人体肠道宏基因组生物信息分析方法

最近5年来,微生物组与人体健康之间的微妙关系已成为全球研究热点,特别是基于高通量测序的宏基因组技术推动了这个领域的发展。然而宏基因组生物信息学分析往往是开展研究过程中的难点。本文对宏基因组生物信息常规分析方法进行了介绍。     

A CRISPR-based strategy for targeted sequencing in biodiversity science

Many applications in molecular ecology require the ability to match specific DNA sequences from single- or mixed-species samples with a diagnostic reference library. Widely used methods for DNA barcoding and metabarcoding employ PCR and amplicon sequencing to identify taxa based on target sequences, but the target-specific enrichment capabilities of CRISPR-Cas systems may offer advantages in some applications. We identified 54,837 CRISPR-Cas guide RNAs that may be useful for enriching chloroplast DNA across phylogenetically diverse plant species. We tested a subset of 17 guide RNAs in vitro to enrich plant DNA strands ranging in size from diagnostic DNA barcodes of 1,428 bp to entire chloroplast genomes of 121,284 bp. We used an Oxford Nanopore sequencer to evaluate sequencing success based on both single- and mixed-species samples, which yielded mean chloroplast sequence lengths of 2,530–11,367 bp, depending on the experiment. In comparison to mixed-species experiments, single-species experiments yielded more on-target sequence reads and greater mean pairwise identity between contigs and the plant species' reference genomes. But nevertheless, these mixed-species experiments yielded sufficient data to provide ≥48-fold increase in sequence length and better estimates of relative abundance for a commercially prepared mixture of plant species compared to DNA metabarcoding based on the chloroplast trnL-P6 marker. Prior work developed CRISPR-based enrichment protocols for long-read sequencing and our experiments pioneered its use for plant DNA barcoding and chloroplast assemblies that may have advantages over workflows that require PCR and short-read sequencing. Future work would benefit from continuing to develop in vitro and in silico methods for CRISPR-based analyses of mixed-species samples, especially when the appropriate reference genomes for contig assembly cannot be known a priori.     

高通量测序技术及其在表观遗传学上的应用

DNA测序技术是现代生命科学研究的重要工具之一,而高通量测序技术在全基因组的研究中发挥着越来越重要的作用。简要回溯DNA测序技术的产生与发展,着重从PCR扩增测序和单分子测序两个方面全面描述了高通量测序中众多代表性的技术及直接测序技术,并从DNA甲基化、组蛋白修饰、非编码RNA调控等方面阐述了高通量测序技术在表观遗传学上的运用。     

Epialleles in plant evolution

Heritable phenotypic differences caused by epigenetic modifications, rather than DNA sequence mutations, pose a challenge to our understanding of natural variation. Here, we review what is known about plant epialleles and the role of epigenetics in evolution.     

Current challenges in de novo plant genome sequencing and assembly

Genome sequencing is now affordable, but assembling plant genomes de novo remains challenging. We assess the state of the art of assembly and review the best practices for the community.     

植物群落和土壤理化性质对碧塔海湿地土壤细菌群落的影响

土壤微生物是湿地生态系统中土壤-植物系统生源要素迁移转化的引擎.探究湿地生态系统地上植物群落、土壤理化性质和空间结构与土壤细菌间的相互关系是维护湿地生态系统健康和稳定的关键.本研究运用双向指示种分析法(TWINSPAN)对碧塔海湿地采集的35个样方中的植物群落进行分类,并采用高通量测序技术对样方的表层土壤细菌进行测序,...     

Low phosphorus supply constrains plant responses to elevated CO2: A meta‐analysis

