Ecological Strategy of Bacteria: Specific Nature of the Problem

An attempt is made to sum up the results of the many years of using the conception of ecological strategy in bacterial ecology. Taking into account the specificities of microorganisms and their natural selection and the coevolution of microorganisms within evolving microbial communities, an inference is derived that the ecological strategy of most bacteria is the sum of a number of particular canonical strategies, some of which are common to higher organisms. It is proposed to call these particular strategies ecological tactics. The author considers this review to be a basis for a discussion.     

The life strategy and self-regulation mechanisms of populations of the causative agents of sapronoses (exemplified by Pseudomonas pseudomallei)

The strategy of the selection (life) of P. pseudomallei has been defined as C-competitiveness, combining the advantages of the limited (r and K) types of the ecological strategies of microorganisms and ensuring their good capacity of survival in soil biota. The self-regulation mechanisms of P. pseudomallei populations in the environment are determined by the type of their strategy of selection, which also determines the place of this species among other organisms inhabiting the soil. C-competitiveness of P. pseudomallei permits the realization of the self-support of its populations under changing conditions of their habitat, in particular in vivo.     

Ecological Strategies of Soil Microbial Communities under Plants of Meadow Ecosystems

Dominant growth strategies of soil microbial communities of mown and unmown meadows were assessed with respect to the constants of saturation and maximal specific growth rate of microorganisms. The microbial community of mown-meadow soil was characterized by a greater biomass and activity due to prevalence of microorganisms with the r strategy, compared to the microbial community of unmown-meadow soil. In contrast to nonrhizosphere soil, rhizosphere soil was dominated by rapidly growing microorganisms with the r strategy. The dependence of the dominant ecological strategy of the rhizosphere microbial community on the vegetation stage of plants has been traced. Study of the effect of plant species on the growth strategies of rhizosphere microorganisms showed that the features of the K strategy are more pronounced in the following rhizosphere microbial communities of grasses at the same growth stage: r strategy–Bromopsis inermis L.–Poa pratensis L., P. compressa L.–Dactylis glomerata L.–Festuca pratensisL.–K strategy. In the absence of limitation by climatic factors, the growth strategies of rhizosphere microorganisms are determined by the competition between microorganisms and plants for nutrients.     

Marine microorganisms as a source of bioactive agents

Several ecological factors of the marine environment were used in developing a strategy for discovering useful bioactive agents from marine microorganisms. By consideration of sea water requirements, production and degradation of marine polymers, and plasmid content, several novel anti-malarial antibiotics, anti-tumor polysaccharides, glucan-degrading enzymes, and aminoglycoside antibiotics were found.     

Exclusion of generalist pathogens in multihost communities

Knowing how to control a pathogen that infects more than one host species is of increasing importance because the incidence of such infections grows with continuing environmental change. Of concern are infections transmitted from wildlife to humans or livestock. To determine which options are available to control a pathogen in these circumstances, we analyze the pathogen invasion matrix for the multihost susceptible-infected-susceptible model. We highlight the importance of both community structure and the column sum or row sum index, an indicator of both force of infection and community stability. We derive a set of guidelines for constructing culling strategies and suggest a hybrid strategy that has the advantages of both the bottom-up and the top-down approaches, which we study in some detail. The analysis holds for an arbitrary number of host species, enabling the analysis of large-scale ecological systems and systems with spatial dimensions. We test the robustness of our methods by making two changes in the structure of the underlying dynamic model, adding direct competition and introducing frequency-dependent infection transmission. In particular, we show that the introduction of an additional host can eliminate the pathogen rather than eliminate the resident host. The discussion is illustrated with a reference to bovine tuberculosis.     

The soil metagenome--a rich resource for the discovery of novel natural products

Soil microorganisms have been the most valuable source of natural products, providing industrially important antibiotics and biocatalysts. But, of late, the discovery rate of novel biomolecules using traditional cultivation techniques has been extremely low, as most soil microorganisms cannot be cultured in this way. The development of novel cultivation-dependent and molecular cultivation-independent approaches has paved the way for a new era of product recovery from soil microorganisms. In particular, gene-mining based on the construction and screening of complex libraries derived from the soil metagenome provides opportunities to fully explore and exploit the enormous genetic and metabolic diversity of soil microorganisms. This strategy has already resulted in the isolation of novel biocatalysts and bioactive molecules.     

