scholarly journals Effect of Long-Term Farming Practices on Agricultural Soil Microbiome Members Represented by Metagenomically Assembled Genomes (MAGs) and Their Predicted Plant-Beneficial Genes

Genes ◽  
2019 ◽  
Vol 10 (6) ◽  
pp. 424 ◽  
Author(s):  
Johanna Nelkner ◽  
Christian Henke ◽  
Timo Wentong Lin ◽  
Wiebke Pätzold ◽  
Julia Hassa ◽  
...  
Keyword(s):  
Plant Growth ◽  
Growth Regulators ◽  
Nitrogen Fertilization ◽  
Soil Samples ◽  
Soil Microbiome ◽  
Farming Practices ◽  
Metagenomic Dna ◽  
Reduced Nitrogen ◽  
Microbiome Profiling

To follow the hypothesis that agricultural management practices affect structure and function of the soil microbiome regarding soil health and plant-beneficial traits, high-throughput (HT) metagenome analyses were performed on Chernozem soil samples from a long-term field experiment designated LTE-1 carried out at Bernburg-Strenzfeld (Saxony-Anhalt, Germany). Metagenomic DNA was extracted from soil samples representing the following treatments: (i) plough tillage with standard nitrogen fertilization and use of fungicides and growth regulators, (ii) plough tillage with reduced nitrogen fertilization (50%), (iii) cultivator tillage with standard nitrogen fertilization and use of fungicides and growth regulators, and (iv) cultivator tillage with reduced nitrogen fertilization (50%). Bulk soil (BS), as well as root-affected soil (RS), were considered for all treatments in replicates. HT-sequencing of metagenomic DNA yielded approx. 100 Giga bases (Gb) of sequence information. Taxonomic profiling of soil communities revealed the presence of 70 phyla, whereby Proteobacteria, Actinobacteria, Bacteroidetes, Planctomycetes, Acidobacteria, Thaumarchaeota, Firmicutes, Verrucomicrobia and Chloroflexi feature abundances of more than 1%. Functional microbiome profiling uncovered, i.a., numerous potential plant-beneficial, plant-growth-promoting and biocontrol traits predicted to be involved in nutrient provision, phytohormone synthesis, antagonism against pathogens and signal molecule synthesis relevant in microbe–plant interaction. Neither taxonomic nor functional microbiome profiling based on single-read analyses revealed pronounced differences regarding the farming practices applied. Soil metagenome sequences were assembled and taxonomically binned. The ten most reliable and abundant Metagenomically Assembled Genomes (MAGs) were taxonomically classified and metabolically reconstructed. Importance of the phylum Thaumarchaeota for the analyzed microbiome is corroborated by the fact that the four corresponding MAGs were predicted to oxidize ammonia (nitrification), thus contributing to the cycling of nitrogen, and in addition are most probably able to fix carbon dioxide. Moreover, Thaumarchaeota and several bacterial MAGs also possess genes with predicted functions in plant–growth–promotion. Abundances of certain MAGs (species resolution level) responded to the tillage practice, whereas the factors compartment (BS vs. RS) and nitrogen fertilization only marginally shaped MAG abundance profiles. Hence, soil management regimes promoting plant-beneficial microbiome members are very likely advantageous for the respective agrosystem, its health and carbon sequestration and accordingly may enhance plant productivity. Since Chernozem soils are highly fertile, corresponding microbiome data represent a valuable reference resource for agronomy in general.

Mineralization and immobilization of soil nitrogen in two Douglas-fir stands 15 and 22 years after nitrogen fertilization

1989 ◽  
Vol 19 (6) ◽  
pp. 798-801 ◽  
Author(s):  
Russell H. Strader ◽  
Dan Binkley
Keyword(s):  
Nitrogen Fertilization ◽  
N Fertilization ◽  
Douglas Fir ◽  
Soil Samples ◽  
N Availability ◽  
Microbial Immobilization ◽  
Mineral N ◽  
Net Mineralization ◽  
Infertile Soils

Additions of 15N-labelled ammonium chloride were used to examine the role of microbial immobilization in long-term growth response of Douglas-fir (Pseudotsugamenziesii (Mirb.) Franco) plantations to nitrogen fertilization. Soil samples were collected in the summer of 1986 from fertilized (448 or 470 kg N/ha) and nonfertilized plots at previously established N fertilization experiments near Shawnigan Lake, British Columbia, and the Wind River Experimental Forest near Carson, Washington. Douglas-fir on these sites were reported to still be responding to N fertilization after 12 and 18 years. Less than 2% of the added 15N was recovered as mineral N after a 14-day laboratory incubation of soil samples from the fertilized and nonfertilized plots. This indicates that gross mineralization could be over 50 times greater than net mineralization in these infertile soils if the remaining 98% of the added 15N was all biologically immobilized. Net mineralization was significantly greater (p ≤ 0.10) in soils from the fertilized plots than in those from the non-fertilized plots at the Wind River site. Though the current differences in N availability did not appear to be related to differences in microbial immobilization, such large rates of immobilization warrant closer scrutiny as a factor in long-term response to fertilization.

scholarly journals Cryopreservation of a soil microbiome using a Stirling 1 cycle approach - a genomic assessment.

