Macroecological distributions of gene variants highlight the functional organization of soil microbial systems

2021 ◽  
Author(s):  
Arthur Escalas ◽  
Fabiana S. Paula ◽  
François Guilhaumon ◽  
Mengting Yuan ◽  
Yunfeng Yang ◽  
...  
2021 ◽  
Vol 26 (1(48)) ◽  
pp. 45-54
Author(s):  
N. E., Ellanska ◽  
O. P. Yunosheva

Problem. Intensive human pressure on urban ecosystems in big cities, such as Kyiv, leads to cenotic and trophic relations disbalance, agronomically useful microbiota and microfauna inhibition, plant resistance to any stressors decrease and disruption of normal soil formation. Therefore, it is important to find new effective, economically viable and environmentally safe methods to overcome soil sickness in city plantations. Aim. To study the structural and functional peculiarities of organization of soil microbial groups in anthropogenically disturbed zones of Kyiv green plantations in order to overcome soil fatigue with the use of natural substances - silicon-containing mineral analcime. Methods. Investigations were carried out on the basis of the National Botanical Garden M.M. Gryshko NAS of Ukraine, Department of Allelopathy. Six research regions in the most сontaminated and anthropogenically disturbed green areas of the Kyiv Obolonsky district were selected as objects. Twice a year, samples of root soil were taken at 0-20 cm depth before application (May) and 3.5 months after application of silicon-containing mixture (analcime) (September). The selection of soil samples, preparation and saving for the study of aerobic microbiota were carried out in accordance with ISO 10381-6-2001. The quantity of microorganisms of main ecological and trophic groups, direction of microbiological processes, identification of soil micromycetes were determined by conventional microbiological methods. Results. The results of this work showed that 3.5 months after the addition of the silicon-containing mixture, there were significant changes in the structure of the soil microbiocenosis. The increase in the number of microorganisms involved in the transformation of nitrogen compounds and the reduction of phytotoxic forms of soil fungi were detected, which indicates favorable conditions for the synthesis of humic compounds. The biggest changes were observed on the side of the highway with active emissions from automobiles and in the park, where higher content of iron ions was determined in the water for irrigation. Conclusions. The conducted research made it possible to estimate the structural and functional organization of microbial groups of the soils in a separate Kyiv district under different anthropogenic influence before and after the addition of silicon-containing mixture.


During the past decade, investigations with microbial systems have provided a model of the structural and functional organization of the genetic material which permits a general understanding of transmissional and functional aspects of heredity in terms of the chemical structure of the genetic material. Of historical interest is the fact that one of the major paths of investigation which led to this state of knowledge was initiated with report of a specific deviation from Mendel’s Law of Segregation first seen in Drosophila melanogaster . Assay of meiotic products of females, heterozygous for different mutant alleles at the lozenge locus, yielded exceptions which were associated with recombination (Oliver 1940). Subsequent investigations of other multiple allelic loci in several higher organisms consistently yielded such exceptions. The term pseudo-alleles was used to describe mutants which formerly were called alleles, but which now yielded to recombination, and pseudo-allelic locus or complex locus were expressions used to describe a locus whose mutant alleles exhibited a low order of recombination. The use of these expressions reflects the classical conceptual framework within which these cases were interpreted. Thus, if a genetic unit is a unit of function and mutation within which there is no recombination, then the evidence of recombination requires that there be two such units in close proximity. Moreover, since mutation of these adjacent genetic units led to a similar array of phenotypic effects, it was inferred that these genes were functionally similar or related. Indeed, their phenotypic interactions in heterozygotes confirmed this interpretation. Thus was erected the notion of a pseudo-allelic locus as consisting of a small number of recombinationally separable units, whose recombinational distinction was paral­leled by functional distinction, and whose phenotypic interactions in heterozygotes reflected some relationship between their separable functions (see reviews by Carlson 1959; Green 1963). An accessory theorem (Lewis 1951) was based upon the observation that several pseudo-allelic systems in Drosophila were associated with salivary chromosome doublet structures, long believed to represent small duplica­tions. This notion suggested that pseudo-alleles were cases of gene duplicates in various stages of evolution, and the investigation of such systems was believed to be concerned essentially with the evolution of new genes and new gene functions. In summation, most of the work with higher organisms has been interpreted in a fashion entirely consistent with classical notions concerning genetic organization, with pseudo-allelism taken as a special situation. In contrast, the work with microbial systems has led to a considerable revision of classical notions concerning genetic organization. From these studies, there emerges a concept of the hereditary material as consisting of a linear order of units called cistrons, which are defined in terms of function (Benzer 1957). Each such unit possesses numerous, separable, linearly ordered sites capable of undergoing independent mutation (Benzer 1959, 1961). Moreover, it now is possible to relate the linear order of recombinational sites within a cistron to the genetic code which determines the linear order of amino acids in a polypeptide (Helinski & Yanofsky 1962; Yanofsky 1963). The microbial evidence has revealed still another order of genetic organization. Cistrons which control physiologically related polypeptides are found to be located adjacent to each other on the genetic map, and evidence is available which provides an understanding of the regulation of the function of these adjacent blocks of cistrons, now termed operons (Ames & Hartman 1963; Jacob & Monod 1961). Despite obvious parallels between the higher organism studies and the microbial work, considerable disagreement exists concerning the relevance of the microbial model of genetic organization for higher organisms. This paper is addressed to this point.