全球变化背景下内蒙古草原土壤微生物多样性维持机制研究进展

全球变化对人类环境的影响是近几十年世界广泛关注的热点之一。内蒙古草原不仅是我国重要的牲畜和饲料生产基地, 而且有着不可替代的生态系统功能。土壤微生物是地球上多样性最高的生物类群, 在驱动碳氮循环等多种生态系统过程中发挥着至关重要的作用。由于研究技术的限制和群落结构复杂等原因, 土壤微生物生态学研究还处于描述性阶段, 理论研究还很缺乏。鉴于此, 利用分子生物学技术尤其是新一代测序技术, 从理论层面上系统地研究全球变化背景下我国北方草地微生物多样性的维持机制具有重要意义。本文在比较各种环境变化对土壤微生物群落的相对影响的基础上, 分析全球变化对微生物多样性影响的物理化学和生态学机制, 并对未来内蒙古草原微生物多样性的重点研究领域进行了展望, 包括: (1)加强全球变化多因素综合研究; (2)加强微生物多样性维持的生态学机制的研究; (3)加强地上与地下多样性关联机制的研究; (4)加强全球大尺度多生态系统的整合研究。     

Hydrophobic properties of gram-negative rods colonizing upper respiratory tract of healthy people

The cell surface hydrophobicity is one of the non specific factors of adhesion influencing the ability of microorganisms to colonize nasopharynx. The aim of this paper was to evaluate via salt aggregation test (SAT) the cell surface hydrophobicity of 150 strains of gram-negative rods isolated from the throat or/and nasal specimens of healthy people. It has been found that among the nonfermenting rods hydrophobic strains were predominant. In contrast, the isolates of Enterobacteriaceae family were characterized by the distinctive features of the cell surface within particular genera or even species. The obtained results show that, despite differences in cell surface hydrophobicity, numerous species of gram-negative rods have the ability to colonize the mucous membrane of upper respiratory tract. This suggests that the cell surface hydrophobicity is rather a feature of species or genus, but it is not related to the ecological niche of microorganisms in human body.     

Novel clades of soil biphenyl degraders revealed by integrating isotope probing,multi-omics,and single-cell analyses

Most microorganisms in the biosphere remain uncultured and poorly characterized. Although the surge in genome sequences has enabled insights into the genetic and metabolic properties of uncultured microorganisms, their physiology and ecological roles cannot be determined without direct probing of their activities in natural habitats. Here we employed an experimental framework coupling genome reconstruction and activity assays to characterize the largely uncultured microorganisms responsible for aerobic biodegradation of biphenyl as a proxy for a large class of environmental pollutants, polychlorinated biphenyls. We used ¹³C-labeled biphenyl in contaminated soils and traced the flow of pollutant-derived carbon into active cells using single-cell analyses and protein–stable isotope probing. The detection of ¹³C-enriched proteins linked biphenyl biodegradation to the uncultured Alphaproteobacteria clade {"type":"entrez-protein","attrs":{"text":"UBA11222","term_id":"2096922005"}}UBA11222, which we found to host a distinctive biphenyl dioxygenase gene widely retrieved from contaminated environments. The same approach indicated the capacity of Azoarcus species to oxidize biphenyl and suggested similar metabolic abilities for species of Rugosibacter. Biphenyl oxidation would thus represent formerly unrecognized ecological functions of both genera. The quantitative role of these microorganisms in pollutant degradation was resolved using single-cell-based uptake measurements. Our strategy advances our understanding of microbially mediated biodegradation processes and has general application potential for elucidating the ecological roles of uncultured microorganisms in their natural habitats.Subject terms: Microbial ecology, Biogeochemistry, Biogeochemistry, Soil microbiology, Biogeochemistry     

Natural roles of biosurfactants

Microorganisms produce a variety of surface-active agents (or surfactants). These can be divided into low-molecular-weight molecules that lower surface and interfacial tensions efficiently and high-molecular-weight polymers that bind tightly to surfaces. These surfactants, produced by a wide variety of microorganisms, have very different chemical structures and surface properties. It is therefore reasonable to assume that different groups of biosurfactants have different natural roles in the growth of the producing microorganisms. Moreover, as their chemical structures and surface properties are so different, each emulsifier probably provides advantages in a particular ecological niche. Several bioemulsifiers have antibacterial or antifungal activities. Other bioemulsifiers enhance the growth of bacteria on hydrophobic water-insoluble substrates by increasing their bioavailability, presumably by increasing their surface area, desorbing them from surfaces and increasing their apparent solubility. Bioemulsifiers also play an important role in regulating the attachment–detachment of microorganisms to and from surfaces. In addition, emulsifiers are involved in bacterial pathogenesis, quorum sensing and biofilm formation. Recent experiments indicate that a high-molecular-weight bioemulsifier that coats the bacterial surface can be transferred horizontally to other bacteria, thereby changing their surface properties and interactions with the environment.     

