Rare but active taxa contribute to community dynamics of benthic biofilms in glacier‐fed streams

Glaciers harbour diverse microorganisms, which upon ice melt can be released downstream. In glacier‐fed streams microorganisms can attach to stones or sediments to form benthic biofilms. We used 454‐pyrosequencing to explore the bulk (16S rDNA) and putatively active (16S rRNA) microbial communities of stone and sediment biofilms across 26 glacier‐fed streams. We found differences in community composition between bulk and active communities among streams and a stronger congruence between biofilm types. Relative abundances of rRNA and rDNA were positively correlated across different taxa and taxonomic levels, but at lower taxonomic levels, the higher abundance in either the active or the bulk communities became more apparent. Here, environmental variables played a minor role in structuring active communities. However, we found a large number of rare taxa with higher relative abundances in rRNA compared with rDNA. This suggests that rare taxa contribute disproportionately to microbial community dynamics in glacier‐fed streams. Our findings propose that high community turnover, where taxa repeatedly enter and leave the ‘seed bank’, contributes to the maintenance of microbial biodiversity in harsh ecosystems with continuous environmental perturbations, such as glacier‐fed streams.     

Chemical and Ultrastructural Characterization of High Arctic Cryptoendolithic Habitats

Cryptoendolithic habitats in the Canadian high Arctic are host to a diverse assemblage of microorganisms including cyanobacteria, algae, fungi and heterotrophic bacteria. Communities grow as biofilms attached to mineral surfaces as well as within the open void spaces between grains and in many cases produce extracellular polysaccharides in response to the extreme environmental conditions. In situ observations of the cryptoendolithic habitat as well as ultrastructural examination of microorganisms show that this EPS provides a substrate for accumulation of allochthonous clay particles that enter the system by winds and rain. The lack of evidence for biomineralization within this habitat contrasts with similar environments in the Antarctic Dry Valleys, a consequence of warmer temperatures and wetter conditions that increase erosion rates and subsequent habitat destruction, effectively limiting the time possible for biomineralization by living microorganisms as well as the formation of biosignatures or microfossils.     

种子微生物生态学研究进展

植物种子微生物生态学是研究与种子相联合的微生物的组成﹑功能﹑演替、它们之间关系及其与宿主之间相互关系的科学。种子中蕴含着丰富的微生物资源,它们对种子以及植物的健康具有重要的影响。不同种类植物种子联合的微生物群落由于受到种子本身及外界环境因素的影响而有所差异。论述了种子微生物生态学的概念、主要研究方法、种子微生物生态系统中的微生物种类、相关影响因素,以及种子微生物生态学研究的发展方向。种子微生物生态学的研究对生产实践有重要意义,同时也将丰富种子生物学的内容,对种子科学的发展起到促进作用。     

微生物种子包衣的应用与研究进展

种子包衣是一种高效、新兴的种子处理技术。该技术将外源性材料与种子紧密结合,从而提高种子性能,最终提高作物产量和品质。植物有益微生物(plant beneficial microorganisms, PBM)是指能够促进植物养分吸收、增强其对生物和非生物胁迫的耐受力,并促进植物生长或减少农业化学投入的微生物。因此,PBM可以作为一种微生物种子包衣剂。微生物种子包衣作为一种能够显著提高作物产量、经济效益和农业系统的可持续性发展的革新性技术,因其生态安全性和社会经济效益被认为是传统农业技术有前途的替代品。本文综述了微生物种子包衣技术及其在作物生产中的应用,并对其局限性和不一致性进行讨论。     

Performance of carrot and onion seed primed with beneficial microorganisms in glasshouse and field trials

