Coexistence and Pattern Formation in Bacterial Mixtures with Contact-Dependent Killing

Multistrain microbial communities often exhibit complex spatial organization that emerges because of the interplay of various cooperative and competitive interaction mechanisms. One strong competitive mechanism is contact-dependent neighbor killing enabled by the type VI secretion system. It has been previously shown that contact-dependent killing can result in bistability of bacterial mixtures so that only one strain survives and displaces the other. However, it remains unclear whether stable coexistence is possible in such mixtures. Using a population dynamics model for two interacting bacterial strains, we found that coexistence can be made possible by the interplay of contact-dependent killing and long-range growth inhibition, leading to the formation of various cellular patterns. These patterns emerge in a much broader parameter range than that required for the linear Turing-like instability, suggesting this may be a robust mechanism for pattern formation.     

Bacterial Synergism or Antagonism in a Gel Cassette System

The growth and the metabolic activity of Shewanella putrfaciens, Brochothrix thermosphacta, and Pseudomonas sp., when cultured individually or in all possible combinations in gel cassettes system supplemented with 0.1% glucose at 5°C, were investigated. The overall outcome was that the coexistence of the above-mentioned microorganisms affected not only each growth rate but also their type of metabolic end products compared to the control cultures. These effects were varied and depended on the selection of the combination of the tested bacteria. For example, the growth of Pseudomonas sp. strains cocultured with either B. thermosphacta or S. putrefaciens strains resulted in different effects: a promoting one for the first and an inhibitory one for the second. Moreover, the production of formic acid and two unidentified organic acids (peaks a and b) was characteristic in all cases in which S. putrefaciens was cultured.     

Extracellular Accumulation of Pyrroles in Bacterial Cultures

Aerobacter aerogenes, Paracolobactrum aerogenoides, Spirillum serpens, and gelatinous strains of Chromobacterium violaceum produced an extracellular, ether-soluble, Ehrlich-positive substance when grown in media prepared with gelatin hydrolysate. The substance has been tentatively identified as pyrrole-2-carboxylic acid. Both hydroxy-l-proline and allo-d-hydroxyproline have been shown to be precursors of the material. Gelatinous strains of Chromobacterium violaceum, but not the other positive cultures, produced two ether-insoluble pyrroles as well, the precursors of which occur in gelatin hydrolysate but have not yet been identified. The property of pyrrole formation in bacteria and its possible use as an aid in identification of bacteria was discussed.     

Competition and Coexistence of Sulfate-Reducing and Methanogenic Populations in Anaerobic Biofilms

The microbial population structure and function of natural anaerobic communities maintained in laboratory fixed-bed biofilm reactors were tracked before and after a major perturbation, which involved the addition of sulfate to the influent of a reactor that had previously been fed only glucose (methanogenic), while sulfate was withheld from a reactor that had been fed both glucose and sulfate (sulfidogenic). The population structure, determined by using phylogenetically based oligonucleotide probes for methanogens and sulfate-reducing bacteria, was linked to the functional performance of the biofilm reactors. Before the perturbation, the methanogenic reactor contained up to 25% methanogens as well as 15% sulfate-reducing bacteria, even though sulfate was not present in the influent of this reactor. Methanobacteriales and Desulfovibrio spp. were the most abundant methanogens and sulfate-reducing bacteria, respectively. The presence of sulfate-reducing bacteria (primarily Desulfovibrio spp. and Desulfobacterium spp.) in the absence of sulfate may be explained by their ability to function as proton-reducing acetogens and/or fermenters. Sulfate reduction began immediately following the addition of sulfate consistent with the presence of significant levels of sulfate-reducing bacteria in the methanogenic reactor, and levels of sulfate-reducing bacteria increased to a new steady-state level of 30 to 40%; coincidentally, effluent acetate concentrations decreased. Notably, some sulfate-reducing bacteria (Desulfococcus/Desulfosarcina/Desulfobotulus group) were more competitive without sulfate. Methane production decreased immediately following the addition of sulfate; this was later followed by a decrease in the relative concentration of methanogens, which reached a new steady-state level of approximately 8%. The changeover to sulfate-free medium in the sulfidogenic reactor did not cause a rapid shift to methanogenesis. Methane production and a substantial increase in the levels of methanogens were observed only after approximately 50 days following the perturbation.     

