhibit reduced growth rates indicating that the function of certain proteins depends on formylated N-termini but it has remained unclear, which cellular processes are abrogated by the lack of formylation.

Results

In order to elucidate how global metabolic processes are affected by the absence of formylated proteins the exometabolome of an S. aureus fmt mutant was compared with that of the parental strain and the transcription of corresponding enzymes was analyzed to identify possible regulatory changes. The mutant consumed glucose and other carbon sources slower than the wild type. While the turnover of several metabolites remained unaltered fmt inactivation led to increases pyruvate release and, concomitantly, reduced pyruvate dehydrogenase activity. In parallel, the release of the pyruvate-derived metabolites lactate, acetoin, and alanine was reduced. The anaerobic degradation of arginine was also reduced in the fmt mutant compared to the wild-type strain. Moreover, the lack of formylated proteins caused increased susceptibility to the antibiotics trimethoprim and sulamethoxazole suggesting that folic acid-dependant pathways were perturbed in the mutant.

Conclusions

These data indicate that formylated proteins are crucial for specific bacterial metabolic processes and they may help to understand why it has remained important during bacterial evolution to initiate protein biosynthesis with a formylated tRNA^Met.

Are uncultivated bacteria really uncultivable?

Many strategies have been used to increase the number of bacterial cells that can be grown from environmental samples but cultivation efficiency remains a challenge for microbial ecologists. The difficulty of cultivating a fraction of bacteria in environmental samples can be classified into two non-exclusive categories. Bacterial taxa with no cultivated representatives for which appropriate laboratory conditions necessary for growth are yet to be identified. The other class is cells in a non-dividing state (also known as dormant or viable but not culturable cells) that require the removal or addition of certain factors to re-initiate growth. A number of strategies, from simple to high throughput techniques, are reviewed that have been used to increase the cultivation efficiency of environmental samples. Some of the underlying mechanisms that contribute to the success of these cultivation strategies are described. Overall this review emphasizes the need of researchers to first understand the factors that are hindering cultivation to identify the best strategies to improve cultivation efficiency.

Increased lysine production by flux coupling of the tricarboxylic acid cycle and the lysine biosynthetic pathway--metabolic engineering of the availability of succinyl-CoA in Corynebacterium glutamicum

In this study, we demonstrate increased lysine production by flux coupling using the industrial work horse bacterium Corynebacterium glutamicum, which was mediated by the targeted interruption of the tricarboxylic acid (TCA) cycle at the level of succinyl-CoA synthetase. The succinylase branch of the lysine production pathway functions as the bridging reaction to convert succinyl-CoA to succinate in this aerobic bacterium. The mutant C. glutamicum ΔsucCD showed a 60% increase in the yield of lysine when compared to the advanced lysine producer which was used as parent strain. This mutant was highly vital and exhibited only a slightly reduced specific growth rate. Metabolic flux analysis with (13)C isotope studies confirmed that the increase in lysine production was mediated by pathway coupling. The novel strain exhibited an exceptional flux profile, which was closer to the optimum performance predicted by in silico pathway analysis than to the large set of lysine-producing strains analyzed thus far. Fluxomics and transcriptomics were applied as further targets for next-level strain engineering to identify the back-up mechanisms that were activated upon deletion of the enzyme in the mutant strain. It seemed likely that the cells partly recruited the glyoxylate shunt as a by-pass route. Additionally, the α-ketoglutarate decarboxylase pathway emerged as the potential compensation mechanism. This novel strategy appears equally promising for Escherichia coli, which is used in the industrial production of lysine, wherein this bacterium synthesizes lysine exclusively by succinyl-CoA activation of pathway intermediates. The channeling of a high flux pathway into a production pathway by pathway coupling is an interesting metabolic engineering strategy that can be explored to optimize bio-production in the future.

Life and death of proteins: a case study of glucose-starved Staphylococcus aureus

The cellular amount of proteins not only depends on synthesis but also on degradation. Here, we expand the understanding of differential protein levels by complementing synthesis data with a proteome-wide, mass spectrometry-based stable isotope labeling with amino acids in cell culture analysis of protein degradation in the human pathogen Staphylococcus aureus during glucose starvation. Monitoring protein stability profiles in a wild type and an isogenic clpP protease mutant revealed that 1) proteolysis mainly affected proteins with vegetative functions, anabolic and selected catabolic enzymes, whereas the expression of TCA cycle and gluconeogenesis enzymes increased; 2) most proteins were prone to aggregation in the clpP mutant; 3) the absence of ClpP correlated with protein denaturation and oxidative stress responses, deregulation of virulence factors and a CodY repression. We suggest that degradation of redundant, inactive proteins disintegrated from functional complexes and thereby amenable to proteolytic attack is a fundamental cellular process in all organisms to regain nutrients and guarantee protein homeostasis.