Beneficial microorganisms (Clonostachys rosea IK726, Pseudomonas chlororaphis MA342, Pseudomonas fluorescens CHA0, Trichoderma harzianum T22 and Trichoderma viride S17a) were successfully applied to carrot and onion seed during a commercial drum priming process. Applied microorganisms were recovered above the target of at least 1 × 10⁵ cfu g⁻¹ seed following subsequent application of pesticides to the seed according to standard commercial practices of film-coating carrot and pelletting onion seed. Two glasshouse experiments consistently showed that priming improved emergence of carrot seed and that C. rosea IK726 further improved emergence time. Priming improved emergence of onion seed in one glasshouse experiment, but had an unexpected negative effect on emergence in the second experiment, possibly due to the proliferation of an unidentified indigenous microorganism during priming, becoming deleterious in high numbers. In this experiment, the application of beneficial microorganisms during priming negated this effect and significantly improved emergence. For each crop, a series of field trials was also carried out over three years, at two different sites each year. Although some positive effects of different seed treatments were seen on emergence or yield in individual field trials, no consistent effects were found for primed or microorganism-treated seed across all sites and years. However, a combined analysis of data for all years and sites indicated that pesticide application did consistently improve emergence and yield for both carrot and onion. This is the first comprehensive study assessing glasshouse and field performance of carrot and onion seed primed with beneficial microorganisms during a commercial process of drum priming in the UK.     

The effects of re-use of polyethylene glycol priming osmotica upon the development of microbial populations and germination of leeks and carrots

Three batches of leek seeds were osmotically primed successively in the same polyethylene glycol solution in a bubble column at a seed concentration of 100 g/litre for seven days at 15°C. Three batches of carrot seeds were similarly primed in a separate solution for six days at 15°C. The concentration of microorganisms in the solutions increased rapidly during priming of the first seed batch for both seed types, but increases during priming of the second and third batches were small. The seeds were the main source of the microorganisms; priming reduced the numbers of colonies of filamentous fungi and increased those of bacteria and yeasts. The priming treatments improved the percentage germination of the three seed batches of primed carrots and reduced the mean time to germination in both species and the mean time to emergence in compost. Percentage emergence was not affected by priming except in the third batch of primed carrot seed. The presence of large numbers of microorganisms in the priming solutions did not greatly affect seed performance when the same osmoticum was used three times with leeks and twice with carrots. Priming did not affect the number of abnormal seedlings.     

Genetic aspects of toxic chemical degradation

All naturally occurring molecules are continuously being recycled in nature, constantly being synthesized, and constantly being degraded. Synthetic molecules on the other hand, often are unable to enter nature's recycling scheme because organisms that have an ability to degrade these xenobiotic compounds simply do not exist. Moreover, many synthetic chemicals are not only recalcitrant to biodegradation, but also are toxic and therefore can cause significant pollution problems even at very low concentrations. The chemical industry will continue to produce an evergrowing number of molecules, even though severe environmental problems have resulted from synthetic molecules already produced. We must find a means of bringing synthetic molecules back into nature's recycling systems if we are to preserve the environment. Biotechnology, through the genetic manipulation of microorganisms, provides a means of accomplishing this goal.     

Biodegradation of halogenated organic compounds.

In this review we discuss the degradation of chlorinated hydrocarbons by microorganisms, emphasizing the physiological, biochemical, and genetic basis of the biodegradation of aliphatic, aromatic, and polycyclic compounds. Many environmentally important xenobiotics are halogenated, especially chlorinated. These compounds are manufactured and used as pesticides, plasticizers, paint and printing-ink components, adhesives, flame retardants, hydraulic and heat transfer fluids, refrigerants, solvents, additives for cutting oils, and textile auxiliaries. The hazardous chemicals enter the environment through production, commercial application, and waste. As a result of bioaccumulation in the food chain and groundwater contamination, they pose public health problems because many of them are toxic, mutagenic, or carcinogenic. Although synthetic chemicals are usually recalcitrant to biodegradation, microorganisms have evolved an extensive range of enzymes, pathways, and control mechanisms that are responsible for catabolism of a wide variety of such compounds. Thus, such biological degradation can be exploited to alleviate environmental pollution problems. The pathways by which a given compound is degraded are determined by the physical, chemical, and microbiological aspects of a particular environment. By understanding the genetic basis of catabolism of xenobiotics, it is possible to improve the efficacy of naturally occurring microorganisms or construct new microorganisms capable of degrading pollutants in soil and aquatic environments more efficiently. Recently a number of genes whose enzyme products have a broader substrate specificity for the degradation of aromatic compounds have been cloned and attempts have been made to construct gene cassettes or synthetic operons comprising these degradative genes. Such gene cassettes or operons can be transferred into suitable microbial hosts for extending and custom designing the pathways for rapid degradation of recalcitrant compounds. Recent developments in designing recombinant microorganisms and hybrid metabolic pathways are discussed.     

