scholarly journals Microbiomes of natural and abandoned agricultural soils of the Central part of Yamal region

2021 ◽  
Vol 941 (1) ◽  
pp. 012029
Author(s):  
E Abakumov ◽  
A Kimeklis ◽  
G Gladkov ◽  
E Andronov ◽  
E Morgun
Keyword(s):  
Soil Fertility ◽  
Agricultural Soil ◽  
Soil Cover ◽  
Agricultural Soils ◽  
Terrestrial Ecosystem ◽  
Nitrogen Sources ◽  
Ecological Niches ◽  
Microbial Biodiversity ◽  
Soil Microbial ◽  
Taiga Soils

Abstract Soil cover of the northern most regions of Eurasia are considered as underestimated in terms of their possible role in expansions of current agriculture to the cryolithozone. In this context, abandoned agricultural soils of Yamal region were investigated in terms of morphology, chemistry and taxonomy microbiome compositions and compared in these terms with mature tundra and taiga soils of pristine environments. The level of soil fertility was low in all cases – former agricultural soils and pristine ones. The level of microorganism’s biodiversity was higher in soils of agricultural lands. This fact indicates that the agricultural soil treatment in polar terrestrial ecosystem results in increasing of soil microbial biodiversity due to diversification of ecological niches. Also the is an essential lack of nitrogen sources in all permafrost affected soils studied.

Bacteria in agricultural soils: Diversity, role and future perspectives

2003 ◽  
Vol 83 (Special Issue) ◽  
pp. 303-309 ◽  
Author(s):  
E. Topp
Keyword(s):  
Soil Bacteria ◽  
Crop Production ◽  
Agricultural Soils ◽  
Future Research ◽  
Functional Biodiversity ◽  
Microbial Biodiversity ◽  
Soil Microbial ◽  
Pesticide Biodegradation ◽  
Important Object ◽  
Bacterial Biodiversity

Bacteria in soil are very diverse, very numerous, and functionally important, and have historically been an important object of research by Canadian microbiologists. Only a small fraction of bacteria in soils are amenable to culturing in the laboratory, limiting the ability to study these organisms. Canadian scientists have contributed to the development and implementation of both nucleic acidbased and chemical biomarker-based methods now widely used for assessing soil microbial biodiversity without the need for isolation and cultivation. Pesticide degradation, and the cycling of nitrogen in soils are used here to illustrate the significance of bacterial biodiversity to soil functions relevant to human and environmental health, and crop production . There remains much to be discovered about the genetic and functional biodiversity of soil bacteria, and much to be gained from this knowledge. A number of recommendations are made for future research in soil bacteriology. Key words: Soil quality, bacteria, microbial biodiversity, pesticide biodegradation, nitrogen cycling.

scholarly journals Microbial responses to chitin and chitosan in oxic and anoxic agricultural soil slurries

2014 ◽  
Vol 11 (12) ◽  
pp. 3339-3352 ◽  
Author(s):  
A. S. Wieczorek ◽  
S. A. Hetz ◽  
S. Kolb
Keyword(s):  
Carbon Dioxide ◽  
Agricultural Soil ◽  
Soil Microbial Communities ◽  
Terrestrial Ecosystems ◽  
Ecological Niches ◽  
Acid Fermentation ◽  
Fermentation Products ◽  
Anoxic Conditions ◽  
Chitin Degradation ◽  
Soil Microbial

Abstract. Microbial degradation of chitin in soil substantially contributes to carbon cycling in terrestrial ecosystems. Chitin is globally the second most abundant biopolymer after cellulose and can be deacetylated to chitosan or can be hydrolyzed to N,N′-diacetylchitobiose and oligomers of N-acetylglucosamine by aerobic and anaerobic microorganisms. Which pathway of chitin hydrolysis is preferred by soil microbial communities is unknown. Supplementation of chitin stimulated microbial activity under oxic and anoxic conditions in agricultural soil slurries, whereas chitosan had no effect. Thus, the soil microbial community likely was more adapted to chitin as a substrate. In addition, this finding suggested that direct hydrolysis of chitin was preferred to the pathway that starts with deacetylation. Chitin was apparently degraded by aerobic respiration, ammonification, and nitrification to carbon dioxide and nitrate under oxic conditions. When oxygen was absent, fermentation products (acetate, butyrate, propionate, hydrogen, and carbon dioxide) and ammonia were detected, suggesting that butyric and propionic acid fermentation, along with ammonification, were likely responsible for anaerobic chitin degradation. In total, 42 different chiA genotypes were detected of which twenty were novel at an amino acid sequence dissimilarity of less than 50%. Various chiA genotypes responded to chitin supplementation and affiliated with a novel deep-branching bacterial chiA genotype (anoxic conditions), genotypes of Beta- and Gammaproteobacteria (oxic and anoxic conditions), and Planctomycetes (oxic conditions). Thus, this study provides evidence that detected chitinolytic bacteria were catabolically diverse and occupied different ecological niches with regard to oxygen availability enabling chitin degradation under various redox conditions on community level.