Phosphorus (P) is an essential macro‐nutrient required for plant metabolism and growth. Low P availability could potentially limit plant responses to elevated carbon dioxide (eCO₂), but consensus has yet to be reached on the extent of this limitation. Here, based on data from experiments that manipulated both CO₂ and P for young individuals of woody and non‐woody species, we present a meta‐analysis of P limitation impacts on plant growth, physiological, and morphological response to eCO₂. We show that low P availability attenuated plant photosynthetic response to eCO₂ by approximately one‐quarter, leading to a reduced, but still positive photosynthetic response to eCO₂ compared to those under high P availability. Furthermore, low P limited plant aboveground, belowground, and total biomass responses to eCO₂, by 14.7%, 14.3%, and 12.4%, respectively, equivalent to an approximate halving of the eCO₂ responses observed under high P availability. In comparison, low P availability did not significantly alter the eCO₂‐induced changes in plant tissue nutrient concentration, suggesting tissue nutrient flexibility is an important mechanism allowing biomass response to eCO₂ under low P availability. Low P significantly reduced the eCO₂‐induced increase in leaf area by 14.3%, mirroring the aboveground biomass response, but low P did not affect the eCO₂‐induced increase in root length. Woody plants exhibited stronger attenuation effect of low P on aboveground biomass response to eCO₂ than non‐woody plants, while plants with different mycorrhizal associations showed similar responses to low P and eCO₂ interaction. This meta‐analysis highlights crucial data gaps in capturing plant responses to eCO₂ and low P availability. Field‐based experiments with longer‐term exposure of both CO₂ and P manipulations are critically needed to provide ecosystem‐scale understanding. Taken together, our results provide a quantitative baseline to constrain model‐based hypotheses of plant responses to eCO₂ under P limitation, thereby improving projections of future global change impacts.     

Design of efficient simplified genomic DNA and bisulfite sequencing in large plant populations

The next generation sequencing enables generation of high resolution and high throughput data for structure sequence of any genome at a fast declining cost. This opens opportunity for population based genetic and genomic analyses. In many applications, whole genome sequencing or re-sequencing is unnecessary or prohibited by budget limits. The Reduced Representation Genome Sequencing (RRGS), which sequences only a small proportion of the genome of interest, has been proposed to deal with the situations. Several forms of RRGS are proposed and implemented in the literature. When applied to plant or crop species, the current RRGS protocols shared a key drawback that a significantly high proportion (up to 60%) of sequence reads to be generated may be of non-genomic origin but attributed to chloroplast DNA or rRNA genes, leaving an exceptional low efficiency of the sequencing experiment. We recommended and discussed here the design of optimized simplified genomic DNA and bisulfite sequencing strategies, which may greatly improves efficiency of the sequencing experiments by bringing down the presentation of the undesirable sequencing reads to less than 10% in the whole sequence reads. The optimized RAD-seq and RRBS-seq methods are potentially useful for sequence variant screening and genotyping in large plant/crop populations.     

Forest floor photosynthesis and respiration in a drained peatland forest in southern Finland

Background: Although forest floor forms a large biomass pool in forested peatlands, little is known about its role in ecosystem carbon (C) dynamics.

Aim: We aimed to quantify forest floor photosynthesis (P _FF) and respiration (R _FF) as a part of overall C dynamics in a drained peatland forest in southern Finland.

Methods: We measured net forest floor CO₂ exchange with closed chambers and reconstructed seasonal CO₂ exchange in the prevailing plant communities.

Results: The vegetation was a mosaic of plant communities that differed in CO₂ exchange dynamics. The reconstructed growing season P _FF was highest in the Sphagnum community and lowest in the feather moss communities. On the contrary, R _FF was highest in the feather moss communities and lowest in the Sphagnum community. CO₂ assimilated by the forest floor was 20–30% of the total CO₂ assimilated by the forest. The forest floor was a net CO₂ source to the atmosphere, because respiration from ground vegetation, tree roots and decomposition of soil organic matter exceeded the photosynthesis of ground vegetation.

Conclusions: Tree stand dominates C fluxes in drained peatland forests. However, forest floor vegetation can have a noticeable role in the C cycle of peatlands drained for forestry. Similarly to natural mires, Sphagnum moss-dominated communities were the most efficient assimilators of C.     

Epigenetic regulation of development and pathogenesis in fungal plant pathogens

Evidently, epigenetics is at forefront in explaining the mechanisms underlying the success of human pathogens and in the identification of pathogen‐induced modifications within host plants. However, there is a lack of studies highlighting the role of epigenetics in the modulation of the growth and pathogenicity of fungal plant pathogens. In this review, we attempt to highlight and discuss the role of epigenetics in the regulation of the growth and pathogenicity of fungal phytopathogens using Magnaporthe oryzae, a devastating fungal plant pathogen, as a model system. With the perspective of wide application in the understanding of the development, pathogenesis and control of other fungal pathogens, we attempt to provide a synthesized view of the epigenetic studies conducted on M. oryzae to date. First, we discuss the mechanisms of epigenetic modifications in M. oryzae and their impact on fungal development and pathogenicity. Second, we highlight the unexplored epigenetic mechanisms and areas of research that should be considered in the near future to construct a holistic view of epigenetic functioning in M. oryzae and other fungal plant pathogens. Importantly, the development of a complete understanding of the modulation of epigenetic regulation in fungal pathogens can help in the identification of target points to combat fungal pathogenesis.     

