scholarly journals Seed Banks Alter the Rate and Direction of Molecular Evolution in Bacillus subtilis

2021 ◽  
Author(s):  
William R. Shoemaker ◽  
Evgeniya Polezhaeva ◽  
Kenzie B. Givens ◽  
Jay T. Lennon
Keyword(s):  
Bacillus Subtilis ◽  
Molecular Evolution ◽  
Seed Bank ◽  
Negative Selection ◽  
Evolutionary Dynamics ◽  
Genetic Manipulation ◽  
Seed Banks ◽  
Rate Of Molecular Evolution ◽  
Over Time ◽  
Growth And Reproduction

Fluctuations in the availability of resources constrains the growth and reproduction of individuals, which in turn effects the evolution of their respective populations. Many organisms are able to respond to fluctuations by entering a reversible state of reduced metabolic activity, a phenomenon known as dormancy. This pool of dormant individuals (i.e., a seed bank) does not reproduce and is expected to act as an evolutionary buffer, though it is difficult to observe this effect directly over an extended evolutionary timescale. Through genetic manipulation, we analyze the molecular evolutionary dynamics of Bacillus subtilis populations in the presence and absence of a seed bank over 700 days. We find that the ability to enter a dormant state increases the accumulation of genetic diversity over time and alters the trajectory of mutations, findings that are recapitulated using simulations based on a simple mathematical model. While the ability to form a seed bank does not alter the degree of negative selection, we find that it consistently alters the direction of molecular evolution across genes. Together, these results show that the ability to form a seed bank affects the direction and rate of molecular evolution over an extended evolutionary timescale.

scholarly journals Evolution with a seed bank: the population genetic consequences of microbial dormancy

2017 ◽  
Author(s):  
WR Shoemaker ◽  
JT Lennon
Keyword(s):  
Seed Bank ◽  
Population Genetic ◽  
Evolutionary Dynamics ◽  
Phenotypic Diversity ◽  
Seed Banks ◽  
Hedging Strategy ◽  
Term Survival ◽  
Evolutionary Forces ◽  
Growth And Reproduction

ABSTRACTDormancy is a bet-hedging strategy that allows organisms to persist through conditions that are sub-optimal 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 microbial evolutionary dynamics.

scholarly journals The significance of the seed bank as a potential for the reestablishment of arable-land vegetation in a marginal cultivated landscape

Web Ecology ◽  
2001 ◽  
Vol 2 (1) ◽  
pp. 83-87 ◽  
Author(s):  
R. Waldhardt ◽  
K. Fuhr-Bossdorf ◽  
A. Otte
Keyword(s):  
Land Use ◽  
Seed Bank ◽  
Arable Land ◽  
Seed Banks ◽  
German Research Foundation ◽  
German Research ◽  
Arable Land Use ◽  
Over Time

Abstract. As part of the German Research Foundation (DFG) project “Land Use Concepts for Marginal Regions”, since 1997 we have made analyses of the seed bank of 22 cultivated allotments, as well as of 15 meadow/pasture and 16 fallow allotments on former arable land of the Lahn-Dill Highlands, a marginal cultivated landscape in Hesse, Germany. One aim of this study is to determine according to which dynamic laws the seed bank of arable-land weeds is depleted after cultivation is abandoned. Depending on the intensity of the arable land use, the seed banks of rankers and cambisols that are presently still cultivated contain up to 1 004 800 seeds of arable-land species capable of germination m−3. Soils that were last cultivated less than ten years ago have much lower seed densities, while the seed bank of arable-land species is largely exhausted after only ca. 20 yr. This points to an exponential depletion of the seed bank of arable-land species and their abundance over time. On the basis of the present results, <20 yr remain in the Lahn-Dill Highlands for the reestablishment of characteristic arable-land vegetation from the seed bank.

scholarly journals Molecular evolutionary dynamics of energy limited microorganisms

2021 ◽  
Author(s):  
William R. Shoemaker ◽  
Evgeniya Polezhaeva ◽  
Kenzie B. Givens ◽  
Jay T. Lennon
Keyword(s):  
Genetic Diversity ◽  
Molecular Evolution ◽  
Evolutionary Dynamics ◽  
Microbial Evolution ◽  
Gene Level ◽  
Rate Of Molecular Evolution ◽  
Energy Limitation ◽  
Low Levels ◽  
Periodic Exposure ◽  
Unique Ability

AbstractMicroorganisms have the unique ability to survive extended periods of time in environments with extremely low levels of exploitable energy. To determine the extent that energy limitation affects microbial evolution, we examined the molecular evolutionary dynamics of a phylogenetically diverse set of taxa over the course of 1,000-days. We found that periodic exposure to energy limitation affected the rate of molecular evolution, the accumulation of genetic diversity, and the rate of extinction. We then determined the degree that energy limitation affected the spectrum of mutations as well as the direction of evolution at the gene level. Our results suggest that the initial depletion of energy altered the direction and rate of molecular evolution within each taxon, though after the initial depletion the rate and direction did not substantially change. However, this consistent pattern became diminished when comparisons were performed across phylogenetically distant taxa, suggesting that while the dynamics of molecular evolution under energy limitation are highly generalizable across the microbial tree of life, the targets of adaptation are specific to a given taxon.

