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At least 145 records · Page 8Linked to original sources
PubMed2006

Effect of methamidophos and urea application on microbial communities in soils as determined by microbial biomass and community level physiological profiles.

In this study, we evaluated the effect of the application by two agrochemicals, methamidophos (O,S-dimethyl phosphoroamidothioate) and urea, on microbial diversity in soil, using the combined approaches of soil microbial biomass analysis and community level physiological profiles (CLPPs). The results showed that both a low and a high level of methamidophos application (CS2 and CS3) and urea application (CS4) significantly decreased microbial biomass C (Cmic) by 41-83% compared with the control (CS1). The soil organic C (Corg) values of CS3 and CS4 were significantly higher and lower by 24% and 14%, respectively, than that of CS1. Similarly to Cmic, the values of Cmic/Corg of the three applied soils which decreased were lower by 31-84% than that of CS1. In contrast, the respiration activity of the three applied soils were significantly higher than the control. Agrochemical application also significantly increased the soil total of N and P (Ntol and Ptol) and decreased the Corg/Ntol and Corg/Ptol values. The CLPPs results showed that the AWCD (average well color development) of the three applied soils were significantly higher than that of CS1 during the incubation period. Substrate richness, Shannon and Simpson indices of microbial communities under chemical stresses, increased significantly. In addition, the CFU (colony-forming unit) numbers of methamidophos metabolized bacteria in CS2 and CS3 also increased significantly by 86.1% and 188.9% compared with that of CS1. The combined results suggest that agrochemicals reduce microbial biomass and enhance functional diversities of soil microbial communities; meanwhile, some species of bacteria may be enriched in soils under methamidophos stress.

Biomass↗
PubMed1993

Recent advances of flow cytometry in fundamental and applied microbiology.

This review focuses on the recent applications of flow cytometry (FCM) in microbiological research (1987-mid 1992). It tries to give a scope of the important breakthroughs which occurred in this field during this period. The technical difficulties of microorganism analysis by flow cytometry is briefly appraised. The significance and the limits of the different microbial cell parameters attainable by flow analyses are systematically evaluated: light scatter for cell size and structure, fluorescence measurements for quantification of cellular components, microbial antigen detection and cell physiological activity estimation. Emphasis is given on the new technological advances which appeared in the last two years. The second part of the review is devoted to the analysis of the usefulness of flow cytometric approach in the different fields of microbiology: fundamental studies in microbial physiology, differentiation, microbial ecology and aquatic sciences, medical microbiology, parasitology, microbial pharmacology and biotechnology.

Biotechnology↗
PubMed2003

Complexity in natural microbial ecosystems: the Guerrero Negro experience.

The goal of this project is to describe and understand the organismal composition, structure, and physiology of microbial ecosystems from hypersaline environments. One collection of such ecosystems occurs at North America's largest saltworks, the Exportadora de Sal, in Guerrero Negro, Baja California Sur. There, seawater flows through a series of evaporative basins with an increase in salinity until saturation is reached and halite crystallization begins. Several of these ponds are lined with thick (10 cm) microbial mats that have received some biological study. To determine the nature and extent of diversity of the microbial organisms that constitute these ecosystems, we are conducting a phylogenetic analysis using molecular approaches, based on cloning and sequencing of small subunit (SSU) rRNA genes (16S for Bacteria and Archaea, 18S for Eukarya). In addition, we report preliminary results on the microbial composition of a laminated community that occurs in a crystallized gypsum-halite matrix in near-saturated salt water. Exposure of the interior of these large (kilogram) wet, endoevaporite crystals reveals a multitude of colors: layers of yellow, green, pink, and purple microbiota. To date, analyses of these two environments indicate the ubiquitous dominance of uncultured organisms of phylogenetic kinds not generally thought to be associated with hypersaline environments.

Bacteria↗
PubMed2026

Amino acid reprogramming and biofilm-specific tricarboxylate transporters in PET-degrading Piscinibacter sakaiensis.