植物种子内生细菌组的研究进展

种子是种子植物的繁殖器官,也是多种有益微生物和病原菌的传递载体。种子微生物与植物的生长发育、健康程度、品质及产量等密切相关。随着微生物生态学和微生物组学技术的发展,国内外有关植物微生物组的研究突飞猛进,尤其植物微生态相关的根际微生物组和叶际微生物组的研究已经成为焦点和热点。相比之下,对植物种子内生微生物组的研究还尚未引起足够的重视。细菌是种子内生微生物的主要类群,本文将重点从种子内生细菌的类群组成、生物学功能、传播途径和核心微生物组四个方面对近年来的研究进展进行概括总结,剖析当前种子内生微生物组研究领域亟待解决的问题以及未来的研究方向与思路。     

New concepts for rapid yeast settling. I. Flocculation with an inert powder

A novel technique for settling microorganisms has been described. The technique involves adding a dense, inert powder to a suspension of microorganisms under conditions where flocculation of the microorganism with the inert poweder occurs. The flocs formed are small and relatively dense and settle rapidly. Suspensions of Saccharomyces cerevisiae yeast have been flocculated with several different inert seed materials achieving rapid settling and separations of up to 99.9%. Nickel powder was used as a seed material for most experiments described here, and iron sand showed promise as a cheaper seed for large-scale use. The degree of flocculation and cell separation obtained depended largely on the seed concentration and the components in solution. Temperature and pH had little effect. When the method was initially applied to a practical fermentation, flocculation was poor because of inhibiting compounds in the fermentation medium, but modification of the technique produced good flocculation in the medium.     

Temporal Stability of the Microbial Community in Sewage-Polluted Seawater Exposed to Natural Sunlight Cycles and Marine Microbiota

Billions of gallons of untreated wastewater enter the coastal ocean each year. Once sewage microorganisms are in the marine environment, they are exposed to environmental stressors, such as sunlight and predation. Previous research has investigated the fate of individual sewage microorganisms in seawater but not the entire sewage microbial community. The present study used next-generation sequencing (NGS) to examine how the microbial community in sewage-impacted seawater changes over 48 h when exposed to natural sunlight cycles and marine microbiota. We compared the results from microcosms composed of unfiltered seawater (containing naturally occurring marine microbiota) and filtered seawater (containing no marine microbiota) to investigate the effect of marine microbiota. We also compared the results from microcosms that were exposed to natural sunlight cycles with those from microcosms kept in the dark to investigate the effect of sunlight. The microbial community composition and the relative abundance of operational taxonomic units (OTUs) changed over 48 h in all microcosms. Exposure to sunlight had a significant effect on both community composition and OTU abundance. The effect of marine microbiota, however, was minimal. The proportion of sewage-derived microorganisms present in the microcosms decreased rapidly within 48 h, and the decrease was the most pronounced in the presence of both sunlight and marine microbiota, where the proportion decreased from 85% to 3% of the total microbial community. The results from this study demonstrate the strong effect that sunlight has on microbial community composition, as measured by NGS, and the importance of considering temporal effects in future applications of NGS to identify microbial pollution sources.     

