酚酸类物质的化感作用研究进展

酚酸类物质是普遍存在于高等植物组织并与植物生长密切相关的次级代谢产物。几十年来,人们对酚酸类化合物的认识逐渐加深,但关于其在生物学、生态学以及农业上的作用机制仍不是很清楚。因此,进一步了解这些生物分子将有助于生态系统的维持与保护。重点介绍了酚酸类物质的来源及化感作用,微生物对酚酸类物质的降解机理,代谢途径及相应分子水平的研究,指出了酚酸类物质研究中存在的问题,同时展望了酚酸类物质的研究方向与前景。     

A novel regulation on developmental gene expression of fruiting body formation in Myxobacteria

Myxobacteria are Gram-negative soil microorganisms that prey on other microorganisms. Myxobacteria have significant potential for applications in biotechnology because of their extraordinary ability to produce natural products such as secondary metabolites. Myxobacteria also stand out as model organisms for the study of cell–cell interactions and multicellular development during their complex life cycle. Cellular morphogenesis during multicellular development in myxobacteria is very similar to that in the eukaryotic soil amoebae. Recent studies have started uncovering molecular mechanisms directing the myxobacterial life cycle. We describe recent studies on signal transduction and gene expression during multicellular development in the myxobacterium Myxococcus xanthus. We provide our current model for signal transduction pathways mediated by a two-component His–Asp phosphorelay system and a Ser/Thr kinase cascade.     

Neutrophilic lithotrophic iron-oxidizing prokaryotes and their role in the biogeochemical processes of the iron cycle

Biology of lithotrophic neutrophilic iron-oxidizing prokaryotes and their role in the processes of the biogeochemical cycle of iron are discussed. This group of microorganisms is phylogenetically, taxonomically, and physiologically heterogeneous, comprising three metabolically different groups: aerobes, nitratedependent anaerobes, and phototrophs; the latter two groups have been revealed relatively recently. Their taxonomy and metabolism are described. Materials on the structure and functioning of the electron transport chain in the course of Fe(II) oxidation by members of various physiological groups are discussed. Occurrence of iron oxidizers in freshwater and marine ecosystems, thermal springs, areas of hydrothermal activity, and underwater volcanic areas are considered. Molecular genetic techniques were used to determine the structure of iron-oxidizing microbial communities in various natural ecosystems. Analysis of stable isotope fractionation of ^56/54Fe in pure cultures and model experiments revealed a predominance of biological oxidation over abiotic ones in shallow aquatic habitats and mineral springs, which was especially pronounced under microaerobic conditions at the redox zone boundary. Discovery of anaerobic bacterial Fe(II) oxidation resulted in development of new hypotheses concerning the possible role of microorganisms and the mechanisms of formation of the major iron ore deposits during Precambrian era until the early Proterozoic epoch. Paleobiological data are presented on the microfossils and specific biomarkers retrieved from ancient ore samples and confirming involvement of anaerobic biogenic processes in their formation.     

From the Cell to the Ecosystem: The Physiological Evolution of Symbiosis

Living organisms constantly interact with their habitats, selectively taking up compounds from their surroundings to meet their particular needs but also excreting metabolic products and thus modifying their environment. The small size, ubiquity, metabolic versatility, flexibility, and genetic plasticity (horizontal transfer) of microbes allow them to tolerate and quickly adapt to unfavorable and/or changing environmental conditions. The consumption of resources and the formation of metabolic products by spatially separated microbial populations constitute the driving forces that lead to chemical gradient formation. Communication and cooperation, both within and among bacterial species, have produced the properties that give these organisms a selective advantage. Observations of a wide range of natural habitats have established that bacteria do not function as individuals; rather, the vast majority of bacteria in natural and pathogenic ecosystems live in biofilms, defined as surface-associated, complex aggregates of bacterial communities that are attached to solid substrates and embedded in a polymer matrix of their own production. The spatial configurations of biofilms reach levels of complexity nearing those of multicellular eukaryotes. Microbial consortia have played important roles throughout the history of life on Earth, from the microbial mats (a type of biofilm) that were probably the first ecosystems in the early Archean, to the complex microbiota of the intestinal tract of different animals.     

