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。     

Size-dependent species richness: trends within plant communities and across latitude

We examine how species richness and species‐specific plant density (number of species and number of individuals per species, respectively) vary within community size frequency distributions and across latitude. Communities from Asia, Africa, Europe, and North, Central and South America were studied (60°4′N–41°4′S latitude) using the Gentry data base. Log–log linear stem size (diameter) frequency distributions were constructed for each community and the species richness and species‐specific plant density within each size class were determined for each frequency distribution. Species richness in the smallest stem size class correlated with the Y‐intercepts (β‐values) of the regression curves describing each log–log linear size distributions. Two extreme community types were identified (designated as type A and type B). Type A communities had steep size distributions (i.e. large β‐values), log–log linear species‐richness size distributions, low species‐specific plant density distributions, and a small size class (2–4 cm) containing the majority of all species but rarely conspecifics of the dominant tree species. Type B communities had shallow size distributions (i.e. small β‐values), more or less uniform (and low) size class species‐ richness and species‐specific density distributions and size‐dominant species resident in the smallest size class. Type A communities were absent in the higher latitudes but increased in number towards the equator, i.e. in the smallest size class, species richness increased (and species‐specific density decreased) towards the tropics. Based on our survey of type A and type B communities (and their intermediates), species richness evinces size‐dependent and latitudinal trends, i.e. species richness increased with decreasing body size and most species increasingly reside in the smallest plant size class towards the tropics. Across all latitudes, a trade‐off exists between the number of species and the number of individuals per species residing in the smaller size classes.     

Interspecies interactions within oral microbial communities.

While reductionism has greatly advanced microbiology in the past 400 years, assembly of smaller pieces just could not explain the whole! Modern microbiologists are learning "system thinking" and "holism." Such an approach is changing our understanding of microbial physiology and our ability to diagnose/treat microbial infections. This review uses oral microbial communities as a focal point to describe this new trend. With the common name "dental plaque," oral microbial communities are some of the most complex microbial floras in the human body, consisting of more than 700 different bacterial species. For a very long time, oral microbiologists endeavored to use reductionism to identify the key genes or key pathogens responsible for oral microbial pathogenesis. The limitations of reductionism forced scientists to begin adopting new strategies using emerging concepts such as interspecies interaction, microbial community, biofilms, polymicrobial disease, etc. These new research directions indicate that the whole is much more than the simple sum of its parts, since the interactions between different parts resulted in many new physiological functions which cannot be observed with individual components. This review describes some of these interesting interspecies-interaction scenarios.     

Priority effects can persist across floral generations in nectar microbial metacommunities

The order of species arrival can influence how species interact with one another and, consequently, which species may coexist in local communities. This phenomenon, called priority effects, has been observed in various types of communities, but it remains unclear whether priority effects persist over the long term spanning multiple generations of local communities in metacommunities. Focusing on bacteria and yeasts that colonize floral nectar of the sticky monkey flower, Mimulus aurantiacus, via hummingbirds and other flower‐visiting animals, we experimentally manipulated initial microbial dominance on plants (regarded as metacommunities) to examine whether its effects persisted across multiple generations of flowers (regarded as local microbial habitats). The experimental introduction of Neokomagataea (= Gluconobacter) bacteria and Metschnikowia yeasts into wild flowers showed that the effects of initial dominance were observable across multiple floral generations. Three weeks after introduction, corresponding approximately to three floral generations, Neokomagataea introduction led to exclusion of yeasts, whereas Metschnikowia introduction did not result in the exclusion of Neokomagataea. Our results suggest that, even when local habitats are ephemeral, priority effects may influence multiple generations of local communities within metacommunities.     

