Outstanding impact of soil tillage on the abundance of soil hydrolases revealed by a metagenomic approach

Abstract

The soil represents the main source of novel biocatalysts and biomolecules of industrial relevance. We searched for hydrolases in silico in four shotgun metagenomes (4,079,223 sequences) obtained in a 13-year field trial carried out in southern Brazil, under the no-tillage (NT), or conventional tillage (CT) managements, with crop succession (CS, soybean/wheat), or crop rotation (CR, soybean/maize/wheat/lupine/oat). We identified 42,631 hydrolases belonging to five classes by comparing with the KEGG database, and 44,928 sequences by comparing with the NCBI-NR database. The abundance followed the order: lipases > laccases > cellulases > proteases > amylases > pectinases. Statistically significant differences were attributed to the tillage system, with the NT showing about five times more hydrolases than the CT system. The outstanding differences can be attributed to the management of crop residues, left on the soil surface in the NT, and mechanically broken and incorporated into the soil in the CT. Differences between the CS and the CR were slighter, 10% higher for the CS, but not statistically different. Most of the sequences belonged to fungi (Verticillium, and Colletotrichum for lipases and laccases, and Aspergillus for proteases), and to the archaea Sulfolobus acidocaldarius for amylases. Our results indicate that agricultural soils under conservative managements may represent a hotspot for bioprospection of hydrolases.

Multi-functional assessment of soil health under Conservation Agriculture in Cambodia

“…CA is based on three technical principles which are (i) minimum soil disturbance, (ii) retention of crop and cover crop residues and (iii) use of diversified cropping patterns (FAO, 2014;Séguy et al, 2006). CA was promoted for providing multiple beneficial effects on soil physical (Indoria et al, 2017;Patra et al, 2019), biological (Lienhard et al, 2013;Mathew et al, 2012;Souza et al, 2018) and chemical properties (Ivy et al, 2017;Parihar et al, 2018;Ranaivoson et al, 2017). Amongst soil chemical properties, soil organic carbon (SOC) was widely studied under CA, due to its potential to adapt farming systems to climate change and variability, and mitigate the effects of climate change through carbon sequestration (Lal, 2013).…”

Microbial Response to Phytostabilization in Mining Impacted Soils Using Maize in Conjunction with Biochar and Compost

“…Extracellular enzymes assayed were as follows: βglucosidase (BG), used as an indicator of C cycling; N-acetyl-β-D-glucosaminidase (NAG), a chitinase involved in chitin degradation and used as an indicator of N cycling in soils; acid phosphomonoesterase (AcP), used as an indicator of P cycling. Esterase (EST), a hydrolase, is an intracellularly located enzyme; as one of the most abundant hydrolase enzymes found in soils, it was used to assess general microbial activity [48].…”

“…This suppression of NAG activity upon addition of compost is potentially due to readily accessible organic N supplied by the compost [49]. hydrolase, is an intracellularly located enzyme; as one of the most abundant hydrolase enzymes found in soils, it was used to assess general microbial activity [48]. For BG, which is frequently implemented in soil health indices as an indicator of nutrient cycling, the lowest activity rate was exhibited in the control soil (mean: 0.02 nmol g −1 soil h −1 ; Figure 4A).…”

Targeted Metagenomics of Retting in Flax: The Beginning of the Quest to Harness the Secret Powers of the Microbiota

“…The study of the effect of agricultural management practices on crop soil microbial communities is also a growing field for the use of shotgun metagenomics and aims to correlate these practices to microbial community taxonomic diversity and the pool of functions (Souza et al, 2018;Nelkner et al, 2019). In their study, Souza et al (2018) analyzed soil samples that were subjected to four different soil and crop management practices (conventional tillage and no tillage, each with crop succession or crop rotation). Although their results revealed a limited impact of management practice on the abundance of each functional category from the SEED database, the use of KEGG pathways identified some practice-related differences in key enzymes involved in the metabolism of fructose and mannose.…”