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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.

SUBMITTER: Souza RC

PROVIDER: S-EPMC6175745 | biostudies-literature | 2018 Oct - Dec

REPOSITORIES: biostudies-literature

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

Souza Renata Carolini RC Cantão Maurício Egídio ME Nogueira Marco Antonio MA Vasconcelos Ana Tereza Ribeiro ATR Hungria Mariangela M

Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] 20180331 4

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 K ...[more]

PMID: 29636299

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Project description:Agriculture is facing a major challenge nowadays: to increase crop production for food and energy while preserving ecosystem functioning and soil quality. Argentine Pampas is one of the main world producers of crops and one of the main adopters of conservation agriculture. Changes in soil chemical and physical properties of Pampas soils due to different tillage systems have been deeply studied. Still, not much evidence has been reported on the effects of agricultural practices on Pampas soil microbiomes. The aim of our study was to investigate the effects of agricultural land use on community structure, composition and metabolic profiles on soil microbiomes of Argentine Pampas. We also compared the effects associated to conventional practices with the effects of no-tillage systems. Our results confirmed the impact on microbiome structure and composition due to agricultural practices. The phyla Verrucomicrobia, Plactomycetes, Actinobacteria, and Chloroflexi were more abundant in non cultivated soils while Gemmatimonadetes, Nitrospirae and WS3 were more abundant in cultivated soils. Effects on metabolic metagenomic profiles were also observed. The relative abundance of genes assigned to transcription, protein modification, nucleotide transport and metabolism, wall and membrane biogenesis and intracellular trafficking and secretion were higher in cultivated fertilized soils than in non cultivated soils. We also observed significant differences in microbiome structure and taxonomic composition between soils under conventional and no-tillage systems. Overall, our results suggest that agronomical land use and the type of tillage system have induced microbiomes to shift their life-history strategies. Microbiomes of cultivated fertilized soils (i.e. higher nutrient amendment) presented tendencies to copiotrophy while microbiomes of non cultivated homogenous soils appeared to have a more oligotrophic life-style. Additionally, we propose that conventional tillage systems may promote copiotrophy more than no-tillage systems by decreasing soil organic matter stability and therefore increasing nutrient availability.

Project description:Tillage intensive cropping practices have deteriorated soil physical quality and decreased soil organic carbon (SOC) levels in rice-growing areas of South Asia. Consequently, crop productivity has declined over the years demonstrating the need for sustainable alternatives. Given that, a field experiment was conducted for six years to assess the impact of four tillage based crop establishment treatments [puddled transplant rice followed by conventional tillage in wheat/maize (CTTPR-CT), non-puddled transplant rice followed by zero-tillage in wheat/maize (NPTPR-ZT), zero-till transplant rice followed by zero-tillage in wheat/maize (ZTTPR-ZT), zero-tillage direct seeded rice followed by zero-tillage in wheat/maize (ZTDSR-ZT)], two residue management treatments [residue removal, residue retention (~33%)], and two cropping systems [rice-wheat, rice-maize] on soil aggregation, carbon pools, nutrient availability, and crop productivity. After six years of rotation, in top 0.2 m soil depth, zero-till crop establishment treatments (ZTTPR-ZT and ZTDSR-ZT) had higher (p < 0.05) total organic carbon (TOC) over conventional tillage treatment (CTTPR-CT). Zero-till crop establishment treatments increased very-labile C faction (Cfrac 1) by 21% followed by labile fraction (Cfrac 2) (16%), non-labile fraction (Cfrac 4) (13%) and less-labile fraction (Cfrac 3) (7%). Notably, higher passive C-pool in conservation tillage practices over CTTPR-CT suggests that conservation tillage could stabilize the recalcitrant form of carbon that persists longer in the soil. Meantime, zero-till crop establishment treatments had higher (p < 0.05) water stable macro-aggregates, macro-aggregates: micro-aggregates ratio and aggregate carbon content over CTTPR-CT. The treatment NPTPR-ZT significantly increased soil quality parameters over CTTPR-CT. However, the effect was not as prominent as that of ZTTPR-ZT and ZTDSR-ZT. Retention of crop residue increased (p < 0.05) TOC (12%) and soil available nutrients mainly available-P (16%), followed by available-K (12%), DTPA-extractable Zn (11%), and available-S (6%) over residue removal treatment. The constructive changes in soil properties following conservation tillage and crop residue retention led to increased crop productivity over conventional CTTPR-CT. Therefore, conservation tillage (particularly ZTTPR-ZT and ZTDSR-ZT) and crop residue retention could be recommended in tropical rice-based cropping systems for improving soil quality and production sustainability.

Dataset Information

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

Publications

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

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