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Implications of saline water irrigation and soil straw amendment for the microbial diversity in semiarid soil and wheat rhizosphere

ABSTRACT: Implications of saline water irrigation and soil straw amendment for the microbial diversity in semiarid soil and wheat rhizosphere

PROVIDER: PRJEB30355 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR3001170_1.fastq.gz	Fastqsanger.gz
	ERR3001170_2.fastq.gz	Fastqsanger.gz
	ERR3001180_1.fastq.gz	Fastqsanger.gz
	ERR3001180_2.fastq.gz	Fastqsanger.gz
	ERR3001190_1.fastq.gz	Fastqsanger.gz

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Project description:Chitin soil amendment is known to improve soil quality, plant growth and plant stress resilience, but the underlying mechanisms are not well understood. In this study, we monitored chitin’s effect on lettuce physiology every two weeks through an eight-week growth period, analyzed the early transcriptional reprogramming and related metabolomic changes of lettuce, in response to crab chitin treatment in peat-based potting soil. In commercial growth conditions, chitin amendment still promoted lettuce growth, increased chlorophyll content, the number of leaves and crop head weight from week six. The flavonoid content in lettuce leaves was altered as well, showing an increase at week two but a decrease from week six. Transcriptomic analysis showed that over 300 genes in lettuce root were significant differentially expressed after chitin soil treatment. Gene Ontology-term (GO) enrichment analysis revealed statistical overrepresentation of GO terms linked to photosynthesis, pigment metabolic process and phenylpropanoid metabolic process. Further analysis of the differentially expressed genes (DEGs) showed that the flavonoid pathway is mostly upregulated whereas the bifurcation of upstream phenylpropanoid pathway towards lignin biosynthesis is mostly downregulated. Metabolomic analysis revealed the upregulation of salicylic acid, chlorogenic acid, ferulic acid, and p-coumaric acid in chitin treated lettuce seedlings. These phenolic compounds mainly influence the phenylpropanoid biosynthesis pathway and may play important roles in plant defense reactions. Our results suggest that chitin soil amendments might activate induced resistance by priming lettuce plants and promote lettuce growth via transcriptional changes.

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Interactive effects of depth and differential irrigation on soil microbiome composition and functioning_PNNLSoilsSFA_Naylor

Project description:GCMS datasets for the soil depth manuscript Abstract Two factors that are well-known to influence soil microbiomes include the depth of the soil as well as the level of moisture. Previous works have demonstrated that climate change will increase the incidence of drought in soils, but it is unknown how fluctuations in moisture availability affect soil microbiome composition and functioning down the depth profile. Here, we investigated soil and wheatgrass rhizosphere microbiomes in a common field setting under four different irrigation regimes and three depths. We demonstrated that there is a significant interactive effect, where fluctuations in soil moisture more strongly influence soil microbiomes at the surface layer than in deeper layers, including for soil community composition, diversity, and for functional profiles. Meanwhile, in rhizosphere communities the influence of irrigation was similar across the different depths, although there were slight discrepancies between the two cultivars of wheatgrass used. The lessened response of deeper soil microbiomes to changes in irrigation may be due to higher incidence of slow-growing, stress-resistant microbes.

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Contrasting microbial community responses to salinization and straw amendment in a semiarid bare soil and its wheat rhizosphere.

Project description:Soil salinization is a major constraint of agriculture in semiarid ecosystems. In this study soil microcosms were applied to evaluate the impact of a lower- and higher-level salinization treatment of a pristine scrubland soil on the abundance of Bacteria, Archaea, and Fungi, and on prokaryotic diversity in bare soil and the rhizosphere of wheat assessed by qPCR and high-throughput sequencing of 16S rRNA gene amplicons. Furthermore, the impact of soil straw amendment as a salt-stress alleviation strategy was studied. While the low-level salinity stimulated plant growth, the seedlings did not survive under the higher-level salinity unless the soil was amended with straw. Without the straw amendment, salinization had only minor effects on the microbial community in bare soil. On the other hand, it decreased prokaryotic diversity in the rhizosphere of wheat, but the straw amendment was effective in mitigating this effect. The straw however, was not a significant nutrient source for the rhizosphere microbiota but more likely acted indirectly by ameliorating the salinity stress on the plant. Members of Proteobacteria, Actinobacteria, and Firmicutes were abundant among the bacteria that reacted to soil salinization and the straw amendment but showed inconsistent responses indicating the large physiological diversity within these phyla.

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Long-term effects of straw return and straw-derived biochar amendment on bacterial communities in soil aggregates.

Project description:Improving soil structure, fertility, and production is of major concern for establishing sustainable agroecosystems. Further research is needed to evaluate whether different methods of straw returning determine the variations of soil aggregation and the microbial community in aggregates in the long term. In this study, we comparatively investigated the effects of long-term fertilization regimes performed over six years, namely, non-fertilization (CK), chemical fertilization (CF), continuous straw return (CS), and continuous straw-derived biochar amendment (CB), on soil aggregation and bacterial communities in rice-wheat rotation systems. The results showed that straw/biochar application increased soil nutrient content and soil aggregate size distribution and stability at both 0-20 cm and 20-40 cm soil depths, compared with those of CF and CK; CB performed better than CS. CB increased bacterial community diversity and richness in 0-20 cm soil, and evenness in 0-40 cm soil (p < 0.05); CS had no significant effect on these aspects. Variations in the relative abundance of Actinobacteria, Chloroflexi, Bacteroidetes, Nitrospirae, Gemmatimonadetes, and Latescibacteria in specific aggregates confirmed the different effects of straw/biochar on bacterial community structure. The partial least squares discrimination analysis and permutation multivariate analysis of variance revealed that fertilization, aggregate size fractions, and soil depth affected the bacterial community, although their effects differed. This study suggests that CB may reduce chemical fertilizer usage and improve the sustainability of rice-wheat cropping systems over the long term, with a better overall outcome than CS.

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