Investigating responses of soil bacterial community composition to hardwood biochar amendment using high-throughput PCR sequencing

Cole, Emily J.; Zandvakili, Omid Reza; Blanchard, Jeffrey L.; Xing, Baoshan; Hashemi, Masoud; Etemadi, Fatemeh

doi:10.1016/j.apsoil.2018.12.010

Cited by 37 publications

(19 citation statements)

References 23 publications

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“…The control soil maintained pH values below 6, whereas the biochar amended soils all had elevated soil pH, increasing throughout the experiment and maintaining pH values of 6.2–6.8 [1] . It is important to note, that all biochar treatment levels significantly increased the soil pH within the acceptable range for field crop growth.…”

Section: Datamentioning

confidence: 97%

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Dataset on the effect of hardwood biochar on soil gravimetric moisture content and nitrate dynamics at different soil depths with FTIR analysis of fresh and aged biochar

et al. 2019

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The goal of this research work was to determine widespread impact kiln-produced hardwood biochar has upon temperate agricultural soil characteristics in a long-term field experiment. This dataset is supplementary to the submitted research by [1] and presents select physical and chemical characteristics of the biochar and field plots amended with hardwood biochar. Data on soil gravimetric moisture content (GMC), soil acidity and soil nitrate-N concentration at lower depth of soil under different biochar application rates is presented. Fourier Transform Infrared (FTIR) spectroscopy is provided to demonstrate the difference between fresh and aged biochar in terms of surface functional group content.

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Section: Datamentioning

confidence: 97%

“… Data source location University of Massachusetts Amherst Crops and Animal Research and Education Farm in South Deerfield, MA. Data accessibility Data are accessible with the article Related research article The associated research article to this data set is [1] . …”

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Dataset on the effect of hardwood biochar on soil gravimetric moisture content and nitrate dynamics at different soil depths with FTIR analysis of fresh and aged biochar

et al. 2019

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“…The microbial community consisting of bacteria tend to respond positively to BC, as several studies have reported a significant increase in abundance, diversity, after BC application, especially in the rhizosphere soil [158][159][160][161]. For example, an increase in specific bacterial families and species such as phosphorous solubilizing [162], nitrifiers [163], and N-fixing and denitrifiers [164] was observations [158]. Similar results with wood (fir, cedar) BC (450°C -550°C) indicated a significant shift towards a bacteria-dominated microbial community in a short-term study (3 months) and was attributed to the increased release of labile C from the BC or stable SOM-BC aggregates [91].…”

Section: Bacteriamentioning

confidence: 99%

“…reported with Malus pumila woodchip BC (500°C), Eucalyptus saligna hardwood BC (550°C), and sugar maple wood BC (400°C) soil amendment, respectively. Additional studies found only modest or no differences[136,155,164,165]. The change in the composition of bacterial communities after incorporation of BC in soil is highly dependent on the preexisting bacterial community, soil type, and overall BC characteristics.Generally, the gram-negative bacterial community are favored in the nutrient-enriched BCamended soils and initially predominate the soil environment since they perform specific and narrow functions.…”

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confidence: 94%

Biochar - A Panacea for Agriculture or Just Carbon?

Tenic¹,

Ghogare‬²,

Dhingra³

2020

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The sustainable production of food faces formidable challenges. Foremost is the availability of arable soils, which have been ravaged by the overuse of fertilizers and detrimental soil management techniques. As such, maintenance of soil quality, and reclamation of marginal soils, has become an increasingly important endeavor. Recently, there has been emerging interest in the use of biochar, a carbon rich, porous material thought to improve various aspects of soil performance. Biochar (BC) is produced through the thermochemical decomposition of organic matter at high temperature in an oxygen limited environment, in a process known as pyrolysis. Importantly, the source of organic material, or ‘feedstock,’ used in this process and different parameters of pyrolysis, especially temperature, determine the chemical and physical properties of biochar. Incorporation of BC impacts soil-water relations, tilth and nutrient status, pH, soil organic matter (SOM), and microbial activity. Soil amendment with BC has been shown to have an overall positive impact on soil health and crop productivity; however, initial soil properties need to be considered prior to the application of BC. There is an urgent need to understand the effects of long-term field application of BC and how it influences the soil microcosm. This knowledge will facilitate predictable enhancement of crop productivity and meaningful carbon sequestration.

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“…Nowadays, many studies in environmental microbiology [ 1 , 2 ], molecular ecology [ 3 , 4 ] and medical diagnostics [ 5 , 6 ] are either based on or accompanied by next-generation sequencing (NGS) analyses. Amplicon-sequencing (e.g.…”

Section: Introductionmentioning

confidence: 99%

CoMA – an intuitive and user-friendly pipeline for amplicon-sequencing data analysis

et al. 2020

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In recent years, there has been a veritable boost in next-generation sequencing (NGS) of gene amplicons in biological and medical studies. Huge amounts of data are produced and need to be analyzed adequately. Various online and offline analysis tools are available; however, most of them require extensive expertise in computer science or bioinformatics, and often a Linux-based operating system. Here, we introduce “CoMA–Comparative Microbiome Analysis” as a free and intuitive analysis pipeline for amplicon-sequencing data, compatible with any common operating system. Moreover, the tool offers various useful services including data pre-processing, quality checking, clustering to operational taxonomic units (OTUs), taxonomic assignment, data post-processing, data visualization, and statistical appraisal. The workflow results in highly esthetic and publication-ready graphics, as well as output files in standardized formats (e.g. tab-delimited OTU-table, BIOM, NEWICK tree) that can be used for more sophisticated analyses. The CoMA output was validated by a benchmark test, using three mock communities with different sample characteristics (primer set, amplicon length, diversity). The performance was compared with that of Mothur, QIIME and QIIME2-DADA2, popular packages for NGS data analysis. Furthermore, the functionality of CoMA is demonstrated on a practical example, investigating microbial communities from three different soils (grassland, forest, swamp). All tools performed well in the benchmark test and were able to reveal the majority of all genera in the mock communities. Also for the soil samples, the results of CoMA were congruent to those of the other pipelines, in particular when looking at the key microbial players.

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Investigating responses of soil bacterial community composition to hardwood biochar amendment using high-throughput PCR sequencing

Cited by 37 publications

References 23 publications

Dataset on the effect of hardwood biochar on soil gravimetric moisture content and nitrate dynamics at different soil depths with FTIR analysis of fresh and aged biochar

Dataset on the effect of hardwood biochar on soil gravimetric moisture content and nitrate dynamics at different soil depths with FTIR analysis of fresh and aged biochar

Biochar - A Panacea for Agriculture or Just Carbon?

CoMA – an intuitive and user-friendly pipeline for amplicon-sequencing data analysis

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