Effect of different treatments on the seed bank of grazed and ungrazed Baltic seashore meadows

1998 ◽  
Vol 76 (7) ◽  
pp. 1188-1197 ◽  
Author(s):  
Heli M. Jutila b. Erkkilä
Keyword(s):  
Seed Bank ◽  
Brackish Water ◽  
Salt Water ◽  
Tap Water ◽  
Cold Treatment ◽  
Abundant Species ◽  
Seed Banks ◽  
The West ◽  
Pesticide Treatment ◽  
Juncus Gerardii

Seed banks of two seashore meadows were studied on the west coast of Finland (latitude 61°30'-61°33'N, longitude 21°28'-21°41'E). Samples were taken in June to a depth of 10 cm in the geolittoral zone of the grazed and ungrazed transects. The grazed samples were halved lengthwise: one half was grown immediately, the other after cold treatment. One third of the all samples was treated as controls, one third was watered with brackish water, and one third was given a pesticide treatment. Altogether, 13 926 seedlings germinated and 25 species were identified (three annuals, two biennials, and the rest perennials). Most seedlings were perennial monocots, with Juncus gerardii Loisel. the most abundant species. The seed bank was significantly larger and richer in the ungrazed site than in the grazed site. Cold treatment reduced the number of germinating species and seedlings. In the grazed and non-cold-treated samples, the numbers of species and seedlings were highest in the pesticide treatment. In ungrazed samples there were no significant differences among treatments. After the cold treatment, the least number of species and seedlings was produced by the salt-water treatment. Changing brackish water to tap water led to a burst of germination, especially of J. gerardii. The seed bank of the upper geolittoral zone was richer than that of the middle geolittoral. The multivariate classification and ordination groupings are based on the abundances of J. gerardii and Glaux maritima L.; different treatments were not distinguishable. There was a low resemblance between the seed bank and the aboveground vegetation.Key words: seed bank, salinity, pesticide, seashore meadow, cold treatment, vegetation.

Seed production and seedling emergence of Giant Parramatta grass on the north coast of New South Wales

1996 ◽  
Vol 36 (3) ◽  
pp. 299 ◽  
Author(s):  
TS Andrews ◽  
RDB Whalley ◽  
CE Jones
Keyword(s):  
Seed Production ◽  
Seed Bank ◽  
New South ◽  
New South Wales ◽  
Seed Banks ◽  
North Coast ◽  
The North ◽  
South Wales ◽  
Seed Fall ◽  
The Impact

Inputs and losses from Giant Parramatta grass [GPG, Sporobolus indicus (L.) R. Br. var. major (Buse) Baaijens] soil seed banks were quantified on the North Coast of New South Wales. Monthly potential seed production and actual seed fall was estimated at Valla during 1991-92. Total potential production was >668 000 seeds/m2 for the season, while seed fall was >146000 seeds/m2. Seed fall >10000 seeds/m2.month was recorded from January until May, with further seed falls recorded in June and July. The impact of seed production on seed banks was assessed by estimating seed banks in the seed production quadrats before and after seed fall. Seed banks in 4 of the 6 sites decreased in year 2, although seed numbers at 1 damp site increased markedly. Defoliation from mid-December until February, April or June prevented seed production, reducing seed banks by 34% over 7 months. Seed banks in undefoliated plots increased by 3300 seeds/m2, although seed fall was estimated at >114 000 seeds/m2. Emergence of GPG seedlings from artificially established and naturally occurring, persistent seed banks was recorded for 3 years from bare and vegetated treatment plots. Sown seeds showed high levels of innate dormancy and only 4% of seeds emerged when sown immediately after collection. Longer storage of seeds after collection resulted in more seedlings emerging. Estimates of persistent seed banks ranged from 1650 to about 21260 seeds/m2. Most seedlings emerged in spring or autumn and this was correlated with rainfall but not with ambient temperatures. Rates of seed bank decline in both bare and vegetated treatment plots was estimated by fitting exponential decay curves to seed bank estimates. Assuming no further seed inputs, it was estimated that it would take about 3 and 5 years, respectively, for seed banks to decline to 150 seeds/m2 in bare and vegetated treatments.