Competition and Coexistence Among Four Estuarine Species of Fundulus

Four sympatric species of Fundulus (F. heteroclitus, F. majalis,F. diaphanus, and F. luciae) are distributed along tidal heightand salinity gradients such that F. heteroclitus co-occurs witheach species, while the remaining species rarely occur together.Feeding habitats of all the species are similar, and food hasbeen shown to limit population size of F. heteroclitus. Thispaper examines whether competition is an important structuringforce within this guild by addressing two questions: 1) is thespatial separation exhibited by three of the species due tophysiological barriers or due to competitive exlusion? and 2)when F. heteroclitus occurs with other Fundulus species doescompetition for resources take place? Laboratory studies indicate that all four species are tolerantof a wide range of environmental conditions; available evidencesuggests that physiological barriers are an unlikely explanationfor spatial segregation among some members of this guild. Competitiveexclusion seems a likely alternate explanation, but is supportedonly by studies of diet overlap. Similarly, only inference fromdiet overlap is available to answer the second question. A fieldexperiment is presented here in which F. heteroclitus and F.majalis were placed in enclosures separately and together. Competitionbetween these species appears to be important, and similar fieldexperiments are recommended to investigate competitive interactionsamong other species pairs within the genus     

Direct Interference on Competition in a Chemostat

Thispaperstudiestheglobaldynamicsofcompetitioninchemostatinwhichtwopopulationsofmicrooganismscompeteexploitativelyforasingle,essential,nonreproducing,growth-limitingsubstrateandthereisadirectinterferencebetweencompetitors.Inordertounderstandthedifferencesintheeffectsofintraspecificandinterspecificinterference,thebothcasesareconsideredrespectively.Keywords:##4Populationdynamicsecology;;chemostat;;competition;;interference;;interspecific;;intraspecific;;principalofcompetitiveexclusion     

Tree Competition and Species Coexistence in a Sub-boreal Forest, Northern Japan

The growth and mortality patterns and the mode of competitionof six tree species forming a sub-boreal climax forest in Hokkaido,northern Japan, were investigated based on the diffusion modelat the level of the individual tree 2 m height in a 2·3-hastudy site. Picea jezoensis, Picea glehnii, Betula ermanii andAbies sachalinensis were dominant species, occupying approx.94% of the total basal area. Sorbus commixta and Acer ukurunduensewere subordinate species occupying approx. 6% of the total basalarea. A model for individual growth was developed, consideringboth intra- and inter-specific competition and the degree ofcompetitive asymmetry. Asymmetry was found in intraspecificcompetition of Sorbus commixta and Acer ukurunduense. Piceajezoensis, Betula ermanii and Abies sachalinensis showed symmetricintraspecific competition. There was little interspecific competitionamongst Picea jezoensis, Picea glehnii and Betula ermanii. Abiessachalinensis competed symmetrically with Picea jezoensis (onlyvery weakly, P < 0·1) and Betula ermanii (P < 0·01).Picea glehnii gave no indication of inter- or intra-specificcompetition. The growth of the four dominant species was neveraffected by the two subordinate species; the growth of the twosubordinate species was governed by the abundances of the fourdominant species, the sum of which almost amounted to standcrowdedness (i.e. symmetric competitive effect and one-sidedcompetitive direction). On the scale of 2·3 ha of thesub-boreal forest, symmetric competition prevailed over one-sidedor asymmetric competition although statistical evidence forany competitive effects was rather weak. This was probably dueto the relatively low tree density and stand crowdedness ofthis climax forest. Little competition between the dominantspecies suggested by relatively low proportions of r²-valuesattributable to competitive effects indicates weak organizationamongst the component species (i.e. species were more or lessindependent of each other) at the level of the individual tree 2 m height on the 2·3-ha scale.Copyright 1995, 1999Academic Press Climax forest, diffusion model, individual growth, one-sided competition, size structure, symmetric competition     

