Silicates,Silicate Weathering,and Microbial Ecology

Mineralogy, microbial ecology, and mineral weathering in the subsurface are an intimately linked biogeochemical system. Although bacteria have been implicated indirectly in the accelerated weathering of minerals, it is not clear if this interaction is simply the coincidental result of microbial metabolism, or if it represents a specific strategy offering the colonizing bacteria a competitive ecological advantage. Our studies provide evidence that silicate weathering by bacteria is sometimes driven by the nutrient requirements of the microbial consortium, and therefore depends on the trace nutrient content of each aquifer mineral. This occurrence was observed in reducing groundwaters where carbon is abundant but phosphate is scarce; here, even resistant feldspars are weathered rapidly. This suggests that the progression of mineral weathering may be influenced by a mineral's nutritional potential, with microorganisms destroying only beneficial minerals. The rock record, therefore, may contain a remnant mineralogy that reflects early microbial destruction of biologically valuable minerals, leaving a residuum of "useless" minerals, where "value" depends on the organism, its metabolic needs, and the diagenetic environment. Conversely, the subsurface distribution of microorganisms may, in part, be controlled by the mineralogy and by the ability of an organism to take advantage of mineral-bound nutrients.     

碳源与氮源限制下细菌代谢调节研究进展

营养限制是微生物最常面临的环境胁迫之一。除了在营养物质匮乏的海洋、冰川、沙漠、深层地表等自然环境中,越来越多的人工环境也出现了营养限制的特征,例如各类微污染水体、提标改造的废水生物处理系统等。基质浓度极大地影响着包括细菌在内的许多微生物的生长、代谢及群落结构,最终导致其功能的改变。为了在营养限制条件下维持生存,微生物首先需感知营养供给的减少,其后通过基因、蛋白质、信号分子、代谢产物等对各代谢过程进行全局调控,最后改变基质亲和力、生长速率、运动能力、形态等以适应营养不足。胞内各种信号物质及其触发的响应是微生物应对营养胁迫的关键。本文分别梳理了以细菌为代表的微生物应对碳源、氮源限制时的关键信号物质、受体蛋白/调控过程及响应结果,并分析了碳氮限制响应过程中的相互作用,以期为极端环境微生物的认识、营养限制条件下微生物的应用,尤其是低浓度污染物生物处理、生物监测等领域提供理论基础。     

Nitrogen-Fixing Bacteria in Eucalyptus globulus Plantations

Eucalypt cultivation is an important economic activity worldwide. In Portugal, Eucalyptus globulus plantations account for one-third of the total forested area. The nutritional requirements of this crop have been well studied, and nitrogen (N) is one of the most important elements required for vegetal growth. N dynamics in soils are influenced by microorganisms, such as diazotrophic bacteria (DB) that are responsible for biological nitrogen fixation (BNF), so the aim of this study was to evaluate and identity the main groups of DB in E. globulus plantations. Samples of soil and root systems were collected in winter and summer from three different Portuguese regions (Penafiel, Gavião and Odemira). We observed that DB communities were affected by season, N fertilization and moisture. Furthermore Bradyrhizobium and Burkholderia were the most prevalent genera in these three regions. This is the first study describing the dynamic of these bacteria in E. globulus plantations, and these data will likely contribute to a better understanding of the nutritional requirements of eucalypt cultivation and associated organic matter turnover.     

Oligotrophic and copiotrophic marine bacteria—observations related to attachment

Abstract The initial selective adhesion of bacteria, expressing growth on solid media with low, intermediate, and high nutrient concentrations, to immersed glass surfaces in seawater was examined. Copiotrophic-type bacteria grown on high nutrient medium did not show a competitive advantage as primary colonizers. As compared to bacterial numbers in bulk water, relatively higher numbers of adhered oligotrophic-type bacteria, exhibiting growth on low-nutrient media, were found during the initial phase of adhesion. Higher numbers of copiotrophic rather than oligotrophic-type bacteria were seen in the bulk water. The majority of the adherent bacteria was irreversibly bound. Characteristics such as cell size, degree of cell surface hydrophobicity, and motility of bacterial isolates from the different nutrient concentrations did not account for the observed, possibly selective, adhesion. Although bacteria expressed nutritionally different requirements and adaptations at the time of sampling, successive reinoculations of a total of 161 isolates essentially failed to show the existence of obligacy of any given nutritional type of bacteria. The expression of different nutritional adaptations of bacteria in low-nutrient marine waters was also suggested by showing the inability of oligotrophic-like bacteria to possess starvation survival mechanisms such as those displayed by copiotrophs [3].     