Plants ◽  
2020 ◽  
Vol 9 (10) ◽  
pp. 1338 ◽  
Author(s):  
Adriano Sofo ◽  
Hazem S. Elshafie ◽  
Ippolito Camele

Plants are affected by soil environments to the same extent that they affect soil functioning through interactions between environmental and genetic factors. Here, five plant species (broad bean, pea, cabbage, fennel, and olive) grown under controlled pot conditions were tested for their ability to differently stimulate the degradation of standard litter. Litter, soil C and N contents were measured for evaluating chemical changes due to plant presence, while soil microbial abundance was evaluated to assess if it had a positive or negative catalyzing influence on litter decomposition. The architecture and morphological traits of roots systems were also evaluated by using specific open-source software (SmartRoot). Soil chemical and microbiological characteristics were significantly influenced by the plant species. Variations in soil C/N dynamics were correlated with the diversity of root traits among species. Early stage decomposition of the standard litter changed on the basis of the plant species. The results indicated that key soil processes are governed by interactions between plant roots, soil C and N, and the microbial metabolism that stimulate decomposition reactions. This, in turn, can have marked effects on soil chemical and microbiological fertility, both fundamental for sustaining crops, and can promote the development of new approaches for optimizing soil C and N cycling, managing nutrient transport, and sustaining and improving net primary production.


1991 ◽  
Vol 10 (1) ◽  
pp. 63-121 ◽  
Author(s):  
José O. Siqueira ◽  
Muraleedharan G. Nair ◽  
Raymond Hammerschmidt ◽  
Gene R. Safir ◽  
Alan R. Putnam

2018 ◽  
Vol 12 (10) ◽  
pp. 2492-2505 ◽  
Author(s):  
Bin Ma ◽  
Kankan Zhao ◽  
Xiaofei Lv ◽  
Weiqin Su ◽  
Zhongmin Dai ◽  
...  

Author(s):  
D.L. Spector ◽  
S. Huang ◽  
S. Kaurin

We have been interested in the organization of RNA polymerase II transcription and pre-mRNA splicing within the cell nucleus. Several models have been proposed for the functional organization of RNA within the eukaryotic nucleus and for the relationship of this organization to the distribution of pre-mRNA splicing factors. One model suggests that RNAs which must be spliced are capable of recruiting splicing factors to the sites of transcription from storage and/or reassembly sites. When one examines the organization of splicing factors in the nucleus in comparison to the sites of chromatin it is clear that splicing factors are not localized in coincidence with heterochromatin (Fig. 1). Instead, they are distributed in a speckled pattern which is composed of both perichromatin fibrils and interchromatin granule clusters. The perichromatin fibrils are distributed on the periphery of heterochromatin and on the periphery of interchromatin granule clusters as well as being diffusely distributed throughout the nucleoplasm. These nuclear regions have been previously shown to represent initial sites of incorporation of 3H-uridine.


Author(s):  
David L. Spector ◽  
Robert J. Derby

Studies in our laboratory are involved in evaluating the structural and functional organization of the mammalian cell nucleus. Since several major classes (U1, U2, U4/U6, U5) of small nuclear ribonucleoprotein particles (snRNPs) play a crucial role in the processing of pre-mRNA molecules, we have been interested in the localization of these particles within the cell nucleus. Using pre-embedding immunoperoxidase labeling combined with 3-dimensional reconstruction, we have recently shown that nuclear regions enriched in snRNPs form a reticular network within the nucleoplasm which extends between the nucleolar surface and the nuclear envelope. In the present study we were inte rested in extending these nuclear localizations using cell preparation techniques which avoid slow penetration of fixatives, chemical crosslinking of potential antigens and solvent extraction. CHOC 400 cells were cryofixed using a CF 100 ultra rapid cooling device (LifeCell Corp.). After cryofixation cells were molecular distillation dried, vapor osmicated, in filtra ted in 100% Spurr resin in vacuo and polymerized in molds a t 60°C. Using this procedure we were able to evaluate the distribution of snRNPs in resin embedded cells which had not been chemically fixed, incubated in cryoprotectants or extracted with solvents.


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