Temporal variability in soil microbial communities across land-use types

Although numerous studies have investigated changes in soil microbial communities across space, questions about the temporal variability in these communities and how this variability compares across soils have received far less attention. We collected soils on a monthly basis (May to November) from replicated plots representing three land-use types (conventional and reduced-input row crop agricultural plots and early successional grasslands) maintained at a research site in Michigan, USA. Using barcoded pyrosequencing of the 16S rRNA gene, we found that the agricultural and early successional land uses harbored unique soil bacterial communities that exhibited distinct temporal patterns. α-Diversity, the numbers of taxa or lineages, was significantly influenced by the sampling month with the temporal variability in α-diversity exceeding the variability between land-use types. In contrast, differences in community composition across land-use types were reasonably constant across the 7-month period, suggesting that the time of sampling is less important when assessing β-diversity patterns. Communities in the agricultural soils were most variable over time and the changes were significantly correlated with soil moisture and temperature. Temporal shifts in bacterial community composition within the successional grassland plots were less predictable and are likely a product of complex interactions between the soil environment and the more diverse plant community. Temporal variability needs to be carefully assessed when comparing microbial diversity across soil types and the temporal patterns in microbial community structure can not necessarily be generalized across land uses, even if those soils are exposed to the same climatic conditions.     

Rapid changes in plasticity across generations within an expanding cedar forest

We investigated the inter‐individual variation of phenotypic plasticity and its evolution across three generations within an expanding forest. Plasticity was assessed in situ from dendrochronological data as the response of radial growth to summer rainfall. A linear mixed model was used to account for spatial effects (environment and stand structure), temporal factors (stand dynamics) and the variation with age. Beyond these effects, our results reveal a significant inter‐individual variance of growth and plasticity within each generation. We also show that the mean values and variances of growth and plasticity changed significantly across generations, with different patterns for both traits. The possible environmental and genetic drivers of these changes are discussed. Contrasting with the trade‐off between stress tolerance and plasticity generally observed among populations, we detected a positive covariance at the individual level, which does not support the cost of plasticity hypothesis in this case.     

Environmental shaping of codon usage and functional adaptation across microbial communities

Microbial communities represent the largest portion of the Earth’s biomass. Metagenomics projects use high-throughput sequencing to survey these communities and shed light on genetic capabilities that enable microbes to inhabit every corner of the biosphere. Metagenome studies are generally based on (i) classifying and ranking functions of identified genes; and (ii) estimating the phyletic distribution of constituent microbial species. To understand microbial communities at the systems level, it is necessary to extend these studies beyond the species’ boundaries and capture higher levels of metabolic complexity. We evaluated 11 metagenome samples and demonstrated that microbes inhabiting the same ecological niche share common preferences for synonymous codons, regardless of their phylogeny. By exploring concepts of translational optimization through codon usage adaptation, we demonstrated that community-wide bias in codon usage can be used as a prediction tool for lifestyle-specific genes across the entire microbial community, effectively considering microbial communities as meta-genomes. These findings set up a ‘functional metagenomics’ platform for the identification of genes relevant for adaptations of entire microbial communities to environments. Our results provide valuable arguments in defining the concept of microbial species through the context of their interactions within the community.     

Trade-offs between flowering time,plant height,and seed size within and across 11 communities of a QingHai-Tibetan flora

Flowering timing is of fundamental biological importance for its tight association with pre-flower growth states and subsequent reproduction success. Here, we selected plant height and seed size to represent plant growth and reproduction states, respectively, and analyzed their associations with flowering time in 11 communities together representing a QingHai-Tibetan flora. Trait associations were examined using Pearson correlation analyses (TIPs) and phylogenetically independent contrasts (PICs) within individual communities and meta-analyses across all communities. The results of TIPs-based and PICs-based analyses were generally congruent, although fewer contrasts were significant with PICs, probably because of low statistical power. Overall, flowering time was negatively correlated with seed size and plant height (i.e., plants with larger seeds and stature started flowering earlier) in various woody communities, but correlations were neutral or positive in herbaceous communities. The seed size–flowering time relationship was negative for woody and herbaceous perennials but not for annual herbs in most communities. The relationship between plant height and flowering time was negative for woody but positive for herbaceous plants. Moreover, the lack of difference in time–size relationships between anemophilous and entomophilous plants suggests that pollination type may only be a secondary force in controlling flowering phenology. Our studies demonstrate that environmental conditions, community structure, and plant life history strategies may affect community flowering time singly or in combination.     