A Novel Nutritional Predictor Links Microbial Fastidiousness with Lowered Ubiquity,Growth Rate,and Cooperativeness

Understanding microbial nutritional requirements is a key challenge in microbiology. Here we leverage the recent availability of thousands of automatically generated genome-scale metabolic models to develop a predictor of microbial minimal medium requirements, which we apply to thousands of species to study the relationship between their nutritional requirements and their ecological and genomic traits. We first show that nutritional requirements are more similar among species that co-habit many ecological niches. We then reveal three fundamental characteristics of microbial fastidiousness (i.e., complex and specific nutritional requirements): (1) more fastidious microorganisms tend to be more ecologically limited; (2) fastidiousness is positively associated with smaller genomes and smaller metabolic networks; and (3) more fastidious species grow more slowly and have less ability to cooperate with other species than more metabolically versatile organisms. These associations reflect the adaptation of fastidious microorganisms to unique niches with few cohabitating species. They also explain how non-fastidious species inhabit many ecological niches with high abundance rates. Taken together, these results advance our understanding microbial nutrition on a large scale, by presenting new nutrition-related associations that govern the distribution of microorganisms in nature.     

Coexistence of mixotrophs, autotrophs, and heterotrophs in planktonic microbial communities

We examine what circumstances allow the coexistence of microorganisms following different nutritional strategies, using a mathematical model. This model incorporates four nutritional types commonly found in planktonic ecosystems: (1) heterotrophic bacteria that consume dissolved organic matter and are prey to some of the other organisms; (2) heterotrophic zooflagellates that depend entirely on bacterial prey; (3) phototrophic algae that depend only on light and inorganic nutrients, and (4) mixotrophs that photosynthesize, take up inorganic nutrients, and consume bacterial prey. Mixotrophs are characterized by a parameter representing proportional mixing of phototrophic and heterotrophic nutritional strategies. Varying this parameter, a range of mixotrophic strategies was examined in hypothetical habitats differing in supplies of light, dissolved organic carbon, and dissolved inorganic phosphorous. Mixotrophs expressing a wide range of mixotrophic strategies persisted in model habitats with low phosphorus supply, but only those with a strategy that is mostly autotrophic persisted with high nutrient supply, and then only when light supply was also high. Organisms representing all four nutritional strategies were predicted to coexist in habitats with high phosphorus and light supplies. Coexistence involves predation by zooflagellates and mixotrophs balancing the high competitive ability of bacteria for phosphorus, the partitioning of partially overlapping resources between all populations, and possibly nonequlibrium dynamics. In most habitats, the strategy predicted to maximize the abundance of mixotrophs is to be mostly photosynthetic and supplement nutritional needs by consuming bacteria.     

Nitrogen-fixing bacteria alleviates competition between arbuscular mycorrhizal fungi and Solidago canadensis for nutrients under nitrogen limitation

丛枝菌根真菌(AMF)能与大多数陆生植物的根系形成共生体, 有助于宿主植物吸收养分。但营养胁迫下, 根系微生物对AMF与宿主植物间关系的影响少见报道。该研究假设: 在营养极度匮乏(如氮胁迫)环境下, AMF与宿主植物可能产生营养竞争, 而固氮菌的介入能够缓解两者对营养的竞争关系。为了验证这一假设, 该文探究了加拿大一枝黄花(Solidago canadensis)生长受限的氮浓度, 并在氮受限条件下检验了AMF、加拿大一枝黄花及固氮菌三者间的关系。结果表明: 低氮处理明显抑制了加拿大一枝黄花的地上生物量和总生物量, 尤其以0.025 mmol·L^-1 N的氨态氮对加拿大一枝黄花的负影响更甚。在此氮浓度下, 单独添加AMF总体上都进一步抑制了加拿大一枝黄花的生长, 而固氮菌的添加在一定程度上提高了氮受限条件下AMF对宿主的根部侵染率及宿主植物生物量。这表明固氮菌能够缓和氮受限条件下AMF和加拿大一枝黄花间的营养竞争关系。研究结果加深了对外来植物在极度营养胁迫环境下与多种微生物互作的入侵机制的理解。     

