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PubMed2004

Genome analysis of marine photosynthetic microbes and their global role.

Four recently completed genome projects on marine Cyanobacteria have started the age of comparative genomics for marine microbes. Cyanobacteria are a group of photoautotrophic bacteria that have traditionally been under-represented in studies of complete genome sequences, as have microbes from the marine environment in general. The new genome information is of crucial importance to understanding their role in oceanic primary production, global carbon cycling and functioning of the biosphere. Marine microbes are a still almost untapped resource for the identification of novel beneficial metabolites and activities. The availability of an increasing number of genome sequences will eventually lead to a sustained development of marine biotechnology.

Bacteriophages↗

PubMed2004

Recycling of pathogenic microbes through survival in ice.

Viable microorganisms (e.g. fungi, bacteria, Archaea and viruses) are distributed by wind over great distances, including globally. Microbes may settle out of the atmosphere or may be incorporated into fog, rain, sleet, hail, or snow. These organisms fall into lakes, streams, oceans, or onto the land or glaciers. When they become incorporated into environmental ice (e.g. glaciers, ice sheets, and snow), those that survive freezing and thawing may persist for years, centuries, millennia, or longer. Once they melt from the ice, they may enter contemporary populations. This mixing of ancient and modern genotypes (i.e. temporal gene flow, or what we term "genome recycling") may lead to a change of allele proportions in the population, which may have effects on mutation rates, fitness, survival, pathogenicity and other characteristics of the organisms. Pathogenic microbes that survive freezing and thawing (e.g. influenza viruses, polioviruses, caliciviruses and tobamoviruses) can remain in these icy reservoirs long enough to avoid resistance mechanisms of the hosts, thereby conveying a selective advantage to these pathogens over those that cannot survive in ice. Ice is an abiotic reservoir of microbes that has been ignored in surveillance activities for human diseases.

Bacteria↗

PubMed2005

Dynamic cellular responses in plant-microbe interactions.

Encounters between plant cells and both 'friendly' and 'hostile' microbes (such as those in symbiotic and pathogenic interactions, respectively) trigger a range of highly dynamic plant cellular responses. These include reorganization of the cytoskeleton, organelle translocation, vesicle trafficking, and alterations in subcellular protein localization. Recent progress in this borderland that bridges the fields of plant-microbe interactions and cell biology heralds the transition from descriptive phenomenology to the identification and characterization of key molecules that are involved in these processes. Intriguingly, molecular events that occur in plant cells in response to microbes also take place upon abiotic wounding and during fundamental plant developmental processes, such as the tip growth of pollen, root hairs and trichomes. Thus, elementary 'activity modules' that are required for the generation of cell polarity in plant morphogenesis appear to be re-used in both abiotic and biotic stress response pathways.

Cytoplasmic Vesicles↗

PubMed1999

Influence of microbes on the mobilization, toxicity and biomethylation of arsenic in soil.

To understand the effects of microbial activity on the mobilization and speciation of arsenic in soil, the cycling of arsenic was studied in microcosm experiments under laboratory conditions. Particular attention was paid to the biomethylation of arsenic and to the toxicity of inorganic and organic arsenic species for microbes. Microbes enhanced mobilization of arsenic from soil by 19-24% compared to formaldehyde inhibited controls. Formation of dissolved methylated arsenic species by microbes was low (< 0.1%) during the 5-day incubation. Even though methylation may function as a detoxification method, it was of minor importance in the soil tested.

Arsenic↗

PubMed2001

Enchytraeids and microbes in Zn polluted soil: no link between organism-level stress responses and ecosystem functioning.

We studied the presence of zinc tolerance in enchytraeid worm (Cognettia sphagnetorum, Oligochaeta) from a metal-polluted forest soil in The Netherlands. In a dose response experiment, we compared Zn sensitivity, measured as body growth and reproduction, of these enchytraeids with that of animals taken from three unpolluted sites. Because C. sphagnetorum is a keystone species, regulating microbial processes in coniferous forest soil, we performed a microcosm experiment to study the interaction of enchytraeids from several sites with soil microbes. The idea was to study whether there is a link between metal stress response of individuals (tolerance level, life history alteration) and changes observed at higher organization levels of the biological system (trophic interaction and decomposition processes). We did not find evidence for increased metal tolerance of C. sphagnetorum. Worms from the polluted site actually had reduced body growth, indicating negative fitness effects caused by long-lasting metal stress. The density and biomass of the worm population from the polluted site was low in Zn contaminated soil. Presence of enchytraeids enhanced and Zn contamination reduced the activity of microbes in the soil. Enchytraeids from different sites with different life histories and population development, however, had the same effect on microbes. Hence, observed stress responses of individuals and populations could not be linked to density-dependent trophic interactions and ecosystem functioning in the soil-decomposer food chain.

