Monitoring the impact of hydrocarbon contamination and nutrient addition on microbial density, activity, and diversity in soil

The development of optimal in situ bioremediation strategies requires a better knowledge of their impact on the soil microbial communities. We have evaluated the impact of hexadecane contamination and different nutrient amendments on soil microbial density and activity. Microbial density was measured via total DNA quantification, and microbial activity via respiration and RNA variation. The RNA/DNA ratio was also determined, as it is a potential indicator of microbial activity. PCR-amplified 16S rRNA genes were cloned and sequenced to analyze the diversity of bacterial communities. Nutrient addition significantly increased respiration and DNA and RNA concentrations in contaminated soil, indicating a limitation of degradation and growth by the availability of nitrogen and phosphorus in unamended microcosms. Hexadecane treatment slightly affected the diversity of the bacterial community, while it was dramatically reduced by nutrient treatments, particularly the addition of nitrogen and phosphorus. Microbial community composition was also altered with the enrichment of populations related to Nocardia in bioremediated soils, while uncultured Proteobacteria were mostly detected in uncontaminated soil.

Download Full-text

Arable agriculture changes soil microbial communities in the South African Grassland Biome

South African Journal of Science ◽

10.17159/sajs.2018/20170288 ◽

2018 ◽

Vol 114 (5/6) ◽

Cited By ~ 1

Author(s):

Gilbert Kamgan Nkuekam ◽

Don A. Cowan ◽

Angel Valverde

Keyword(s):

Microbial Communities ◽

Agricultural Soils ◽

Soil Microbial Communities ◽

Fungal Communities ◽

16S Rrna Genes ◽

Rrna Genes ◽

Soil Microbial Diversity ◽

Soil Microbial ◽

The Impact ◽

Natural Grassland

Many studies, mostly in temperate regions of the northern hemisphere, have demonstrated that agricultural practices affect the composition and diversity of soil microbial communities. However, very little is known about the impact of agriculture on the microbial communities in other regions of the world, most particularly on the African continent. In this study, we used MiSeq amplicon sequencing of bacterial 16S rRNA genes and fungal ITS regions to characterise microbial communities in agricultural and natural grassland soils located in the Mpumalanga Province of South Africa. Nine soil chemical parameters were also measured to evaluate the effects of edaphic factors on microbial community diversity. Bacterial and fungal communities were significantly richer and more diverse in natural grassland than in agricultural soils. Microbial taxonomic composition was also significantly different between the two habitat types. The phylum Acidobacteria was significantly more abundant in natural grassland than in agricultural soils, while Actinobacteria and the family Nectriaceae showed the opposite pattern. Soil pH and phosphorus significantly influenced bacterial communities, whereas phosphorus and calcium influenced fungal communities. These findings may be interpreted as a negative impact of land-use change on soil microbial diversity and composition.

Download Full-text

Biochar and compost effects on soil microbial communities and nitrogen induced respiration in turfgrass soils

PLoS ONE ◽

10.1371/journal.pone.0242209 ◽

2020 ◽

Vol 15 (11) ◽

pp. e0242209

Author(s):

Muhammad Azeem ◽

Lauren Hale ◽

Jonathan Montgomery ◽

David Crowley ◽

Milton E. McGiffen

Keyword(s):

Microbial Community ◽

Soil Microbial Communities ◽

16S Rrna Genes ◽

Rrna Genes ◽

Community Structures ◽

Soil Microbial Community Structure ◽

Amended Soils ◽

Soil Microbial ◽

Compost Amendment ◽

Microbial Community Structures

We examined the effect of a labile soil amendment, compost, and recalcitrant biochar on soil microbial community structure, diversity, and activity during turfgrass establishment. Two application rates of biochar (B1 at 12.5 t ha-1and B2 at 25 t ha-1), a 5 centimeter (cm) green waste compost treatment (CM) in top soil, a treatment with 12.5 t ha-1 biochar and 5 cm compost (B1+CM), and an unamended control (CK) treatment were prepared and seeded with tall fescue. Overall, results of phospholipid fatty acid analysis (PLFA) profiling and Illumina high-throughput sequencing of 16S rRNA genes amplified from soil DNA revealed significant shifts in microbial community structures in the compost amended soils whereas in biochar amended soils communities were more similar to the control, unamended soil. Similarly, increases in enzymatic rates (6–56%) and nitrogen-induced respiration (94%) were all largest in compost amended soils, with biochar amended soils exhibiting similar patterns to the control soils. Both biochar and compost amendments impacted microbial community structures and functions, but compost amendment, whether applied alone or co-applied with biochar, exhibited the strongest shifts in the microbial community metrics examined. Our results suggest application of compost to soils in need of microbiome change (reclamation projects) or biochar when the microbiome is functioning and long-term goals such as carbon sequestration are more desirable.