固氮菌缓解氮限制环境中丛枝菌根真菌对加拿大一枝黄花的营养竞争

丛枝菌根真菌(AMF)能与大多数陆生植物的根系形成共生体, 有助于宿主植物吸收养分。但营养胁迫下, 根系微生物对AMF与宿主植物间关系的影响少见报道。该研究假设: 在营养极度匮乏(如氮胁迫)环境下, AMF与宿主植物可能产生营养竞争, 而固氮菌的介入能够缓解两者对营养的竞争关系。为了验证这一假设, 该文探究了加拿大一枝黄花(Solidago canadensis)生长受限的氮浓度, 并在氮受限条件下检验了AMF、加拿大一枝黄花及固氮菌三者间的关系。结果表明: 低氮处理明显抑制了加拿大一枝黄花的地上生物量和总生物量, 尤其以0.025 mmol·L^-1 N的氨态氮对加拿大一枝黄花的负影响更甚。在此氮浓度下, 单独添加AMF总体上都进一步抑制了加拿大一枝黄花的生长, 而固氮菌的添加在一定程度上提高了氮受限条件下AMF对宿主的根部侵染率及宿主植物生物量。这表明固氮菌能够缓和氮受限条件下AMF和加拿大一枝黄花间的营养竞争关系。研究结果加深了对外来植物在极度营养胁迫环境下与多种微生物互作的入侵机制的理解。     

The nutritional consequences of foraging in primates: the relationship of nutrient intakes to nutrient requirements.

Many studies have examined the proportion of time that primates devote to feeding on various types of food, but relatively little is known about the intake rates associated with each food. However, the nutritional consequences of foraging can only be interpreted by comparing nutrient intakes with estimated nutrient requirements. The energy available to primates from ingested foods will depend both on the composition of the food and the extent to which various constituents, including fibre fractions, are digested. Both human and non-human primates have relatively low requirements for protein as a consequence of slow growth rates, small milk yields and relatively dilute milk. Because the nutrient demands of growth and reproduction are spread out over time, it appears that primates do not need to seek out foods of particularly high nutrient density, except perhaps during weaning. Although food selection in some species of primates appears to be correlated with the protein concentration of foods, it is unlikely that high dietary protein levels are required, at least when foods of balanced amino acid composition (such as leaves) are included in the diet.     

Achievements and perspectives to overcome the poor solvent resistance in acetone and butanol-producing microorganisms

Anaerobic bacteria such as the solventogenic clostridia can ferment a wide range of carbon sources (e.g., glucose, galactose, cellobiose, mannose, xylose, and arabinose) to produce carboxylic acids (acetic and butyric) and solvents such as acetone, butanol, and ethanol (ABE). The fermentation process typically proceeds in two phases (acidogenic and solventogenic) in a batch mode. Poor solvent resistance by the solventogenic clostridia and other fermenting microorganisms is a major limiting factor in the profitability of ABE production by fermentation. The toxic effect of solvents, especially butanol, limits the concentration of these solvents in the fermentation broth, limiting solvent yields and adding to the cost of solvent recovery from dilute solutions. The accepted dogma is that toxicity in the ABE fermentation is due to chaotropic effects of butanol on the cell membranes of the fermenting microorganisms, which poses a challenge for the biotechnological whole-cell bio-production of butanol. This mini-review is focused on (1) the effects of solvents on inhibition of cell metabolism (nutrient transport, ion transport, and energy metabolism); (2) cell membrane fluidity, death, and solvent tolerance associated with the ability of cells to tolerate high concentrations of solvents without significant loss of cell function; and (3) strategies for overcoming poor solvent resistance in acetone and butanol-producing microorganisms.     

Effects of drugs on nutrition

Drugs can increase nutrient requirements through various mechanisms and if these requirements are not met by dietary modification or provision of nutrient supplements, deficiency disease will result. Commoner nutritional effects of drugs consist in the insidious development of hypovitaminoses; other serious nutritional consequences of drug intake include growth impairment and, in the case of vitamin antagonists, poisoning through interference with metabolic processes dependent on the activity of vitamins or coenzymes. Interactions may exist between pharmacologic agents and nutrients with respect to their absorption, transport, metabolism and excretion. Single drugs can cause nutrient depletion by more than one mechanism and multiple drug regimens can deplete nutrient stores by a synergistic effect. Risks of drug-induced malnutrition with drugs increase with dose and duration of intake, marginal diets and co-existence of disease which increases requirements for the same nutrients that are affected by the drug.     

