A novel microcosm for recruiting biofertilizer-candidate microorganisms from inherently competitive soil environments
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB39145 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR4326360_1.fastq.gz | Fastqsanger.gz | |||
| ERR4326360_2.fastq.gz | Fastqsanger.gz | |||
| ERR4326370_1.fastq.gz | Fastqsanger.gz | |||
| ERR4326370_2.fastq.gz | Fastqsanger.gz | |||
| ERR4326361_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 40 |
Similar Datasets
Project description:Microbial ecology surrounding persistent phytate in agricultural soils
| PRJEB39274 | ENA
Project description:Naegleria fowleri causes deadly primary amoebic meningoencephalitis (PAM) in humans. Humans obtain the infection by inhaling water or dust contaminated with amebae into the nostrils, wherefrom the pathogen migrates via the olfactory nerve to cause brain inflammation and necrosis. Current PAM treatment is ineffective and toxic. Seeking new effective and less toxic drugs for the environmental control of the amoeba population to reduce human exposure is logical for the management of N. fowleri infection. On the basis of the concept of competitive exclusion, where environmental microorganisms compete for resources by secreting factors detrimental to other organisms, we tested cell-free culture supernatants (CFSs) of three bacteria isolated from a fresh water canal, i.e., Pseudomonas aeruginosa, Pseudomonas otitidis, and Enterobacter cloacae, were tested against N. fowleri. The CFSs inhibited growth and caused morphological changes in N. fowleri. At low dose, N. fowleri trophozoites exposed to P. aeruginosa pyocyanin were seen to shrink and become rounded, while at high dose, the trophozoites were fragmented. While the precise molecular mechanisms of pyocyanin and products of P. otitidis and E. cloacae that also exert anti-N. fowleri activity await clarification. Our findings suggest that P. aeruginosa pyocyanin may have a role in the control of amphizoic N. fowleri in the environment.
| S-EPMC7911858 | biostudies-literature
Project description:Cellulose is the most abundant component of plant litter, which is critical for terrestrial carbon cycling. Nonetheless, it remains unknown how climate changes affect cellulose-decomposing microorganisms. Here, we carried out a multi-year litterbag experiment to examine cellulose decomposition undergoing +3°C warming in an Oklahoma tallgrass prairie, USA. GeoChip 5.0M was employed to detect microbial functional genes.
2024-06-01 | GSE237659 | GEO
Project description:Seed germination is important to soybean (Glycine max) growth and development, ultimately affecting soybean yield. A lower seed field emergence has been the main hindrance for breeding soybeans low in phytate. Although this reduction could be overcome by additional breeding and selection, the mechanisms of seed germination in different low phytate mutants remain unknown. In this study, we performed a comparative transcript analysis of two low phytate soybean mutants (TW-1 and TW-1-M), which have the same mutation, a 2 bp deletion in GmMIPS1, but show a significant difference in seed field emergence.
2016-12-05 | GSE83152 | GEO
Project description:Most yeast genes are dispensable for optimal growth in laboratory cultures. However, this apparent lack of fitness contribution is difficult to reconcile with the theory of natural selection. Here we use stochastic modeling to show that environmental fluctuations can select for a genetic mechanism that does not affect growth in static laboratory environments. We then present a novel experimental platform for measuring the fitness levels of specific genotypes in fluctuating environments. We test this platform by monitoring a mixed culture of two yeast strains that differ in their ability to respond to changes in carbon source yet exhibit the same fitness level in static conditions. When the sugar in the growth medium was switched between galactose and glucose, the wild-type strain gained a growth advantage over the mutant strain. Interestingly, both our computational and experimental results show that the strength of the adaptive advantage conveyed by the wild-type genotype depends on the total number of carbon source switches, not on the frequency of these fluctuations. Our results illustrate the selective power of environmental fluctuations on seemingly slight phenotypic differences in cellular response dynamics and underscore the importance of dynamic processes in the evolution of species.
