Seed bank characteristics of the Nymphoides peltata population in Lake Taihu.
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ABSTRACT:
SUBMITTER: Huang W
PROVIDER: S-EPMC4539606 | biostudies-other | 2015
REPOSITORIES: biostudies-other
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Project description:Using quantitative PCR, the abundances of six phytoplankton viruses DNA polymerase (polB) gene fragments were estimated in water samples collected from Lake Ontario, Canada over 26 months. Four of the polB fragments were most related to marine prasinoviruses, while the other two were most closely related to cultivated chloroviruses. Two Prasinovirus-related genes reached peak abundances of >1000?copies?ml(-1) and were considered 'high abundance', whereas the other two Prasinovirus-related genes peaked at abundances <1000?copies?ml(-1) and were considered 'low abundance'. Of the genes related to chloroviruses, one peaked at ca 1600?copies?ml(-1), whereas the other reached only ca 300?copies?ml(-1). Despite these differences in peak abundance, the abundances of all genes monitored were lowest during the late fall, winter and early spring; during these months the high abundance genes persisted at 100-1000?copies?ml(-1) while the low abundance Prasinovirus- and Chlorovirus-related genes persisted at fewer than ca 100?copies?ml(-1). Clone libraries of psbA genes from Lake Ontario revealed numerous Chlorella-like algae and two prasinophytes demonstrating the presence of candidate hosts for all types of viruses monitored. Our results corroborate recent metagenomic analyses that suggest that aquatic virus communities are composed of only a few abundant populations and many low abundance populations. Thus, we speculate that an ecologically important characteristic of phycodnavirus communities is seed-bank populations with members that can become numerically dominant when their host abundances reach appropriate levels.
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Project description:Dormancy is a bet-hedging strategy that allows organisms to persist through conditions that are suboptimal for growth and reproduction by entering a reversible state of reduced metabolic activity. Dormancy allows a population to maintain a reservoir of genetic and phenotypic diversity (i.e., a seed bank) that can contribute to the long-term survival of a population. This strategy can be potentially adaptive and has long been of interest to ecologists and evolutionary biologists. However, comparatively little is known about how dormancy influences the fundamental evolutionary forces of genetic drift, mutation, selection, recombination, and gene flow. Here, we investigate how seed banks affect the processes underpinning evolution by reviewing existing theory, implementing novel simulations, and determining how and when dormancy can influence evolution as a population genetic process. We extend our analysis to examine how seed banks can alter macroevolutionary processes, including rates of speciation and extinction. Through the lens of population genetic theory, we can understand the extent that seed banks influence the evolutionary dynamics of microorganisms as well as other taxa.
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Project description:Dormancy is an adaptation to living in fluctuating environments. It allows individuals to enter a reversible state of reduced metabolic activity when challenged by unfavorable conditions. Dormancy can also influence species interactions by providing organisms with a refuge from predators and parasites. Here we test the hypothesis that, by generating a seed bank of protected individuals, dormancy can modify the patterns and processes of antagonistic coevolution. We conducted a factorially designed experiment where we passaged a bacterial host (Bacillus subtilis) and its phage (SPO1) in the presence versus absence of a seed bank consisting of dormant endospores. Owing in part to the inability of phages to attach to spores, seed banks stabilized population dynamics and resulted in minimum host densities that were 30-fold higher compared to bacteria that were unable to engage in dormancy. By supplying a refuge to phage-sensitive strains, we show that seed banks retained phenotypic diversity that was otherwise lost to selection. Dormancy also stored genetic diversity. After characterizing allelic variation with pooled population sequencing, we found that seed banks retained twice as many host genes with mutations, whether phages were present or not. Based on mutational trajectories over the course of the experiment, we demonstrate that seed banks can dampen bacteria-phage coevolution. Not only does dormancy create structure and memory that buffers populations against environmental fluctuations, it also modifies species interactions in ways that can feed back onto the eco-evolutionary dynamics of microbial communities.