Large variability of bathypelagic microbial eukaryotic communities across the world's oceans

In this work, we study the diversity of bathypelagic microbial eukaryotes (0.8–20 μm) in the global ocean. Seawater samples from 3000 to 4000 m depth from 27 stations in the Atlantic, Pacific and Indian Oceans were analyzed by pyrosequencing the V4 region of the 18S ribosomal DNA. The relative abundance of the most abundant operational taxonomic units agreed with the results of a parallel metagenomic analysis, suggesting limited PCR biases in the tag approach. Although rarefaction curves for single stations were seldom saturated, the global analysis of all sequences together suggested an adequate recovery of bathypelagic diversity. Community composition presented a large variability among samples, which was poorly explained by linear geographic distance. In fact, the similarity between communities was better explained by water mass composition (26% of the variability) and the ratio in cell abundance between prokaryotes and microbial eukaryotes (21%). Deep diversity appeared dominated by four taxonomic groups (Collodaria, Chrysophytes, Basidiomycota and MALV-II) appearing in different proportions in each sample. Novel diversity amounted to 1% of the pyrotags and was lower than expected. Our study represents an essential step in the investigation of bathypelagic microbial eukaryotes, indicating dominating taxonomic groups and suggesting idiosyncratic assemblages in distinct oceanic regions.     

武夷山植被带土壤微生物量沿海拔梯度的变化

土壤微生物量是陆地生态系统碳循环的重要组成部分,在森林生态系统物质循环和能量转化中占有特别重要的地位.以武夷山常绿阔叶林(EBF)、针叶林(CF)、亚高山矮林(DF)和高山草甸(AM)为试验对象,研究了土壤微生物量沿海拔梯度的变化特征.结果表明:在0～10cm土壤层,随着海拔高度的增加,年平均土壤微生物量增大,AM的年平均土壤微生物量为4.07 g·kg-1,分别为DF、CF和EBF的2.06、3.21倍和3.91倍;AM的年平均土壤微生物量显著大于DF、CF和AM(p<0.01),DF的年平均土壤微生物量显著大于EBF、CF(p<0.05),EBF和CF的年平均土壤微生物量无显著性差异(p>0.05),10～25cm土壤层的年平均土壤微生物量的变化规律与上层基本一致;在0～10cm土壤层,不同海拔年平均土壤微生物量分别与土壤有机碳、全氮、全硫含量以及土壤湿度呈显著正相关(p<0.05),在10～25cm土壤层,不同海拔年平均土壤微生物量分别与土壤有机碳、全氮含量呈显著正相关(p<0.05).研究表明,武夷山亚热带森林年平均土壤微生物量随海拔高度升高而增加,土壤有机碳、全氮、全硫和土壤湿度可能是调控土壤微生物量沿海拔梯度变化的主要因子.     

Variable influences of soil and seed-associated bacterial communities on the assembly of seedling microbiomes

Plants grown in distinct soils typically harbor distinct microbial communities, but the degree of the soil microbiome influence on plant microbiome assembly remains largely undetermined. We also know that the microbes associated with seeds can contribute to the plant microbiome, but the magnitude of this contribution is likely variable. We quantified the influence of soil and seed microbiomes on the bacterial community composition of seedlings by independently inoculating seeds from a single cultivar of wheat (Triticum aestivum) with 219 unique soil slurries while holding other environmental factors constant, determining the composition of the seed, soil, and seedling bacterial communities via cultivation-independent methods. Soil bacterial communities exert a strong, but variable, influence on seedling bacterial community structure, with the extent of the soil bacterial contribution dependent on the soil in question. By testing a wide range of soils, we were able to show that the specific composition of the seedling microbiome is predictable from knowing which bacterial taxa are found in soil. Although the most ubiquitous taxa associated with the seedlings were seed derived, the contributions of the seed microbiome to the seedling microbiome were variable and dependent on soil bacterial community composition. Together this work improves our predictive understanding of how the plant microbiome assembles and how the seedling microbiome could be directly or indirectly manipulated to improve plant health.Subject terms: Microbial ecology, Next-generation sequencing, Microbial ecology     

Association between translation efficiency and horizontal gene transfer within microbial communities