| S-EPMC3808460 | biostudies-literature
Project description:Exogenic deposits are an important source of rare earth elements (REEs), especially heavy REEs (HREEs). It is generally accepted that microorganisms are able to dissolve minerals and mobilize elements in supergene environments. However, little is known about the roles of microorganisms in the formation of exogenic deposits such as regolith-hosted REE deposits that are of HREE enrichment and provide over 90% of global HREE demand. In this study, we characterized the microbial community composition and diversity along a complete weathering profile drilled from a regolith-hosted REE deposit in Southeastern China and report the striking contributions of microorganisms to the enrichment of REEs and fractionation between HREEs and light REEs (LREEs). Our results provide evidence that the variations in REE contents are correlated with microbial community along the profile. Both fungi and bacteria contributed to the accumulation of REEs, whereas bacteria played a key role in the fractionation between HREEs and LREEs. Taking advantage of bacteria strains isolated from the profile, Gram-positive bacteria affiliated with Bacillus and Micrococcus preferentially adsorbed HREEs, and teichoic acids in the cell wall served as the main sites for HREE adsorption, leading to an enrichment of HREEs in the deposit. The present study provides the first database of microbial community in regolith-hosted REE deposits. These findings not only elucidate the crucial contribution of fungi and bacteria in the supergene REE mineralization but also provide insights into efficient utilization of mineral resources via a biological pathway. IMPORTANCE Understanding the role of microorganisms in the formation of regolith-hosted rare earth element (REE) deposits is beneficial for improving the metallogenic theory and deposit exploitation, given that such deposits absolutely exist in subtropical regions with strong microbial activities. Little is known of the microbial community composition and its contribution to REE mineralization in this kind of deposit. Using a combination of high-throughput sequencing, batch adsorption experiments, and spectroscopic characterization, the functional microorganisms contributing to REE enrichment and fractionation are disclosed. For bacteria, the surface carboxyl and phosphate groups are active sites for REE adsorption, while teichoic acids in the cell walls of G+ bacteria lead to REE fractionation. The above-mentioned findings not only unravel the importance of microorganisms in the formation of supergene REE deposits but also provide experimental evidence for the bioutilization of REE resources.
| S-EPMC9275249 | biostudies-literature
Project description:Soil biogeochemical processes and the ecological stability of wetland ecosystems under global warming scenarios have gained increasing attention worldwide. Changes in the capacity of microorganisms to maintain stoichiometric homeostasis, or relatively stable internal concentrations of elements, may serve as an indicator of alterations to soil biogeochemical processes and their associated ecological feedbacks. In this study, an outdoor computerized microcosm was set up to simulate a warmed (+5°C) climate scenario, using novel, minute-scale temperature manipulation technology. The principle of stoichiometric homeostasis was adopted to illustrate phosphorus (P) biogeochemical cycling coupled with carbon (C) dynamics within the soil-microorganism complex. We hypothesized that enhancing the flux of P from soil to water under warming scenarios is tightly coupled with a decrease in homeostatic regulation ability in wetland ecosystems. Results indicate that experimental warming impaired the ability of stoichiometric homeostasis (H) to regulate biogeochemical processes, enhancing the ecological role of wetland soil as an ecological source for both P and C. The potential P flux from soil to water ranged from 0.11 to 34.51 mg m(-2) d(-1) in the control and 0.07 to 61.26 mg m(-2) d(-1) in the warmed treatment. The synergistic function of C-P acquisition is an important mechanism underlying C∶P stoichiometric balance for soil microorganisms under warming. For both treatment groups, strongly significant (p<0.001) relationships fitting a negative allometric power model with a fractional exponent were found between n-HC∶P (the specialized homeostatic regulation ability as a ratio of soil highly labile organic carbon to dissolved reactive phosphorus in porewater) and potential P flux. Although many factors may affect soil P dynamics, the n-HC∶P term fundamentally reflects the stoichiometric balance or interactions between the energy landscape (i.e., C) and flow of resources (e.g., N and P), and can be a useful ecological tool for assessing potential P flux in ecosystems.
