Profiles of wheat rhizobacterial communities in response to repeated glyphosate applications, crop rotation, and tillage

2020 ◽  
pp. 1-11 ◽  
Author(s):  
Newton Z. Lupwayi ◽  
Myriam R. Fernandez ◽  
Derrick A. Kanashiro ◽  
Renee M. Petri
Keyword(s):  
Crop Rotation ◽  
Relative Abundance ◽  
Triticum Turgidum ◽  
Soil Microbial Communities ◽  
Soil Microbial ◽  
No Till ◽  
Α Diversity ◽  
Candidate Division ◽  
Relative Abundances ◽  
Bacterial Groups

Due to widespread adoption of no-till management and use of glyphosate-resistant transgenic crops, glyphosate is the most widely used herbicide worldwide. However, its effect on soil microbial communities is inconsistent. We studied the effects of glyphosate, tillage, and crop rotation on the diversity and composition of soil bacterial communities in wheat (Triticum turgidum var. durum Desf.) rhizosphere after 6 and 7 yr of glyphosate applications. In a 2 × 2 × 2 factorial design, there were two crop rotation treatments: continuous wheat (W–W) and wheat in rotation with field pea (Pisum sativum L.) (P–W); two tillage treatments: minimum tillage (MT) and no-till (NT); and two glyphosate treatments: no application or pre-seeding application at the recommended rate. None of the treatments affected wheat rhizobacterial α-diversity or the relative abundances of most bacterial groups. The most abundant phyla were Proteobacteria (25.1% relative abundance), Actinobacteria (21.7%), Acidobacteria (8.7%), Bacteroidetes (5.9%), Firmicutes (1.4%), Armatimonadetes (1.3%), and Verrucomicrobia (1.2%). Glyphosate reduced the relative abundance of Alphaproteobacteria in W–W rotation but increased it in P–W rotation, and it reduced the relative abundance of Opitutus spp. The W–W rotation had greater relative abundances of the classes Bacilli (Firmicutes) and Gammaproteobacteria, and genera Bacillus and Opitutus (Verrucomicrobia), than the P–W rotation. Compared with MT, NT increased the relative abundance of the phylum candidate division WPS-1, but it reduced that of Phenylobacterium spp. in W–W rotation. These treatment effects probably had implications for soil functioning, including nutrient cycling and biological disease/pest control.

scholarly journals Soil Bacterial and Fungal Composition and Diversity Responses to Seasonal Deer Grazing in a Subalpine Meadow

Diversity ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 84
Author(s):  
Andéole Niyongabo Turatsinze ◽  
Baotian Kang ◽  
Tianqi Zhu ◽  
Fujiang Hou ◽  
Saman Bowatte
Keyword(s):  
Relative Abundance ◽  
Soil Microbial Communities ◽  
Gansu Province ◽  
Total Carbon ◽  
Mountain Range ◽  
Microbial Composition ◽  
Soil Microbial ◽  
Β Diversity ◽  
Α Diversity ◽  
Soil Bacterial

Soil microbial composition and diversity are widely recognized for their role in ecological functioning. This study examined the differences of soil microbial communities between two seasonally grazed grasslands. The study area was in the Gansu red deer farm located on the Qilian Mountain range in the Gansu province of northwestern China. This farm adopted a seasonal rotation grazing system whereby grasslands at higher altitudes are grazed in summer (SG), whilst grasslands at lower altitudes are grazed in winter (WG). The soil bacterial and fungal communities were examined by Illumina MiSeq sequencing. We found that soil water content (SWC), organic carbon (OC), total carbon (TC), and total nitrogen (TN) were significantly higher, whereas the C/N ratio was significantly lower in SG than WG pastures. The α-diversity of bacteria was greater than that of fungi in both pastures, while both bacterial and fungal α-diversity were not significantly different between the pastures. The bacterial β-diversity was significantly different between the pastures, but fungal β-diversity was not. The bacterial phylum Actinobacteria and fungal phylum Ascomycota were dominant in both pastures. The relative abundance of Actinobacteria in soil was significantly higher in WG pastures, whereas the relative abundance of Proteobacteria in soil was significantly higher in SG pastures. Significant correlations between bacterial and fungal phyla and soil properties were observed, but this varied between the two grasslands. This study showed that distinct microbial community structures developed in two pastures within the same geographic location that were grazed in different seasons.