scholarly journals Sociality and the Rate of Molecular Evolution

2005 ◽  
Vol 22 (6) ◽  
pp. 1393-1402 ◽  
Author(s):  
Lindell Bromham ◽  
Remko Leys
Keyword(s):  
Molecular Evolution ◽  
Rate Of Molecular Evolution

Temperature predicts the rate of molecular evolution in Australian Eugongylinae skinks

Evolution ◽  
2021 ◽  
Author(s):  
Jeremias Ivan ◽  
Craig Moritz ◽  
Sally Potter ◽  
Jason Bragg ◽  
Rust Turakulov ◽  
...  
Keyword(s):  
Molecular Evolution ◽  
Rate Of Molecular Evolution

scholarly journals Similarity between seed bank and herb layer in a natural deciduous temperate lowland forest

2011 ◽  
Vol 79 (2) ◽  
pp. 157-166 ◽  
Author(s):  
Maciej Wódkiewicz ◽  
Anna Justyna Kwiatkowska-Falińska
Keyword(s):  
Seed Bank ◽  
Soil Seed Bank ◽  
Similarity Index ◽  
Seed Banks ◽  
Herb Layer ◽  
Managed Forests ◽  
Lowland Forest ◽  
Soil Seed Banks ◽  
Dominance Structure ◽  
Species Similarity

Forest seed banks mostly studied in managed forests proved to be small, species poor and not reflecting aboveground species composition. Yet studies conducted in undisturbed communities indicate a different seed bank characteristic. Therefore we aimed at describing soil seed bank in an undisturbed forest in a remnant of European lowland temperate forests, the Białowieża Forest. We compared similarity between the herb layer and seed bank, similarity of seed bank between different patches, and dominance structure of species in the herb layer and in the seed bank of two related oak-hornbeam communities. We report relatively high values of Sorensen species similarity index between herb layer and seed bank of both patches. This suggests higher species similarity of the herb layer and soil seed bank in natural, unmanaged forests represented by both plots than in fragmented communities influenced by man. Although there was a set of core seed bank species present at both plots, yielding high Sorensen species similarity index values, considerable differences between plots in seed bank size and dominance structure of species were found, indicating spatial variability of studied seed bank generated by edaphic conditions. Dominance structure of species in the herb layer was not reflected in the underlying seed bank. This stresses, that natural forest regeneration cannot rely only on the seed bank, although some forest species are capable of forming soil seed banks. While forest seed banks may not reflect vegetation composition of past successional stages, they may inform on history and land use of a specific plot.

scholarly journals Responses of weed community, soil nutrients, and microbes to different weed management practices in a fallow field in Northern China

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7650 ◽  
Author(s):  
Xian Gu ◽  
Yu Cen ◽  
Liyue Guo ◽  
Caihong Li ◽  
Han Yuan ◽  
...  
Keyword(s):  
Soil Fertility ◽  
Soil Nutrients ◽  
Seed Bank ◽  
Weed Management ◽  
Seed Banks ◽  
Total Biomass ◽  
Weed Seed ◽  
Soil Biodiversity ◽  
Deep Tillage ◽  
Positive Effects

The long-term use of herbicides to remove weeds in fallow croplands can impair soil biodiversity, affect the quality of agricultural products, and threaten human health. Consequently, the identification of methods that can effectively limit the weed seed bank and maintain fallow soil fertility without causing soil pollution for the next planting is a critical task. In this study, four weeding treatments were established based on different degrees of disturbance to the topsoil: natural fallow (N), physical clearance (C), deep tillage (D), and sprayed herbicide (H). The changes in the soil weed seed banks, soil nutrients, and soil microbial biomass were carefully investigated. During the fallow period, the C treatment decreased the annual and biennial weed seed bank by 34% against pretreatment, whereas the H treatment did not effectively reduce the weed seed bank. The D treatment had positive effects on the soil fertility, increasing the available nitrogen 108% over that found in the N soil. In addition, a pre-winter deep tillage interfered with the rhizome propagation of perennial weeds. The total biomass of soil bacterial, fungal, and actinomycete in H treatment was the lowest among the four treatments. The biomass of arbuscular mycorrhizal fungi in the N treatment was respectively 42%, 35%, and 91%, higher than that in the C, D, and H treatments. An ecological weeding strategy was proposed based on our findings, which called for exhausting seed banks, blocking seed transmission, and taking advantage of natural opportunities to prevent weed growth for fallow lands. This study could provide a theoretical basis for weed management in fallow fields and organic farming systems.

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