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ABSTRACT: Soil bacteria attributes in a mixed forest

PROVIDER: PRJNA817877 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR18383659.fastq.gz	Fastqsanger.gz
	SRR18383659_1.fastq.gz	Fastqsanger.gz
	SRR18383659_2.fastq.gz	Fastqsanger.gz
	SRR18383660_1.fastq.gz	Fastqsanger.gz
	SRR18383660_2.fastq.gz	Fastqsanger.gz

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Project description:Soil microbial attributes in a mixed forest

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Cellulose and hemicellulose decomposition by forest soil bacteria proceeds by the action of structurally variable enzymatic systems

Project description:Evidence shows that bacteria contribute actively to the decomposition of cellulose and hemicellulose in forest soil; however, their role in this process is still unclear. Here we performed the screening and identification of bacteria showing potential cellulolytic activity from litter and organic soil of a temperate oak forest. The genomes of three cellulolytic isolates previously described as abundant in this ecosystem were sequenced and their proteomes were characterized during the growth on plant biomass and on microcrystalline cellulose. Pedobacter and Mucilaginibacter showed complex enzymatic systems containing highly diverse carbohydrate-active enzymes for the degradation of cellulose and hemicellulose, which were functionally redundant for endoglucanases, -glucosidases, endoxylanases, -xylosidases, mannosidases and carbohydrate-binding modules. Luteibacter did not express any glycosyl hydrolases traditionally recognized as cellulases. Instead, cellulose decomposition was likely performed by an expressed GH23 family protein containing a cellulose-binding domain. Interestingly, the presence of plant lignocellulose as well as crystalline cellulose both trigger the production of a wide set of hydrolytic proteins including cellulases, hemicellulases and other glycosyl hydrolases. Our findings highlight the extensive and unexplored structural diversity of enzymatic systems in cellulolytic soil bacteria and indicate the roles of multiple abundant bacterial taxa in the decomposition of cellulose and other plant polysaccharides.

2016-05-02 | PXD003844 | Pride

Project description:Soil fungi in a mixed forest

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Metaproteome analysis of different soil types

Project description:Metaproteome analysis of a forest soil and a potting soil. Different protein extraction methods were compared to investigate protein extraction efficiency and compatibility with sample downstream processing.

2015-03-26 | PRD000542 | Pride

Transcription profiling of mycorrhized European beech (Fagus sylvatica L.) roots in response to fertilization with different forms of inorganic nitrogen

Project description:Young Fagus sylvatica trees (approximately 7 to 8 years) were collected from a natural regeneration beech forest. The trees were excavated with intact soil cores, roots and top organic layer. The trees were then kept outdoors at the Department of Forest Botany, Georg-August-Universität Göttingen. Plants were protected from rain, and light conditions were matched to those of the natural stand using a shading net; otherwise, plants were exposed to natural climatic conditions. The soil moisture was regularly measured; plants were watered with deionized water as needed to keep soil moisture close to the original conditions. Trees was randomly relocated on a weekly basis throughout the experiment to avoid biasses caused by location or light effects. After 21 weeks, a treatment was applied to understand the physiological mechanisms of inorganic nitrogen uptake and assimilation under conditions of an inorganic nitrogen saturated forest simulation: Plants were fertilized with either a 20 mM solution of KNO3, a 20 mM solution of NH4Cl, or demineralized water (control) for 2 days. On the third day, the trees were harvested. Root tips were immediately shock-frozen in liquid nitrogen and used for RNA extraction.

2020-12-14 | E-MTAB-8931 | biostudies-arrayexpress

Transcriptome profiling of lung immune responses potentially related to acute respiratory distress syndrome in forest musk deer

Project description:ARDS-mediated lung transcriptome alterations were identified in forest musk deer. Moreover, multiple transcripts/genes involved in lung development and lung defense responses to bacteria/viruses/fungi in ARDS were filtered out in forest musk deer.

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Expression of lignin-degrading enzymes in soils using targeted microarrays

Project description:Microarrays have become established tools for describing microbial systems, however the assessment of expression profiles for environmental microbial communities still presents unique challenges. Notably, the concentration of particular transcripts are likely very dilute relative to the pool of total RNA, and PCR-based amplification strategies are vulnerable to amplification biases and the appropriate primer selection. Thus, we apply a signal amplification approach, rather than template amplification, to analyze the expression of selected lignin-degrading enzymes in soil. Controls in the form of known amplicons and cDNA from Phanerochaete chrysosporium were included and mixed with the soil cDNA both before and after the signal amplification in order to assess the dynamic range of the microarray. We demonstrate that restored prairie soil expresses a diverse range of lignin-degrading enzymes following incubation with lignin substrate, while farmed agricultural soil does not. The mixed additions of control cDNA with soil cDNA indicate that the mixed biomass in the soil does interfere with low abundance transcript changes, nevertheless our microarray approach consistently reports the most robust signals. Keywords: comparative analysis, microbial ecology, soil microbial communities

2009-06-01 | GSE13977 | GEO

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