Plastic-degrading bacteria predominantly colonize polymer surfaces as biofilms, yet it remains unclear whether the biofilm phenotype contributes to metabolism beyond retaining extracellular enzymes. Here, we combine population-level RNA-sequencing across three conditions-biofilm cells on polyethylene terephthalate (PET), planktonic cells incubated with PET, and planktonic cells on maltose-with single-cell Raman spectroscopy to characterize the PET response of Piscinibacter sakaiensis (formerly Ideonella sakaiensis). This integrated approach reveals two metabolically distinct response layers. A carbon-source-driven response shared by all PET-exposed cells is dominated by a broad amino acid reprogramming, led by upregulation of branched-chain amino acid transport genes, enhanced serine biosynthesis, and reduced chemotaxis. A biofilm-specific layer selectively induces tripartite tricarboxylate transporter genes from three distinct genomic loci. This transcriptional feature is accompanied by a single-cell phenotype consistent with a protein-rich and saturated membrane. These results suggest that biofilm formation is not limited to enzyme retention but is associated with selective activation of transport systems, consistent with a putative role in capturing PET-derived intermediates at the polymer interface. This two-layer model separates general metabolic adaptation to PET from biofilm-specific functions and provides a framework for understanding how surface-associated bacterial physiology contributes to plastic degradation.IMPORTANCEPolyethylene terephthalate (PET) degradation in natural and engineered environments is largely mediated by surface-attached microbial communities, yet the physiological role of biofilm state during plastic degradation remains poorly understood. Using the model PET degrader Piscinibacter sakaiensis, we show that biofilm-associated cells are not simply retained near the polymer surface but exhibit a distinct metabolic program characterized by selective induction of tripartite tricarboxylate transporters. In contrast, extensive amino acid reprogramming occurs in both biofilm and planktonic PET-exposed cells, indicating that it is driven by carbon source rather than surface attachment. These findings reveal that PET degradation involves two separable physiological layers: a general metabolic response to PET-derived carbon shared across cell phenotypes, and a biofilm-specific transport response potentially linked to substrate capture at the plastic interface. This work advances our understanding of how microbial physiology is organized during plastic biodegradation and identifies transport processes as previously unrecognized components of PET-degrading biofilms.

PET biodegradation↗
PubMed2006

Interactive cellular and physiological responses of the freshwater crab Potamonautes warreni to cadmium and microbial gill infestations.

Cellular and physiological responses of the freshwater crab, Potamonautes warreni, to cadmium and microbial gill infestations were investigated. Infested crabs were collected from the Mooi River, at Noordbrug, Northwest Province, South Africa in the autumn of 1995 and exposed to 0.2mg Cd(2+)L(-1) or kept unexposed under constant laboratory conditions for 7, 14 and 21 days at 24 degrees C. Cellular lesions with microbial gill infestations were persistent over 21 days and showed a similar species diversity and density as recorded in the previous summer [Schuwerack et al., 2001a. Pathological and physiological changes in the South African freshwater crab, P. warreni Calman induced by microbial gill infestations. J. Invertebrate Pathol. 77(4), 259-269]. With Cd exposure the microbial community disappeared and crabs showed a higher mean but wider range in ammonia excretion and lower mean O:N ratio after 7 days. After 14 days exposure to Cd, time- and stressor-specific cellular and physiological responses included degeneration of oxygen and gas exchange gill tissues and a mean reduced growth rate, ion exchange, a significantly reduced O:N ratio (P<or=0.05) and induced hemolymph pH (P<or=0.05). Both stressors, i.e. gill infestation and Cd, produce a barrier, which obstructs pathways in ion exchange and oxygen uptake, resulting in NH(3)/NH(4)(+) retention and similar physiological responses after 21 days. The interactive cellular and physiological mechanisms in P. warreni exposed to multiple stress are discussed.

Adaptation, Physiological↗
PubMed2004

Bacterial sensitivity to bacteriophage in the aquatic environment.