Animals↗

PubMed2025

Label-free structural imaging of plant roots and microbes using third-harmonic generation microscopy.

Root biology is pivotal in addressing global challenges including sustainable agriculture and climate change. However, roots have been relatively understudied among plant organs, partly due to the difficulties in imaging root structures in their natural environment. Here we used microfabricated ecosystems (EcoFABs) to establish growing environments with optical access and employed nonlinear multimodal microscopy of third-harmonic generation (THG) and three-photon fluorescence (3PF) to achieve label-free, in situ imaging of live roots and microbes at high spatiotemporal resolution. THG enabled us to observe key plant root structures including the vasculature, Casparian strips, dividing meristematic cells, and root cap cells, as well as subcellular features including nuclear envelopes, nucleoli, starch granules, and putative stress granules. THG from the cell walls of bacteria and fungi also provides label-free contrast for visualizing these microbes in the root rhizosphere. With simultaneously recorded 3PF signal, we demonstrated our ability to investigate root-microbe interactions by achieving single-bacterium tracking and subcellular imaging of fungal spores and hyphae in the rhizosphere.

Plant Roots↗

PubMed1999

Microbes and sequestered substances as mechanisms for disease: Bartonella and L-forms as common global etiological agents.

The pathogenicity of microbes may be determined by substances sequestered from blood and bound to their constituent lipid. The brain may not perceive substances sequestered by microbes, to interfere with control to maintain normal levels. Pathological conditions can be induced as organisms exposed to antimicrobial substances/conditions and/or deprived of nutrients essential to cell wall synthesis, disintegrate to free lipid-bound compounds and produce L-forms that can deplete nutrients as they revert to bacteria. Microbes may act as active carriers for the continuing interaction of sequestered substances. Changes in the molecular structure of substances effected during sequesteration could cause them to be seen as substances 'synthesized' by an organism. In media that contain substances to inhibit 'contaminants', L-forms can be seen as mycoplasma. Elementary bodies of L-forms with a specific substance or tissue affinity may be seen as 'receptors'. Bartonella are global agents for disease--pleomorphic organisms (description suits Proteus)--and they can be seen as 'contaminants'.

Bartonella↗

PubMed2002

Modulating airway defenses against microbes.

Prevention and treatment of respiratory infections remain an important health care challenge as the US population ages, contains more susceptible or high-risk people, and encounters new pathogens or antibiotic resistant bacteria. Reasonably protective vaccines against very common microbes are available for childhood and adult immunization, but, generally, these are underutilized. A broader definition of higher risk individuals is evolving, which will include more for immunization. Different approaches to vaccine development through design of new component vaccines are necessary. This review has updated host defense mechanisms at three levels in the human respiratory tract: naso-oropharynx (upper airways), conducting airways, and alveolar space. Examples of representative pathogenic microbes have been inserted at the respective airway segment where they may colonize or create infection (influenza, measles virus, Porphyromonas gingivalis causing periodontitis, Bordetella pertussis, Chlamydia pneumoniae, Streptococcus pneumoniae, and Bacillus anthracis ). Hopefully, microbe-host interactions will suggest new approaches for preventing these kinds of infections.

Animals↗

PubMed2003

Enhancement of plant-microbe interactions using a rhizosphere metabolomics-driven approach and its application in the removal of polychlorinated biphenyls.

Persistent organic pollutants, such as polychlorinated biphenyls (PCBs), are a global problem. We demonstrate enhanced depletion of PCBs using root-associated microbes, which can use plant secondary metabolites, such as phenylpropanoids. Using a "rhizosphere metabolomics" approach, we show that phenylpropanoids constitute 84% of the secondary metabolites exuded from Arabidopsis roots. Phenylpropanoid-utilizing microbes are more competitive and are able to grow at least 100-fold better than their auxotrophic mutants on roots of plants that are able to synthesize or overproduce phenylpropanoids, such as flavonoids. Better colonization of the phenylpropanoid-utilizing strain in a gnotobiotic system on the roots of flavonoid-producing plants leads to almost 90% removal of PCBs in a 28-d period. Our work complements previous approaches to engineer soil microbial populations based on opines produced by transgenic plants and used by microbes carrying opine metabolism genes. The current approach based on plant natural products can be applied to contaminated soils with pre-existing vegetation. This strategy is also likely to be applicable to improving the competitive abilities of biocontrol and biofertilization strains.