Download Full-text

Microbial community analysis of soils under different soybean cropping regimes in the Argentinean south-eastern Humid Pampas

FEMS Microbiology Ecology ◽

10.1093/femsec/fiab007 ◽

2021 ◽

Author(s):

Gabriela Fernandez-Gnecco ◽

Kornelia Smalla ◽

Lorrie Maccario ◽

Søren J Sørensen ◽

Pablo Barbieri ◽

...

Keyword(s):

Microbial Community ◽

Cover Crops ◽

Microbial Community Composition ◽

Soil Microbial Communities ◽

16S Rrna Genes ◽

Rrna Genes ◽

Temporal Shift ◽

Soil Microbial ◽

No Till

Abstract Soil microbial communities are key players of ecosystem processes and important for crop and soil health. The Humid Pampas region in Argentina concentrates 75% of the national soybean production, which is based on intensive use of agrochemicals, monocropping and no-till. A long-term field experiment under no-till management in the southeast of the Argentinean Pampas provides a unique opportunity to compare soybean under monocropping with cultivation including alternating cover crops or in a three-phase rotation. We hypothesized that cropping regimes and season affect soil microbial community composition and diversity. Amplicon sequencing of 16S rRNA genes and internal transcribed spacer fragments showed a stronger microbial seasonal dynamic in conservation regimes compared to monocropping. In addition, several bacterial (e.g. Catenulispora, Streptomyces and Bacillus) and fungal genera (e.g. Exophiala) with cropping regime-dependent differential relative abundances were identified. Despite a temporal shift in microbial and chemical parameters, this study shows that long-term cropping regimes shaped the soil microbiota. This might have important implications for soil quality and soybean performance and should therefore be considered in the development of sustainable agricultural managements.

Download Full-text

Diversity and composition of the Panax ginseng rhizosphere microbiome in various cultivation modesand ages

BMC Microbiology ◽

10.1186/s12866-020-02081-2 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Ai-Zi Tong ◽

Wei Liu ◽

Qiang Liu ◽

Guang-Qing Xia ◽

Jun-Yi Zhu

Keyword(s):

Microbial Community ◽

Microbial Diversity ◽

Panax Ginseng ◽

Soil Microbial Communities ◽

16S Rrna Genes ◽

Rrna Genes ◽

Continuous Cropping ◽

Soil Microbial Diversity ◽

Soil Microbial ◽

Soil Borne Pathogens

Abstract Background Continuous cropping of ginseng (Panax ginseng Meyer) cultivated in farmland for an extended period gives rise to soil-borne disease. The change in soil microbial composition is a major cause of soil-borne diseases and an obstacle to continuous cropping. The impact of cultivation modes and ages on the diversity and composition of the P. ginseng rhizosphere microbial community and technology suitable for cropping P. ginseng in farmland are still being explored. Methods Amplicon sequencing of bacterial 16S rRNA genes and fungal ITS regions were analyzed for microbial community composition and diversity. Results The obtained sequencing data were reasonable for estimating soil microbial diversity. We observed significant variations in richness, diversity, and relative abundances of microbial taxa between farmland, deforestation field, and different cultivation years. The bacterial communities of LCK (forest soil where P. ginseng was not grown) had a much higher richness and diversity than those in NCK (farmland soil where P. ginseng was not grown). The increase in cultivation years of P. ginseng in farmland and deforestation field significantly changed the diversity of soil microbial communities. In addition, the accumulation of P. ginseng soil-borne pathogens (Monographella cucumerina, Ilyonectria mors-panacis, I. robusta, Fusarium solani, and Nectria ramulariae) varied with the cropping age of P. ginseng. Conclusion Soil microbial diversity and function were significantly poorer in farmland than in the deforestation field and were affected by P. ginseng planting years. The abundance of common soil-borne pathogens of P. ginseng increased with the cultivation age and led to an imbalance in the microbial community.

Download Full-text

Phylogenetic Clustering of Soil Microbial Communities by 16S rRNA but Not 16S rRNA Genes

Applied and Environmental Microbiology ◽

10.1128/aem.07547-11 ◽

2012 ◽

Vol 78 (7) ◽

pp. 2459-2461 ◽

Cited By ~ 18

Author(s):

Kristen M. DeAngelis ◽

Mary K. Firestone

Keyword(s):

16S Rrna ◽

Soil Microbial Communities ◽

16S Rrna Genes ◽

Rrna Genes ◽

Rrna Gene ◽

Phylogenetic Clustering ◽

Soil Microbial ◽

Highly Active ◽

Bacterial And Archaeal Communities ◽

Archaeal Communities

ABSTRACTWe evaluated phylogenetic clustering of bacterial and archaeal communities from redox-dynamic subtropical forest soils that were defined by 16S rRNA and rRNA gene sequences. We observed significant clustering for the RNA-based communities but not the DNA-based communities, as well as increasing clustering over time of the highly active taxa detected by only rRNA.