Isolation and typing methods for the epidemiologic investigation of thermotolerant campylobacters.

Thermotolerant campylobacters, C. jejuni, C. coli, C. lari and C. upsaliensis, are spiral bacteria involved in human enteric disease. The prevalence of these emerging pathogens, mainly C. jejuni and to a lesser extent C. coli, as etiologic agents of enteric disease in industrialized countries has increased over the last decade. The isolation and culture of these microorganisms is tedious and time-consuming mainly due to their complex nutritional and environmental requirements. This review discusses the techniques and methods developed for the selective isolation of thermotolerant campylobacters from food, environmental and clinical samples. Additionally, both traditional and newer molecular biology techniques applied to this group of thermophilic organisms for typing and taxonomic purposes are summarized.     

Digestion of dead bacteria by germ-free rats

In fecal smears from germ-free rats on ordinary diets, varying amounts of bacteria can be demonstrated by morphological methods. Due to the present knowledge of the fastidiousness of many intestinal microbes, the origin and status of viability of these bacteria are important. On a diet that was shown by microscopic examination not to contain any microorganisms, the feces of germ-free rats became free of bacteria within 1 week. When animals on such a diet were fed killed bacteria, all Gram-negative strains and certain strains of clostridia were digested, whereas nearly all Gram-positive strains were not. Such differences in digestibility could have both immunological and nutritional implications.     

The reduction of formaldehyde by bacterial cells

Formaldehyde is reduced to methyl alcohol by living cells of a creatinine-decomposing strain of Pseudomonas aeruginosa. The amount of HCHO taken up in 30 minutes by 3 x 10(10) cells of this organism is termed its reducing capacity. It was found to be 400 to 480 microg. The reaction takes place over wide pH and temperature ranges, is independent of the concentration of formaldehyde as long as the latter is not high enough to exert a toxic effect on the cell, but depends on the number of bacteria present. In cultures, 3 to 7 days old, there is a decline in reducing capacity without a proportionate decrease in the number of viable cells. On the other hand in cultures, 2 to 4 weeks old, the number of viable cells determines the amount of HCHO taken up. N/100 NaOH depresses the reducing capacity of the organism without affecting bacterial viability. Exposure of bacterial suspensions to temperatures of 46-52 degrees C. for 10 minutes causes a far more rapid decrease in the number of viable cells than in reducing capacity. Incubation of cellular suspensions with nutrient substances, which are able to support adequately the growth of the organism, for 30 minutes prior to the addition of HCHO, induces increases in reducing capacity. The uptake of HCHO by different microorganisms seems to be related to their gaseous and nutritional requirements. Strains of P. aeruginosa and P. fluorescens are predominantly aerobic, least fastidious in their nutritional requirements, most active against HCHO, and least susceptible to the action of aureomycin and chloromycetin. The potential significance of cellular reducing capacity is discussed.     

Microbial interactions involving sulfur bacteria: implications for the ecology and evolution of bacterial communities

A major goal of microbial ecology is the identification and characterization of those microorganisms which govern transformations in natural ecosystems. This review summarizes our present knowledge of microbial interactions in the natural sulfur cycle. Central to the discussion is the recent progress made in understanding the co-occurrence in natural ecosystems of sulfur bacteria with contrasting nutritional requirements and of the spatially very close associations of bacteria, the so-called phototrophic consortia (e.g. 'Chlorochromatium aggregatum' or 'Pelochromatium roseum'). In a similar way, microbial interactions may also be significant during microbial transformations other than the sulfur cycle in natural ecosystems, and could also explain the low culturability of bacteria from natural samples.     

Recycling of waste products in the induction of biofilms to remediate the visual impact generated by quartz mining

The present study was undertaken to investigate the viability of the use of two waste products, cheese whey and composted organic waste, as nutrient sources in the induction of biological films on quartz surfaces, with the final aim of reducing the visual impact generated by quartz mining. Experiments were carried in laboratory in which quartz samples were colonized with microorganisms (mainly cyanobacteria) forming biofilms. Previous studies have shown that a nutritional supplement must be added for good development of biofilms and, therefore, application of the two waste products was compared with application of the chemical nutrient medium on which these types of microorganisms are usually cultivated. Both products provided better results than the culture medium, in terms of the speed of formation of the biofilm, faster with the waste products, and the degree of cover of the brilliant white colour of the quartz, better masked by the biofilms formed when the waste products were applied as a darker biofilm was obtained.     