Significance of microbial interactions in control of microbial ecosystems

A microbial ecosystem represents a delicately balanced population of microorganisms each interacting with and influencing the other members of the population. An understanding of the nature and effects of these interactions is essential to improving the performance of these ecologies, which are important, in such diverse processes as biological waste treatment procedures, water pollution abatement, industrial fermentations, human or animal digestives processes and in soil. There are several types of mocrobial interactions, such as commensalism, inhibition, food competition, predation, parasitism, and synergism, which either singly or in combination may influence the functioning of the microbial ecology. To understand interactions, it is necessary to perform a detailed study of the physiology of the individual predominating microorganisms to establish their requirements with respect to such environmental factors as nutrients, temperature, pH, oxidation-reduction potential, removal of waste products, or toxic materials which may be involved in control processes and to determine how these factors affect their capabilities. The sum total of this information will indicate the possible interactions between the microorganisms and will form the basis for conducting experiments either in the laboratory or with mathematical models. Such experiments will lead to an understanding of microbial activities and to the formulation of control measures, often using an alteration of the environmental factors for regulation of the microbial ecologies. Extensive research remains to be done on the microbial interact inns in obtain the desired, precise control of these ecological processes.     

Transbiome invasions of femtoplankton

The results of ecological and phylogenetic studies of femtoplankton, the smallest size fraction of plankton formed by viruses and ultramicrobacteria (UMB), are overviewed to shed light on the problem of transbiome invasions by microbes. Phylogenetic lineages of viruses and UMB are shown to be associated with particular biomes, thus indicating infrequent transbiome transitions in the microbial world. An alternative hypothesis of widespread cross-colonization events requires a deeper analysis of the factors that form the barrier between biomes and are responsible for the adaptation of microorganisms to different environments.     

小城镇土地利用变化的生态效应分析

采用系统生态学方法,尤其是应用了Simpson生物多样性指数法,前后相隔10年为时间跨度,对小城镇发展典型地区浙江省绍兴县某镇土地利用变化导致的生态效应进行了初步定量分析与研究.结果表明,由于土地使用功能的改变,导致了以绿色植物为计数的Simpson指数增加近2倍,而以土壤微生物为参照的工业和居住用地的Simpson指数均高于农业用地,反映该小城镇发展过程中生物多样性明显降低,并出现了局部气候的恶化(表现为镇区内年平均气温上升,而年平均相对湿度下降)等不良生态效应.     

Microbial communities of ancient seeds derived from permanently frozen Pleistocene deposits

Microbial communities from the surface of ancient seeds of higher plants and embedding frozen material dated to the late Pleistocene (formed about 30 thousand years ago) were studied by various methods: scanning electron microscopy, epifluorescence microscopy, and inoculation of nutrient media, followed by identification of isolated cultures. Both prokaryotic and eukaryotic microorganisms were found on the surface of ancient seeds. The total quantity of bacterial cells determined by direct counting and dilution plating (CFU) for the samples of ancient seeds exceeded the value in the embedding frozen material by one to two orders of magnitude. This pattern was not maintained for mycelial fungi; their quantity in the embedding material was also rather high. A significant difference was revealed between the microbial communities of ancient seeds and embedding frozen material. These findings suggest that ancient plant seeds are a particular ecological niche for microorganisms existing in permafrost and require individual detailed study.     

Effect of new antimicrobial agents on the ecological balance of human microflora

The human normal microflora is relatively stable at each ecological habitat under normal circumstances and acts as a barrier against colonization by potentially pathogenic microorganisms and against overgrowth of already present opportunistic microorganisms. Administration of antimicrobial agents causes disturbances in the ecological balance between the host and the normal microflora. The risk of emergence and spread of resistant strains between patients and dissemination of resistant determinants between microorganisms is reduced if colonization resistance is not disturbed by antimicrobial agents. In this article, the potential ecological effects of administration of new antimicrobial agents on the intestinal and oropharyngeal microflora are summarized. The review is based on clinical studies published during the past 10 years.     

