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PubMed2002

Metabolic commensalism and competition in a two-species microbial consortium.

We analyzed metabolic interactions and the importance of specific structural relationships in a benzyl alcohol-degrading microbial consortium comprising two species, Pseudomonas putida strain R1 and Acinetobacter strain C6, both of which are able to utilize benzyl alcohol as their sole carbon and energy source. The organisms were grown either as surface-attached organisms (biofilms) in flow chambers or as suspended cultures in chemostats. The numbers of CFU of P. putida R1 and Acinetobacter strain C6 were determined in chemostats and from the effluents of the flow chambers. When the two species were grown together in chemostats with limiting concentrations of benzyl alcohol, Acinetobacter strain C6 outnumbered P. putida R1 (500:1), whereas under similar growth conditions in biofilms, P. putida R1 was present in higher numbers than Acinetobacter strain C6 (5:1). In order to explain this difference, investigations of microbial activities and structural relationships were carried out in the biofilms. Insertion into P. putida R1 of a fusion between the growth rate-regulated rRNA promoter rrnBP1 and a gfp gene encoding an unstable variant of the green fluorescent protein made it possible to monitor the physiological activity of P. putida R1 cells at different positions in the biofilms. Combining this with fluorescent in situ hybridization and scanning confocal laser microscopy showed that the two organisms compete or display commensal interactions depending on their relative physical positioning in the biofilm. In the initial phase of biofilm development, the growth activity of P. putida R1 was shown to be higher near microcolonies of Acinetobacter strain C6. High-pressure liquid chromatography analysis showed that in the effluent of the Acinetobacter strain C6 monoculture biofilm the metabolic intermediate benzoate accumulated, whereas in the biculture biofilms this was not the case, suggesting that in these biofilms the excess benzoate produced by Acinetobacter strain C6 leaks into the surrounding environment, from where it is metabolized by P. putida R1. After a few days, Acinetobacter strain C6 colonies were overgrown by P. putida R1 cells and new structures developed, in which microcolonies of Acinetobacter strain C6 cells were established in the upper layer of the biofilm. In this way the two organisms developed structural relationships allowing Acinetobacter strain C6 to be close to the bulk liquid with high concentrations of benzyl alcohol and allowing P. putida R1 to benefit from the benzoate leaking from Acinetobacter strain C6. We conclude that in chemostats, where the organisms cannot establish in fixed positions, the two strains will compete for the primary carbon source, benzyl alcohol, which apparently gives Acinetobacter strain C6 a growth advantage, probably because it converts benzyl alcohol to benzoate with a higher yield per time unit than P. putida R1. In biofilms, however, the organisms establish structured, surface-attached consortia, in which heterogeneous ecological niches develop, and under these conditions competition for the primary carbon source is not the only determinant of biomass and population structure.

Acinetobacter↗

PubMed2005

Microbial community activities during establishment, performance, and decline of bench-scale passive treatment systems for mine drainage.

Permeable reactive barrier (PRB) technology, in which sulfate-reducing bacteria (SRB) facilitate precipitation of metal sulfides, is a promising approach for remediation of sulfate- and metal-laden mine drainage. While PRBs are easily established, they often decline for reasons not well understood. SRB depend on or compete with multiple dynamic microbial populations within a PRB; as a result, performance depends on the changing PRB chemical composition and on succession and competition within the microbial community. To investigate these interactions, we constructed and monitored eight bench-scale PRBs to define periods of establishment, performance, and decline. We then conducted short-term batch studies, using substrate-supplemented column materials, on Days 0 (pre-establishment), 27 (establishment), 41 (performance), and 99 (decline) to reveal potential activities of cellulolytic bacteria, fermenters + anaerobic respirers, SRB, and methanogens. PRBs showed active sulfate reduction, with sulfate removal rates (SRR) of approximately 1-3 mol/m3/d, as well as effective removal of Zn2+. Potential activities of fermentative + anaerobic respiratory bacteria were initially high but diminished greatly during establishment and dropped further during performance and decline. In contrast, potential SRB activity rose during establishment, peaked during performance, and diminished as performance declined. Potential methanogen activity was low; in addition, SRB-methanogen substrate competition was shown not to limit SRB activity. Cellulolytic bacteria showed no substrate limitation at any time. However, fermenters experienced substrate limitation by Day 0, SRB by Day 27, and methanogens by Day 41, showing the dependence of each group on upstream populations to provide substrates. All potential activities, except methanogenesis, were ultimately limited by cellulose hydrolysis; in addition, all potential activities except methanogenesis declined substantially by Day 99, showing that long-term substrate deprivation strongly diminished the intrinsic capacity of the PRB community to perform.