液质发酵食品中微生物群落及与乳酸菌间相互作用研究进展

液质发酵食品发酵过程中微生物组成复杂,复杂的微生物发酵体系会影响微生物的生长和代谢,继而改变微生物的群落结构与功能,最终影响液质发酵食品的品质.乳酸菌在食品发酵中对形成风味物质、提高营养价值、抑制腐败菌生长具有重要的作用.本文主要对近年来食醋、酱油和饮料酒等液质发酵食品中微生物群落及与乳酸菌间相互作用关系进行综述,了解...     

Effects of Interactions of Auxin-Producing Bacteria and Bacterial-Feeding Nematodes on Regulation of Peanut Growths

The influences of an IAA (indole-3-acetic acid)-producing bacterium (Bacillus megaterium) and two bacterial-feeding nematodes (Cephalobus sp. or Mesorhabditis sp.) on the growth of peanut (Arachis hypogaea L. cv. Haihua 1) after various durations of time were investigated in natural soils. The addition of bacteria and nematodes and incubation time all significantly affected plant growth, plant root growth, plant nutrient concentrations, soil nutrient concentrations, soil microorganisms and soil auxin concentration. The addition of nematodes caused greater increases in these indices than those of bacteria, while the addition of the combination of bacteria and nematodes caused further increases. After 42-day growth, the increases in soil respiration differed between the additions of two kinds of nematodes because of differences in their life strategies. The effects of the bacteria and nematodes on the nutrient and hormone concentrations were responsible for the increases in plant growth. These results indicate the potential for promoting plant growth via the addition of nematodes and bacteria to soil.     

Aciduric Proteobacteria isolated from pH 2.9 soil

Acidic (pH 2.9) soil was used as an inoculum to culture heterotrophic bacteria at pH values of 3-4. Four isolates were obtained; on the basis of 16S rDNA sequence, they were shown to be members of the beta- and gamma-Proteobacteria. The three isolates that were most closely related to Burkholderia spp. had simple nutritional requirements and could grow in glucose-mineral salts media; two of these used a broad array of organic substrates. The 16S rDNA sequence of the fourth isolate was most similar (96%) to Frateuria aurantia. The isolates were aciduric rather than acidophilic; their pH ranges for growth were approximately 3.5-8. Unlike many bacteria whose acid tolerance represents the capacity to survive acid exposure, these microorganisms carried out exponential growth at pH<4 and their growth rates at pH 3.9 ranged from 60 to 98% of those found at pH 7. The cell yields on glucose of two strains were identical at pH 4 and pH 7. The acidic soils appeared to contain a very diverse bacterial community as assessed by denaturing gradient gel electrophoresis fingerprinting of PCR amplicons of a portion of the 16S rDNA gene. Electronic supplementary material to this paper can be obtained by using the Springer LINK server located at http://dx.doi.org/10.1007/s00203-002-0427-1.     

新疆叶城两种主栽红枣土壤养分、微生物多样性与营养品质的比较分析

比较新疆叶城两种主栽红枣—骏枣与灰枣的土壤养分、微生物多样性和枣营养品质之间的差异,分析土壤养分、微生物与枣营养品质之间的相关性,从土壤养分、微生物角度研究枣营养品质的影响因素。通过化学分析法测定叶城骏枣与灰枣土壤养分、枣营养品质指标,高通量测序分析土壤微生物多样性,将土壤养分和微生物优势门属微生物进行冗余分析,研究枣营养品质指标与土壤养分、微生物功能类群的相关性。结果显示,新疆叶城两种主栽红枣土壤的全氮、速效氮、有机质含量显著不同;细菌群落变化的主要原因是土壤TN(全氮)值,真菌群落变化的主要原因是土壤AN(速效氮)值。两种主栽红枣土壤微生物多样性显示,骏枣土壤微生物在细菌水平上具有更高的物种丰富性和多样性,薄壁杆菌属(Gracilibacillus)、芽胞杆菌目(Bacillales)等溶磷微生物、固氮微生物等功能土壤微生物相对丰度和占比较高,差异显著;枣营养品质,尤其是不可溶膳食纤维、Fe、K、Zn的含量差异明显。而不可溶膳食纤维、K、蔗糖含量与TP(全磷)、OM(有机质)存在显著负相关;Fe、Zn含量与薄壁杆菌属、芽胞杆菌目等九类功能微生物存在显著正相关;Mg、可溶性糖、可溶性...