Ontology highlight
ABSTRACT:
PROVIDER: PRJNA804565 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR17951200.fastq.gz | Fastqsanger.gz | |||
| SRR17951201.fastq.gz | Fastqsanger.gz | |||
| SRR17951202.fastq.gz | Fastqsanger.gz | |||
| SRR17951203.fastq.gz | Fastqsanger.gz | |||
| SRR17951204.fastq.gz | Fastqsanger.gz |
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Project description:Permafrost soil in high latitude tundra is one of the largest terrestrial carbon (C) stocks and is highly sensitive to climate warming. Understanding microbial responses to warming induced environmental changes is critical to evaluating their influence on soil biogeochemical cycles. In this study, a functional gene array (i.e. GeoChip 4.2) was used to analyze the functional capacities of soil microbial communities collected from a naturally degrading permafrost region in Central Alaska. Varied thaw history was reported to be the main driver of soil and plant differences across a gradient of minimally, moderately and extensively thawed sites. Compared with the minimally thawed site, the number of detected functional gene probes across the 15-65 cm depth profile at the moderately and extensively thawed sites decreased by 25 % and 5 %, while the community functional gene beta-diversity increased by 34% and 45%, respectively, revealing decreased functional gene richness but increased community heterogeneity along the thaw progression. Particularly, the moderately thawed site contained microbial communities with the highest abundances of many genes involved in prokaryotic C degradation, ammonification, and nitrification processes, but lower abundances of fungal C decomposition and anaerobic-related genes. Significant correlations were observed between functional gene abundance and vascular plant primary productivity, suggesting that plant growth and species composition could be co-evolving traits together with microbial community composition. Altogether, this study reveals the complex responses of microbial functional potentials to thaw related soil and plant changes, and provides information on potential microbially mediated biogeochemical cycles in tundra ecosystems.
2019-06-03 | GSE97107 | GEO
Project description:<p>Drought stress negatively impacts microbial activity, but the magnitude of stress responses are likely dependent on a diversity of below ground interactions. Populus trichocarpa individuals and no plant bulk soils were exposed to extended drought (~0.03% gravimetric water content (GWC) after 12d), re-wet, and a 12-d 'recovery' period to determine the effects of plant presence in mediating soil microbiome stability to water stress. Plant metabolomic analyses indicated that drought exposure increased host investment in C and N metabolic pathways (amino acids, fatty-acids, phenolic glycosides) regardless of recovery. Several metabolites positively correlated with root-associated microbial alpha diversity, but not those of soil communities. Soil bacterial community composition shifted with P. trichocarpa presence and with drought relative to irrigated controls, whereas soil fungal composition only shifted with plant presence. However, root fungal communities strongly shifted with drought, whereas root bacterial communities changed to a lesser degree. The proportion of bacterial water-stress opportunistic OTUs (enriched counts in drought) were high (~11%) at the end of drying phases, and maintained after re-wet, and recovery phases in bulk soils, but declined over time in soils with plants present. For root fungi opportunistic OTUs were high at the end of recovery in drought treatments (~17% abundance), although relatively not responsive in soils, particularly planted soils (< 0.5% abundance for sensitive or opportunistic). These data indicate that plants modulate soil and root associated microbial drought responses via tight plant-microbe linkages during extreme drought scenarios, but trajectories after extreme drought vary with plant habitat and microbial functional groups.</p>
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Project description:Plants are naturally associated with diverse microbial communities, which play significant roles in plant performance, such as growth promotion or fending off pathogens. The roots of Alkanna tinctoria L. are rich in naphthoquinones, particularly the medicinally used chiral compounds alkannin, shikonin and their derivatives. Former studies already have shown that microorganisms may modulate plant metabolism. To further investigate the potential interaction between A. tinctoria and associated microorganisms we performed a greenhouse experiment, in which A. tinctoria plants were grown in the presence of three distinct soil microbiomes. At four defined plant developmental stages we made an in-depth assessment of bacterial and fungal root-associated microbiomes as well as all primary and secondary metabolites. Our results showed that the plant developmental stage was the most important driver influencing the plant metabolite content, revealing peak contents of alkannin/shikonin at the fruiting stage. In contrast, the soil microbiome had the biggest impact on the plant root microbiome. Correlation analyses performed on the measured metabolite content and the abundance of individual bacterial and fungal taxa suggested a dynamic, at times positive or negative relationship between root-associated microorganisms and root metabolism. In particular, the bacterial Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium group and the fungal species Penicillium jensenii were found to be positively correlated with higher content of alkannins.
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Project description:Understanding the mechanisms underlying the establishment of invasive plants is critical in community ecology. According to a widely accepted theory, plant-soil-microbe interactions mediate the effects of invasive plants on native species, thereby affecting invasion success. However, the roles and molecular mechanisms associated with such microbes remain elusive. Using high throughput sequencing and a functional gene microarray, we found that soil taxonomic and functional microbial communities in plots dominated by Ageratina adenophora developed to benefit the invasive plant. There were increases in nitrogen-fixing bacteria and labile carbon degraders, as well as soil-borne pathogens in bulk soil, which potentially suppressed native plant growth. Meanwhile, there was an increase of microbial antagonism in the A. adenophora rhizosphere, which could inhibit pathogenicity against plant invader. These results suggest that the invasive plant A. adenophora establishes a self-reinforcing soil environment by changing the soil microbial community. It could be defined as a ‘bodyguard/mercenary army’ strategy for invasive plants, which has important insights for the mitigation of plant invasion.