单细胞稳定同位素标记技术在固氮微生物中的应用研究

生物固氮是指固氮微生物将大气中氮气还原为生物可利用氨的过程,是环境中新氮的主要来源,调控初级生产力并影响氮储库的收支平衡。由于环境中大部分固氮微生物不可纯培养,不依赖培养且具有高空间分辨率水平的单细胞技术,成为研究固氮微生物的有力手段。~(15)N_2稳定同位素标记技术,以微生物对~(15)N的同化量或速率为依据,是表征微生物固氮活性的最直接手段。本文对~(15)N_2稳定同位素标记结合两种单细胞技术,即纳米二次离子质谱(Nano SIMS)和单细胞拉曼光谱,用于固氮微生物研究的最新进展进行了综述,内容包括揭示环境中高活性固氮微生物、空间分布、与其他生物的共生关系、细胞生理状态等,并进一步对近期发展的基于单细胞拉曼光谱的固氮微生物研究进行了展望。     

水圈微生物：推动地球重要元素循环的隐形巨人

正生活在水圈环境中的微生物数量巨大、遗传与代谢方式极为多样,它们驱动着地球上重要元素的循环。水圈微生物研究已经成为生命科学与地球科学的研究热点。国家自然科学基金委员会于2017年启动了"水圈微生物驱动地球元素循环的机制"重大研究计划(简称"水圈微生物"计划)。"水圈微生物"计划拟选择典型水圈生境,通过多学科交叉研究,借助新技术、新方法,揭示水圈微生物在物种、群落和生态水平驱动碳氮硫循环的机制及其环境响应,     

Application of FISH technology for microbiological analysis: current state and prospects

In order to identify and quantify the microorganisms present in a certain ecosystem, it has become necessary to develop molecular methods avoiding cultivation, which allows to characterize only the countable part of the microorganisms in the sample, therefore losing the information related to the microbial component which presents a vitality condition, although it cannot duplicate in culture medium. In this context, one of the most used techniques is fluorescence in situ hybridization (FISH) with ribosomal RNA targeted oligonucleotide probes. Owing to its speed and sensitivity, this technique is considered a powerful tool for phylogenetic, ecological, diagnostic and environmental studies in microbiology. Through the use of species-specific probes, it is possible to identify different microorganisms in complex microbial communities, thus providing a solid support to the understanding of inter-species interaction. The knowledge of the composition and distribution of microorganisms in natural habitats can be interesting for ecological reasons in microbial ecology, and for safety and technological aspects in food microbiology. Methodological aspects, use of different probes and applications of FISH to microbial ecosystems are presented in this review.     

Ecological role of energy taxis in microorganisms

Motile microorganisms rapidly respond to changes in various physico-chemical gradients by directing their motility to more favorable surroundings. Energy generation is one of the most important parameters for the survival of microorganisms in their environment. Therefore it is not surprising that microorganisms are able to monitor changes in the cellular energy generating processes. The signal for this behavioral response, which is called energy taxis, originates within the electron transport system. By coupling energy metabolism and behavior, energy taxis is fine-tuned to the environment a cell finds itself in and allows efficient adaptation to changing conditions that affect cellular energy levels. Thus, energy taxis provides cells with a versatile sensory system that enables them to navigate to niches where energy generation is optimized. This behavior is likely to govern vertical species stratification and the active migration of motile cells in response to shifting gradients of electron donors and/or acceptors which are observed within microbial mats, sediments and soil pores. Energy taxis has been characterized in several species and might be widespread in the microbial world. Genome sequencing revealed that many microorganisms from aquatic and soil environments possess large numbers of chemoreceptors and are likely to be capable of energy taxis. In contrast, species that have a fewer number of chemoreceptors are often found in specific, confined environments, where relatively constant environmental conditions are expected. Future studies focusing on characterizing behavioral responses in species that are adapted to diverse environmental conditions should unravel the molecular mechanisms underlying sensory behavior in general and energy taxis in particular. Such knowledge is critical to a better understanding of the ecological role of energy taxis.     

松材线虫与伴生微生物的生态关系

松材线虫是重要的外来有害生物,造成松树大量死亡,带来严重的经济损失和生态破坏.松材线虫与伴生微生物存在密切的生态关系.本文综述了松材线虫伴生微生物的种类及其在松材线虫繁殖和致病过程中的重要生态作用,从微生态系统角度对松材线虫病进行探讨.伴生真菌能为松材线虫提供食物,维持松材线虫次生侵染循环,提高分散型第三龄幼虫在种群中的比例,利于松材线虫侵染扩散;伴生细菌能够提高松材线虫致病性,促进其繁殖,并菌有助于松材线虫降解松萜类物质,从而提高松材线虫的适应性.