There are several unusual features about phage when you first encounter them as a biologist. They are small, but conform to one of a few morphological types. Next their genomes can be composed of DNA or RNA and be single or double stranded. Finally they are numerically more abundant than prokaryotes and a significant proportion of them form an association in their microbial host populations termed lysogeny. The latter findings indicate that they are numerically significant in microbial populations. Since bacterial and phage abundance or lack of it is related in environments, this implies that the phage populations 'titrate' their hosts, and more probably the host's physiological status. Microbial populations wax and wane with nutritional inputs and there is a dynamic relationship between phage population sizes and host numbers and physiology. Overlay this with the different phage life cycle strategies, exemplified at the extremes by phage lambda (temperate) and phage T4 (virulent), then it becomes apparent that phage are a component in nutrient cycling in ecology. But their contribution does not stop there. Many are capable of transduction, moving DNA from one cell into another. So they can also aid the evolutionary progress of microbial populations by allowing them to share genes, just as gene exchange via plasmids and transformation does. Our perception of bacteria has been derived from pure culture studies and we are just being able to appreciate how subtle their ecological interactions are. This is no less true of the studies on bacteriophage, which are almost all based on laboratory experimentation, where the hosts are physiologically stressed by growing in 'high nutritional and optimum conditions'. The natural environment is naturally discontinuous and life evolved in this. Thus our perceptions of bacteriophage and their life cycle patterns derived from laboratory experimentation may be a little off the mark when we come to understand how they and their hosts interact in the niches available to them. It is worth just considering this as you read the article, as I suspect phage behaviours are more intimately involved in, and moderated by the physiological stresses in the life cycle of bacteria than we currently believe.

Bacteria↗
PubMed1990

[What are toxins to microbes? (the role of toxins in bacterial ecology)].

The author attempts to answer two questions: whether the toxins, in particular the toxins having their specificity connected with enzymatic activity, are needed for microbial cell physiology and their significance for bacteria that are not the obligate parasites for warm blooded animals. The analysis of literary data supposes the toxins to be essential cellular metabolites since many of them participate in energy acquiring. Besides that a number of toxins is shown to be relevant to microbial life and to affect the micropredators, especially the monocellular organisms feeding the microbes. In connection with the above mentioned, special attention is paid to extrachromosomal location of many toxins genes relating them to bacteriocins. The possibility is not excluded that in the future the new toxins might come to be found having the enzymatic activities.

Bacteria↗
PubMed2002

Composition and physiological profiling of sprout-associated microbial communities.

The native microfloras of various types of sprouts (alfalfa, clover, sunflower, mung bean, and broccoli sprouts) were examined to assess the relative effects of sprout type and inoculum factors (i.e., sprout-growing facility, seed lot, and inoculation with sprout-derived inocula) on the microbial community structure of sprouts. Sprouts were sonicated for 7 min or hand shaken with glass beads for 2 min to recover native microfloras from the surface, and the resulting suspensions were diluted and plated. The culturable fraction was characterized by the density (log CFU/g), richness (e.g., number of types of bacteria), and diversity (e.g., microbial richness and evenness) of colonies on tryptic soy agar plates incubated for 48 h at 30 degrees C. The relative similarity between sprout-associated microbial communities was assessed with the use of community-level physiological profiles (CLPPs) based on patterns of utilization of 95 separate carbon sources. Aerobic plate counts of 7.96 +/- 0.91 log CFU/g of sprout tissue (fresh weight) were observed, with no statistically significant differences in microbial cell density, richness, or diversity due to sprout type, sprout-growing facility, or seed lot. CLPP analyses revealed that the microbial communities associated with alfalfa and clover sprouts are more similar than those associated with the other sprout types tested. Variability among sprout types was more extensive than any differences between microbial communities associated with alfalfa and clover sprouts from different sprout-growing facilities and seed lots. These results indicate that the subsequent testing of biocontrol agents should focus on similar organisms for alfalfa and clover, but alternative types may be most suitable for the other sprout types tested. The inoculation of alfalfa sprouts with communities derived from various sprout types had a significant, source-independent effect on microbial community structure, indicating that the process of inoculation alters the dynamics of community development regardless of the types of organisms involved.

Brassica↗
PubMed2002

Control of the bacterial cell cycle by cytoplasmic growth.