Global analysis of the Staphylococcus aureus response to mupirocin

In the present study, we analyzed the response of S. aureus to mupirocin, the drug of choice for nasal decolonization. Mupirocin selectively inhibits the bacterial isoleucyl-tRNA synthetase (IleRS), leading to the accumulation of uncharged isoleucyl-tRNA and eventually the synthesis of (p)ppGpp. The alarmone (p)ppGpp induces the stringent response, an important global transcriptional and translational control mechanism that allows bacteria to adapt to nutritional deprivation. To identify proteins with an altered synthesis pattern in response to mupirocin treatment, we used the highly sensitive 2-dimensional gel electrophoresis technique in combination with mass spectrometry. The results were complemented by DNA microarray, Northern blot, and metabolome analyses. Whereas expression of genes involved in nucleotide biosynthesis, DNA metabolism, energy metabolism, and translation was significantly downregulated, expression of isoleucyl-tRNA synthetase, the branched-chain amino acid pathway, and genes with functions in oxidative-stress resistance (ahpC and katA) and putative roles in stress protection (the yvyD homologue SACOL0815 and SACOL1759 and SACOL2131) and transport processes was increased. A comparison of the regulated genes to known regulons suggests the involvement of the global regulators CodY and SigB in shaping the response of S. aureus to mupirocin. Of particular interest was the induced transcription of genes encoding virulence-associated regulators (i.e., arlRS, saeRS, sarA, sarR, sarS, and sigB), as well as genes directly involved in the virulence of S. aureus (i.e., fnbA, epiE, epiG, and seb).

Metabolome analysis of gram-positive bacteria such as Staphylococcus aureus by GC-MS and LC-MS

The field of metabolomics has become increasingly important in the context of functional genomics. Together with other "omics" data, the investigation of the metabolome is an essential part of systems biology. Beside the analysis of human and animal biofluids, the investigation of the microbial physiology by methods of metabolomics has gained increased attention. For example, the analysis of metabolic processes during growth or virulence factor expression is crucially important to understand pathogenesis of bacteria. Common bioanalytical techniques for metabolome analysis include liquid and gas chromatographic methods coupled to mass spectrometry (LC-MS and GC-MS) and spectroscopic approaches such as NMR. In order to achieve metabolome data representing the physiological status of a microorganism, well-verified protocols for sampling and analysis are necessary. This chapter presents a detailed protocol for metabolome analysis of the Gram-positive bacterium Staphylococcus aureus. A detailed manual for cell sampling and metabolite extraction is given, followed by the description of the analytical procedures GC-MS and LC-MS. The advantages and limitations of each experimental setup are discussed. Here, a guideline specified for S. aureus metabolomics and information for important protocol steps are presented, to avoid common pitfalls in microbial metabolome analysis.

Exometabolome analysis identifies pyruvate dehydrogenase as a target for the antibiotic triphenylbismuthdichloride in multiresistant bacterial pathogens

The desperate need for new therapeutics against notoriously antibiotic-resistant bacteria has led to a quest for novel antibacterial target structures and compounds. Moreover, defining targets and modes of action of new antimicrobial compounds remains a major challenge with standard technologies. Here we characterize the antibacterial properties of triphenylbismuthdichloride (TPBC), which has recently been successfully used against device-associated infections. We demonstrate that TPBC has potent antimicrobial activity against many bacterial pathogens. Using an exometabolome profiling approach, a unique TPBC-mediated change in the metabolites of Staphylococcus aureus was identified, indicating that TPBC blocks bacterial pyruvate catabolism. Enzymatic studies showed that TPBC is a highly efficient, uncompetitive inhibitor of the bacterial pyruvate dehydrogenase complex. Our study demonstrates that metabolomics approaches can offer new avenues for studying the modes of action of antimicrobial compounds, and it indicates that inhibition of the bacterial pyruvate dehydrogenase complex may represent a promising strategy for combating multidrug-resistant bacteria.

Staphylococcus aureus physiological growth limitations: insights from flux calculations built on proteomics and external metabolite data

Comparing proteomics and metabolomics allows insights into Staphylococcus aureus physiological growth. We update genome and proteome information and deliver strain-specific metabolic models for three S. aureus strains (COL, N315, and Newman). We find a number of differences in metabolism and enzymes. Growth experiments (glucose or combined with oxygen limitation) were conducted to measure external metabolites. Fluxes of the central metabolism were calculated from these data with low error. In exponential phase, glycolysis is active and amino acids are used for growth. In later phases, dehydroquinate synthetase is suppressed and acetate metabolism starts. There are strain-specific differences for these phases. A time series of 2-D gel protein expression data on COL strain delivered a second data set (glucose limitation) on which fluxes were calculated. The comparison with the metabolite-predicted fluxes shows, in general, good correlation. Outliers point to different regulated enzymes for S. aureus COL under these limitations. In exponential growth, there is lower activity for some enzymes in upper glycolysis and pentose phosphate pathway and stronger activity for some in lower glycolysis. In transition phase, aspartate kinase is expressed to meet amino acid requirements and in later phases there is high expression of glyceraldehyde-3-phosphate dehydrogenase and lysine synthetase. Central metabolite fluxes and protein expression of their enzymes correlate in S. aureus.

