92 research outputs found
Sigma-phase in Fe-Cr and Fe-V alloy systems and its physical properties
A review is presented on physical properties of the sigma-phase in Fe-Cr and
Fe-V alloy systems as revealed both with experimental -- mostly with the
Mossbauer spectroscopy -- and theoretical methods. In particular, the following
questions relevant to the issue have been addressed: identification of sigma
and determination of its structural properties, kinetics of alpha-to-sigma and
sigma-to-alpha phase transformations, Debye temperature and Fe-partial phonon
density of states, Curie temperature and magnetization, hyperfine fields,
isomer shifts and electric field gradients.Comment: 26 pages, 23 figures and 83 reference
A benzene-degrading nitrate-reducing microbial consortium displays aerobic and anaerobic benzene degradation pathways
All sequence data from this study were deposited at the European Bioinformatics Institute under the accession numbers ERS1670018 to ERS1670023. Further, all assigned genes, taxonomy, function, sequences of contigs, genes and proteins can be found in Table S3.In this study, we report transcription of genes involved in aerobic and anaerobic benzene degradation pathways in a benzene-degrading denitrifying continuous culture. Transcripts associated with the family Peptococcaceae dominated all samples (2136% relative abundance) indicating their key role in the community. We found a highly transcribed gene cluster encoding a presumed anaerobic benzene carboxylase (AbcA and AbcD) and a benzoate-coenzyme A ligase (BzlA). Predicted gene products showed >96% amino acid identity and similar gene order to the corresponding benzene degradation gene cluster described previously, providing further evidence for anaerobic benzene activation via carboxylation. For subsequent benzoyl-CoA dearomatization, bam-like genes analogous to the ones found in other strict anaerobes were transcribed, whereas gene transcripts involved in downstream benzoyl-CoA degradation were mostly analogous to the ones described in facultative anaerobes. The concurrent transcription of genes encoding enzymes involved in oxygenase-mediated aerobic benzene degradation suggested oxygen presence in the culture, possibly formed via a recently identified nitric oxide dismutase (Nod). Although we were unable to detect transcription of Nod-encoding genes, addition of nitrite and formate to the continuous culture showed indication for oxygen production. Such an oxygen production would enable aerobic microbes to thrive in oxygen-depleted and nitrate-containing subsurface environments contaminated with hydrocarbons.This study was supported by a grant of BE-Basic-FES funds from the Dutch Ministry of Economic Affairs. The research of A.J.M. Stams is supported by an ERC grant (project 323009) and the gravitation grant “Microbes for Health and Environment” (project 024.002.002) of the Netherlands Ministry of Education, Culture and Science. F. Hugenholtz was supported by the same gravitation grant (project 024.002.002). B. Hornung is supported by Wageningen University and the Wageningen Institute for Environment and Climate Research (WIMEK) through the IP/OP program Systems Biology (project KB-17-003.02-023).info:eu-repo/semantics/publishedVersio
A Novel Acyl-CoA Beta-Transaminase Characterized from a Metagenome
BACKGROUND: Bacteria are key components in all ecosystems. However, our knowledge of bacterial metabolism is based solely on the study of cultivated organisms which represent just a tiny fraction of microbial diversity. To access new enzymatic reactions and new or alternative pathways, we investigated bacterial metabolism through analyses of uncultivated bacterial consortia. METHODOLOGY/PRINCIPAL FINDINGS: We applied the gene context approach to assembled sequences of the metagenome of the anaerobic digester of a municipal wastewater treatment plant, and identified a new gene which may participate in an alternative pathway of lysine fermentation. CONCLUSIONS: We characterized a novel, unique aminotransferase that acts exclusively on Coenzyme A (CoA) esters, and proposed a variant route for lysine fermentation. Results suggest that most of the lysine fermenting organisms use this new pathway in the digester. Its presence in organisms representative of two distinct bacterial divisions indicate that it may also be present in other organisms
Genome analysis and physiological comparison of Alicycliphilus denitrificans strains BC and K601T