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Project description:Dispersal is an important factor in plant community assembly, but assembly studies seldom include information on actual dispersal into communities, i.e. the local propagule pool. The aim of this study was to determine which factors influence plant community assembly by focusing on two phases of the assembly process: the dispersal phase and the establishment phase. At 12 study sites in grazed ex-arable fields in Sweden the local plant community was determined and in a 100-m radius around the centre of each site, the regional species pool was measured. The local seed bank and the seed rain was explored to estimate the local propagule pool. Trait-based models were then applied to investigate if species traits (height, seed mass, clonal abilities, specific leaf area and dispersal method) and regional abundance influenced which species from the regional species pool, dispersed to the local community (dispersal phase) and which established (establishment phase). Filtering of species during the dispersal phase indicates the effect of seed limitation while filtering during the establishment phase indicates microsite limitation. On average 36% of the regional species pool dispersed to the local sites and of those 78% did establish. Species with enhanced dispersal abilities, e.g. higher regional abundance, smaller seeds and dispersed by cattle, were more likely to disperse to the sites than other species. At half the sites, dispersal was influenced by species height. Species establishment was however mainly unlinked to the traits included in this study. This study underlines the importance of seed limitation in local plant community assembly. It also suggests that without information on species dispersal into a site, it is difficult to distinguish between the influence of dispersal and establishment abilities, and thus seed and microsite limitation, as both can be linked to the same trait.
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Project description:AimsConsidered as an essential measure in the application of soil seed bank (SSB) projects, the mixing of substrate and surface soil can effectively improve soil condition. This research is aimed at exploring the diversity characteristics of SSBs and the relationships between SSBs and soil properties.MethodsCanonical correspondence analysis (CCA) was adopted to describe the ordination of SSBs on soil properties' gradients; multiple linear regressions were adopted to analyze the relationship between average growth height and soil properties, density and soil properties.ResultsExperimental groups of mixed substrate (the mixture of organic and inorganic substrates) had high diversity indexes, especially the Shannon-Wiener Index compared with those of single substrate. Meanwhile, a higher number of species and increased density were also noted in those of mixed substrate. The best test group, No.16, had the highest diversity indexes with a Shannon-Wiener of 1.898, Simpson of 0.633 and Pielou of 0.717, and also showed the highest density of 14000 germinants /m2 and 21 species. In addition, an improvement of the soil's chemical and physical properties was noted when the substrates were mixed. The mixed substrate of turfy soil and perlite could effectively enhance the soil moisture content, whilst a mixed substrate of rice husk carbon and vermiculite could improve the content of available potassium (AK) and phosphorus (AP) and strengthen soil fertility. The germinated plants also reflected obvious regularities of ordination on soil factor gradients. Three distinct cluster groups were presented, of which the first cluster was distributed in an area with a relatively higher content of AK and AP; the second cluster was distributed at places with relatively higher soil moisture content; and the third cluster of plants didn't show any obvious relationship with soil physical and chemical properties. Through CCA analysis, AK and AP were considered the most important soil factors to influence the SSB, which was illustrated in regression analysis with a high correlation coefficient when dependent values were growth height and density respectively. The linear regression equations with: growth height = 142.728 - 1.514TC + 30.218AP - 5.083TN + 10.839AK + 1.234mc; density = -68.216 - 4.609TC + 9.566AP - 35.492TN + 19.779AK - 1.591mc.were established by multiple linear regression.Conclusions(1) The mixed substrates showed a greater advantage for SSBs than single substrates, both in improving the number of species, density and diversity indexes. (2) The germinated plants reflected an obvious preference to different soil conditions, which different mixed substrates could improve accordingly. (3) AK, AP were important soil factors to influence SSBs, especially in the growth of plants and density.
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Project description:BackgroundFood banks are a common community-based response to household food insecurity in high-income countries. While the profile of their users and nature of the quality of food they provide have been researched, few studies have examined their operational characteristics to explore the accessibility of their services for people at risk of food insecurity. This study describes the nature of operations in a food bank network operating in Britain and explores how operations are associated with volume of use.MethodsData from The Trussell Trust Foodbank's network of 1145 distribution centres in 2015/16 on hours of operation, locations, and usage were combined with national statistics on Working Tax Credit claimants, disability and unemployment. Descriptive statistics focused on how often and when food banks were open within local authorities. The relationships between operational characteristics and volume of use were examined using regression analyses. Interaction terms tested how relationships between indicators of need with food bank usage changed with operational characteristics.ResultsWeekday operating hours were primarily between the hours of 10 a.m. and 2 p.m., but at any given hour no more than 20% of distribution centres were open, with fewer than 3% open after 4 pm. Where food banks had fewer distribution centres and operating hours, the volume of food bank usage was lower. In-work poverty, disability, and unemployment rates were all associated with higher volume of usage; however, the relationship between disability and food bank use was modified by the density of food banks and number of operating hours. Where food banks were less accessible, the relationship between disability and food bank use was diminished.ConclusionsThese findings suggest operational characteristics are an important part of access to food banks and raise questions about the ability of food banks to meet the needs of people at risk of food insecurity in Britain.