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Project description:Fire is a crucial event regulating the structure and functioning of many ecosystems. Yet few studies focused on how fire affects both the taxonomic and functional diversity of soil microbial communities, along with plant diversity and soil carbon (C) and nitrogen (N) dynamics. Here, we analyze these effects for a grassland ecosystem 9-months after an experimental fire at the Jasper Ridge Global Change Experiment (JRGCE) site in California, USA. Fire altered soil microbial communities considerably, with community assembly process analysis indicating that environmental selection pressure was higher in burned sites. However, a small subset of highly connected taxa were able to withstand the disturbance. In addition, fire decreased the relative abundances of most genes associated with C degradation and N cycling, implicating a slow-down of microbial processes linked to soil C and N dynamics. In contrast, fire stimulated plant growth, likely enhancing plant-microbe competition for soil inorganic N. To synthesize our findings, we performed structural equation modeling, which showed that plants but not microbial communities were responsible for the significantly higher soil respiration rates in burned sites. In conclusion, fire is well-documented to considerable alter the taxonomic and functional composition of soil microorganisms, along with the ecosystem functioning, thus arousing feedback of ecosystem responses to affect global climate.
2022-02-19 | GSE126737 | GEO
Project description:Plants in their natural and agricultural environments are continuously exposed to a plethora of diverse microorganisms resulting in microbial colonization of plants in the rhizosphere. This process is believed to be accompanied by an intricate network of ongoing simultaneous interactions. In this study, we compared transcriptional patterns of Arabidopsis thaliana roots and shoots in the presence and absence of whole microbial communities extracted from compost soil. The results show a clear growth promoting effect of Arabidopsis shoots in the presence of soil microbes compared to axenically grown plants under identical conditions. Element analyses showed that iron uptake was facilitated by these mixed microbial communities which also lead to transcriptional downregulation of genes required for iron transport. In addition, soil microbial communities suppressed the expression of marker genes involved in oxidative stress/redox signalling, cell wall modification and plant defense. While most previous studies have focussed on individual plant-microbe interactions, our data suggest that multi-species transcriptional profiling, using simultaneous plant and metatranscriptomics coupled to metagenomics may be required to further increase our understanding of the intricate networks underlying plant-microbe interactions in their diverse environments.
2013-03-09 | GSE44984 | GEO
Project description:The melting of permafrost and its potential impact on greenhouse gas emissions is a major concern in the context of global warming. The fate of the carbon trapped in permafrost will largely depend on soil physico-chemical characteristics, among which are the quality and quantity of organic matter, pH and water content, and on microbial community composition. In this study, we used microarrays and real-time PCR (qPCR) targeting 16S rRNA genes to characterize the bacterial communities in three different soil types representative of various Arctic settings. The microbiological data were linked to soil physico-chemical characteristics and CO2 production rates. Microarray results indicated that soil characteristics, and especially the soil pH, were important parameters in structuring the bacterial communities at the genera/species levels. Shifts in community structure were also visible at the phyla/class levels, with the soil CO2 production rate being positively correlated to the relative abundance of the Alphaproteobacteria, Bacteroidetes, and Betaproteobacteria. These results indicate that CO2 production in Arctic soils does not only depend on the environmental conditions, but also on the presence of specific groups of bacteria that have the capacity to actively degrade soil carbon.
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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.
2017-07-07 | PXD003572 | Pride
Project description:Plants in their natural and agricultural environments are continuously exposed to a plethora of diverse microorganisms resulting in microbial colonization of plants in the rhizosphere. This process is believed to be accompanied by an intricate network of ongoing simultaneous interactions. In this study, we compared transcriptional patterns of Arabidopsis thaliana roots and shoots in the presence and absence of whole microbial communities extracted from compost soil. The results show a clear growth promoting effect of Arabidopsis shoots in the presence of soil microbes compared to axenically grown plants under identical conditions. Element analyses showed that iron uptake was facilitated by these mixed microbial communities which also lead to transcriptional downregulation of genes required for iron transport. In addition, soil microbial communities suppressed the expression of marker genes involved in oxidative stress/redox signalling, cell wall modification and plant defense. While most previous studies have focussed on individual plant-microbe interactions, our data suggest that multi-species transcriptional profiling, using simultaneous plant and metatranscriptomics coupled to metagenomics may be required to further increase our understanding of the intricate networks underlying plant-microbe interactions in their diverse environments. Four samples were analysed in total. One corresponded to a pooled sample of RNA extracted from root tissues of 60 plants. The other three were biological replicates from shoot tissues, each of which contained 20 plants. Controls were used as reference and corresponded to tissues of plants grown in sterile conditions.
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