抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

KEGG(Kyoto Encyclopedia of Genes and Genomes)〔和文〕 (特集 ゲノム医学の現在と未来--基礎と臨床) -- (データベース)

Publisher Summary This chapter reviews the rates at which Coarse Woody Debris (CWD) is added and removed from ecosystems, the biomass found in streams and forests, and many functions that CWD serves. CWD is an important component of temperate stream and forest ecosystems and is added to the ecosystem by numerous mechanisms, including wind, fire, insect attack, pathogens, competition, and geomorphic processes. Many factors control the rate at which CWD decomposes, including temperature, moisture, the internal gas composition of CWD, substrate quality, the size of the CWD, and the types of organisms involved. The mass of CWD in an ecosystem ideally represents the balance between addition and loss. In reality, slow decomposition rates and erratic variations in input of CWD cause the CWD mass to deviate markedly from steady-state projections. Many differences correspond to forest type, with deciduous-dominated systems having generally lower biomass than conifer-dominated systems. Stream size also influences CWD mass in lotic ecosystems, while successional stage dramatically influences CWD mass in boat aquatic and terrestrial settings. This chapter reviews many of these functions and concludes that CWD is an important functional component of stream and forest ecosystems. Better scientific understanding of these functions and the natural factors influencing CWD dynamics should lead to more enlightened management practices.

Ecology of Coarse Woody Debris in Temperate Ecosystems

The BLOLOG redox technology based on tetrazolium dye reduction as an indicator of sole-carbon-source utilization was evaluated as a rapid, community-level method to characterize and classify heterotrophic microbial communities. Direct incubation of whole environmental samples (aquatic, soil, and rhizosphere) in BIOLOG plates containing 95 separate carbon sources produced community-dependent patterns of sole-carbon-source utilization. Principal-component analysis of color responses quantified from digitized images of plates revealed distinctive patterns among microbial habitats and spatial gradients within soil and estuarine sites. Correlation of the original carbon source variables to the principal components gives a functional basis to distinctions among communities. Intensive spatial and temporal analysis of microbial communities with this technique can produce ecologically relevant classifications of heterotrophic microbial communities.

Classification and characterization of heterotrophic microbial communities on the basis of patterns of community-level sole-carbon-source utilization.

Inputs of biologically fixed nitrogen derived from the symbiotic relationship between legumes and their root-nodule bacteria into terrestrial ecosystems amount to at least 70 million metric tons per year. It is obvious that this enormous quantity will need to be augmented as the world's population increases and as the natural resources that supply fertilizer nitrogen diminish. This objective will be achieved through the development of superior legume varieties, improvement in agronomic practice, and increased efficiency of the nitrogen fixation process itself by better management of the symbiotic relationship between plant and bacteria. This paper considers ways and means by which populations of root-nodule bacteria, established and introduced, can be manipulated ecologically, agronomically, edaphically and genetically to improve legume productivity and, as a consequence, soil fertility.

Manipulation of rhizobia microflora for improving legume productivity and soil fertility: a critical assessment

Root-deposited photosynthate (rhizodeposition) is an important source of readily available carbon (C) for microbes in the vicinity of growing roots. Plant nutrient availability is controlled, to a large extent, by the cycling of this and other organic materials through the soil microbial community. Currently, our understanding of microbial community dynamics associated with rhizodeposition is limited. We used a 13C pulse-chase labeling procedure to examine the incorporation of rhizodeposition into individual phospholipid fatty acids (PLFAs) in the bulk and rhizosphere soils of greenhouse-grown annual ryegrass (Lolium multiflorum Lam. var. Gulf). Labeling took place during a growth stage in transition between active root growth and rapid shoot growth on one set of plants (labeling period 1) and 9 days later during the rapid shoot growth stage on another set of plants (labeling period 2). Temporal differences in microbial community composition were more apparent than spatial differences, with a greater relative abundance of PLFAs from gram-positive organisms (i15:0 and a15:0) in the second labeling period. Although more abundant, gram-positive organisms appeared to be less actively utilizing rhizodeposited C in labeling period 2 than in labeling period 1. Gram-negative bacteria associated with the 16:1ω5 PLFA were more active in utilizing 13C-labeled rhizodeposits in the second labeling period than in the first labeling period. In both labeling periods, however, the fungal PLFA 18:2ω6,9 was the most highly labeled. These results demonstrate the effectiveness of using 13C labeling and PLFA analysis to examine the microbial dynamics associated with rhizosphere C cycling by focusing on the members actively involved.