Alkalies↗

PubMed1990

Model of carbon fixation in microbial mats from 3,500 Myr ago to the present.

Biological carbon fixation is an important part of global carbon cycling and ecology. Fixation that took place 3,500 million years ago is recorded in the laminated sedimentary rock structures known as stromatolites, which are fossilized remains of microbial mat communities. Stromatolites are the most abundant type of fossil found in the Proterozoic (2,500 to 590 Myr ago), but they then declined, possibly because of predation and competition. Using modern microbial mats as analogues for ancient stromatolites, we show that the rate of carbon fixation is higher at the greater levels of atmospheric CO2 that were probably present in the past. We suggest that carbon fixation in microbial mats was not carbon-limited during the early Precambrian, but became carbon-limited as the supply of inorganic carbon decreased. Carbon limitation led to a lower rate of carbon fixation, especially towards the end of the Precambrian. Thus, another reason for the decline of the stromatolites could have been a decrease in available CO2.

Atmosphere↗

PubMed1993

Inhibitory effect against pathogenic and spoilage bacteria of Pseudomonas strains isolated from spoiled and fresh fish.

The antibacterial effects of 209 Pseudomonas strains isolated from spoiled iced fish and newly caught fish were assessed by screening target organisms in agar diffusion assays. One-third (67 strains) inhibited the growth of one or several of six target organisms (Escherichia coli, Shewanella putrefaciens, Aeromonas sobria, Pseudomonas fluorescens, Listeria monocytogenes, and Staphylococcus aureus), of which S. aureus and A. sobria were the most sensitive. The inhibitory action was most pronounced among the strains producing siderophores, and the presence of iron eliminated the antibacterial effect of two-thirds of the inhibitory strains. Siderophore-mediated competition for iron may explain the inhibitory activity of these strains. All but nine of the inhibiting strains were found to inhibit the growth of 38 psychrotrophic S. putrefaciens strains isolated from spoiling fish and fish products. Siderophore-containing Pseudomonas culture supernatants inhibited growth of S. putrefaciens, as did the addition of iron chelators (ethylenediamine dihydroxyphenylacetic acid [EDDHA]). In particular, Pseudomonas strains isolated from newly caught and spoiled Nile perch (Lates niloticus) inhibited S. putrefaciens. This suggests that microbial interaction (e.g., competition or antagonism) may influence the selection of a microflora for some chilled food products.

Animals↗

PubMed2026

Cross-Kingdom Siderophores: Biosynthesis, Ecology, and Biotechnological Applications.

Microbial siderophores are high-affinity iron-binding compounds which are produced by bacteria, fungi, and actinomycetes to obtain iron and survive and interact with different species in an iron-deficient environment. While the conventional research on siderophore systems deals mainly with the study within the same taxa, modern researchers have increased their inclination toward cross-kingdom integration of siderophore behavior and their impact on host-associated environments. This can be largely attributed to differences in biosynthetic gene clusters, receptor systems, and regulatory networks, which produce distinct genotype-to-phenotype results determining microbial cooperation and competition. Current advancements in genomic research, together with omics studies like transcriptomics, proteomics, and metabolomics, have created newer insights into how siderophores function. However, the present literature evidences multiple major gaps in multi-omics data because the link between genomes and metabolomes remains weak due to inconsistent regulatory data sets and failure in identifying producer-consumer relationships in polymicrobial systems. Additionally, major constraints like molecular instability, delivery system limitations, host toxicity, limitations in upscaling, and regulatory issues delimit the use of siderophores in medical treatment, agricultural practices, and environmental biotechnology. This review aims to bridge the existing knowledge about siderophore biochemistry, biosynthesis, ecological functions, and genetic regulation across kingdoms while integrating multi-omics outlook with translational considerations. Thus, by connecting molecular mechanisms with evolutionary cross-talk, this study aims to provide a system-level framework in the world of siderophore-mediated iron uptake and therefore shapes future directions in emerging fields of microbial engineering, precision therapies, and sustainable biotechnology.

Fur regulation↗

PubMed2006

Reduced folate supply as a key to enhanced L-serine production by Corynebacterium glutamicum.