scholarly journals Draft Genome Sequence of Burkholderia cordobensis Type Strain LMG 27620, Isolated from Agricultural Soils in Argentina

2015 ◽  
Vol 3 (5) ◽  
Author(s):  
Walter Omar Draghi ◽  
Ulises M. Mancini Villagra ◽  
Luis Gabriel Wall ◽  
Angeles Zorreguieta
Keyword(s):  
Genome Sequence ◽  
Type Strain ◽  
Agricultural Soil ◽  
Agricultural Soils ◽  
Phenol Degradation ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Ecological Niches ◽  
Interesting Candidate ◽  
Xenobiotic Degradation

Bacteria of the genus Burkholderia are commonly found in diverse ecological niches in nature. We report here the draft genome sequence of Burkholderia cordobensis type strain LMG 27620, isolated from agricultural soil in Córdoba, Argentina. This strain harbors several genes involved in chitin utilization and phenol degradation, which make it an interesting candidate for biocontrol purposes and xenobiotic degradation in polluted environments.

scholarly journals Microbial responses to chitin and chitosan in oxic and anoxic agricultural soil slurries

2014 ◽  
Vol 11 (2) ◽  
pp. 2155-2188
Author(s):  
A. S. Wieczorek ◽  
S. A. Hetz ◽  
S. Kolb
Keyword(s):  
Carbon Dioxide ◽  
Agricultural Soil ◽  
Soil Microbial Communities ◽  
Terrestrial Ecosystems ◽  
Ecological Niches ◽  
Acid Fermentation ◽  
Fermentation Products ◽  
Anoxic Conditions ◽  
Chitin Degradation ◽  
Soil Microbial

Abstract. Chitin is the second most abundant biopolymer in terrestrial ecosystems and is subject to microbial degradation. Chitin can be deacetylated to chitosan or can be hydrolyzed to N,N′-diacetylchitobiose and oligomers of N-acetylglucosamine by aerobic and anaerobic microorganisms. Which pathway of chitin hydrolysis is preferred by soil microbial communities has previously been unknown. Supplementation of chitin stimulated microbial activity under oxic and anoxic conditions in agricultural soil slurries, whereas chitosan had no effect. Thus, the soil microbial community likely was more adapted to chitin as a substrate. In addition, this finding suggested that direct hydrolysis of chitin was preferred to the pathway that starts with deacetylation. Chitin was apparently degraded by aerobic respiration, ammonification, and nitrification to carbon dioxide and nitrate under oxic conditions. When oxygen was absent, fermentation products (acetate, butyrate, propionate, hydrogen, carbon dioxide) and ammonia were detected, suggesting that butyric and propionic acid fermentation were along with ammonification likely responsible for apparent anaerobic chitin degradation. In total, 42 different chiA genotypes were detected of which twenty were novel at an amino acid sequence dissimilarity of >50%. Various chiA genotypes responded to chitin supplementation and affiliated with a novel deep-branching bacterial chiA genotype (anoxic conditions), genotypes of Beta- and Gammaproteobacteria (oxic and anoxic conditions), and Planctomycetes (oxic conditions). Thus, this study provides evidence that detected chitinolytic bacteria were catabolically diverse and occupied different ecological niches with regard to oxygen availability enabling chitin degradation under various redox conditions at the level of the community.

scholarly journals Microbial Diversity of Reconstituted, Degraded, and Agricultural Soils Assessed by 16S rDNA Multi-Amplicon Sequencing