Horizontal gene transfer (HGT) is a major force in microbial evolution. Previous studies have suggested that a variety of factors, including restricted recombination and toxicity of foreign gene products, may act as barriers to the successful integration of horizontally transferred genes. This study identifies an additional central barrier to HGT-the lack of co-adaptation between the codon usage of the transferred gene and the tRNA pool of the recipient organism. Analyzing the genomic sequences of more than 190 microorganisms and the HGT events that have occurred between them, we show that the number of genes that were horizontally transferred between organisms is positively correlated with the similarity between their tRNA pools. Those genes that are better adapted to the tRNA pools of the target genomes tend to undergo more frequent HGT. At the community (or environment) level, organisms that share a common ecological niche tend to have similar tRNA pools. These results remain significant after controlling for diverse ecological and evolutionary parameters. Our analysis demonstrates that there are bi-directional associations between the similarity in the tRNA pools of organisms and the number of HGT events occurring between them. Similar tRNA pools between a donor and a host tend to increase the probability that a horizontally acquired gene will become fixed in its new genome. Our results also suggest that frequent HGT may be a homogenizing force that increases the similarity in the tRNA pools of organisms within the same community.     

Endophytes inconsistently affect plant communities across Schedonorus arundinaceus hosts

Fungal endophytes in cool-season grasses may affect communities at multiple trophic levels. However, it is unclear whether community-scale endophyte effects arise due to the endophyte itself or as a result of unique, endophyte–host interactions. We used a long-term field experiment to test whether common-toxic (CT) and non-ergot alkaloid-producing (novel) endophytes in Schedonorus arundinaceus (tall fescue) forage cultivars consistently affect communities across tall fescue hosts. Tilled plots (2 × 2 m; Guelph, ON) were seeded with Georgia 5 and Jesup cultivars containing either the CT or AR542 (novel) endophyte and allowed to be re-colonized by plant species from the local propagule pool. Non-seeded control plots were included to assess effects of seeding the non-native grass. We assessed plant, invertebrate, soil moisture, and soil nutrient responses to the endophyte–cultivar treatments after four growing seasons. Seeding tall fescue affected plant species abundances, but not richness, and did not consistently alter soil moisture and nutrient pools. Endophyte identity in the tall fescue cultivars affected the communities, but effects were not consistent between cultivars. Within Georgia 5, the AR542 endophyte reduced tall fescue abundance and altered the invertebrate community relative to CT plots. Within Jesup, the AR542 endophyte reduced species evenness and decreased soil moisture during dry periods relative to CT plots. Endophyte effects were not consistent between cultivars, and it is probable that the community-scale effects of endophyte infection in tall fescue cultivars arise due to unique interactions between cultivar and endophyte.     

Belowground responses of bacterial communities to foliar SA application over four plant generations

Plant and Soil - Jacobaea vulgaris plants grow better in sterilized than in live soil. Foliar application of SA mitigates this negative effect of live soil on plant growth. To examine what causes...     

Functional trait variation of forest understorey plant communities across Europe

Global environmental changes are expected to alter the functional characteristics of understorey herb-layer communities, potentially affecting forest ecosystem functioning. However, little is known about what drives the variability of functional traits in forest understories. Here, we assessed the role of different environmental drivers in shaping the functional trait distribution of understorey herbs in fragmented forests across three spatial scales. We focused on 708 small, deciduous forest patches located in 16 agricultural landscape windows, spanning a 2500-km macroclimatic gradient across the temperate forest biome in Europe. We estimated the relative effect of patch-scale, landscape-scale and macroclimatic variables on the community mean and variation of plant height, specific leaf area and seed mass. Macroclimatic variables (monthly temperature and precipitation extremes) explained the largest proportion of variation in community trait means (on average 77% of the explained variation). In contrast, patch-scale factors dominated in explaining community trait variation (on average 68% of the explained variation). Notably, patch age, size and internal heterogeneity had a positive effect on the community-level variability. Landscape-scale variables explained only a minor part of the variation in both trait distribution properties. The variation explained by shared combinations of the variable groups was generally negligible. These findings highlight the importance of considering multiple spatial scales in predictions of environmental-change effects on the functionality of forest understories. We propose that forest management sustainability could benefit from conserving larger, historically continuous and internally heterogeneous forest patches to maximise ecosystem service diversity in rural landscapes.     