| S-EPMC3903482 | biostudies-literature
Project description:AlkB and CYP153 are important alkane hydroxylases responsible for aerobic alkane degradation in bioremediation of oil-polluted environments and microbial enhanced oil recovery. Since their distribution in nature is not clear, we made the investigation among thus-far sequenced 3,979 microbial genomes and 137 metagenomes from terrestrial, freshwater, and marine environments. Hundreds of diverse alkB and CYP153 genes including many novel ones were found in bacterial genomes, whereas none were found in archaeal genomes. Moreover, these genes were detected with different distributional patterns in the terrestrial, freshwater, and marine metagenomes. Hints for horizontal gene transfer, gene duplication, and gene fusion were found, which together are likely responsible for diversifying the alkB and CYP153 genes adapt to the ubiquitous distribution of different alkanes in nature. In addition, different distributions of these genes between bacterial genomes and metagenomes suggested the potentially important roles of unknown or less common alkane degraders in nature.
| S-EPMC4021335 | biostudies-literature
Project description:Cellulose is the most abundant component of plant litter, which is critical for terrestrial carbon cycling. Nonetheless, it remains unknown how global warming affects cellulose-decomposing microorganisms. Here, we carried out a 3-year litterbag experiment to examine cellulose decomposition undergoing +3°C warming in a tallgrass prairie. Most cellulose-associated bacteria and fungi in litterbags were also detected in bulk soil, and bacteria in litterbags had higher community-level rrn copy numbers, larger genome sizes, and higher genome guanine-cytosine (GC) contents than those in bulk soil, implying higher growth rates. Warming stimulated soil respiration by 32.3% and accelerated mass loss of cellulose, concurring with the increase in relative abundances of most functional genes associated with carbon decomposition in litterbags. Incorporating cellulose-decomposing genes into an ecosystem model reduced model parameter uncertainty and showed that warming stimulated microbial biomass, activity, and soil carbon decomposition. Collectively, our study supports a trait-centric view since cellulose-decomposing genes or genomic traits are amenable for ecosystem modeling. By characterizing the phylogenetically diverse yet functionally similar cellulose-associated microorganisms and their responses to warming, we take a step toward more precise predictions of soil carbon dynamics under future climate scenarios.
| S-EPMC11892950 | biostudies-literature
Project description:This paper aims to review the literature on 'Effective Microorganism (EM)' and 'Fertilizer' from the Scopus database and to discuss EMs using Halal-based sources for biofertilizer production from socio economic insights. Based on EM and fertilizer publications on the Scopus database, all the 17 papers reviewed provided no detailed information on the Halal-status of the biofertilizers inoculated with EM. The impacts of Halal-certified biofertilizers will trigger the Halal certification in food products by (a) catering for the increasing Halal food demand due to expectedly Muslim population expansion, (b) contributing to the sustainable buying behaviour of Halal products' consumers in the future, (c) catering for the increasing number of Muslim travellers around the world, (d) becoming a positive driver for higher production of more Halal foods that can enhance food safety, human health and well-being, and (e) creating a cost-effective and increasing food marketability. The later three points (c, d and e) play a very important role in a country's societal well-being and economic growth and development. Although Halal-status is not a must for the world's food marketing, Halal-certified biofertilizer for the Halal-status of food carries the greatest potential to enter the ever-expanding Muslim markets. Finally, it is postulated that the successful usage of EM using Halal-based sources for biofertilizer production will result in two major outcomes from the points of United Nations' Sustainable Development Goals # 9 (Industry, Innovation and Infrastructure) and # 12 (Responsible Consumption and Production). Hence, the presented review provides a starting point for future research considering sustainability and innovation as priorities.
| S-EPMC10138028 | biostudies-literature