Arabidopsis↗

PubMed2004

The rate and pattern of cladogenesis in microbes.

Theories of macroevolution rarely have been extended to include microbes; however, because microbes represent the most ancient and diverse assemblage of organismal diversity, such oversight limits our understanding of evolutionary history. Our analysis of phylogenetic trees for microbes suggests that macroevolution may differ between prokaryotes and both micro- and macroeukaryotes (mainly plants and animals). Phylogenetic trees inferred for prokaryotes and some microbial eukaryotes conformed to expectations assuming a constant rate of cladogenesis over time and among lineages: nevertheless, microbial eukaryote trees exhibited more variation in rates of cladogenesis than prokaryote trees. We hypothesize that the contrast of macroevolutionary dynamics between prokaryotes and many eukaryotes is due, at least in part, to differences in the prevalence of lateral gene transfer (LGT) between the two groups. Inheritance is predominantly, if not wholly, vertical within eukaryotes, a feature that allows for the emergence and maintenance of heritable variation among lineages. By contrast, frequent LGT in prokaryotes may ameliorate heritable variation in rate of cladogenesis resulting from the emergence of key innovations; thus, the inferred difference in macroevolution might reflect exclusivity of key innovations in eukaryotes and their promiscuous nature in prokaryotes.

Archaea↗

PubMed2006

Gnotobiotically grown aquatic animals: opportunities to investigate host-microbe interactions.

The culture of aquatic organisms is still hampered by the occurrence of unpredictable diseases in their early life stages, which are responsible for massive mortalities and considerable economic losses. A better understanding of the host-microbe interactions is certainly essential to develop effective solutions of disease control for the aquaculture industry. As demonstrated in terrestrial animals, the use of gnotobiotic systems (animals cultured in axenic conditions or with a known microflora) can be an excellent tool to extent the understanding of the mechanisms involved in host-microbe interactions and to evaluate new treatments of disease control. Several aquatic animals were cultured so far in germ-free conditions, such as fish, molluscs, crustaceans, rotifers, echinoderms, cnidarians, turbellarians, ascidians and echiurans. The aim of the present review is to recapitulate the findings obtained with gnotobiotic aquatic animals over the last decades, with special emphasis to the host-microbe interactions, as well as the perspectives for future research in this field. In addition, the procedures utilized to culture axenic aquatic animals and to verify contaminations are summarized, and the standardization of these procedures is proposed.

Animals↗

PubMed2006

Identification and cultivation of anaerobic, syntrophic long-chain fatty acid-degrading microbes from mesophilic and thermophilic methanogenic sludges.

We investigated long-chain fatty acid (LCFA)-degrading anaerobic microbes by enrichment, isolation, and RNA-based stable isotope probing (SIP). Primary enrichment cultures were made with each of four LCFA substrates (palmitate, stearate, oleate, or linoleate, as the sole energy source) at 55 degrees C or 37 degrees C with two sources of anaerobic granular sludge as the inoculum. After several transfers, we obtained seven stable enrichment cultures in which LCFAs were converted to methane. The bacterial populations in these cultures were then subjected to 16S rRNA gene-based cloning, in situ hybridization, and RNA-SIP. In five of seven enrichment cultures, the predominant bacteria were affiliated with the family Syntrophomonadaceae. The other two enrichment cultures contained different bacterial populations in which the majority of members belonged to the phylum Firmicutes and the class Deltaproteobacteria. After several attempts to isolate these dominant bacteria, strain MPA, belonging to the family Syntrophomonadaceae, and strain TOL, affiliated with the phylum Firmicutes, were successfully isolated. Strain MPA converts palmitate to acetate and methane in syntrophic association with Methanospirillum hungatei. Even though strain TOL assimilated [(13)C]palmitate in the original enrichment culture, strain TOL has not shown the ability to degrade LCFAs after isolation. These results suggest that microbes involved in the degradation of LCFAs under methanogenic conditions might not belong only to the family Syntrophomonadaceae, as most anaerobic LCFA-degrading microbes do, but may also be found in phylogenetically diverse bacterial groups.