2022 ◽  
Vol 9 ◽  
Author(s):  
Laura Maretto ◽  
Saptarathi Deb ◽  
Samathmika Ravi ◽  
Claudia Chiodi ◽  
Paolo Manfredi ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Diversity ◽  
16S Rdna ◽  
Agricultural Soil ◽  
Agricultural Soils ◽  
Amplicon Sequencing ◽  
Soil Samples ◽  
Biogeochemical Cycle ◽  
Soil Microbial Diversity ◽  
Soil Microbial

The microbial diversity is, among soil key factors, responsible for soil fertility and nutrient biogeochemical cycles, and can be modified upon changes in main soil physicochemical properties and soil pollution. Over the years, many restoration techniques have been applied to restore degraded soils. However, the effect of these approaches on soil microbial diversity is less understood and thus requires more investigation. In this study, we analyzed the impact, on soil microbial diversity of a patented novel technology, used to restore degraded soils. Soil samples were collected from three nearby sites located in Borgotrebbia, Piacenza, Italy, and categorized as reconstituted, degraded, and agricultural soils. After total soil DNA extraction, 16S rDNA multi-amplicon sequencing was carried out using an Ion GeneStudio S5 System to compare soils’ bacterial community profiles. Sequenced reads were processed to assign taxonomy and then key microbial community differences were identified across the sampling sites. Species diversity featured significant abatement at all rank levels in the degraded soil when compared to the agricultural control. The 5 year restoration technique showed full recovery of this index at the genus level but not at the phylum level, displaying a rank-dependent gradient of restored richness. In parallel, the abundance of genes involved in the nitrogen (N) biogeochemical cycle was assessed using quantitative Real-Time PCR (qPCR). Total DNA content was significantly higher (p < 0.05) in degraded (μ = 12.69 ± 2.58 μg g−1) and reconstituted (μ = 11.73 ± 1.65 μg g−1) soil samples when compared to the agricultural soil samples (μ = 2.39 ± 0.50 μg g−1). The taxonomic diversity of each soil site was significantly different, with some instances unique of the agricultural soil even at the phylum level. The analysis of N functional genes showed that the relative abundance of bacterial amoA (p < 0.05) and nosZ (p < 0.01) genes were significantly lower in the agricultural than in the reconstituted and degraded soils. We concluded that the application of the soil reconstitution technique appears to enhance the active microbial community, with distinct diversity and functionality towards genes involved in N biogeochemical cycle, as compared to both the degraded and the agricultural soil.

scholarly journals Ammonia-oxidizing archaea are integral to nitrogen cycling in a highly fertile agricultural soil

2021 ◽  
Vol 1 (1) ◽  
Author(s):  
Laibin Huang ◽  
Seemanti Chakrabarti ◽  
Jennifer Cooper ◽  
Ana Perez ◽  
Sophia M. John ◽  
...  
Keyword(s):  
Nitrogen Cycle ◽  
Agricultural Soil ◽  
Agricultural Soils ◽  
Ammonia Oxidizing Bacteria ◽  
Central Process ◽  
Soil Nitrification ◽  
Plant Nitrogen ◽  
Ammonia Oxidizing Archaea ◽  
Activity Measurements ◽  
Nitrite Oxidizing Bacteria

AbstractNitrification is a central process in the global nitrogen cycle, carried out by a complex network of ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), complete ammonia-oxidizing (comammox) bacteria, and nitrite-oxidizing bacteria (NOB). Nitrification is responsible for significant nitrogen leaching and N2O emissions and thought to impede plant nitrogen use efficiency in agricultural systems. However, the actual contribution of each nitrifier group to net rates and N2O emissions remain poorly understood. We hypothesized that highly fertile agricultural soils with high organic matter mineralization rates could allow a detailed characterization of N cycling in these soils. Using a combination of molecular and activity measurements, we show that in a mixed AOA, AOB, and comammox community, AOA outnumbered low diversity assemblages of AOB and comammox 50- to 430-fold, and strongly dominated net nitrification activities with low N2O yields between 0.18 and 0.41 ng N2O–N per µg NOx–N in cropped, fallow, as well as native soil. Nitrification rates were not significantly different in plant-covered and fallow plots. Mass balance calculations indicated that plants relied heavily on nitrate, and not ammonium as primary nitrogen source in these soils. Together, these results imply AOA as integral part of the nitrogen cycle in a highly fertile agricultural soil.