2021 ◽  
Author(s):  
Giovanni Cafa ◽  
Juan Miguel Bonnin ◽  
Nicola Holden ◽  
Jacob G. Malone ◽  
Tim H. Mauchline ◽  
...  
Keyword(s):  
Liquid Medium ◽  
Soil Sample ◽  
Soil Samples ◽  
Soil Microbiome ◽  
Similar Response ◽  
Before And After ◽  
Microbiome Research ◽  
Health And Disease ◽  
And Function

Abstract Soil microbiomes are dynamic systems that respond to biotic and abiotic environmental factors such as those presented at seasonal scales or due to long-term anthropogenic regime shifts. These can affect the composition and function of microbiomes. Investigation of microbiomes can uncover hidden microbial roles in health and disease and discover microbiome-based interventions. Collections of soil samples are kept by various institutions in either a refrigerated or occasionally frozen state, but conditions are not optimised to ensure the integrity of soil microbiome. In this manuscript, we describe cryopreservation with a controlled rate cooler and estimate the genomic content of an exemplar soil sample before and after cryopreservation. The first hypothesis was to test the genomic integrity of the microbiome. We also enriched the soil sample with a liquid medium to estimate the growth of bacteria and compared their growth before and after cryopreservation. Sequence-based rRNA metabarcoding was used to demonstrate that the controlled rate cooler maintains intact the DNA content of the microbiome. Two methods of cryopreservation were applied and compared with control aliquots of soil. An optimised cryopreservation of soil samples is essential for the development of microbiome research in order to retain stable, functionally intact microbiomes. Our results showed that metabarcoding of 16S and ITS rRNA were useful methods to estimate successful cryopreservation. The soil microbiome after enrichment with liquid medium exhibited a similar response of cryopreserved soil and this was estimated with the comparison of the ten most abundant bacterial taxa. These findings support a successful process of cryopreservation and are promising for future use of this technology. To the best of our knowledge, this study is the first report of cryopreservation of soil using a Stirling cycle cooling approach.

scholarly journals 783 PB 427 LEATHERLEAF FERN DAMAGE AND BENLATE USE

HortScience ◽  
1994 ◽  
Vol 29 (5) ◽  
pp. 545b-545
Author(s):  
David N. Sasseville ◽  
Robert J. Kremer ◽  
Wm. Alan Bergfield ◽  
Thourava Souissi Lincoln
Keyword(s):  
Plant Growth ◽  
Electron Micrographs ◽  
Growth Regulators ◽  
Soil Bacteria ◽  
Root Hairs ◽  
Root Surface ◽  
Growth Suppression ◽  
Growing Media ◽  
History Of

Benlate 50 DF has been implicated in causing long term damage to leatherleaf ferns. Damage to leatherleaf fern including frond distortion, discoloration and growth suppression continues to occur even after two or more years following last Benlate application. Electron micrographs of affected plants roots indicate a loss of root hairs and a proliferation of associated soil bacteria on the root surface compared to healthy plants. Plants with history of continued Benlate application have extensive bacterial colonies embedded on the root surface, but these colonies were not parasitic. Lcatherleaf fern plants which only had their rhizomes dipped in Benlate at planting lacked the embedded colonies, but were extensively covered with bacteria. Bioassays of bacteria taken from the rhizoplane and rhizosphere of the these leatherleaf ferns showed that these bacteria have the ability to produce growth regulators and/or toxins which may be detrimental to plant growth when absorbed through the root. Consequently, Benlate may be influencing fern growth indirectly by modifying bacteria composition of the growing media to favor proliferation of deleterious, non-parasitic bacteria.

scholarly journals Growth of Common Bermudagrass as Influenced by Plant Growth Regulators, Soil Type and Nitrogen Fertility

1989 ◽  
Vol 7 (1) ◽  
pp. 1-8 ◽  
Author(s):  
D. A. Devitt ◽  
R. L. Morris
Keyword(s):  
Plant Growth ◽  
Plant Growth Regulators ◽  
Growth Regulators ◽  
Cynodon Dactylon ◽  
Sandy Loam ◽  
Sandy Loam Soil ◽  
Nitrogen Levels ◽  
Loam Soil ◽  
Common Bermudagrass