For free-living single-celled organisms, it can be assumed that it is their success in acquiring resources and converting them into cytoplasm that controls the timing of their cell cycles. Cytoplasm is the sink for the bulk of the environmental resources. It must be the case that this type of control must operate in dilute cultures under adequate nutrition in a constant environment. It follows that there ought to be mechanisms that measure or count the cell's biomass or some component of the cytoplasm to measure their growth success. Besides sensing their biomass, they need to know when a certain value of the cell size has been achieved. When this critical state has been achieved, the cell needs to have an all-or-none trigger that either initiates chromosome replication, the completion of cell replication, cell division, or the process of separating sister cells physiologically or physically. Any of these four different stages, in principle, may be the one triggered in response to cell growth in different species of microorganisms. Alternatively, multiple triggers at different cell sizes may be activated at different cell cycle stages. Although initiation of chromosome replication has been believed to be the event triggered in Escherichia coli, this probably is not generally the case and other control mechanisms may act in other prokaryotes. How the increase in cell biomass is self-assessed and used to carry out critical cell cycle events is not understood in any case. This deficiency in our knowledge of microbial cell physiology is grave. The factor that probably has prevented the elucidation of the mechanisms in any organism is that enzymatic processes deal with concentrations, and a cell cycle trigger must respond to the total amount of material present in a cell. This article discusses the theoretically possible classes of mechanisms for the cell to respond when it has achieved its appropriate critical size. These breakdown into three groups: those mechanisms that assess the total amount of biomass or some special subcellular component, and those that measure the ratio of one component to another component where their two syntheses are differently controlled by cell physiology and morphology, and a third group with some specialized mechanisms.

Allosteric Regulation↗
PubMed2026

Glutathione acts as an exometabolite that promotes growth recovery in fission yeast with defects in amino acid metabolism and cell polarity.

UNLABELLED: Microorganisms in nature form communities through diverse interactions, such as mutualism and competition, to adapt to their ecological environments. These interactions seem to be mediated by extracellular metabolites (exometabolites), yet the chemical and biological diversity underlying these processes remains largely unexplored. In this study, we examined the chemical basis of exometabolite-mediated interactions in the fission yeast Schizosaccharomyces pombe by a genome-wide screen employing 3,420 viable gene deletion mutants. We identified 37 strains that exhibited growth defects in monoculture on a minimal medium but exhibited growth recovery in the vicinity of wild-type colonies (co-culture), suggesting that exometabolites derived from wild-type cells compensated for the gene deletion. Both lipophilic and water-soluble fractions obtained by solvent partitioning of the wild-type culture supernatant promoted growth recovery. Among the 11 mutants rescued by the water-soluble fraction, 6 were cysteine auxotrophs, prompting analyses of thiol-containing metabolites by liquid chromatography-mass spectrometry (LC-MS), revealing the presence of glutathione (GSH) in the culture supernatant. GSH restored growth in most strains as a nutrient source. In contrast, GSH rescued cell morphology defects in the hob3&#x2206; mutant, lacking the Bin/amphiphysin/Rvs (BAR) adaptor protein Hob3, through a mechanism independent of nutrition. This research advances understanding of exometabolite-mediated interactions in S. pombe by identifying GSH as an exometabolite that influences cellular processes and potentially shapes microbial communities. IMPORTANCE: Microorganisms secrete a wide range of metabolites that control microbial community behavior. These extracellular metabolites (exometabolites) include not only well-studied signaling molecules but also diverse primary and secondary metabolites, suggesting complex interactions among microbes. However, the molecular basis of these interactions remains poorly understood, partly due to challenges in detecting them experimentally. In this study, we surveyed exometabolites involved in cell-cell interactions in the model eukaryotic microorganism Schizosaccharomyces pombe. S. pombe releases a wide variety of metabolites outside the cells, including previously reported nitrogen signaling factors (NSFs) and glutathione (GSH) identified in this work. By analyzing gene deletion mutants whose growth is supported by extracellular GSH, we provide new insights into how secreted primary exometabolites compensate for specific genetic defects and influence cell physiology in microbial populations.

exometabolite↗
PubMed2006

A new approach to non-destructive analysis of biofilms by confocal Raman microscopy.