Comparative analysis of antimicrobial activities of valinomycin and cereulide, the Bacillus cereus emetic toxin

Cereulide and valinomycin are highly similar cyclic dodecadepsipeptides with potassium ionophoric properties. Cereulide, produced by members of the Bacillus cereus group, is known mostly as emetic toxin, and no ecological function has been assigned. A comparative analysis of the antimicrobial activity of valinomycin produced by Streptomyces spp. and cereulide was performed at a pH range of pH 5.5 to pH 9.5, under anaerobic and aerobic conditions. Both compounds display pH-dependent activity against selected Gram-positive bacteria, including Staphylococcus aureus, Listeria innocua, Listeria monocytogenes, Bacillus subtilis, and Bacillus cereus ATCC 10987. Notably, B. cereus strain ATCC 14579 and the emetic B. cereus strains F4810/72 and A529 showed reduced sensitivity to both compounds, with the latter two strains displaying full resistance to cereulide. Both compounds showed no activity against the selected Gram-negative bacteria. Antimicrobial activity against Gram-positive bacteria was highest at alkaline pH values, where the membrane potential (ΔΨ) is the main component of the proton motive force (PMF). Furthermore, inhibition of growth was observed in both aerobic and anaerobic conditions. Determination of the ΔΨ, using the membrane potential probe DiOC(2)(3) (in the presence of 50 mM KCl) in combination with flow cytometry, demonstrated for the first time the ability of cereulide to dissipate the ΔΨ in sensitive Gram-positive bacteria. The putative role of cereulide production in the ecology of emetic B. cereus is discussed.

A metabolomic view of Staphylococcus aureus and its ser/thr kinase and phosphatase deletion mutants: involvement in cell wall biosynthesis

Little is known about intracellular metabolite pools in pathogens such as Staphylococcus aureus. We have studied a particular metabolome by means of the presented LC-MS method. By investigating the central carbon metabolism which includes most of the energy transfer molecules like nucleotides, sugar mono- and biphosphates, and cofactors, a conclusion about phenotypes and stress answers in microorganisms is possible. Quantitative metabolite levels of S. aureus grown in complex lysogeny broth and in minimal medium were compared in the wild-type S. aureus strain 8325 and the isogenic eukaryotic-like protein serine/threonine kinase (DeltapknB) and phosphatase (Deltastp) deletion mutants. Detection of several remarkable differences, e.g., in nucleotide metabolism and especially cell wall precursor metabolites, indicates a previously unreported importance of serine/threonine kinase/phosphatase on peptidoglycan and wall teichoic acid biosynthesis. These findings may lead to new insights into the regulation of staphylococcal cell wall metabolism.

Pyruvate formate lyase acts as a formate supplier for metabolic processes during anaerobiosis in Staphylococcus aureus

Previous studies demonstrated an upregulation of pyruvate formate lyase (Pfl) and NAD-dependent formate dehydrogenase (Fdh) in Staphylococcus aureus biofilms. To investigate their physiological role, we constructed fdh and pfl deletion mutants (Δfdh and Δpfl). Although formate dehydrogenase activity in the fdh mutant was lost, it showed little phenotypic alterations under oxygen-limited conditions. In contrast, the pfl mutant displayed pleiotropic effects and revealed the importance of formate production for anabolic metabolism. In the pfl mutant, no formate was produced, glucose consumption was delayed, and ethanol production was decreased, whereas acetate and lactate production were unaffected. All metabolic alterations could be restored by addition of formate or complementation of the Δpfl mutant. In compensation reactions, serine and threonine were consumed better by the Δpfl mutant than by the wild type, suggesting that their catabolism contributes to the refilling of formyl-tetrahydrofolate, which acts as a donor of formyl groups in, e.g., purine and protein biosynthesis. This notion was supported by reduced production of formylated peptides by the Δpfl mutant compared to that of the parental strain, as demonstrated by weaker formyl-peptide receptor 1 (FPR1)-mediated activation of leukocytes with the mutant. FPR1 stimulation could also be restored either by addition of formate or by complementation of the mutation. Furthermore, arginine consumption and arc operon transcription were increased in the Δpfl mutant. Unlike what occurred with the investigated anaerobic conditions, a biofilm is distinguished by nutrient, oxygen, and pH gradients, and we thus assume that Pfl plays a significant role in the anaerobic layer of a biofilm. Fdh might be critical in (micro)aerobic layers, as formate oxidation is correlated with the generation of NADH/H(+), whose regeneration requires respiration.