Bioactive Compounds from Marine Bacteria and Fungi

Marine bacteria and fungi are of considerable importance as new promising sources of a huge number of biologically active products. Some of these marine species live in a stressful habitat, under cold, lightless and high pressure conditions. Surprisingly, a large number of species with high diversity survive under such conditions and produce fascinating and structurally complex natural products. Up till now, only a small number of microorganisms have been investigated for bioactive metabolites, yet a huge number of active substances with some of them featuring unique structural skeletons have been isolated. This review covers new biologically active natural products published recently (2007–09) and highlights the chemical potential of marine microorganisms, with focus on bioactive products as well as on their mechanisms of action.     

Biofilm formation and dispersal and the transmission of human pathogens

Several pathogenic bacterial species that are found in the environment can form complex multicellular structures on surfaces known as biofilms. Pseudomonas aeruginosa, Vibrio cholerae and certain species of nontuberculous mycobacteria are examples of human pathogens that form biofilms in natural aquatic environments. We suggest that the dynamics of biofilm formation facilitates the transmission of pathogens by providing a stable protective environment and acting as a nidus for the dissemination of large numbers of microorganisms; both as detached biofilm clumps and by the fluid-driven dispersal of biofilm clusters along surfaces. We also suggest that emerging evidence indicates that biofilm formation conveys a selective advantage to certain pathogens by increasing their ability to persist under diverse environmental conditions.     

Physiological and Transcriptional Responses of Different Industrial Microbes at Near-Zero Specific Growth Rates

The current knowledge of the physiology and gene expression of industrially relevant microorganisms is largely based on laboratory studies under conditions of rapid growth and high metabolic activity. However, in natural ecosystems and industrial processes, microbes frequently encounter severe calorie restriction. As a consequence, microbial growth rates in such settings can be extremely slow and even approach zero. Furthermore, uncoupling microbial growth from product formation, while cellular integrity and activity are maintained, offers perspectives that are economically highly interesting. Retentostat cultures have been employed to investigate microbial physiology at (near-)zero growth rates. This minireview compares information from recent physiological and gene expression studies on retentostat cultures of the industrially relevant microorganisms Lactobacillus plantarum, Lactococcus lactis, Bacillus subtilis, Saccharomyces cerevisiae, and Aspergillus niger. Shared responses of these organisms to (near-)zero growth rates include increased stress tolerance and a downregulation of genes involved in protein synthesis. Other adaptations, such as changes in morphology and (secondary) metabolite production, were species specific. This comparison underlines the industrial and scientific significance of further research on microbial (near-)zero growth physiology.     

Approaches to cultivation of “nonculturable” bacteria: Cyclic cultures

The work deals with more efficient procedures for the isolation and cultivation of “nonculturable” microorganisms (NM) from environmental sources. The techniques for NM cultivation in situ and under laboratory conditions are discussed. A new approach is considered, viz., cultivation under cyclically varying conditions with the cycle duration comparable to the duration of the cell cycle. Cyclic cultivation implies sequential changes of several cultivation phases with different growth conditions. An established sequence of growth phases provides for the competitiveness of the target microorganisms and for accumulation of their biomass. Cultivation of phosphate-accumulating bacteria, nonculturable microorganisms which have not been previously isolated in pure culture, in an SBR reactor is discussed as an example of cyclic cultures.     

Leben und Überleben im Boden

Myxobacteria - survivalists in soil Myxobacteria like Myxococccus xanthus are soil-living microorganisms featuring a complex lifestyle, including movement by coordinated swarming on surfaces, predatory feeding on other microorganisms, and the formation of multicellular fruiting bodies when unfavorable environmental conditions are encountered. Bioinformatic analysis of the large myxobacterial genomes has enabled fascinating insights into the molecular basis for the biosynthesis of complex secondary metabolite structures by myxobacteria, and has set the stage for the discovery of novel natural products. Moreover, well-characterized myxobacteria like M. xanthus increasingly play a role as “biochemical factories” for the biotechnological production of bioactive molecules using synthetic biology approaches.     