Confocal Raman microscopy (CRM) of biofilms enables one to determine the distribution of different microorganisms and other substances inside physiological intact microbial communities. These biofilms are of outstanding interest for biological wastewater treatment. In contrast to invasive techniques, such as fluorescent in situ hybridization (FISH), we were able to identify anaerobically ammonium-oxidising (anammox) bacteria without pretreatment processes of the samples just by its Raman vibrational signature. The presented results provide new insights into the complex interactions of different organisms in microbial communities without interfering with them.

Anaerobiosis↗
PubMed2006

Changes in communities of Fusarium and arbuscular mycorrhizal fungi as related to different asparagus cultural factors.

Asparagus (Asparagus officinalis) is a high-value perennial vegetable crop that has shown a marked decline in productivity after many years of continuous harvesting. This decline is caused by an increase in both abiotic (autotoxicity, harvesting pressure) and biotic stresses [fungal infections, mainly Fusarium crown and root rot (FCRR)]. To gain insight into disease development and possible mitigation strategies, we studied the effects of harvesting, time in the growing season, and field age on FCRR development, Fusarium species composition, and arbuscular mycorrhizal fungi (AMF) communities in both a controlled field experiment and an ecological survey of commercial fields. In one experiment, a 3-year-old asparagus field was subdivided into plots that were harvested or not and sampled throughout the growing season to assess short-term dominant Fusarium species shifts. In addition, diseased and healthy asparagus plants sampled from six commercial fields in the same geographical region were used to assess Fusarium and AMF communities in relation to different parameters. Fusarium and AMF communities were described by using a polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE) approach, and results were analyzed by mainly correspondence analysis and canonical correspondence analysis. Results showed that dominant Fusarium taxa assemblages changed throughout the growing season. Harvested plots had significantly more FCRR symptomatic plants at the end of the growing season, but this effect was not related with any trend in Fusarium community structure. Sampling site and plant age significantly influenced AMF community structure, whereas only sampling site consistently influenced the Fusarium community. Diseased and healthy plants harbored similar Fusarium and AMF communities. Shifts in Fusarium community might not be responsible for different disease incidence because they are ubiquitous regardless of plant health status or harvesting regime. The different incidence noted might rather be related to plant physiology, antagonist microbial communities, or soil parameters.

Asparagus Plant↗
PubMed2026

Effects of acute hypoxia followed by reoxygenation on intestinal histomorphology, oxidative stress and hypoxia signaling biomarkers, and microbiota in pikeperch (Sander lucioperca).

In aquatic environments, natural and anthropogenic factors commonly reduce dissolved oxygen (DO) and trigger hypoxia, which threatens the health and survival of aquatic organisms. As an important economic fish species in China, pikeperch (Sander lucioperca) is extremely sensitive to hypoxia. However, there are relatively few reports on how hypoxia and reoxygenation affect its intestinal physiology and microbial community. Three treatment groups were set for pikeperch: normoxia (DO&#xa0;=&#xa0;8.5&#xa0;&#xb1;&#xa0;0.5&#xa0;mg/L), 48&#xa0;h hypoxia (DO&#xa0;=&#xa0;2.5&#xa0;&#xb1;&#xa0;0.1&#xa0;mg/L), and reoxygenation (48&#xa0;h hypoxia followed by 6&#xa0;h reoxygenation at normal DO), to evaluate alterations in intestinal histopathology, tight junction gene expression, oxidative stress, hypoxia signaling molecules and intestinal microbiota composition. The results showed that hypoxia significantly decreased muscularis thickness by approximately 32.5% and reduced the expression of tight junction genes (Occludin, Claudin2, and ZO-2). Moreover, hypoxia significantly increased oxidative stress index levels (GSH-Px, CAT, and MDA), markedly upregulated the expression of Bax, Caspase3, and HIF-1&#x3b1;, while significantly downregulating the expression of Bcl-2, Egln1, and Egln2. Notably, reoxygenation elicited partial compensatory effects against these hypoxia-induced changes. 16S rRNA sequencing analysis revealed that hypoxic stress altered the intestinal microbial community composition of pikeperch and increased its diversity. In the hypoxia group, the abundance of the phylum Bacillota, along with the genera Halomonas and Acinetobacter, was significantly elevated, whereas in the reoxygenation group, the genus Lactobacillus increased approximately 180-fold. The results indicated that hypoxia caused intestinal oxidative damage, cell apoptosis, and intestinal microbiota dysbiosis in pikeperch, while short-term reoxygenation achieved partial recovery from these hypoxia-triggered intestinal injuries. The present research provides valuable references for in-depth exploration of the molecular mechanisms behind the response of pikeperch to acute hypoxia and reoxygenation stress, while also offering a novel perspective to understand the mechanism by which hypoxia impacts intestinal health in fish.