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 Effects of Soil Microbes on Forest Recovery to Climax Community through the Regulation of Nitrogen Cycling

Forests ◽  
2020 ◽  
Vol 11 (10) ◽  
pp. 1027
Author(s):  
Dandan Qi ◽  
Fujuan Feng ◽  
Yanmei Fu ◽  
Ximei Ji ◽  
Xianfa Liu
Keyword(s):  
Relative Abundance ◽  
Soil Microbes ◽  
Microbial Community Composition ◽  
Soil Microbial Communities ◽  
N Cycling ◽  
Forest Recovery ◽  
Forest Types ◽  
Ecosystem Recovery ◽  
Soil Microbial ◽  
Clear Cutting

Microbes, as important regulators of ecosystem processes, play essential roles in ecosystem recovery after disturbances. However, it is not clear how soil microbial communities and functions change and affect forest recovery after clear-cutting. Here, we used metagenome sequencing to systematically analyse the differences in soil microbial community composition, functions, and nitrogen (N) cycling pathways between primary Korean pine forests (PF) and secondary broad-leaved forests (SF) formed after clear-cutting. Our results showed that the dominant phyla of the two forest types were consistent, but the relative abundance of some phyla was significantly different. Meanwhile, at the genus level, the fold-changes of rare genera were larger than the dominant and common genera. The genes related to microbial core metabolic functions, virulence factors, stress response, and defence were significantly enriched in SF. Additionally, based on the relative abundance of functional genes, a schema was proposed to analyse the differences in the whole N cycling processes between the two forest types. In PF, the stronger ammoniation and dissimilatory nitrate reduction (DNRA) and the weaker nitrification provided a genetic explanation for PF dominated by ammonium (NH4+) rather than nitrate (NO3−). In SF, the weaker DNRA, the stronger nitrification and denitrification, the higher soil available phosphorus (AP), and the lower nitrogen to phosphorus ratio (N/P) comprehensively suggested that SF was faced with a greater degree of N limitation. These results offer insights into the potential relationship between soil microbes and forest recovery, and aid in implementing proper forestry management.

scholarly journals Impact of Olive Saplings and Organic Amendments on Soil Microbial Communities and Effects of Mineral Fertilization

2021 ◽  
Vol 12 ◽  
Author(s):  
Miquel Llimós ◽  
Guillem Segarra ◽  
Marc Sancho-Adamson ◽  
M. Isabel Trillas ◽  
Joan Romanyà
Keyword(s):  
Relative Abundance ◽  
Soil Microbial Communities ◽  
Organic Amendments ◽  
Basal Respiration ◽  
Soil Microbiome ◽  
Organic Fertilization ◽  
Mineral Fertilization ◽  
Substrate Induced Respiration ◽  
Relative Abundances ◽  
Olive Trees

Plant communities and fertilization may have an impact on soil microbiome. Most commercial olive trees are minerally fertilized, while this practice is being replaced by the use of organic amendments. Organic amendments can both fertilize and promote plant growth-promoting organisms. Our aims were (i) to describe the changes in soil bacterial and fungal communities induced by the presence of young olive trees and their interaction with organic amendments and (ii) to compare the effects of mineral and organic fertilization. We set up two parallel experiments in pots using a previously homogenized soil collected from a commercial olive orchard: in the first one, we grew olive saplings in unamended and organically amended soils with two distinct composts and compared these two soils incubated without a plant, while in the second experiment, we comparatively tested the effects of organic and mineral fertilization. OTUs and the relative abundances of bacterial and fungal genera and phyla were analyzed by 16S rRNA and ITS1 gene amplicon using high-throughput sequencing. Basal respiration and substrate-induced respiration were measured by MicroRespTM. The effects of the different treatments were analyzed in all phyla and in the 100 most abundant genera. The presence of olive saplings increased substrate-induced respiration and bacterial and fungal richness and diversity. Organic amendments greatly affected both bacterial and fungal phyla and increased bacterial richness while not affecting fungal richness. Mineral fertilization increased the relative abundance of the less metabolically active bacterial phyla (Actinobacteria and Firmicutes), while it reduced the most metabolically active phylum, Bacteroidetes. Mineral fertilization increased the relative abundance of three N2-fixing Actinobacteria genera, while organic fertilization only increased one genus of Proteobacteria. In organically and minerally fertilized soils, high basal respiration rates were associated with low fungal diversity. Basidiomycota and Chytridiomycota relative abundances positively correlated with basal respiration and substrate-induced respiration, while Ascomycota correlated negatively. Indeed, the Ascomycota phyla comprised most of the fungal genera decreased by organic amendments. The symbiotrophic phylum Glomeromycota did not correlate with any of the C sources. The relative abundance of this phylum was promoted by the presence of plants but decreased when amending soils with composts.

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

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.