角百灵和小云雀的巢址选择与竞争共存

于 2 0 0 0— 2 0 0 2年的鸟类繁殖期在中国科学院海北高寒草甸生态系统定位站 ,测定了 2 7窝角百灵(Eremophilaalpestris)和 4 3窝小云雀 (Alaudagulgula)的巢址特征 ,观察了两者在繁殖期巢数的季节变化 ,并运用稳定性同位素技术测定了育雏食物 ,对两种百灵的巢址特征和食物重叠度进行了比较。结果表明两者的巢址特征存在着显著的不同 :角百灵的巢开放度为 92 16 % ,小云雀的为 34 6 1% ,前者的巢开放度显著大于后者(P <0 0 1) ;角百灵距巢 10 0cm范围内遮蔽物的数量为 0 0 7± 0 2 6 ,小云雀的为 2 5 7± 1 19,前者显著少于后者 (P <0 0 1) ;角百灵巢址植被的高度和盖度也显著小于小云雀的 (P <0 0 1)。角百灵和小云雀均以小型昆虫育雏 ,育雏食物的资源重叠程度很高 ,为 0 895 7;而且两者的繁殖季节和繁殖强度也是相互重叠的。这两种百灵鸟类在巢址的选择上存在着一种代价和利益的权衡关系 ,巢址选择是捕食压和热条件共同作用的结果。二者共存的机制是巢址上的分化     

Multifactorial Competition and Resistance in a Two-Species Bacterial System

Microorganisms exist almost exclusively in interactive multispecies communities, but genetic determinants of the fitness of interacting bacteria, and accessible adaptive pathways, remain uncharacterized. Here, using a two-species system, we studied the antagonism of Pseudomonas aeruginosa against Escherichia coli. Our unbiased genome-scale approach enabled us to identify multiple factors that explained the entire antagonism observed. We discovered both forms of ecological competition–sequestration of iron led to exploitative competition, while phenazine exposure engendered interference competition. We used laboratory evolution to discover adaptive evolutionary trajectories in our system. In the presence of P. aeruginosa toxins, E. coli populations showed parallel molecular evolution and adaptive convergence at the gene-level. The multiple resistance pathways discovered provide novel insights into mechanisms of toxin entry and activity. Our study reveals the molecular complexity of a simple two-species interaction, an important first-step in the application of systems biology to detailed molecular dissection of interactions within native microbiomes.     

Comparison of Bacterial Extracellular Polymer Extraction Methods

Five different bacterial extracellular polymer extraction methods and a combination of two of these methods were compared on cultures of activated sludge, synthetic activated sludge, and Klebsiella aerogenes. High-speed centrifugation was the most effective extraction method for the K. aerogenes culture, based on the comparatively small amount of cell disruption and the relatively high extracellular polymer yield. Steaming treatment was the most effective extraction method for the activated sludges, since it released a significant quantity of extracellular polymers from the flocs and caused less cellular disruption than ethylenediaminetetraacetic acid and sodium hydroxide treatments. Sodium hydroxide treatment caused extensive disruption in all cultures. Ultrasonication released low concentrations of extracellular polymers from all cultures. However, it caused no significant cell disruption and therefore may be useful as a preliminary treatment in conjunction with another extraction method.     

Apparatus for Preparation of Bacterial Extracellular Enzymes

A method is described for the growth of bacteria within dialysis tubing to yield extracellular enzymes, or, possibly, other nondialyzable extracellular products, in concentrated form.     

Switching Between Cooperation and Competition in the Use of Extracellular Glucose

This paper addresses some questions related to the evolution of cooperative behaviors, in the context of energetic metabolism. Glycolysis can perform either under a dissipative working regime suitable for rapid proliferation or under an efficient regime that entails a good modus operandi under conditions of glucose shortage. A cellular mechanism allowing switching between these two regimes may represent an evolutionary achievement. Thus, we have explored the conditions that might have favored the emergence of such an accommodative mechanism. Because of an inevitable conflict for resources between individual interests and the common good, rapid and inefficient use of glucose is always favored by natural selection in spatially homogeneous environment, regardless of the external conditions. In contrast, when the space is structured, the behavior of the system is determined by its free energy content. If the fuel is abundant, the dissipative strategy dominates the space. However, under famine conditions the efficient regime represents an evolutionary stable strategy in a Harmony game. Between these two extreme situations, both metabolic regimes are engaged in a Prisoner’s Dilemma game, where the output depends on the extracellular free energy. The energy transition values that lead from one domain to another have been calculated. We conclude that an accommodative mechanism permitting alternation between dissipative and efficient regimes might have evolved in heterogeneous and highly fluctuating environments. Overall, the current work shows how evolutionary optimization and game-theoretical approaches can be complementary in providing useful insights into biochemical systems. Reviewing Editor: Dr. Antony Dean     