Animals↗
PubMed2002

Kinetics of electron transfer through the respiratory chain.

We show that the rate at which electrons pass through the respiratory chain in mitochondria and respiring prokaryotic cells is described by the product of three terms, one describing electron donation, one acceptance, and a third, the thermodynamic drive. We apply the theory of nonequilibrium thermodynamics in the context of the chemiosmotic model of proton translocation and energy conservation. This approach leads to a closed-form expression that predicts steady-state electron flux as a function of chemical conditions and the proton motive force across the mitochondrial inner membrane or prokaryotic cytoplasmic membrane. The rate expression, derived considering reverse and forward electron flow, is the first to account for both thermodynamic and kinetic controls on the respiration rate. The expression can be simplified under specific conditions to give rate laws of various forms familiar in cellular physiology and microbial ecology. The expression explains the nonlinear dependence of flux on electrical potential gradient, its hyperbolic dependence on substrate concentration, and the inhibiting effects of reaction products. It provides a theoretical basis for investigating life under unusual conditions, such as microbial respiration in alkaline waters.

Animals↗
PubMed2000

Glucose uptake rates of single E. coli cells grown in glucose-limited chemostat cultures.

To evaluate the extent to which single-cell glucose uptake rates determine the overall specific growth rate of a culture, dilute chemostat cultures of Escherichia coli BL21 were grown in defined medium under glucose limitation. The glucose uptake dynamics of the cell population was examined at the single-cell level using the fluorescent glucose analog, 2-NBDG. Between dilution rates of 0.12 h(-1) and 0.40 h(-1), mean cellular protein content and steady-state, extracellular glucose concentrations increased with increasing dilution rate. However, the distribution of 2-NBDG uptake rates in the population remained constant over the range of dilution rates studied. This indicates that the growth of cells in continuous culture is not limited by the maximum rate of uptake of glucose but by the availability of glucose for transport. The work represents an example of how quantitative flow cytometry can be applied to gain detailed insight into microbial growth physiology.

4-Chloro-7-nitrobenzofurazan↗
PubMed2002

Microfloral contamination and hydrolytic enzyme differences between monsooned and non-monsooned coffees.

AIMS: To analyse and compare, for the first time, fungal and bacterial populations and hydrolytic enzyme production in four monsooned and non-monsooned Arabica and Robusta coffee types. METHODS AND RESULTS: Overall, using serial dilution, the populations of bacteria (approximately 10(8) cfu g(-1)) were highest in monsooned coffees of both varieties. Fungal populations were lower (10(5) cfu g(-1)) and found predominantly on monsooned coffee beans. The major fungal species were Aspergillus terreus, A. restrictus and A. ochraceus. Of 19 semi-quantitative enzymes analysed, significantly higher concentrations of 2-naphthyl-butyrate, caprylate and 2-naphthyl-D-galactopyranosidase were present in Arabica monsooned coffee. CONCLUSIONS: The results suggest that speciality monsooned coffee has markedly different microbial and physiological characteristics from normally produced green coffees. SIGNIFICANCE AND IMPACT OF THE STUDY: Monsooned coffee may have a higher contamination with spoilage moulds, especially mycotoxigenic species.

Bacteria↗