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Agricultural soil

ABSTRACT: The effect of chemical fumigation and substrate carbon availability on soil bacterial and fungal diversity

PROVIDER: PRJNA832601 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR19188500_1.fastq.gz	Fastqsanger.gz
	SRR19188500_2.fastq.gz	Fastqsanger.gz
	SRR19188600_1.fastq.gz	Fastqsanger.gz
	SRR19188600_2.fastq.gz	Fastqsanger.gz
	SRR19188700_1.fastq.gz	Fastqsanger.gz

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Project description:The availability of organic carbon represents a major bottleneck for the development of soil microbial communities and the regulation of microbially-mediated ecosystem processes. However, there is still a lack of knowledge on how the lifestyle and population abundances are physiologically regulated by the availability of energy and organic carbon in soil ecosystems. To date, functional insights into the lifestyles of microbial populations have been limited by the lack of straightforward approaches to the tracking of the active microbial populations. Here, by the use of an comprehensiv metaproteomics and genomics, we reveal that C-availability modulates the lifestyles of bacterial and fungal populations in drylands and determines the compartmentalization of functional niches. This study highlights that the active diversity (evaluated by metaproteomics) but not the diversity of the whole microbial community (estimated by genome profiling) is modulated by the availability of carbon and is connected to the ecosystem functionality in drylands.

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An Aspergillus niger colony locally adapts its molecular responses to spatially separated substrates

Project description:Saprotrophic fungi, such as Aspergillus niger, grow as mycelial colonies that are often considered uniform entities. To test this uniformity, we analyzed pie-slice sections of a colony grown on spatially separated substrates (glucose, wheat bran, sugar beet pulp) using transcriptomics, proteomics and metabolomics. The colony tuned its response to the local carbon source composition. Plant biomass degrading CAZymes and intracellular carbon catabolic enzymes were more abundant in parts of the colony containing the corresponding sugars. For example a stronger pectinolytic response was observed in the part of the colony grown on the pectin-rich sugar beet pulp. Our results argue against a situation in which small molecules are transported efficiently through the colony and favour high diversity within the fungal colony in natural biotopes, where the substrate is typically heterogeneous. It also demonstrates the high level of plasticity of A. niger in reponse to the composition of the prevailing lignocellulose.

2019-08-23 | GSE118894 | GEO

Dynamic utilization of low-molecular-weight organic substrates across a microbial growth rate gradient

Project description:AIM: Low-molecular-weight organic substances (LMWOSs) are at the nexus between micro-organisms, plant roots, detritus and the soil mineral matrix. The nominal oxidation state of carbon (NOSC) has been suggested as a potential parameter for modelling microbial uptake rates of LMWOSs and the efficiency of carbon incorporation into new biomass.METHODS AND RESULTS: In this study, we assessed the role of compound class and oxidation state on uptake kinetics and substrate-specific carbon use efficiency (SUE) during the growth of three model soil micro-organisms, a fungal isolate (Penicillium spinulosum) and two bacterial isolates (Paraburkholderia solitsugae, and Ralstonia pickettii). Isolates were chosen that spanned a growth rate gradient (0.046-0.316 h-1) in media containing 34 common LMWOSs at realistically low initial concentrations (25 μM each). Clustered, co-utilization of LMWOSs occurred for all three organisms. Potential trends (p < 0.05) for early utilization of more oxidized substrates were present for the two bacterial isolates (P. solitsugae and R. pickettii), but high variability (R2 < 0.15) and a small effect of NOSC indicate these relationships are not useful for prediction. The SUEs of selected substrates ranged from 0.16 to 0.99 and there was no observed relationship between NOSC and SUE.CONCLUSION: Our results do not provide compelling population-level support for NOSC as a predictive tool for either uptake kinetics or the efficiency of use of LMWOS in soil solution.SIGNIFICANCE AND IMPACT OF THE STUDY: Metabolic strategies of organisms are likely more important than chemical identity in determining LMWOS cycling in soils. Previous community-level observations may be biased towards fast-responding bacterial community members.

2023-08-14 | MTBLS3558 | MetaboLights

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