Impacts of Crop Rotation and Irrigation on Soilborne Diseases and Soil Microbial Communities

2012 ◽  
pp. 23-41 ◽  
Author(s):  
Robert P. Larkin ◽  
C. Wayne Honeycutt ◽  
O. Modesto Olanya ◽  
John M. Halloran ◽  
Zhongqi He
Keyword(s):  
Microbial Communities ◽  
Crop Rotation ◽  
Soil Microbial Communities ◽  
Soilborne Diseases ◽  
Soil Microbial

scholarly journals Short-Term Effects of Different Forest Management Methods on Soil Microbial Communities of a Natural Quercus aliena var. acuteserrata Forest in Xiaolongshan, China

Forests ◽  
2019 ◽  
Vol 10 (2) ◽  
pp. 161 ◽  
Author(s):  
Pan Wan ◽  
Gongqiao Zhang ◽  
Zhonghua Zhao ◽  
Yanbo Hu ◽  
Wenzhen Liu ◽  
...  
Keyword(s):  
Microbial Community ◽  
Forest Management ◽  
Bacterial Community ◽  
Microbial Communities ◽  
Relative Abundance ◽  
Fungal Community ◽  
Soil Microbial Community ◽  
Soil Microbial Communities ◽  
Short Term ◽  
Soil Microbial

One of the aims of sustainable forest management is to preserve the diversity and resilience of ecosystems. Unfortunately, changes in the soil microbial communities after forest management remain unclear. We analyzed and compared the soil microbial community of a natural Quercus aliena var. acuteserrata forest after four years of four different management methods using high-throughput sequencing technology. The forest management methods were close-to-nature management (CNFM), structure-based forest management (SBFM), secondary forest comprehensive silviculture (SFCS) and unmanaged control (CK). The results showed that: (1) the soil microbial community diversity indices were not significantly different among the different management methods. (2) The relative abundance of Proteobacteria in the SBFM treatment was lower than in the CK treatment, while the relative abundance of Acidobacteria in the SBFM was significantly higher than that in the CK treatment. The relative abundance of Ascomycota was highest in the CNFM treatment, and that of Basidiomycota was lowest in the CNFM treatment. However, the relative abundance of dominant bacterial and fungal phyla was not significantly different in CK and SFCS. (3) Redundancy analysis (RDA) showed that the soil organic matter (SOM), total nitrogen (TN), and available nitrogen (AN) significantly correlated with the bacterial communities, and the available potassium (AK) was the only soil nutrient, which significantly correlated with the composition of the fungal communities. The short-term SBFM treatment altered microbial bacterial community compositions, which may be attributed to the phyla present (e.g., Proteobacteria and Acidobacteria), and the short-term CNFM treatment altered microbial fungal community compositions, which may be attributed to the phyla present (e.g., Ascomycota and Basidiomycota). Furthermore, soil nutrients could affect the dominant soil microbial communities, and its influence was greater on the bacterial community than on the fungal community.

Soil microbial communities of no-till dryland agroecosystems across an evapotranspiration gradient

2007 ◽  
Vol 35 (1) ◽  
pp. 94-106 ◽  
Author(s):  
Mary Stromberger ◽  
Zahir Shah ◽  
Dwayne Westfall
Keyword(s):  
Microbial Communities ◽  
Soil Microbial Communities ◽  
Soil Microbial ◽  
No Till

scholarly journals Erosion reduces soil microbial diversity, network complexity and multifunctionality

2021 ◽  
Author(s):  
Liping Qiu ◽  
Qian Zhang ◽  
Hansong Zhu ◽  
Peter B. Reich ◽  
Samiran Banerjee ◽  
...  
Keyword(s):  
Soil Erosion ◽  
Microbial Diversity ◽  
Microbial Communities ◽  
Negative Impact ◽  
Microbial Community Composition ◽  
Soil Microbial Communities ◽  
Soil Microbial Diversity ◽  
Soil Microbial ◽  
Relative Abundances ◽  
The Impact

AbstractWhile soil erosion drives land degradation, the impact of erosion on soil microbial communities and multiple soil functions remains unclear. This hinders our ability to assess the true impact of erosion on soil ecosystem services and our ability to restore eroded environments. Here we examined the effect of erosion on microbial communities at two sites with contrasting soil texture and climates. Eroded plots had lower microbial network complexity, fewer microbial taxa, and fewer associations among microbial taxa, relative to non-eroded plots. Soil erosion also shifted microbial community composition, with decreased relative abundances of dominant phyla such as Proteobacteria, Bacteroidetes, and Gemmatimonadetes. In contrast, erosion led to an increase in the relative abundances of some bacterial families involved in N cycling, such as Acetobacteraceae and Beijerinckiaceae. Changes in microbiota characteristics were strongly related with erosion-induced changes in soil multifunctionality. Together, these results demonstrate that soil erosion has a significant negative impact on soil microbial diversity and functionality.

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