Five xerotolerant new species of Penicillium from soils
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PROVIDER: PRJEB31761 | ENA |
REPOSITORIES: ENA
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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
Project description:In this work, we used a functional gene microarray approach (GeoChip) to assess the soil microbial community functional potential related to the different wine quality. In order to minimize the soil variability, this work was conducted at a “within-vineyard” scale, comparing two similar soils (BRO11 and BRO12) previously identified with respect to pedological and hydrological properties within a single vineyard in Central Tuscany and that yielded highly contrasting wine quality upon cultivation of the same Sangiovese cultivar
2020-03-04 | GSE146289 | GEO
Project description:Understanding biological diversity and distribution patterns at multiple spatial scales is a central issue in ecology. Here, we investigated the biogeographical patterns of functional genes in soil microbes from 24 arctic heath sites using GeoChip-based metagenomics and principal coordinates of neighbour matrices (PCNM)-based analysis. Functional gene richness varied considerably among sites, while the proportions of each major functional gene category were evenly distributed. Functional gene composition varied significantly at most medium and broad spatial scales, and the PCNM analyses indicated that 14-20% of the variation in total and major functional gene categories could be attributed primarily to relatively broad-scale spatial effects that were consistent with broad-scale variation in soil pH and total nitrogen. The combination of variance partitioning and multi-scales analysis indicated that spatial distance effects contributed 12% to variation in functional gene composition，whereas environmental factors contributed only 3%. This relatively strong influence of spatial as compared to environmental variation in determining functional gene distributions contrasts sharply with typical microbial phylotype/species-based biogeographical patterns in the Arctic and elsewhere. Our results suggest that the distributions of soil functional genes cannot be predicted from phylogenetic distributions because spatial factors associated with historical contingencies are relatively important determinants of their biogeography.
2014-12-10 | GSE63927 | GEO
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 We used lignin degradation as a model process to demonstrate the use of an oligonucleotide microarray for directly detecting gene expression in soil communities using signal amplification instead of template amplification to avoid the introduction of PCR bias. In the current study, we analyzed mRNA isolated from two distinct soil microbial communities and demonstrate our ability to detect the expression of a small subset of lignin degrading genes following exposure to a lignitic substrate. We also included purified control amplicons and mixed target experiments with pure P. chrysosporium genomic cDNA to determine the level of interference from soil biomass on target hybridization.
2010-05-18 | E-GEOD-13977 | biostudies-arrayexpress
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.
2011-01-01 | GSE24800 | GEO
Project description:Aluminum (Al)–tolerant phosphobacteria can improve plant performance in acidic soils by increasing Al complexing and phosphorus (P) availability. However, it is almost unknown how Al stress along with P deficiency affect the bacterial biochemistry and physiology. Because high Al levels and low P availability often occur simultaneously in acidic soils, we have evaluated the single and mutual effects of a high Al stress and P deficiency on the proteome of the Al‒tolerant phosphobacteria strain Klebsiella sp. RCJ4. This strain was previously isolated from the rhizosphere of Lollium perenne plants grown in acidic soil. The strain was cultivated in mineral media modified to contain i) high P (1.4 mM) in the absence of Al, ii) high P (1.4 mM) and high Al (10 mM), iii) low P (0.05 mM) in the absence of Al, and iv) low P (0.05 mM) and high Al (10 mM). Total proteins from bacterial cells were extracted at the end of the exponential phase of growth and subjected to high–throughput proteomics analysis. The results showed that P deficiency was mainly associated with an upregulation of the P metabolism proteins subject to Pho regulon control, including phosphatases and transporters involved in the uptake of organophosphorus compounds such as phosphomonoesters, phosphonates and glycerol–3–phosphate. Aluminum exposure primarily decreased the expression of iron (Fe)–sulfur and haem-containing proteins with a concomitant upregulation of Fe acquisition and metabolism proteins, including siderophore precursors and receptors of Fe–chelator complexes. Here, we demonstrated the preponderant role that Al plays in the adjustment of Fe homeostasis, and consequently in the central metabolism of the bacteria. This is the first report of a proteomic study of the interaction between high Al and P deficiency in acidic soil–adapted bacteria. This knowledge is crucial for developing bioinoculants for crops affected by both Al toxicity and P deficiency.