The genomes of the Betaproteobacteria Alicycliphilus denitrificans strains BC and K601T have been sequenced to get insight into the physiology of the two strains. Strain BC degrades benzene with chlorate as electron acceptor. The cyclohexanol-degrading denitrifying strain K601T is not able to use chlorate as electron acceptor, while strain BC cannot degrade cyclohexanol. The 16S rRNA sequences of strains BC and K601T are identical and the fatty acid methyl ester patterns of the strains are similar. Basic Local Alignment Search Tool (BLAST) analysis of predicted open reading frames of both strains showed most hits with Acidovorax sp. JS42, a bacterium that degrades nitro-aromatics. The genomes include strain-specific plasmids (pAlide201 in strain K601T and pAlide01 and pAlide02 in strain BC). Key genes of chlorate reduction in strain BC were located on a 120 kb megaplasmid (pAlide01), which was absent in strain K601T. Genes involved in cyclohexanol degradation were only found in strain K601T. Benzene and toluene are degraded via oxygenase-mediated pathways in both strains. Genes involved in the meta-cleavage pathway of catechol are present in the genomes of both strains. Strain BC also contains all genes of the ortho-cleavage pathway. The large number of mono- and dioxygenase genes in the genomes suggests that the two strains have a broader substrate range than known thus far.This research was supported by the Technology Foundation, the Applied Science Division (STW) of the Netherlands Organization for Scientific Research (NWO), project number 08053, the graduate school WIMEK (Wageningen Institute for Environment and Climate Research, which is part of SENSE Research School for Socio-Economic and Natural Sciences of the Environment, www.wimek-new.wur.nl and www.sense.nl), SKB (Dutch Centre for Soil Quality Management and Knowledge Transfer, www.skbodem.nl) and the Consolider project CSD-2007-00055. The research was incorporated in the TRIAS (TRIpartite Approaches 469 toward Soil systems processes) program (http://www.nwo.nl/en/research-and-results/programmes/alw/trias-tripartite-approach-to-soil-system-processes/index. html). Flávia Talarico Saia was supported by a FAPESP (the State of São Paulo Research Foundation) scholarship (2006-01997/5). The work conducted by the DOE JGI is supported by the Office of Science of the United States Department of Energy under contract number DE-AC02-05CH11231. Alfons Stams acknowledges support by an ERC (European Research Counsil) advanced grant (project 323009). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript
The self-organizing fractal theory as a universal discovery method: the phenomenon of life
A universal discovery method potentially applicable to all disciplines studying organizational phenomena has been developed. This method takes advantage of a new form of global symmetry, namely, scale-invariance of self-organizational dynamics of energy/matter at all levels of organizational hierarchy, from elementary particles through cells and organisms to the Universe as a whole. The method is based on an alternative conceptualization of physical reality postulating that the energy/matter comprising the Universe is far from equilibrium, that it exists as a flow, and that it develops via self-organization in accordance with the empirical laws of nonequilibrium thermodynamics. It is postulated that the energy/matter flowing through and comprising the Universe evolves as a multiscale, self-similar structure-process, i.e., as a self-organizing fractal. This means that certain organizational structures and processes are scale-invariant and are reproduced at all levels of the organizational hierarchy. Being a form of symmetry, scale-invariance naturally lends itself to a new discovery method that allows for the deduction of missing information by comparing scale-invariant organizational patterns across different levels of the organizational hierarchy
Origin and fate of methane in the Eastern Tropical North Pacific oxygen minimum zone
This work was funded by the Natural Environment Research Council (grant NE/E01559X/1)
Distribution and activity of the anaerobic methanotrophic community in a nitrogen-fertilized Italian paddy soil
In order to mitigate methane emissions from paddy fields, it is important to understand the sources and sinks. Most paddy
fields are heavily fertilized with nitrite and nitrate, which can be used as electron acceptors by anaerobic methanotrophs.
Here we show that slurry incubations of Italian paddy field soil with nitrate and 13C-labelled methane have the potential for
nitrate-dependent anaerobic oxidation of methane (79.9 nmol g 121
dw d 121). Community analysis based on 16S rRNA amplicon
sequencing and qPCR of the water-logged soil and the rhizosphere showed that anaerobic oxidation of methane-associated
archaea (AAA), including Methanoperedens nitroreducens, comprised 9% (bulk soil) and 1% (rhizosphere) of all archaeal reads.