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Project description:ObjectiveWe aimed to understand the basic characteristics of the underground seed bank of Pinus densata forest and its relationship with aboveground vegetation, to provide a theoretical basis for vegetation restoration.MethodsThe study sites were Dongjiu Bridge (DJ), Linji Bridge (LZ), and Birishen Mountain Scenic Spot (RB) in Gongbu Nature Reserve, Southeast Tibet, China. Species composition and distribution pattern of the underground seed bank in P. densata forest were analyzed. Germination data and field investigations were used to examine the similarities between aboveground vegetation and underground seed banks, and their responses to the environment.ResultsThere were 47 species belonging to 27 families in the underground seed bank of the P. densata forest. Asteraceae, Rosaceae, Labiatae, and Poaceae were dominant, accounting for 40.4% of the total number of families. Underground seed density was 2,114, 1,952, and 1,141 seeds/m2 in DJ, LZ, and BR, respectively. The percentage of different life-forms in each sampling location was shown to be perennial herbs > shrubs > annual herbs > trees > subshrubs. The Shannon-Wiener diversity index, Margalef richness index, and Simpson's dominance index of each sample showed that species decreased with higher elevation, while the Pielou evenness index showed the opposite trend. Elevation, slope position, slope aspect, and slope were positively correlated with the Pielou evenness index and negatively correlated with the Shannon-Wiener diversity index, Margalef richness index, and Simpson's dominance index. The Sørensen index, comparing the similarity between the underground seed bank and aboveground vegetation of DJ, LZ, and BR was 0.46, 0.35, and 0.31, respectively.ConclusionThe underground seed bank of P. densata forest has high seed density and high species richness, but there was little similarity between aboveground vegetation and underground seed bank. Elevation and slope position had a great influence on the uniformity of species distribution.
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Project description:ddRAD sequence reads: Rapid evolution of multiple European plant species based on seed bank and current seed
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Project description:BACKGROUND:Genotyping by sequencing, a new low-cost, high-throughput sequencing technology was used to genotype 2,815 maize inbred accessions, preserved mostly at the National Plant Germplasm System in the USA. The collection includes inbred lines from breeding programs all over the world. RESULTS:The method produced 681,257 single-nucleotide polymorphism (SNP) markers distributed across the entire genome, with the ability to detect rare alleles at high confidence levels. More than half of the SNPs in the collection are rare. Although most rare alleles have been incorporated into public temperate breeding programs, only a modest amount of the available diversity is present in the commercial germplasm. Analysis of genetic distances shows population stratification, including a small number of large clusters centered on key lines. Nevertheless, an average fixation index of 0.06 indicates moderate differentiation between the three major maize subpopulations. Linkage disequilibrium (LD) decays very rapidly, but the extent of LD is highly dependent on the particular group of germplasm and region of the genome. The utility of these data for performing genome-wide association studies was tested with two simply inherited traits and one complex trait. We identified trait associations at SNPs very close to known candidate genes for kernel color, sweet corn, and flowering time; however, results suggest that more SNPs are needed to better explore the genetic architecture of complex traits. CONCLUSIONS:The genotypic information described here allows this publicly available panel to be exploited by researchers facing the challenges of sustainable agriculture through better knowledge of the nature of genetic diversity.
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Project description:Robust seasonal dynamics in microbial community composition have previously been observed in the English Channel L4 marine observatory. These could be explained either by seasonal changes in the taxa present at the L4 site, or by the continuous modulation of abundance of taxa within a persistent microbial community. To test these competing hypotheses, deep sequencing of 16S rRNA from one randomly selected time point to a depth of 10,729,927 reads was compared with an existing taxonomic survey data covering 6 years. When compared against the 6-year survey of 72 shallow sequenced time points, the deep sequenced time point maintained 95.4% of the combined shallow OTUs. Additionally, on average, 99.75%±0.06 (mean±s.d.) of the operational taxonomic units found in each shallow sequenced sample were also found in the single deep sequenced sample. This suggests that the vast majority of taxa identified in this ecosystem are always present, but just in different proportions that are predictable. Thus observed changes in community composition are actually variations in the relative abundance of taxa, not, as was previously believed, demonstrating extinction and recolonization of taxa in the ecosystem through time.
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