Bacteria, Anaerobic↗

PubMed1979

Microbial oxidation of gaseous hydrocarbons: production of methyl ketones from their corresponding secondary alcohols by methane- and methanol-grown microbes.

Cultures of methane- or methanol-utilizing microbes, including obligate (both types I and II) and facultative methylotrophic bacteria, obligate methanol utilizers, and methanol-grown yeasts were isolated from lake water of Warinanco Park, Linden, N.J., and lake and soil samples of Bayway Refinery, Linden, N.J. Resting-cell suspensions of these, and of other known C1-utilizing microbes, oxidized secondary alcohols to their corresponding methyl ketones. The product methyl ketones accumulated extracellularly. Succinate-grown cells of facultative methylotrophs did not oxidize secondary alcohols. Among the secondary alcohols, 2-butanol was oxidized at the highest rate. The optimal conditions for in vivo methyl ketone formation were compared among five different types of C1-utilizing microbes. Some enzymatic degradation of 2-butanone was observed. The product, 2-butanone, did not inhibit the oxidation of 2-butanol. The rate of the 2-butanone production was linear for the first 4 h of incubation for all five cultures tested. A yeast culture had the highest production rate. The optimum temperature for the production of 2-butanone was 35 degrees C for all the bacteria tested. The yeast culture had a higher temperature optimum (40 degrees C), and there was a reasonably high 2-butanone production rate even at 45 degrees C. Metal-chelating agents inhibit the production of 2-butanone, suggesting the involvement of metal(s) in the oxidation of secondary alcohols. Secondary alcohol dehydrogenase activity was found in the cell-free soluble extract of sonically disrupted cells. The cell-free system requires a cofactor, specifically nicotinamide adenine dinucleotide, for its activity. This is the first report of a nicotinamide adenine dinucleotide-dependent, secondary alcohol-specific enzyme.

Butanols↗

PubMed1973

Quantitative extraction of adenosine triphosphate from cultivable and host-grown microbes: calculation of adenosine triphosphate pools.

EXISTING DATA ON ADENOSINE TRIPHOSPHATE (ATP) POOLS IN MICROBES ARE DEFICIENT FOR TWO REASONS: (i) incomplete extractions of ATP, and (ii) the failure to take into account that the adverse effects of extracting procedures on standard ATP exert analogous effects on the ATP released from bacterial cells. Methods for correcting observed yields and calculating ATP pools have been demonstrated. Three bacterial species were used in the studies on extraction of ATP: Escherichia coli, Mycobacterium phlei, and Mycobacterium lepraemurium. Perchloric acid and n-butanol were disqualified because of their failure to extract total bacterial ATP even from E. coli and because of inconvenient procedures. The new extraction procedure had minimal effects on standard ATP, liberated 100% of the ATP pools from the three representative species of microbes, and caused no ionic imbalance or quenching of bioluminescence. This method involves vortexing of cell suspensions for 10 s with 23% chloroform (vol/vol), heating at 98 C for the required time (E. coli, 3 min; M. phlei, 5 min; M. lepraemurium, 10 min) and then 1 min at 98 C with vacuum to dry the samples. Heat or chloroform alone may suffice for some microbes and release total ATP from plant and animal cells.

Adenosine Triphosphate↗

PubMed1984

Kinetic analysis of microbe opsonification based on stimulated polymorphonuclear leukocyte oxygenation activity.

With Pseudomonas aeruginosa as the target microbes and polymorphonuclear leukocytes (PMNL) as effector phagocytes, the microbe-specific, immunoglobulin G (IgG)-dependent opsonic capacities of preimmune and immune sera were measured as the rate of stimulated PMNL dioxygenation of luminol yielding chemiluminescence (CL). When the reactants other than opsonin are present in concentrations that are not rate limiting, the information-effector relationship linking specific opsonin concentration to effector PMNL stimulation is described by the rate equation: L' = k'[IgG]i, where L' is the peak CL velocity (photons per minute), k' is the proportionality constant, [IgG] is the concentration of specific opsonin, and the exponent i is the order of the reaction with respect to opsonin. Since the specific opsonins were polyclonal IgG of unknown absolute serum concentration, the reciprocal rate expression, L' = k'D-i, was employed for data presentation; D is the serum dilution (final volume/initial serum volume), and the sign of i is changed to negative. The relationships of integral, first-derivative, and second-derivative expressions of the CL response to opsonin concentration are illustrated with experimentally obtained data. Based on peak CL velocity or peak CL acceleration measurements taken over different time intervals of testing, the estimated order with respect to opsonin is highest, and probably most accurate, using the shortest test interval allowing reasonably good precision of measurement. As an alternative temporal approach, microbe opsonification kinetics are analyzed based on nodal time (Tn) measurements. The Tn is the time point separating the acceleration and deceleration phases of the PMNL oxygenation response to stimulation and as such satisfies the criterion of a selected condition of PMNL activation.