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Microbial Community Dynamics Associated with Rhizosphere Carbon Flow

We investigated communities of denitrifying bacteria from adjacent meadow and forest soils. Our objectives were to explore spatial gradients in denitrifier communities from meadow to forest, examine whether community composition was related to ecological properties (such as vegetation type and process rates), and determine phylogenetic relationships among denitrifiers. nosZ, a key gene in the denitrification pathway for nitrous oxide reductase, served as a marker for denitrifying bacteria. Denitrifying enzyme activity (DEA) was measured as a proxy for function. Other variables, such as nitrification potential and soil C/N ratio, were also measured. Soil samples were taken along transects that spanned meadow-forest boundaries at two sites in the H. J. Andrews Experimental Forest in the Western Cascade Mountains of Oregon. Results indicated strong functional and structural community differences between the meadow and forest soils. Levels of DEA were an order of magnitude higher in the meadow soils. Denitrifying community composition was related to process rates and vegetation type as determined on the basis of multivariate analyses of nosZ terminal restriction fragment length polymorphism profiles. Denitrifier communities formed distinct groups according to vegetation type and site. Screening 225 nosZ clones yielded 47 unique denitrifying genotypes; the most dominant genotype occurred 31 times, and half the genotypes occurred once. Several dominant and less-dominant denitrifying genotypes were more characteristic of either meadow or forest soils. The majority of nosZ fragments sequenced from meadow or forest soils were most similar to nosZ from the Rhizobiaceae group in α-Proteobacteria species. Denitrifying community composition, as well as environmental factors, may contribute to the variability of denitrification rates in these systems.

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Community composition and functioning of denitrifying bacteria from adjacent meadow and forest soils.

Although no accurate information is available, it seems clear that world-wide production of legume inoculant is static or in decline. This is a paradoxical situation in a world where improved strategies for augmenting biological N2 fixation have the potential to contribute enormous returns in the quality and quantity of food for humans and domestic animals. Here we examine some of the reasons.

Peat or related materials of biological origin have been used as carries for legume inoculants for more than 90 yr. Little progress has been made with alternative carriers that might enhance the numerical quality of inoculants. The traditional means of delivery of inoculant into the soil is by seed inoculation. There are now other methods of delivery which are both practical and ecologically sound. The most efficient strategy for many situations would be to breed or select promiscuous lines of legume with enhanced capacity to fix N with populations of rhizobia resident in the soil. This strategy would bypass the act of legume inoculation. These and related matters are discussed in the paper.

Recent advances in inoculant technology and prospects for the future

Degradation of soil properties following deforestation and long-term soil cultivation may lead to decreases in soil microbial diversity and functional stability. In this study, we investigated the differences in the stability (resistance and resilience) of microbial community composition and enzyme activities in adjacent soils under either native tropical forest (FST) or in agricultural cropping use for 14 years (AGR). Mineral soil samples (0 to 5 cm) from both areas were incubated at 40°C, 50°C, 60°C, or 70°C for 15 min in order to successively reduce the microbial biomass. Three and 30 days after the heat shocks, fluorescein diacetate (FDA) hydrolysis, cellulase and laccase activities, and phospholipid-derived fatty acids-based microbial community composition were measured. Microbial biomass was reduced up to 25% in both soils 3 days after the heat shocks. The higher initial values of microbial biomass, enzyme activity, total and particulate soil organic carbon, and aggregate stability in the FST soil coincided with higher enzymatic stability after heat shocks. FDA hydrolysis activity was less affected (more resistance) and cellulase and laccase activities recovered more rapidly (more resilience) in the FST soil relative to the AGR counterpart. In the AGR soil, laccase activity did not show resilience to any heat shock level up to 30 days after the disturbance. Within each soil type, the microbial community composition did not differ between heat shock and control samples at day 3. However, at day 30, FST soil samples treated at 60°C and 70°C contained a microbial community significantly different from the control and with lower biomass regardless of high enzyme resilience. Results of this study show that deforestation followed by long-term cultivation changed microbial community composition and had differential effects on microbial functional stability. Both soils displayed similar resilience to FDA hydrolysis, a composite measure of a broad range of hydrolases, supporting the concept of high functional redundancy in soil microbial communities. In contrast, the resilience of the substrate-specific activities of laccase and cellulase were lower in AGR soils, indicating a less diverse community of microorganisms capable of producing these enzymes and confirming that specific microbial functions are more sensitive measurements for evaluating change in the ecological stability of soils.

Peter J. Bottomley

Papers

Manipulation of rhizobia microflora for improving legume productivity and soil fertility: a critical assessment

Microbial Community Dynamics Associated with Rhizosphere Carbon Flow

Community composition and functioning of denitrifying bacteria from adjacent meadow and forest soils.

Recent advances in inoculant technology and prospects for the future

Comparative Resistance and Resilience of Soil Microbial Communities and Enzyme Activities in Adjacent Native Forest and Agricultural Soils