Ecosystem CO2 exchange and plant biomass in the littoral zone of a boreal eutrophic lake

• 1 In order to study the dynamics of primary production and decomposition in the lake littoral, an interface zone between the pelagial, the catchment and the atmosphere, we measured ecosystem/atmosphere carbon dioxide (CO₂) exchange in the littoral zone of an eutrophic boreal lake in Finland during two open water periods (1998–1999). We reconstructed the seasonal net CO₂ exchange and identified the key factors controlling CO₂ dynamics. The seasonal net ecosystem exchange (NEE) was related to the amount of carbon accumulated in plant biomass.
• 2 In the continuously inundated zones, spatial and temporal variation in the density of aerial shoots controlled CO₂ fluxes, but seasonal net exchange was in most cases close to zero. The lower flooded zone had a net CO₂ uptake of 1.8–6.2 mol m^?2 per open water period, but the upper flooded zone with the highest photosynthetic capacity and above‐ground plant biomass, had a net CO₂ loss of 1.1–7.1 mol m^?2 per open water period as a result of the high respiration rate. The excess of respiration can be explained by decomposition of organic matter produced on site in previous years or leached from the catchment.
• 3 Our results from the two study years suggest that changes in phenology and water level were the prime cause of the large interannual difference in NEE in the littoral zone. Thus, the littoral is a dynamic buffer and source for the load of allochthonous and autochthonous carbon to small lakes.

     

A hemiparasite in the forest understorey: photosynthetic performance and carbon balance of Melampyrum pratense

• Melampyrum pratense is an annual root‐hemiparasitic plant growing mostly in forest understorey, an environment with unstable light conditions. While photosynthetic responses of autotrophic plants to variable light conditions are in general well understood, light responses of root hemiparasites have not been investigated.
• We carried out gas exchange measurements (light response and photosynthetic induction curves) to assess the photosynthetic performance of M. pratense in spring and summer. These data and recorded light dynamics data were subsequently used to model carbon balance of the hemiparasite throughout the entire growth season.
• Summer leaves had significantly lower rates of saturated photosynthesis and dark respiration than spring leaves, a pattern expected to reflect the difference between sun‐ and shade‐adapted leaves. However, even the summer leaves of the hemiparasite exhibited a higher rate of light‐saturated photosynthesis than reported in non‐parasitic understorey herbs. This is likely related to its annual life history, rare among other understorey herbs. The carbon balance model considering photosynthetic induction still indicated insufficient autotrophic carbon gain for seed production in the summer months due to limited light availability and substantial carbon loss through dark respiration.
• The results point to potentially high importance of heterotrophic carbon acquisition in M. pratense, which could be of at least comparable importance as in other mixotrophic plants growing in forests – mistletoes and partial mycoheterotrophs. It is remarkable that despite apparent evolutionary pressure towards improved carbon acquisition from the host, M. pratense retains efficient photosynthesis and high transpiration rate, the ecophysiological traits typical of related root hemiparasites in the Orobanchaceae.

     

Carbon emission along a eutrophication gradient in temperate riverine wetlands: effect of primary productivity and plant community composition

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A meta-analysis of leaf gas exchange and nitrogen in trees grown under elevated carbon dioxide