Abstract An experiment was conducted on common bermudagrass [Cynodon dactylon (L.) Pers.] in the greenhouse using three soil types, four nitrogen(N) levels and three plant growth regulators. Growth response was compared to a control. Cutting biomass, cumulative height, turf color, and evapotranspiration were studied over a 9 week period. Cutless® (flurprimidol) reduced cumulative height by as much as 83% and water consumption by as much as 27%. Embark® (mefluidide) and Limit® (amidochlor) did not provide significant long-term height suppression at any rate or any N level on the three soils. Biomass, cummulative height and color ratings of the bermudagrass were higher on the loam and clay soils compared to the sandy loam soil after growth regulators were applied. Phytotoxicity was observed in the form of leaf tip dieback and discoloration only with Cutless®. Turf discoloration was offset by increased nitrogen levels. However, nitrogen reduced the efficacy of Cutless®. By the ninth week, on the sandy loam soil, color exceeded the acceptable rating for Cutless® only at the 1.5 kg ai/ha (1.34 lb ai/ac) level and 73 kg/halmo (65/lb/ac/mo) nitrogen.

scholarly journals Use of winter cover crops improves maize productivity under reduced nitrogen fertilization: a long-term study

Bragantia ◽  
2021 ◽  
Vol 80 ◽  
Author(s):  
Jonatas Thiago Piva ◽  
Felipe Bratti ◽  
Jorge Luiz Locatelli ◽  
Ricardo Henrique Ribeiro ◽  
Marcos Renan Besen ◽  
...  
Keyword(s):  
Cover Crops ◽  
Nitrogen Fertilization ◽  
Term Study ◽  
Maize Productivity ◽  
Long Term Study ◽  
Reduced Nitrogen ◽  
Winter Cover ◽  
Winter Cover Crops

scholarly journals Effect of Streptomyces Metabolites on Some Physiological Parameters of Maize Seeds

2012 ◽  
Vol 69 (1) ◽  
Author(s):  
Olga POSTOLAKY POSTOLAKY ◽  
Kristinac BALTSAT ◽  
Svetlana BURTSEVA ◽  
Serghei MASLOBROD
Keyword(s):  
Plant Growth ◽  
Growth Regulators ◽  
Dry Weight ◽  
Soil Samples ◽  
Physiological Parameters ◽  
Main Root ◽  
Streptomyces Sp ◽  
Maize Seeds ◽  
Different Content ◽  
Control Water

The influence of metabolites of actinomycetes on some physiological parameters of maize seeds of hybrid of Debut variety (roots formation, growth of coleoptiles) has been studied. The strains of actinomycetes genus Streptomyces were isolated from various soil samples of R.Moldova with different content of humus. The obtained data showed that the number of roots increased considerably under the influence of metabolites of Streptomyces sp .47, Streptomyces sp .123, Streptomyces sp .154 and Streptomyces sp .182 (19,4%, 16,6% and 13,8% respectively, compared with the control - water). The increasing by 33,0 and 44,8% of the main root in comparison with the control was determined after the treatment with metabolites of Streptomyces sp .11 and Streptomyces sp .123 strains. The metabolites of Streptomyces sp .154 and Streptomyces sp .182 strains led to an increasing of coleoptiles length on 31,3 and 38,1% respectively. The dry weight of the roots and coleoptiles exceeded the control on 30-80% and 25-75% respectively in experimental variants. Our research showed that the investigated streptomycetes strains are capable to synthesize the substances which stimulate roots forming and development of stems. In summary, the isolated from Moldavian soils strains of streptomycetes can be considered as potential producers of plant growth regulators.

scholarly journals EFFECTS OF CALLUS AGE, GENOTYPE, AND PLANT GROWTH REGULATORS ON PLANT REGENERATION FROM ONION SUSPENSION CULTURES

HortScience ◽  
1992 ◽  
Vol 27 (6) ◽  
pp. 696h-697
Author(s):  
Song Ping ◽  
Ellen B. Peffley
Keyword(s):  
Plant Regeneration ◽  
Plant Growth ◽  
Plant Growth Regulators ◽  
Growth Regulators ◽  
Interspecific Hybrids ◽  
Suspension Cultures ◽  
Liquid Media ◽  
Solid Media ◽  
Cells Cultured

Callus of five onion genotypes representing two species. Allium cepa and A. fistulosum, and their interspecific hybrid were used for establishing suspension cultures. Cultures were derived from callus that had been maintained on solid media and routinely subcultured for four years and from callus induced within six months of this experiment. Long-term callus from which plants were routinely regenerated and newly-induced callus were composed of cells which were, for the most-part, meristem-like with higher mitotic indices than cells from long-term callus which had been maintained as callus but had lost us capability to regenerate plants, these cells were large with small nuclei. Callus from newly-induced and long-term regenerable cultures were selected for further studies. Eight liquid media with factorial combinations of plant growth regulators were tested. Cells cultured in BDS liquid medium supplemented with 0.5 mg/l ABA and 1.0 or 2.0 mg/l 2,4-D without e-BA had higher mitotic indices and plant regeneration percentages than did cells cultured in the same media without ABA and with 6-BA. Suspension cultures from A. fistulosum and interspecific hybrids with A. fistulosum produced the highest numbers of plants regenerated.

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