2023-09-27 | PXD041867 | Pride
Project description:Aluminum (Al)–tolerant phosphobacteria can improve plant performance in acidic soils by increasing Al complexing and phosphorus (P) availability. However, it is almost unknown how Al stress along with P deficiency affect the bacterial biochemistry and physiology. Because high Al levels and low P availability often occur simultaneously in acidic soils, we have evaluated the single and mutual effects of a high Al stress and P deficiency on the proteome of the Al‒tolerant phosphobacteria strain Enterobacter sp. RJAL6. This strain was previously isolated from the rhizosphere of Lollium perenne plants grown in acidic soil. The strain was cultivated in mineral media modified to contain i) high P (1.4 mM) in the absence of Al, ii) high P (1.4 mM) and high Al (10 mM), iii) low P (0.05 mM) in the absence of Al, and iv) low P (0.05 mM) and high Al (10 mM). Total proteins from bacterial cells were extracted at the end of the exponential phase of growth and subjected to high–throughput proteomics analysis. The results showed that P deficiency was mainly associated with an upregulation of the P metabolism proteins subject to Pho regulon control, including phosphatases and transporters involved in the uptake of organophosphorus compounds such as phosphomonoesters, phosphonates and glycerol–3–phosphate. Aluminum exposure primarily decreased the expression of iron (Fe)–sulfur and haem-containing proteins with a concomitant upregulation of Fe acquisition and metabolism proteins, including siderophore precursors and receptors of Fe–chelator complexes. Here, we demonstrated the preponderant role that Al plays in the adjustment of Fe homeostasis, and consequently in the central metabolism of the bacteria. This is the first report of a proteomic study of the interaction between high Al and P deficiency in acidic soil–adapted bacteria. This knowledge is crucial for developing bioinoculants for crops affected by both Al toxicity and P deficiency.
2023-09-27 | PXD041868 | Pride
Project description:Aluminum (Al)–tolerant phosphobacteria can improve plant performance in acidic soils by increasing Al complexing and phosphorus (P) availability. However, it is almost unknown how Al stress along with P deficiency affect the bacterial biochemistry and physiology. Because high Al levels and low P availability often occur simultaneously in acidic soils, we have evaluated the single and mutual effects of a high Al stress and P deficiency on the proteome of the Al‒tolerant phosphobacteria strain Enterobacter sp. 198. This strain was previously isolated from the rhizosphere of Lollium perenne plants grown in acidic soil. The strain was cultivated in mineral media modified to contain i) high P (1.4 mM) in the absence of Al, ii) high P (1.4 mM) and high Al (10 mM), iii) low P (0.05 mM) in the absence of Al, and iv) low P (0.05 mM) and high Al (10 mM). Total proteins from bacterial cells were extracted at the end of the exponential phase of growth and subjected to high–throughput proteomics analysis. The results showed that P deficiency was mainly associated with an upregulation of the P metabolism proteins subject to Pho regulon control, including phosphatases and transporters involved in the uptake of organophosphorus compounds such as phosphomonoesters, phosphonates and glycerol–3–phosphate. Aluminum exposure primarily decreased the expression of iron (Fe)–sulfur and haem-containing proteins with a concomitant upregulation of Fe acquisition and metabolism proteins, including siderophore precursors and receptors of Fe–chelator complexes. Here, we demonstrated the preponderant role that Al plays in the adjustment of Fe homeostasis, and consequently in the central metabolism of the bacteria. This is the first report of a proteomic study of the interaction between high Al and P deficiency in acidic soil–adapted bacteria. This knowledge is crucial for developing bioinoculants for crops affected by both Al toxicity and P deficiency.
2023-09-27 | PXD041866 | Pride
Project description:Understanding the environmental factors that shape microbial communities is crucial, especially in extreme environments, like Antarctica. Two main forces were reported to influence Antarctic soil microbes: birds and plants. Both birds and plants are currently undergoing unprecedented changes in their distribution and abundance due to global warming. However, we need to clearly understand the relationship between plants, birds and soil microorganisms. We therefore collected rhizosphere and bulk soils from six different sampling sites subjected to different levels of bird influence and colonized by Colobanthus quitensis and Deschampsia antarctica in the Admiralty Bay, King George Island, Maritime Antarctic. Microarray and qPCR assays targeting 16S rRNA genes of specific taxa were used to assess microbial community structure, composition and abundance and analyzed with a range of soil physico-chemical parameters. The results indicated significant rhizosphere effects in four out of the six sites, including areas with different levels of bird influence. Acidobacteria were significantly more abundant in soils with little bird influence (low nitrogen) and in bulk soil. In contrast, Actinobacteria were significantly more abundant in the rhizosphere of both plant species. At two of the sampling sites under strong bird influence (penguin colonies), Firmicutes were significantly more abundant in D. antarctica rhizosphere but not in C. quitensis rhizosphere. The Firmicutes were also positively and significantly correlated to the nitrogen concentrations in the soil. We conclude that the microbial communities in Antarctic soils are driven both by bird and plants, and that the effect is taxa-specific.
2012-06-01 | GSE33847 | GEO