The amino acid L-serine is required for pharmaceutical purposes, and the availability of a sugar-based microbial process for its production is desirable. However, a number of intracellular utilization routes prevent overproduction of L-serine, with the essential serine hydroxymethyltransferase (SHMT) (glyA) probably occupying a key position. We found that constructs of Corynebacterium glutamicum strains where chromosomal glyA expression is dependent on Ptac and lacIQ are unstable, acquiring mutations in lacIQ, for instance. To overcome the inconvenient glyA expression control, we instead considered controlling SHMT activity by the availability of 5,6,7,8-tetrahydrofolate (THF). The pabAB and pabC genes of THF synthesis were identified and deleted in C. glutamicum, and the resulting strains were shown to require folate or 4-aminobenzoate for growth. Whereas the C. glutamicum DeltasdaA strain (pserACB) accumulates only traces of L-serine, with the C. glutamicum DeltapabABCDeltasdaA strain (pserACB), L-serine accumulation and growth responded in a dose-dependent manner to an external folate supply. At 0.1 mM folate, 81 mM L-serine accumulated. In a 20-liter controlled fed-batch culture, a 345 mM L-serine accumulation was achieved. Thus, an efficient and highly competitive process for microbial l-serine production is available.

Bacterial Proteins↗

PubMed1981

Asterixis and encephalopathy following metrizamide myelography: investigations into possible mechanisms and review of the literature.

Marked asterixis occurred in two patients following metrizamide myelography. One also suffered generalized seizures and the other had severe stuttering speech for seven days. The spectrum of toxic manifestations of metrizamide is reviewed with emphasis on the unusual lethargy and other depressive effects seen with this relatively safe agent. The hypothesis that metrizamide exerts a ouabain-like effect on the cortical surface was tested. Metrizamide in concentrations as high as 20 mM had no inhibitory effect on rat cerebral K+-para-nitrophenylphosphatase, a partial reaction of (Na+K+)-adenosine triphosphatase. Because metrizamide is a 2-deoxyglucose analogue, a competitive inhibition of hexokinase at the first step in glycolysis was also postulated. Metrizamide was found to competitively inhibit commercial (microbial) hexokinase. The Michaelis constant for glucose rises from 0.13 to 0.25 to 0.33 to 0.91 mM in the presence of 0, 0.4, 1.0, and 2.0 mM metrizamide, respectively. Since the concentration of metrizamide over the cerebral cortex after routine myelography may be approximately 50 mM compared with a glucose concentration of only 3.6 mM (65 mg/dl), it is postulated that impaired brain glucose metabolism may be responsible for some of the toxic effects of metrizamide.

Animals↗

PubMed1994

Steady-state coexistence of three pure and simple competitors in a four-membered reactor network.

In this study we investigate the dynamics of pure and simple competition among three microbial populations in a spatially heterogeneous environment. The environment is modeled as a network of four interconnected bioreactors. Growth has been assumed to be noninhibitory, while maintenance requirements have been neglected. Results of numerical studies indicate that the three competitors may coexist in a stable steady state in a domain of the operating parameters space. Results are presented in the form of two-dimensional operating diagrams. No domain was found in the operating parameter space where more than one steady state is meaningful and stable. Since earlier theoretical studies have shown that two pure and simple microbial competitors may coexist in two interconnected bioreactors while numerical studies have shown that three pure and simple competitors cannot coexist in three interconnected bioreactors, the results of the present study may lead one to speculate the N pure and simple competitors may coexist in a network made of 2N-1 bioreactors.

Ecosystem↗

PubMed2001

Effect of metals on Candida albicans growth in the presence of chemical chelators and human abscess fluid.

Calprotectin is a calcium- and zinc-binding protein that is present in abscess fluid supernatants and appears to inhibit microbial growth through competition for zinc. In the present study, growth inhibition by chemical chelators was compared with that produced by human abscess fluid to determine whether other chelators, perhaps with different metal specificities, would have the same or different patterns of metal reversibility as abscess fluid. Zinc was found to be more potent than the other metals tested in reversing C. albicans growth inhibition by human abscess fluid and three chemical chelators, even though in some cases the stability constants of certain of these chelators were higher for other metals. For example, in the presence of the chelator diethylenetriaminopentaacetic acid, zinc stimulated Candida growth at a 10-fold lower concentration than did iron, even though this chelator has a stability constant for iron that is almost 10(10) higher than that for zinc. These results suggest that the zinc specificity of calprotectin's C. albicans growth inhibition can best be explained by the marked sensitivity of this organism to zinc deprivation rather than by selective binding of this metal by the protein.

Calcium↗

PubMed1998

Histidine-based zinc-binding sequences and the antimicrobial activity of calprotectin.