The NC10 phylum bacteria made up less than 1% of all bacterial sequences. The phylogenetic analysis was complemented
by qPCR showing that AAA ranged from 0.28
7 106 to 3.9
7 106 16S rRNA gene copies g 121
dw in bulk soil and 0.27
7 106 to
2.8
7 106 in the rhizosphere. The abundance of NC10 phylum bacteria was an order of magnitude lower. Revisiting
published diversity studies, we found that AAA have been detected, but not linked to methane oxidation, in several paddy
fields. Our data suggest an important role of AAA in methane cycling in paddy fields
Symbiosis revisited: phosphorus and acid buffering stimulate N<sub>2</sub> fixation but not <i>Sphagnum</i> growth
In pristine Sphagnum-dominated peatlands, (di)nitrogen (N2)
fixing (diazotrophic) microbial communities associated with Sphagnum
mosses contribute substantially to the total nitrogen input, increasing
carbon sequestration. The rates of symbiotic nitrogen fixation reported for
Sphagnum peatlands, are, however, highly variable, and experimental
work on regulating factors that can mechanistically explain this variation is
largely lacking. For two common fen species (Sphagnum palustre and
S. squarrosum) from a high nitrogen deposition area
(25 kg N ha−1 yr−1), we found that diazotrophic activity (as
measured by 15 − 15N2 labeling) was still present at a rate of
40 nmol N gDW−1 h−1. This was surprising, given that nitrogen
fixation is a costly process. We tested the effects of phosphorus
availability and buffering capacity by bicarbonate-rich water, mimicking a
field situation in fens with stronger groundwater or surface water influence,
as potential regulators of nitrogen fixation rates and Sphagnum
performance. We expected that the addition of phosphorus, being a limiting
nutrient, would stimulate both diazotrophic activity and Sphagnum
growth. We indeed found that nitrogen fixation rates were doubled. Plant
performance, in contrast, did not increase. Raised bicarbonate levels also
enhanced nitrogen fixation, but had a strong negative impact on
Sphagnum performance. These results explain the higher nitrogen
fixation rates reported for minerotrophic and more nutrient-rich peatlands.
In addition, nitrogen fixation was found to strongly depend on light, with
rates 10 times higher in light conditions suggesting high reliance on
phototrophic organisms for carbon. The contrasting effects of phosphorus and
bicarbonate on Sphagnum spp. and their diazotrophic communities
reveal strong differences in the optimal niche for both partners with respect
to conditions and resources. This suggests a trade-off for the symbiosis of
nitrogen fixing microorganisms with their Sphagnum hosts, in which a
sheltered environment apparently outweighs the less favorable environmental
conditions. We conclude that microbial activity is still nitrogen limited
under eutrophic conditions because dissolved nitrogen is being monopolized by
Sphagnum. Moreover, the fact that diazotrophic activity can
significantly be upregulated by increased phosphorus addition and acid
buffering, while Sphagnum spp. do not benefit, reveals remarkable
differences in optimal conditions for both symbiotic partners and calls into
question the regulation of nitrogen fixation by Sphagnum under these
eutrophic conditions. The high nitrogen fixation rates result in high
additional nitrogen loading of 6 kg ha−1 yr−1 on top of the
high nitrogen deposition in these ecosystems
Nitrogen removal from wastewater by coupling anammox and methane-dependent denitrification in a membrane biofilm reactor
This work demonstrates, for the first time, the feasibility of nitrogen removal by using the synergy of anammox and denitrifying anaerobic methane oxidation (DAMO) microorganisms in a membrane biofilm reactor (MBfR). The reactor was fed with synthetic wastewater containing nitrate and ammonium. Methane was delivered from the interior of hollow fibres in the MBfR to the biofilm that grew on the fiber's outer wall. After 24 months of operation, the system achieved a nitrate and an ammonium removal rate of about 190 mgN L -1 d-1 (or 86 mgN m-2 d-1, with m2 referring to biofilm surface area) and 60 mgN L-1 d-1 (27 mgN m-2 d-1), respectively. No nitrite accumulation was observed. Fluorescence in situ hybridization (FISH) analysis indicated that DAMO bacteria (20-30%), DAMO archaea (20-30%) and anammox bacteria (20-30%) jointly dominated the microbial community. Based on the known metabolism of these microorganisms, mass balance, and isotope studies, we hypothesize that DAMO archaea converted nitrate, both externally fed and produced by anammox, to nitrite, with methane as the electron donor. Anammox and DAMO bacteria jointly removed the nitrite produced, with ammonium and methane as the electron donor, respectively. The process could potentially be used for anaerobic nitrogen removal from wastewater streams containing ammonium and nitrate/nitrite
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