Download Full-text

Effect of Phenylurea Herbicides on Soil Microbial Communities Estimated by Analysis of 16S rRNA Gene Fingerprints and Community-Level Physiological Profiles

Applied and Environmental Microbiology ◽

10.1128/aem.65.3.982-988.1999 ◽

1999 ◽

Vol 65 (3) ◽

pp. 982-988 ◽

Cited By ~ 233

Author(s):

Saïd el Fantroussi ◽

Laurent Verschuere ◽

Willy Verstraete ◽

Eva M. Top

Keyword(s):

16S Rrna ◽

Microbial Communities ◽

16S Rdna ◽

Soil Microbial Communities ◽

16S Rrna Genes ◽

Rrna Genes ◽

Rrna Gene ◽

Metabolic Potential ◽

Soil Microbial ◽

Enrichment Cultures

ABSTRACT The effect of three phenyl urea herbicides (diuron, linuron, and chlorotoluron) on soil microbial communities was studied by using soil samples with a 10-year history of treatment. Denaturing gradient gel electrophoresis (DGGE) was used for the analysis of 16S rRNA genes (16S rDNA). The degree of similarity between the 16S rDNA profiles of the communities was quantified by numerically analysing the DGGE band patterns. Similarity dendrograms showed that the microbial community structures of the herbicide-treated and nontreated soils were significantly different. Moreover, the bacterial diversity seemed to decrease in soils treated with urea herbicides, and sequence determination of several DGGE fragments showed that the most affected species in the soils treated with diuron and linuron belonged to an uncultivated bacterial group. As well as the 16S rDNA fingerprints, the substrate utilization patterns of the microbial communities were compared. Principal-component analysis performed on BIOLOG data showed that the functional abilities of the soil microbial communities were altered by the application of the herbicides. In addition, enrichment cultures of the different soils in medium with the urea herbicides as the sole carbon and nitrogen source showed that there was no difference between treated and nontreated soil in the rate of transformation of diuron and chlorotoluron but that there was a strong difference in the case of linuron. In the enrichment cultures with linuron-treated soil, linuron disappeared completely after 1 week whereas no significant transformation was observed in cultures inoculated with nontreated soil even after 4 weeks. In conclusion, this study showed that both the structure and metabolic potential of soil microbial communities were clearly affected by a long-term application of urea herbicides.

Download Full-text

Elevated Carbon Dioxide Alters the Structure of Soil Microbial Communities

Applied and Environmental Microbiology ◽

10.1128/aem.06924-11 ◽

2012 ◽

Vol 78 (8) ◽

pp. 2991-2995 ◽

Cited By ~ 51

Author(s):

Ye Deng ◽

Zhili He ◽

Meiying Xu ◽

Yujia Qin ◽

Joy D. Van Nostrand ◽

...

Keyword(s):

Carbon Dioxide ◽

Microbial Communities ◽

Microbial Community Composition ◽

Soil Microbial Communities ◽

16S Rrna Genes ◽

Rrna Genes ◽

Soil Microbial ◽

Composition And Structure ◽

Pyrosequencing Analysis ◽

Soil Microbial Community Composition

ABSTRACTPyrosequencing analysis of 16S rRNA genes was used to examine impacts of elevated CO2(eCO2) on soil microbial communities from 12 replicates each from ambient CO2(aCO2) and eCO2settings. The results suggest that the soil microbial community composition and structure significantly altered under conditions of eCO2, which was closely associated with soil and plant properties.

Download Full-text

Impact of Maize Formulated Herbicides Mesotrione and S-Metolachlor, Applied Alone and in Mixture, on Soil Microbial Communities.

ISRN Ecology ◽

10.5402/2012/329898 ◽

2012 ◽

Vol 2012 ◽

pp. 1-9 ◽

Cited By ~ 9

Author(s):

Pierre Joly ◽

Pascale Besse-Hoggan ◽

Frédérique Bonnemoy ◽

Isabelle Batisson ◽

Jacques Bohatier ◽

...

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Microbial Activity ◽

Synergetic Effect ◽

Soil Microbial Communities ◽

Soil Microbial Activity ◽

Soil Microbial ◽

Lower Weight ◽

Global Soil ◽

The Impact

In order to reduce the amounts of pesticides used, and thereby their associated risks, new generations of less environmentally dangerous molecules with lower weight are currently being used in the mixtures sprayed on crops. Few studies have been made, however, to analyse their impact on the soil, and more particularly on the microorganisms living in the soil which maintain the essential functions of this ecosystem. By taking a microcosmic approach, we were able to assess the impact of the maize herbicides “cocktail” Mesotrione and S-metolachlor on global soil microbial activity, biomass, and structures, by using the formulated compounds, respectively, Callisto and Dual Gold (both registered brands of Syngenta). Our results highlighted a synergetic effect in “cocktail” microcosms resulting in an increase in the Mesotrione herbicide dissipation time and in an impact on the microbial community at onefold field rate equally to more than a single herbicide used at tenfold field rate.

Download Full-text