The response of trees to rising atmospheric CO₂ concentration ([CO₂]) is of concern to forest ecologists and global carbon modellers and is the focus of an increasing body of research work. I review studies published up to May 1994, and several unpublished works, which reported at least one of the following: net CO₂ assimilation (A), stomatal conductance (g_s), leaf dark respiration (R_d) leaf nitrogen or specific leaf area (SLA) in woody plants grown at <400 μmol mol^?1 CO₂ or at 600–800 μmol mol^?1 CO₂. The resulting data from 41 species were categorized according to growth conditions (unstressed versus stressed), length of CO₂ exposure, pot size and exposure facility [growth chamber (GC), greenhouse (GH), or open-top chamber (OTC)] and interpreted using meta-analytic methods. Overall, A showed a large and significant increase at elevated [CO₂] but length of CO₂ exposure and the exposure facility were important modifiers of this response. Plants exposed for < 50 d had a significantly greater response, and those from GCs had a significantly lower response than plants from longer exposures or from OTC studies. Negative acclimation of A was significant and general among stressed plants, but in unstressed plants was influenced by length of CO₂ exposure, the exposure facility and/or pot size. Growth at elevated [CO₂] resulted in moderate reductions in gs in unstressed plants, but there was no significant effect of CO₂ on gs in stressed plants. Leaf dark respiration (mass or area basis) was reduced strongly by growth at high [CO₂] > while leaf N was reduced only when expressed on a mass basis. This review is the first meta-analysis of elevated CO₂ studies and provides statistical confirmation of several general responses of trees to elevated [CO₂]. It also highlights important areas of continued uncertainty in our understanding of these responses.     

A field study of the effects of elevated CO2 and plant species diversity on ecosystem-level gas exchange in a planted calcareous grassland

The relationship between plant species diversity and ecosystem CO₂ and water vapour fluxes was investigated for planted calcareous grassland communities composed of 5, 12, or 32 species assembled from the native plant species pool. These diversity manipulations were done in factorial combination with a CO₂ enrichment experiment in order to investigate the degree to which ecosystem responses to elevated CO₂ are altered by a loss of plant diversity. Ecosystem CO₂ and H₂O fluxes were measured over several 24-h periods during the 1994 and 1995 growing seasons. Ecosystem CO₂ assimilation on a ground area basis decreased with decreasing plant diversity in the first year and this was related to a decline in above-ground plant biomass. In the second year, however, CO₂ assimilation was not affected by diversity, and this corresponded to the disappearance of a diversity effect on above-ground biomass. Irrespective of diversity treatment, CO₂ assimilation on a ground area basis was linearly related to peak above-ground biomass in both years. Elevated CO₂ significantly increased ecosystem CO₂ assimilation in both years with no interaction between diversity and CO₂ treatment, and no corresponding increase in above-ground biomass. There were no significant effects of diversity on water vapour flux, which was measured only in the second year. There were indications of a small CO₂ effect on water vapour flux (3–9% lower at elevated CO₂ depending on the light level). Our findings suggest that decreasing plant species diversity may substantially decrease ecosystem CO₂ assimilation during the establishment of such planted calcareous grassland communities, but also suggest that this effect may not persist. In addition, we find no evidence that plant species diversity alters the response of ecosystem CO₂ assimilation to elevated CO₂.     

Responses of nitrogen metabolism in N-sufficient barley primary leaves to plant growth in elevated atmospheric carbon dioxide

Effects of atmospheric carbon dioxide enrichment on nitrogen metabolism were studied in barley primary leaves (Hordeum vulgare L. cv. Brant). Seedlings were grown in chambers under ambient (36 Pa) and elevated (100 Pa) carbon dioxide and were fertilized daily with complete nutrient solution providing 12 millimolar nitrate and 2.5 millimolar ammonium. Foliar nitrate and ammonium were 27% and 42% lower (P ≤ 0.01) in the elevated compared to ambient carbon dioxide treatments, respectively. Enhanced carbon dioxide affected leaf ammonium levels by inhibiting photorespiration. Diurnal variations of total nitrate were not observed in either treatment. Total and Mg²⁺inhibited nitrate reductase activities per gram fresh weight were slightly lower (P ≤ 0.01) in enhanced compared to ambient carbon dioxide between 8 and 15 DAS. Diurnal variations of total nitrate reductase activity in barley primary leaves were similar in either treatment except between 7 and 10 h of the photoperiod when enzyme activities were decreased (P ≤ 0.05) by carbon dioxide enrichment. Glutamate was similar and glutamine levels were increased by carbon dioxide enrichment between 8 and 13 DAS. However, both glutamate and glutamine were negatively impacted by elevated carbon dioxide when leaf yellowing was observed 15 and 17 DAS. The above findings showed that carbon dioxide enrichment produced only slight modifications in leaf nitrogen metabolism and that the chlorosis of barley primary leaves observed under enhanced carbon dioxide was probably not attributable to a nutritionally induced nitrogen limitation. This revised version was published online in June 2006 with corrections to the Cover Date.