Ultrastructure in Bean Leaves Infiltrated with Bacterial Extracellular Polysaccharides

Ultrastructural observations were carried out in bean leaf tissue infiltrated with bacterial extracellular polysaccharides. These investigations revealed changes m the cell fine structure, especially related with chloroplast organization. Up to 24 h after EPS infiltration alterations consisted in irregularly running thylakoids and distortions of stacked regions. Invaginations of the plastid envelope and appearance of cytoplasm pockets inside the stroma were also noted. The most severe alterations, consisting in stroma dilations and envelope infoldings, were noted 24 h after EPS infiltration, parallehng the yellowing of the treated leaf areas; chloroplast shrinkage and collapse of thylakoid system were also sometimes observed. Chloroplast ultrastructure generally recovered 48 h after treatment; at this time local detachment of the plasma membrane and vesicle formation in the periplasmic space were observed, resembling a non specific, locahzed cellular response. The observed, permanent chlorosis and ultrastructural alterations suggest an interference of the EPS in the global metabolism of the bean mesophyll cell.     

Context-Dependent Competition in a Model Gut Bacterial Community

Understanding the ecological processes that generate complex community structures may provide insight into the establishment and maintenance of a normal microbial community in the human gastrointestinal tract, yet very little is known about how biotic interactions influence community dynamics in this system. Here, we use natural strains of Escherichia coli and a simplified model microbiota to demonstrate that the colonization process on the strain level can be context dependent, in the sense that the outcome of intra-specific competition may be determined by the composition of the background community. These results are consistent with previous models for competition between organisms where one competitor has adapted to low resource environments whereas the other is optimized for rapid reproduction when resources are abundant. The genomic profiles of E. coli strains representing these differing ecological strategies provide clues for deciphering the genetic underpinnings of niche adaptation within a single species. Our findings extend the role of ecological theory in understanding microbial systems and the conceptual toolbox for describing microbial community dynamics. There are few, if any, concrete examples of context-dependent competition on a single trophic level. However, this phenomenon can have potentially dramatic effects on which bacteria will successfully establish and persist in the gastrointestinal system, and the principle should be equally applicable to other microbial ecosystems.     

盐渍海带盐中可培养嗜盐古菌多样性、胞外酶活及拮抗作用探究

盐渍海带盐是一种高盐环境,其中可能生存有嗜盐微生物,如嗜盐古菌。嗜盐古菌是一类生活于高盐环境的极端环境微生物。为了探究盐渍海带盐中嗜盐微生物的物种多样性,筛查分离了菌株的几种常见胞外功能酶活性和拮抗活性。采用纯培养技术,从盐渍海带盐样品中分离培养嗜盐微生物,并对其16S rRNA基因进行扩增和测序;基于16S rRNA基因序列的相似度分析,确定分离菌株在属级水平的分类地位;依据种属信息,挑选代表菌株,进行胞外常见功能酶活性和拮抗作用测定。从盐渍海带盐样品中分离到来自Haloarcula(盐盒菌属)、Halorubrum(盐红菌属)、Halarchaeum、Halobacterium(盐杆菌属)、Halococcus(盐球菌属)、Halolamina(盐薄片形菌属)和Haloplanus(盐扁平菌属)等7个属的131株嗜盐古菌;检测到产胞外蛋白酶菌株1株,产酯酶菌2株,产明胶酶菌7株,产氧化酶菌1株和产触菌酶5株;此外,筛选到6株具有拮抗活性的菌株,其中来自盐红菌属菌株Halorubrum sp. ZSA68较其他菌株生长快,产抑菌活性物质快,并显示出较强的抑菌活性和较广的抑菌谱,初步推...     

Resistance to Gonorrhea Possibly Mediated by Bacterial Interference

Two men with no prior history of urethritis failed to develop gonorrhea after sexual exposures to women with genital gonococcal infection. Usual methods of prophylaxis, such as antibiotics or condoms, were not employed. The aerobic bacterial flora of these men's urethras consisted of several bacteria, some of which inhibited the in vitro growth of Neisseria gonorrhoeae. The hypothesis is suggested that bacterial interference may have played a role in protecting these men from gonorrhea.