Growing Yeast into Cylindrical Colonies

Microorganisms often form complex multicellular assemblies such as biofilms and colonies. Understanding the interplay between assembly expansion, metabolic yield, and nutrient diffusion within a freely growing colony remains a challenge. Most available data on microorganisms are from planktonic cultures, due to the lack of experimental tools to control the growth of multicellular assemblies. Here, we propose a method to constrain the growth of yeast colonies into simple geometric shapes such as cylinders. To this end, we designed a simple, versatile culture system to control the location of nutrient delivery below a growing colony. Under such culture conditions, yeast colonies grow vertically and only at the locations where nutrients are delivered. Colonies increase in height at a steady growth rate that is inversely proportional to the cylinder radius. We show that the vertical growth rate of cylindrical colonies is not defined by the single-cell division rate, but rather by the colony metabolic yield. This contrasts with cells in liquid culture, in which the single-cell division rate is the only parameter that defines the population growth rate. This method also provides a direct, simple method to estimate the metabolic yield of a colony. Our study further demonstrates the importance of the shape of colonies on setting their expansion. We anticipate that our approach will be a starting point for elaborate studies of the population dynamics, evolution, and ecology of microbial colonies in complex landscapes.     

Mini-review: Biofilm responses to oxidative stress

Biofilms constitute the predominant microbial style of life in natural and engineered ecosystems. Facing harsh environmental conditions, microorganisms accumulate reactive oxygen species (ROS), potentially encountering a dangerous condition called oxidative stress. While high levels of oxidative stress are toxic, low levels act as a cue, triggering bacteria to activate effective scavenging mechanisms or to shift metabolic pathways. Although a complex and fragmentary picture results from current knowledge of the pathways activated in response to oxidative stress, three main responses are shown to be central: the existence of common regulators, the production of extracellular polymeric substances, and biofilm heterogeneity. An investigation into the mechanisms activated by biofilms in response to different oxidative stress levels could have important consequences from ecological and economic points of view, and could be exploited to propose alternative strategies to control microbial virulence and deterioration.     

Growing Yeast into Cylindrical Colonies

Microorganisms often form complex multicellular assemblies such as biofilms and colonies. Understanding the interplay between assembly expansion, metabolic yield, and nutrient diffusion within a freely growing colony remains a challenge. Most available data on microorganisms are from planktonic cultures, due to the lack of experimental tools to control the growth of multicellular assemblies. Here, we propose a method to constrain the growth of yeast colonies into simple geometric shapes such as cylinders. To this end, we designed a simple, versatile culture system to control the location of nutrient delivery below a growing colony. Under such culture conditions, yeast colonies grow vertically and only at the locations where nutrients are delivered. Colonies increase in height at a steady growth rate that is inversely proportional to the cylinder radius. We show that the vertical growth rate of cylindrical colonies is not defined by the single-cell division rate, but rather by the colony metabolic yield. This contrasts with cells in liquid culture, in which the single-cell division rate is the only parameter that defines the population growth rate. This method also provides a direct, simple method to estimate the metabolic yield of a colony. Our study further demonstrates the importance of the shape of colonies on setting their expansion. We anticipate that our approach will be a starting point for elaborate studies of the population dynamics, evolution, and ecology of microbial colonies in complex landscapes.     