scholarly journals Effects of Monoculture, Crop Rotation, and Soil Moisture Content on Selected Soil Physicochemical and Microbial Parameters in Wheat Fields

2012 ◽  
Vol 2012 ◽  
pp. 1-13 ◽  
Author(s):  
A. Marais ◽  
M. Hardy ◽  
M. Booyse ◽  
A. Botha
Keyword(s):  
Soil Moisture ◽  
Microbial Communities ◽  
Crop Rotation ◽  
Management Practices ◽  
Agricultural Soils ◽  
Soil Microbial Communities ◽  
Soil Microbial Activity ◽  
Most Probable Number ◽  
Probable Number ◽  
Soil Microbial

Different plants are known to have different soil microbial communities associated with them. Agricultural management practices such as fertiliser and pesticide addition, crop rotation, and grazing animals can lead to different microbial communities in the associated agricultural soils. Soil dilution plates, most-probable-number (MPN), community level physiological profiling (CLPP), and buried slide technique as well as some measured soil physicochemical parameters were used to determine changes during the growing season in the ecosystem profile in wheat fields subjected to wheat monoculture or wheat in annual rotation with medic/clover pasture. Statistical analyses showed that soil moisture had an over-riding effect on seasonal fluctuations in soil physicochemical and microbial populations. While within season soil microbial activity could be differentiated between wheat fields under rotational and monoculture management, these differences were not significant.

scholarly journals Possibilities of the Use of Aerial Photographs in the Protection of Agricultural Soil Fund

Geografie ◽  
1990 ◽  
Vol 95 (2) ◽  
pp. 87-95
Author(s):  
Zdeněk Lipský
Keyword(s):  
Agricultural Soil ◽  
Agricultural Soils ◽  
Water Erosion ◽  
Negative Influence ◽  
Aerial Photographs ◽  
Black And White ◽  
Soil Wetting

The author considers two main processes showing a negative influence on the quality and use of agricultural soils, namely water erosion and wetting. The paper treats of general advantages of aerial photographs. Practical examples are presented of direct and indirect interpretation of erosion phenomena and soil wetting by means of black-and-white, multispectral and infrared aerial photographs. In the conclusion, the main spheres of the problem of the soil fund protection are dealt with. Most of these problems could be solved by the application of aerial photographs.

Accumulation of As and Pb in Vegetables Grown in Agricultural Soils Contaminated by Historical Mining in Zacatecas, Mexico

2021 ◽  
Author(s):  
Silvia Salas Muñoz ◽  
Elvia Valdez Valdez ◽  
Jorge Armando Mauricio Castillo ◽  
Fátima Berenice Salazar Badillo ◽  
Héctor René Vega Carrillo ◽  
...  
Keyword(s):  
Agricultural Soil ◽  
Agricultural Soils ◽  
Arsenic Concentration ◽  
Pollution Index ◽  
Lead Content ◽  
National Standard ◽  
Mining Activities ◽  
Human Beings ◽  
Historical Mining ◽  
Edible Parts

Abstract Historical mining activities are a source of environmental pollution that affects the food chain and the health of human beings. The aim of this study was assessment the accumulation of arsenic and lead in vegetables grown in agricultural soils contaminated by old mining in Zacatecas, Mexico. The concentration of arsenic and lead in agricultural soil and edible parts of carrot, garlic, and pepper was analyzed by atomic absorption spectrometry. The soil-vegetable bioconcentration factor and pollution load index were determined. The pH values of the farmland were alkaline. The concentration of arsenic in agricultural soil exceeds the permissible limit for arsenic of Mexican standards and international representing health risks. The lead content in most soil samples they were low. The arsenic and lead content in edible parts of species vegetable exceeded the national standard from various countries and the values established by the Codex Alimentarius (FAO-WHO). The highest arsenic concentration was found both in Capsicum annum and Allium sativum. The highest concentration of Pb was in pepper fruits. Among vegetable the high BCF value was for arsenic, ranging from 2.33 to 0.64, and the average for all vegetable samples was 1.01. The pollution index indicates that arsenic is the dominant pollutant accumulated in soil and vegetables grown in agricultural soils. According to the findings, the state and national agricultural and health authorities should not recommend the cultivation of vegetables in agricultural soil located in this area of historical mining activities. Likewise, preventive measures must be taken on the consumption of contaminated vegetables and certifying their safety.

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