Calprotectin is a protein in neutrophil cytoplasm and abscess fluids that appears to inhibit microbial growth through competition for zinc. This study was undertaken to identify specific sites that might be responsible for the protein's zinc-binding antimicrobial activity. A review of published calprotectin amino acid sequences revealed the HEXXH motif of thermolysin-type metalloproteases and an HHH polyhistidine sequence near the C-terminus of the protein's heavy chain. Reagent polyhistidine had antimicrobial activity against Candida albicans similar to that of calprotectin. Also, one type of HEXXH-containing thermolysin was inactive in the C. albicans assay, whereas a protein tagged with six C-terminal histidines did have calprotectin-like zinc-reversible antimicrobial activity. The activity of polyhistidine, as well as that of calprotectin itself, was reversed by addition of zinc or treatment with the histidine-modifying compound diethylpyrocarbonate. These results suggest that calprotectin's antimicrobial activity may be related to certain histidine-based zinc-binding sequences.

Amino Acid Sequence↗

PubMed1996

Inhibition of Candida albicans growth by calprotectin in the absence of direct contact with the organisms.

Calprotectin is a calcium- and zinc-binding protein that is present in neutrophil cytoplasm and abscess fluid supernatants. This protein appears to inhibit microbial growth through competition for zinc; however, experiments to show that calprotectin can inhibit growth of microorganisms across filter membranes have yielded conflicting results to date. To prevent recontamination of the filtrate by zinc in this type of experiment, Candida albicans was cultured on filter membranes placed on top of an agarose gel containing calprotectin. In these studies, calprotectin in the gels underneath did suppress growth on top of the filters, an effect reversible by 30 microM ZnSO4. In other experiments, the protein did not adhere to the organisms and later suppress their growth. These results indicate that calprotectin inhibits C. albicans growth in the absence of direct contact with the organisms; the findings support a zinc-deprivation mechanism of antimicrobial activity for this protein.

Bacteriological Techniques↗

PubMed1983

Role of catabolite regulatory mechanisms in control of carbohydrate utilization by the rumen anaerobic fungus Neocallimastix frontalis.

Neocallimastix frontalis PN-1 utilized the soluble sugars D-glucose, D-cellobiose, D-fructose, maltose, sucrose, and D-xylose for growth. L-Arabinose, D-galactose, D-mannose, and D-xylitol did not support growth of the fungus. Paired substrate test systems were used to determine whether any two sugars were utilized simultaneously or sequentially. Of the paired monosaccharides tested, glucose was found to be preferentially utilized compared with fructose and xylose. The disaccharides cellobiose and sucrose were preferentially utilized compared with fructose and glucose, respectively, an cellobiose was also the preferred substrate compared with xylose. Xylose was the preferred substrate compared with maltose. In further incubations, the fungus was grown on the substrate utilized last in the two-substrate tests. After moderate growth was attained, the preferred substrate was added to the culture medium. Inhibition of nonpreferred substrate utilization by the addition of the preferred substrate was taken as evidence of catabolite regulation. For the various combinations of substrates tested, fructose and xylose utilization was found to be inhibited in the presence of glucose, indicating that catabolite regulation was involved. No clear-cut inhibition was observed with any of the other substrate combinations tested. The significance of these findings in relation to rumen microbial interactions and competitions is discussed.

Animals↗

PubMed2000

Chemical signaling processes in the marine environment.

Understanding the mechanisms by which environmental chemical signals, chemical defenses, and other chemical agents mediate various life-history processes can lead to important insights about the forces driving the ecology and evolution of marine systems. For chemical signals released into the environment, establishing the principles that mediate chemical production and transport is critical for interpreting biological responses to these stimuli within appropriate natural, historical contexts. Recent technological advancements provide outstanding opportunities for new discoveries, thus allowing quantification of interactions between hydrodynamic, chemical, and biological factors at numerous spatial and temporal scales. Past work on chemically mediated processes involving organisms and their environment have emphasized habitat colonization by larvae and trophic relationships. Future research priorities should include these topics as well as courtship and mating, fertilization, competition, symbiosis, and microbial chemical ecology. There are now vast new opportunities for determining how organisms respond to chemical signals and employ chemical defenses under environmentally realistic conditions. Integrating these findings within a larger ecological and evolutionary framework should lead to improved understanding of natural physicochemical phenomena that constrain biological responses at the individual, population, and community levels of organization.

Animals↗

PubMed2006

Competitive metagenomic DNA hybridization identifies host-specific microbial genetic markers in cow fecal samples.