Fed-batch process for the psychrotolerant marine bacterium Pseudoalteromonas haloplanktis

Background

Pseudoalteromonas haloplanktis is a cold-adapted γ-proteobacterium isolated from Antarctic sea ice. It is characterized by remarkably high growth rates at low temperatures. P. haloplanktis is one of the model organisms of cold-adapted bacteria and has been suggested as an alternative host for the soluble overproduction of heterologous proteins which tend to form inclusion bodies in established expression hosts. Despite the progress in establishing P. haloplanktis as an alternative expression host the cell densities obtained with this organism, which is unable to use glucose as a carbon source, are still low. Here we present the first fed-batch cultivation strategy for this auspicious alternative expression host.

Results

The key for the fed-batch cultivation of P. haloplanktis was the replacement of peptone by casamino acids, which have a much higher solubility and allow a better growth control. In contrast to the peptone medium, on which P. haloplanktis showed different growth phases, on a casamino acids-containing, phosphate-buffered medium P. haloplanktis grew exponentially with a constant growth rate until the stationary phase. A fed-batch process was established by feeding of casamino acids with a constant rate resulting in a cell dry weight of about 11 g l^-1 (OD₅₄₀ = 28) which is a twofold increase of the highest densities which have been obtained with P. haloplanktis so far and an eightfold increase of the density obtained in standard shake flask cultures.

The cell density was limited in the fed-batch cultivation by the relatively low solubility of casamino acids (about 100 g l^-1), which was proven by pulse addition of casamino acid powder which increased the cell density to about 20 g l^-1 (OD₅₄₀ = 55).

Conclusion

The growth of P. haloplanktis to higher cell densities on complex medium is possible. A first fed-batch fermentation strategy could be established which is feasible to be used in lab-scale or for industrial purposes. The substrate concentration of the feeding solution was found to influence the maximal biomass yield considerably. The bottleneck for growing P. haloplanktis to high cell densities still remains the availability of a highly concentrated substrate and the reduction of the substrate complexity. However, our results indicate glutamic acid as a major carbon source, which provides a good basis for further improvement of the fed-batch process.

Advantage of upregulation of succinate dehydrogenase in Staphylococcus aureus biofilms

Previous studies have demonstrated that various tricarboxylic acid (TCA) cycle genes, particularly the succinate dehydrogenase genes (sdhCAB), are upregulated in Staphylococcus aureus biofilms. To better study the role of this enzyme complex, an sdhCAB deletion mutant (Deltasdh) was constructed. Compared to the wild type (wt) the mutant was impaired in planktonic growth under aerobic conditions, excreted acetic acid could not be reused and accumulated continuously, succinate was excreted and found in the culture supernatant, and metabolome analysis with cells grown in chemically defined medium revealed reduced uptake/metabolism of some amino acids from the growth medium. Moreover, the mutant was able to counteract the steadily decreasing extracellular pH by increased urease activity. The addition of fumarate to the growth medium restored the wt phenotype. The mutant showed a small-colony variant (SCV)-like phenotype, a slight increase in resistance to various aminoglycoside antibiotics, and decreased pigmentation. The decreased growth under aerobic conditions is due to the interruption of the TCA cycle (indicated by the accumulation of succinate and acetic acid) with the consequence that many fewer reduction equivalents (NADH and FADH2) can fuel the respiratory chain. The results indicate that the TCA cycle is required for acetate and amino acid catabolism; its upregulation under biofilm conditions is advantageous under such nutrient- and oxygen-limited conditions.

Proteolysis during long-term glucose starvation in Staphylococcus aureus COL

A combination of pulse-chase experiments and 2-D PAGE revealed that protein degradation appears to play a crucial role for the cell physiology of Staphylococcus aureus COL during extended periods of glucose starvation. The synthesis rate of virtually all cytosolic and radioactively labeled proteins from growing cells seemed dramatically reduced in the first 3.5 h of glucose starvation. The stability of proteins synthesized in growing cells was monitored by a pulse-chase approach on a proteome wide scale. Especially, enzymes involved in nucleic acid and amino acid biosyntheses, energy metabolism and biosynthesis of cofactors were found rather rapidly degraded within the onset of the stationary phase, whereas the majority of glycolytic and tricarboxylic acid cycle enzymes remained more stable. Furthermore, single enzymes of biosynthetic pathways were differentially degraded. A metabolite analysis revealed that glucose completely depleted from the medium in the transient phase, and amino acids such as alanine and glycine were taken up by the cells in the stationary phase. We suggest that vegetative proteins no longer required in non-growing cells and thus no longer protected by integration into functional complexes were degraded. Proteolysis of putative non-substrate-bound or "unemployed" proteins appears to be a characteristic feature of S. aureus in order to access nutrients as an important survival strategy under starvation conditions.