环境微生物不依赖于培养的基因组学研究及应用

微生物在生物圈中分布广泛,并且在地球物质循环中占有重要地位,但是约99﹪的微生物目前还不能通过传统的培养方法得到纯培养物（即未培养微生物）,给这些未培养微生物的研究带来很大的困难。随着分子生物学的快速发展及其在微生物研究中的广泛运用,促进了以环境中未培养微生物为研究对象的新兴学科--环境基因组学的产生和发展。在不进行相关微生物培养分离的情况下,通过从环境样品中直接提取获得所有微小生物的全部遗传物质,并构建环境基因组文库;进一步利用功能基因组学研究策略,从文库中寻找编码产生新的有生物活性产物的基因;通过对系统发育相关锚定位点基因序列分析,从而确定特定生态环境体系中未培养微生物的种类结构组成及进化地位,并最终重建该体系中微生物群体的基本物质循环模式。此外,环境基因组学也可以在对未培养微生物生理生化特性深入了解的基础上,建立发展合适的培养体系,最终获得某些特定微生物的纯培养物。本文对环境基因组的构建及相关分析研究策略的进展进行了综述;同时介绍了其在微生物分类及生态学研究的应用。     

Seed number and environmental conditions do not explain seed size variability for the invasive herb Lupinus polyphyllus

Intraspecific variation in seed size may result from life-history constraints or environmental conditions experienced. This variation in seed size is likely to affect the early stage of invasion as seed size may contribute to the success or failure of population establishment. However, only a few studies have examined seed size variability and its causes and consequences for invaders so far. Using the invasive herb Lupinus polyphyllus, we estimated seed mass variation within and among 39 populations from two different geographic regions in a part of the invaded range. We empirically and experimentally evaluated the effect of seed number and environmental conditions (e.g. geographic region, habitat type, intraspecific competition) on seed mass, emergence and seedling performance. Seed mass varied threefold, being largest among individual plants within populations and smallest among populations. Variation in seed mass was neither related to seed number nor the environmental conditions examined, but led to differences in offspring performance, with emergence and seedling size increasing with seed mass. Larger L. polyphyllus seeds were better establishers than smaller seeds regardless of environmental conditions, indicating that the success of L. polyphyllus invasions is likely to depend positively on seed mass. Our results suggest that some plant species such as the invasive L. polyphyllus may not show an adaptive response in seed mass to resources or environmental conditions, which may partly explain their ability to colonise a range of different habitats.     

The role of abscisic acid in plant tissue culture: a review of recent progress

Abscisic acid (ABA) plays a significant role in the regulation of many physiological processes of plants. It is often used in tissue culture systems to promote somatic embryogenesis and enhance somatic embryo quality by increasing desiccation tolerance and preventing precocious germination. ABA is also employed to induce somatic embryos to enter a quiescent state in plant tissue culture systems and during synthetic seed research. Application of exogenous ABA improves in vitro conservation and the adaptive response of plant cell and tissues to various environmental stresses. ABA can act as anti-transpirant during the acclimatization of tissue culture-raised plantlets and reduces relative water loss of leaves during the ex vitro transfer of plantlets even when non-functional stomata are present. This review focuses on the possible roles of ABA in plant tissue culture and recent developments in this area.     

Microbial transformations of tin and tin compounds

Summary The use of organotins for agricultural and industrial purposes and in the marine environment has been increasing steadily for more than 20 years. Recently, reliable methodologies have been developed to permit quantification of individual molecular species of organotins in cultures and in the environment. Particular attention has been given to methyltins which can be formed abiotically and by microorganisms, and to tributyltins which are toxic components of effective antifouling paints. In the aquatic environment tin, tributyltins and other organotins accumulate in the surface microlayer, in sediments, and on suspended particulates. Tin compounds are toxic to a variety of organisms and some aquatic organisms can bioaccumulate them. When tin compounds, particularly di-or tri-substituted tins, enter an ecosystem, a portion of the microbial population is killed. Among the survivors are organisms which can methylate inorganic or organic tins, but the relative contribution of biotic and abiotic mechanisms is not clear. While many details of methylations and demethylations need to be worked out, it is clear that transformations of tins can influence the toxicity, volatility and mobility of tin in natural ecosystems. Tributyltins can be debutylated by microorganisms, and hydroxybutyl tins may be intermediates, as they are in mammalian systems. Little is known of the potential and probable microbial transformations of other economically important organotins, but the transformations should be studied for they may have industrial and environmental importance.     