Hydrocarbon-oxidizing microorganisms in the waters of certain regions of the Western and Central Atlantic

The incidence of hydrocarbon-oxidizing microorganisms in water was determined by the method of plating on solid media. Vertical distribution of hydrocarbon-oxidizing microflora was different near the shore and in the open ocean; the incidence of the microorganisms was low in the surface water layer but increased at depths of 25 and 75 m in the open ocean in contrast to regions near the shore. Pure bacterial and fungal cultures were isolated and their properties were described. The cultures were grown in a liquid mineral medium with diesel fuel and 50 cultures out of 66 were found to be true hydrocarbon-oxidizing microorganisms surviving under the laboratory conditions. It was shown that bacteria and fungi have grown on tarballs collected from the surface of the ocean during their incubation at 30 degrees C.     

Impacts of engineered nanomaterials on microbial community structure and function in natural and engineered ecosystems

In natural and engineered environments, microorganisms often exist as complex communities, which are key to the health of ecosystems and the success of bioprocesses in various engineering applications. With the rapid development of nanotechnology in recent years, engineered nanomaterials (ENMs) have been considered one type of emerging contaminants that pose great potential risks to the proper function of microbial communities in natural and engineered ecosystems. The impacts of ENMs on microorganisms have attracted increasing research attentions; however, most studies focused on the antimicrobial activities of ENMs at single cell and population level. Elucidating the influence of ENMs on microbial communities represents a critical step toward a comprehensive understanding of the ecotoxicity of ENMs. In this mini-review, we summarize and discuss recent research work on the impacts of ENMs on microbial communities in natural and engineered ecosystems, with an emphasis on their influences on the community structure and function. We also highlight several important research topics which may be of great interest to the research community.     

Natural ecosystem design and control imperatives for sustainable ecosystem services

Sustainability of ecosystem services to humanity will depend on knowledge of how ecosystems work in their natural states, which can then be carried over to managed states. The objective of this paper is to describe four properties of ecosystems taken as natural conditions to be maintained under exploitation. Three of these are design properties: near-steady-state or extremal dynamics, dominance of indirect effects, and positive utility in network organization. One is a regulatory property: distributed multivariable control. The methodology of the paper is mathematical modeling. The design properties are drawn from the inherent formalism in models. The control property is demonstrated by manipulating model parameters to achieve a management goal. The results show that: (1) natural ecosystems operate near, but not at, steady states or extrema, and ecosystems exploited for human purposes should be similarly maintained (near-steady-state imperative); (2) indirect effects are dominant in natural ecosystem networks, and should be taken into account in managing ecosystems for human benefits (nonlocal imperative); (3) natural ecosystems enhance positive relationships among their constituents, and ecosystems maintained for human services should be managed to maximize their expression of mutualistic and synergistic network properties (nonzero imperative); and (4) natural ecosystems are regulated by checks and balances distributed across many control variables in interactive networks, so that obtaining human services from ecosystems should similarly be through coordinated use of many, not few, control variables (multifactorial control imperative). The conclusion from these results is that ecosystems under natural conditions evidence organizational properties evolved over evolutionary time, and management for sustainable extraction of ecosystem services should seek to preserve and emulate these properties in the new exploited states.     

Carbon metabolism of intracellular bacteria

Bacterial metabolism has been studied intensively since the first observations of these 'animalcules' by Leeuwenhoek and their isolation in pure cultures by Pasteur. Metabolic studies have traditionally focused on a small number of model organisms, primarily the Gram negative bacillus Escherichia coli, adapted to artificial culture conditions in the laboratory. Comparatively little is known about the physiology and metabolism of wild microorganisms living in their natural habitats. For approximately 500-1000 species of commensals and symbionts, and a smaller number of pathogenic bacteria, that habitat is the human body. Emerging evidence suggests that the metabolism of bacteria grown in vivo differs profoundly from their metabolism in axenic cultures.     

Inorganic carbon acquisition in algal communities: are the laboratory data relevant to the natural ecosystems?