Several PCR methods have recently been developed to identify fecal contamination in surface waters. In all cases, researchers have relied on one gene or one microorganism for selection of host-specific markers. Here we describe the application of a genome fragment enrichment (GFE) method to identify host-specific genetic markers from fecal microbial community DNA. As a proof of concept, bovine fecal DNA was challenged against a porcine fecal DNA background to select for bovine-specific DNA sequences. Bioinformatic analyses of 380 bovine enriched metagenomic sequences indicated a preponderance of Bacteroidales-like regions predicted to encode membrane-associated and secreted proteins. Oligonucleotide primers capable of annealing to select Bacteroidales-like bovine GFE sequences exhibited extremely high specificity (>99%) in PCR assays with total fecal DNAs from 279 different animal sources. These primers also demonstrated a broad distribution of corresponding genetic markers (81% positive) among 148 different bovine sources. These data demonstrate that direct metagenomic DNA analysis by the competitive solution hybridization approach described is an efficient method for identifying potentially useful fecal genetic markers and for characterizing differences between environmental microbial communities.

Animals↗

PubMed1994

Periodic, quasi-periodic, and chaotic coexistence of two competing microbial populations in a periodically operated chemostat.

It is well known that when two microbial populations competing for a single rate-limiting nutrient are grown in a chemostat with time-invariant inputs, with competition being the only interaction between them, they cannot coexist, but eventually one of the two populations prevails and the other becomes extinct. It has been suggested that periodic variation of one of the chemostat's operating parameters can stabilize the coexistence state of the two microbial populations. A systematic numerical study of the model equations describing microbial competition in a chemostat with periodically varying dilution rate is performed, and it is shown that coexistence of the competing microbial populations is obtained for a wide range of operating conditions. The coexistence state is usually in the form of limit cycle oscillations. However, cases of chaotic behavior resulting from successive period doublings and quasi-periodicity are also observed.

Ecosystem↗

PubMed2001

Combination of competitive quantitative PCR and constant-denaturant capillary electrophoresis for high-resolution detection and enumeration of microbial cells.

A novel quantitative PCR (QPCR) approach, which combines competitive PCR with constant-denaturant capillary electrophoresis (CDCE), was adapted for enumerating microbial cells in environmental samples using the marine nanoflagellate Cafeteria roenbergensis as a model organism. Competitive PCR has been used successfully for quantification of DNA in environmental samples. However, this technique is labor intensive, and its accuracy is dependent on an internal competitor, which must possess the same amplification efficiency as the target yet can be easily discriminated from the target DNA. The use of CDCE circumvented these problems, as its high resolution permitted the use of an internal competitor which differed from the target DNA fragment by a single base and thus ensured that both sequences could be amplified with equal efficiency. The sensitivity of CDCE also enabled specific and precise detection of sequences over a broad range of concentrations. The combined competitive QPCR and CDCE approach accurately enumerated C. roenbergensis cells in eutrophic, coastal seawater at abundances ranging from approximately 10 to 10(4) cells x ml(-1). The QPCR cell estimates were confirmed by fluorescent in situ hybridization counts, but estimates of samples with <50 cells x ml(-1) by QPCR were less variable. This novel approach extends the usefulness of competitive QPCR by demonstrating its ability to reliably enumerate microorganisms at a range of environmentally relevant cell concentrations in complex aquatic samples.

Animals↗

PubMed2003

Biofiltration of waste gases containing both ethyl acetate and toluene using different combinations of bacterial cultures.

To investigate the microbial degradation of ethyl acetate and toluene mixtures in biofiltration, three strains were selected, identified and studied in a shake-flask culture, and finally inoculated into biofilters. These strains, namely AC6, TO3 and B5, can degrade different substrates at a different rate. The results showed that competitive inhibition from substrate and microbial community would affect the toluene degradation efficiency. Owing to substrate competition, the toluene degradation efficiency of strain B5 would decrease in the presence of high concentration of ethyl acetate. However, the addition of strain AC6 would alleviate such inhibition because it could remove ethyl acetate rapidly. Microbial community competition from strain AC6 or B5 would impede the toluene degradation efficiency of strain TO3 unless a large amount of strain TO3 was inoculated. In biofiltration, strain B5 would be a better choice for inoculation into biofilters than strains AC6 and TO3, as it would grow rapidly under a low concentration of ethyl acetate.

Acetates↗

PubMed2004

Considering the complexity of microbial community dynamics in food safety risk assessment.

The potential for competitive inhibition to limit the growth of microbial pathogens in food raises questions about the external validity of typical predictive microbiology studies and suggests the need to consider microbial community dynamics in food safety risk assessment. Ecological theory indicates, however, that community dynamics are highly complex and may be very sensitive to initial conditions and random variation. Seemingly incongruous empirical results for Escherichia coli O157:H7 in ground beef are shown to be consistent with a simple theoretical model of interspecific competition. A potential means of incorporating community-level microbial dynamics into the food safety risk assessment process is explored.

Antibiosis↗