Development of methods to measure virus inactivation in fresh waters

This study concerns the identification and correction of deficiencies in methods used to measure inactivation rates of enteric viruses seeded into environmental waters. It was found that viable microorganisms in an environmental water sample increased greatly after addition of small amounts of nutrients normally present in the unpurified seed virus preparation. This burst of microbial growth was not observed after seeding the water with purified virus. The use of radioactively labeled poliovirus revealed that high percentages of virus particles, sometimes greater than 99%, were lost through adherence to containers, especially in less turbid waters. This effect was partially overcome by the use of polypropylene containers and by the absence of movement during incubation. Adherence to containers clearly demonstrated the need for labeled viruses to monitor losses in this type of study. Loss of viral infectivity in samples found to occur during freezing was avoided by addition of broth. Finally, microbial contamination of the cell cultures during infectivity assays was overcome by the use of gentamicin and increased concentrations of penicillin, streptomycin, and amphotericin B.     

Persister cells, dormancy and infectious disease

Several well-recognized puzzles in microbiology have remained unsolved for decades. These include latent bacterial infections, unculturable microorganisms, persister cells and biofilm multidrug tolerance. Accumulating evidence suggests that these seemingly disparate phenomena result from the ability of bacteria to enter into a dormant (non-dividing) state. The molecular mechanisms that underlie the formation of dormant persister cells are now being unravelled and are the focus of this Review.     

Development of methods to measure virus inactivation in fresh waters.

This study concerns the identification and correction of deficiencies in methods used to measure inactivation rates of enteric viruses seeded into environmental waters. It was found that viable microorganisms in an environmental water sample increased greatly after addition of small amounts of nutrients normally present in the unpurified seed virus preparation. This burst of microbial growth was not observed after seeding the water with purified virus. The use of radioactively labeled poliovirus revealed that high percentages of virus particles, sometimes greater than 99%, were lost through adherence to containers, especially in less turbid waters. This effect was partially overcome by the use of polypropylene containers and by the absence of movement during incubation. Adherence to containers clearly demonstrated the need for labeled viruses to monitor losses in this type of study. Loss of viral infectivity in samples found to occur during freezing was avoided by addition of broth. Finally, microbial contamination of the cell cultures during infectivity assays was overcome by the use of gentamicin and increased concentrations of penicillin, streptomycin, and amphotericin B.     

Functional aspects of mature seed coat of theCannaceae

Cannaceae seeds have been analysed regarding seed coat structure, germination and macromolecular composition of the seed coats. Data of several mass spectrometric techniques were combined with those of microscopic and histochemical techniques to acquire insight into the functions of the seed coat.Cannaceae seeds have an exotestal layer of Malpighian cells with a hydrophobic and a hydrophilic part. The hydrophobic part is mainly responsible for the impermeability of the seed and contains silica, callose, lignin as water repellent substances. Water can only enter the seed after a certain temperature-induced opening of an imbibition lid. During imbibition the hydrophilic part of the Malpighian cells swells and the seed coat ruptures due to differences in pressure in the upper and lower part of the Malpighian cells.     

Predicting changes in dormancy level in natural seed soil banks

The possibility of accurately predicting timing and extent of seedling emergence from natural seed soil banks has long been an objective of both ecologist and agriculturalist. However, as dormancy is a common attribute of many wild seed populations, we should first be able to predict dormancy changes if we intend to predict seedling emergence in the field. In this paper, we discuss the most relevant environmental factors affecting seed dormancy of natural seed soil banks, and present a conceptual framework as an attempt to understand how these factors affect seed-bank dormancy level. Based on this conceptual framework we show approaches that can be used to establish quantitative functional relationship between environmental factors regulating dormancy and changes in the seed-bank dormancy status. Finally, we briefly explain how we can utilize population-based threshold models as a framework to characterize and quantify changes in seed sensitivity to environmental factors as a consequence of dormancy loss and/or induction.