Most of the experimental work on the effects of ocean acidification on the photosynthesis of algae has been performed in the laboratory using monospecific cultures. It is frequently assumed that the information obtained from these cultures can be used to predict the acclimation response in the natural environment. CO(2) concentration is known to regulate the expression and functioning of the CCMs in the natural communities; however, ambient CO(2) can become quite variable in the marine ecosystems even in the short- to mid-term. We propose that the degree of saturation of the photosynthesis for a given algal community should be defined in relation to the particular characteristics of its habitat, and not only in relation to its taxonomic composition. The convenience of high CO(2) experiments to infer the degree of photosynthesis saturation by CO(2) in the natural algal communities under the present ocean conditions, as well as its trend in a coming future is discussed taking into account other factors such as the availability of light and nutrients, and seasonality.     

Problems posed by natural environments for monitoring microorganisms

Microorganisms in natural environments have evolved to withstand fluctuations in physical and chemical conditions. This means that they often manifest very different biochemical and morphological features compared with those seen during laboratory culture. A major limitation in natural ecosystems is nutrient limitation under which microorganisms are exposed to starvation conditions and grow slowly or not at all. This review identifies the role of inimical processes on microbial properties such as the responses to starvation that may result in the adoption of viable but nonculturable (VBNC) states, discusses the problems that altered physiological states pose for detection and identification and highlights novel methods that have been developed to circumvent these difficulties. These factors dictate that to survive and respond to environmental stimuli, a cell must have evolved sophisticated programs of gene expression. These include the sigma factor rpoS that directs RNA polymerase to transcribe genes whose expression aids survival during severe nutrient limitation or cell-cell communication systems that promote a concerted population response termed quorum sensing.     

Interactions of certain sapronotic infection pathogens in mixed cultures on a solid medium at different temperatures

Under experimental conditions within the time limit of 21-35 days the causative agents of sapronotic infections in binary cultures, grown on a solid medium at 37 degrees C, 25-27 degrees C and 6-8 degrees C, interacted with one another transbiotically and through contact, their interactions having the character of amensalism, commensalisms-amensalism, competitive equilibrium, antibiosis. Irrespective of the initial density, a change in the species composition was observed, one of them playing the dominating role. At 37 degrees C mutual antagonism of Yersinia pseudotuberculosis and Pseudomonas aeruginosa killed both cultures. P. aeruginosa cells were also killed when cultivated at 37 degrees C jointly with Listeria monocytogenes, the most resistant species under experimental conditions. While studying the character of microorganisms interactions the method of contacting cultures on a solid medium was shown to give more information in comparison with the "cross-strip" method. Possible interspecific relationships between the causative agents of sapronotic infections under natural conditions are discussed.     

Some like it toxic

Humans are notorious for disturbing terrestrial ecosystems worldwide, especially those that are in close proximity to urban areas. This disturbance has involved the accumulation of various types of chemical pollutants, of either agricultural or industrial origins, in both soil and water ecosystems. Pollutants have sometimes included essential plant nutrients, such as phosphate and nitrate, which have piled up throughout the years in many ecosystems as a consequence of aggressive agricultural practices, and a number of toxic or trace metals, e.g. iron, nickel or zinc that are important at low levels for the fitness of living organisms, but otherwise toxic at high concentrations ( Ker & Charest 2010 ; Audet & Charest 2008 ). In order to reduce the load of toxic elements, scientists have used the natural capacity of several plant species to sequestrate them from the soil and, ultimately, render them harmless. This process, called phytoremediation, is rather slow, as most plants take years to build up their biomass but has been shown to be ‘boostable’ under experimental conditions in the presence of a particular group of plant symbionts in the soil – the arbuscular mycorrhizal fungi (AMF) ( Gohre & Paszkowski 2006 ). These latter organisms are now widely recognized as being very beneficial for purposes of phytoremediation, but their biodiversity in the most disturbed ecosystems is still virtually unknown. Are these fungi really abundant in heavily polluted soils, or are their communities shrunken down like those of other microorganisms in the presence of heavy pollution? In this issue of Molecular Ecology, the study by Hassan et al. (2011) provides answers to these specific questions by determining the extent of AMF biodiversity across several urbanized areas in the City of Montréal.