Diversity partitioning of moorland plant communities across hierarchical spatial scales

Understanding of the scaling of diversity is critical to enhance conservation strategies for subalpine moorland ecosystems vulnerable to future environmental changes. However, a paucity of quantitative data strongly limits such attempts. In this study, we used an additive diversity partitioning framework and quantified diversity patterns of moorland plant communities across hierarchical spatial scales, within- and between-sample transects, and between sites (corresponding to α and two levels of β diversity). Moorland sites markedly differed in size (range 1,000–160,000 m²) and were isolated from each other to varying extents within an inhospitable matrix (i.e., forests). We found that β diversity components were consistently higher, whereas the local α diversity component was consistently lower than expected by chance. We observed substantial contribution at the between-site scale to total species richness. By focusing on diversity patterns of moorland plant communities across multiple hierarchical spatial scales, we could thus identify the scale at which regional diversity is maximized. Our results suggest that protection of as many moorland sites as possible, to ensure beta diversity between sites, will effectively conserve total diversity. The use of additive diversity partitioning is a major step forward in providing strategies for the biological conservation of subalpine moorland ecosystems vulnerable to future environmental changes.     

The phylogenetic structure of primate communities: variation within and across continents

Aim Our goals are: (1) to examine the relative degree of phylogenetic overdispersion or clustering of species in communities relative to the entire species pool, (2) to test for across‐continent differences in community phylogenetic structure, and (3) to examine the relationship between species richness and community phylogenetic structure. Location Africa, Madagascar, Asia, and the Neotropics. Methods We collected species composition and phylogenetic data for over 100 primate communities. For each community, we calculated two measures of phylogenetic structure: (1) the net relatedness index (NRI), which provides a measure of the mean pairwise phylogenetic distance among all species in the community; and (2) the nearest taxon index (NTI), which measures the relative phylogenetic distance among the closest related species in a community. Both measures are relative to the phylogeny of the species in the entire species pool. The phylocom package uses a randomization procedure to test whether the NRI and NTI values are higher or lower than expected by chance alone. In addition, we used a Kruskal–Wallis test to examine differences in NRI and NTI across continents, and linear regressions to examine the relationship between species richness and NRI/NTI. Results We found that the majority of individual primate communities in Africa, Asia and the Neotropics consist of member species that are neither more nor less closely related than expected by chance alone. Yet 37% of Malagasy communities contain species that are more distantly related to each other compared with random species assemblages. Also, we found that the average degree of relatedness among species in communities differed significantly across continents, with African and Malagasy communities consisting of more distantly related taxa compared with communities in Asia and the Neotropics. Finally, we found a significant negative relationship between species richness and phylogenetic distance among species in African, Asian and Malagasy communities. The average relatedness among species in communities decreased as community size increased. Main conclusions The majority of individual primate communities exhibit a phylogenetic structure no different from random. Yet there are across‐continent differences in the phylogenetic structure of primate communities that probably result from the unique ecological and evolutionary characteristics exhibited by the endemic species found on each continent. In particular, the recent extinctions of numerous primates on Madagascar are likely responsible for the low levels of evolutionary relatedness among species in Malagasy communities.     

Consistent effects of nitrogen amendments on soil microbial communities and processes across biomes

Ecosystems worldwide are receiving increasing amounts of reactive nitrogen (N) via anthropogenic activities with the added N having potentially important impacts on microbially mediated belowground carbon dynamics. However, a comprehensive understanding of how elevated N availability affects soil microbial processes and community dynamics remains incomplete. The mechanisms responsible for the observed responses are poorly resolved and we do not know if soil microbial communities respond in a similar manner across ecosystems. We collected 28 soils from a broad range of ecosystems in North America, amended soils with inorganic N, and incubated the soils under controlled conditions for 1 year. Consistent across nearly all soils, N addition decreased microbial respiration rates, with an average decrease of 11% over the year‐long incubation, and decreased microbial biomass by 35%. High‐throughput pyrosequencing showed that N addition consistently altered bacterial community composition, increasing the relative abundance of Actinobacteria and Firmicutes, and decreasing the relative abundance of Acidobacteria and Verrucomicrobia. Further, N‐amended soils consistently had lower activities in a broad suite of extracellular enzymes and had decreased temperature sensitivity, suggesting a shift to the preferential decomposition of more labile C pools. The observed trends held across strong gradients in climate and soil characteristics, indicating that the soil microbial responses to N addition are likely controlled by similar wide‐spread mechanisms. Our results support the hypothesis that N addition depresses soil microbial activity by shifting the metabolic capabilities of soil bacterial communities, yielding communities that are less capable of decomposing more recalcitrant soil carbon pools and leading to a potential increase in soil carbon sequestration rates.