Making big data smart—how to use metagenomics to understand soil quality

Vestergaard, Gisle; Schulz, Stefanie; Schöler, Anne; Schloter, Michael

doi:10.1007/s00374-017-1191-3

Cited by 171 publications

(63 citation statements)

References 45 publications

(56 reference statements)

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“…As suggested by Vestergaard et al . (), three cores were collected for each plot, pooled and subsequently homogenized on a 5 mm sieve. A total of twenty‐four (24) samples were taken (6 per site, in three replicates, per season).…”

Section: Methodsmentioning

confidence: 99%

“…Samples were taken from both sites in April and September of 2015 using a soil auger of 3 cm diameter to a depth of 10 cm. As suggested by Vestergaard et al (2017), three cores were collected for each plot, pooled and subsequently homogenized on a 5 mm sieve. A total of twenty-four (24) samples were taken (6 per site, in three replicates, per season).…”

Section: Methodsmentioning

confidence: 99%

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Bacterial potentials for uptake, solubilization and mineralization of extracellular phosphorus in agricultural soils are highly stable under different fertilization regimes

Gräfe

Goers

Tucher

et al. 2018

Environ Microbiol Rep

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Phosphorus is one of the most important macronutrient for plants. In agriculture, amending fertilizer with phosphorus (P) is common practice. However, natural phosphorus sources are finite, making research for more sustainable management practices necessary. We postulated that the addition of carbon (C) and nitrogen (N) would stimulate phosphorus mobilization by bacteria because of their desire to maintain a stable intracellular C:N:P stoichiometry. Therefore, we chose a metagenomic approach to investigate two agricultural soils, which only received mineral N fertilizer or mineral N and organic fertilizer for more than 20 years. The most abundant genes involved in the acquisition of external P sources in our study were those involved in solubilization and subsequent uptake of inorganic phosphorus. Independent of site and season, the relative abundance of genes involved in P turnover was not significantly affected by the addition of fertilizers. However, the type of fertilization had a significant impact on the diversity pattern of bacterial families harbouring genes coding for the different P transformation processes. This gives rise to the possibility that fertilizers can substantially change phosphorus turnover efficiency by favouring different families. Additionally, none of the families involved in phosphorus turnover covered all investigated processes. Therefore, promoting bacteria which play an essential role specifically in mobilization of hardly accessible phosphorus could help to secure the phosphorus supply of plants in soils with low P input.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Bacterial potentials for uptake, solubilization and mineralization of extracellular phosphorus in agricultural soils are highly stable under different fertilization regimes

Gräfe

Goers

Tucher

et al. 2018

Environ Microbiol Rep

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“…Raw sequences were processed as described by Vestergaard et al (2017). Specifically, adapter removal and read trimming was done using AdapterRemoval (Schubert et al, 2016) set to minimum Phred quality of 15, and a minimum read length of 50.…”

Section: Data Filtering Taxonomic and Functional Analysismentioning

confidence: 99%

Shifts in reclamation management strategies shape the role of exopolysaccharide and lipopolysaccharide‐producing bacteria during soil formation

Vuko

Cania

Vogel

et al. 2020

Microbial Biotechnology

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Summary Polymeric substances produced by microbes play a key role for the development of soil aggregates. Here, we investigated the dynamics of bacterial families contributing to the formation of exopolysaccharides and lipopolysaccharides, major constituents of polymeric substances, at a managed land reclamation site of a post‐mining area. We collected soil samples from the initial and the agricultural management phase and expected a peak in the abundance of bacteria capable for exopolysaccharide and lipopolysaccharide production at the points of the biggest disturbances. We used shotgun metagenomic sequencing in combination with measurements of exopolysaccharide concentrations. Our results underline the importance of exopolysaccharide and lipopolysaccharide‐producing bacteria after nutrient input combined with structural disturbance events, caused here by the initial planting of alfalfa and the introduction of a tillage regime together with organic fertilization in the agricultural management phase. Moreover, the changes in management caused a shift in the exopolysaccharide/lipopolysaccharide‐producing community. The initial phase was dominated by typical colonizers of oligotrophic environments, specifically nitrogen fixers (Rhizobiaceae, Comamonadaceae, Hyphomicrobiaceae), while bacteria common in agricultural soils, such as Sphingomonadaceae, Oxalobacteraceae and Nitrospiraceae, prevailed in the agricultural management phase.

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“…Key quality control steps include adapter trimming, quality and length filtering, chimeric sequence and contaminant removal (e.g., PhiX and host DNA), and are discussed in detail by Vestergaard et al (2017). Bokulich et al (2013) provide guidelines for Illumina® 16s rRNA amplicon sequencing analysis, showing that filtering for high-quality read length and using abundance cut-offs significantly improve diversity estimates.…”

Section: Bioinformatic Processingmentioning

confidence: 99%

“…For other issues including soil sampling strategies, DNA extraction, and metadata collection, we refer to Vestergaard et al (2017).…”

Section: Introductionmentioning

confidence: 99%

Analysis of soil microbial communities based on amplicon sequencing of marker genes

Schöler¹,

Jacquiod²,

Vestergaard³

et al. 2017

Biol Fertil Soils

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213

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The use of cultivation independent methods has revolutionized soil biology in the last decades. Most popular approaches are based on directly extracted DNA from soil and subsequent analysis of PCR-amplified marker genes by nextgeneration sequencing. While these high-throughput methods offer novel possibilities over cultivation-based approaches, several key points need to be considered to minimize potential biases during library preparation and downstream bioinformatic analysis. This opinion paper highlights crucial steps that should be considered for accurate analysis and data interpretation.

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Making big data smart—how to use metagenomics to understand soil quality

Cited by 171 publications

References 45 publications

Bacterial potentials for uptake, solubilization and mineralization of extracellular phosphorus in agricultural soils are highly stable under different fertilization regimes

Bacterial potentials for uptake, solubilization and mineralization of extracellular phosphorus in agricultural soils are highly stable under different fertilization regimes

Shifts in reclamation management strategies shape the role of exopolysaccharide and lipopolysaccharide‐producing bacteria during soil formation

Analysis of soil microbial communities based on amplicon sequencing of marker genes

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