Kinetics↗

PubMed1990

Complex regulation of the immunoglobulin mu heavy-chain gene enhancer: microB, a new determinant of enhancer function.

The B-lymphocyte-specific activity of the immunoglobulin mu heavy-chain gene enhancer has been attributed to the octamer motif (ATTTGCAT) present within the enhancer that binds a B-cell-specific factor designated NF-A2/OTF-2. However, significant residual enhancer activity even after deletion of this element has suggested the presence of a second critical functional determinant. We have used deletion and mutational analyses to define an element, microB (TTTGGGGAA), that is essential for B-cell-specific enhancer activity in S194 myeloma cells in the absence of the octamer. Transfection analysis in a panel of lymphoid cell lines suggests that the presence of either microB or octamer leads to considerable enhancer activity in cell lines representing later stages of B-cell differentiation, whereas both elements are needed for function in cell lines representing earlier stages. Furthermore, in contrast to the results in pre-B-cell lines, both microB and octamer elements function independently in certain T-cell lines in which the mu enhancer is active.

Animals↗

PubMed2005

Detection of and response to signals involved in host-microbe interactions by plant-associated bacteria.

Diverse interactions between hosts and microbes are initiated by the detection of host-released chemical signals. Detection of these signals leads to altered patterns of gene expression that culminate in specific and adaptive changes in bacterial physiology that are required for these associations. This concept was first demonstrated for the members of the family Rhizobiaceae and was later found to apply to many other plant-associated bacteria as well as to microbes that colonize human and animal hosts. The family Rhizobiaceae includes various genera of rhizobia as well as species of Agrobacterium. Rhizobia are symbionts of legumes, which fix nitrogen within root nodules, while Agrobacterium tumefaciens is a pathogen that causes crown gall tumors on a wide variety of plants. The plant-released signals that are recognized by these bacteria are low-molecular-weight, diffusible molecules and are detected by the bacteria through specific receptor proteins. Similar phenomena are observed with other plant pathogens, including Pseudomonas syringae, Ralstonia solanacearum, and Erwinia spp., although here the signals and signal receptors are not as well defined. In some cases, nutritional conditions such as iron limitation or the lack of nitrogen sources seem to provide a significant cue. While much has been learned about the process of host detection over the past 20 years, our knowledge is far from being complete. The complex nature of the plant-microbe interactions makes it extremely challenging to gain a comprehensive picture of host detection in natural environments, and thus many signals and signal recognition systems remain to be described.

Chemotaxis↗

PubMed2004

Genetic and phenotypic traits of streptomycetes used to characterize antibiotic activities of field-collected microbes.

Although antibiotic production may contribute significantly to microbial fitness, there is limited information on the ecology of antibiotic-producing microbial populations in soil. Indeed, quantitative information on the variation in frequency and intensity of specific antibiotic inhibitory and resistance abilities within soil microbial communities is lacking. Among the streptomycetes, antibiotic production is highly variable and resistance to antibiotics is highly specific to individual microbial strains. The objective of this work was to genetically and phenotypically characterize a reference collection of streptomycetes for use in distinguishing inhibition and resistance phenotypes of field-collected microbes. Specifically, we examined inhibition and resistance abilities of all isolates in all possible pairwise combinations, genetic relatedness using BOX-PCR and 16S rDNA sequence analyses, nutrient utilization profiles, and antibiotic induction among all possible three-way combinations of isolates. Each streptomycete isolate possessed a unique set of phenotypic and genetic characteristics. However, there was little correspondence between phenotypic and genetic traits. This collection of reference isolates provides the potential for distinguishing 1024 inhibition and resistance phenotypes in field-collected microbes. Relationships between the genetic and phenotypic characteristics examined may provide preliminary insight into the distinct strategies that microbes use in optimizing their fitness in natural environments.

Anti-Bacterial Agents↗