scholarly journals A Win–Loss Interaction on Fe0 Between Methanogens and Acetogens From a Climate Lake

2021 ◽  
Vol 12 ◽  
Author(s):  
Paola Andrea Palacios ◽  
Warren Russell Francis ◽  
Amelia-Elena Rotaru
Keyword(s):  
Small Molecules ◽  
Lake Sediments ◽  
Amplicon Sequencing ◽  
Electron Donors ◽  
Interspecies Interactions ◽  
Group Interactions ◽  
Abiotic Controls ◽  
Metagenome Sequencing ◽  
Flavin Biosynthesis ◽  
Spent Media

Diverse physiological groups congregate into environmental corrosive biofilms, yet the interspecies interactions between these corrosive physiological groups are seldom examined. We, therefore, explored Fe0-dependent cross-group interactions between acetogens and methanogens from lake sediments. On Fe0, acetogens were more corrosive and metabolically active when decoupled from methanogens, whereas methanogens were more metabolically active when coupled with acetogens. This suggests an opportunistic (win–loss) interaction on Fe0 between acetogens (loss) and methanogens (win). Clostridia and Methanobacterium were the major candidates doing acetogenesis and methanogenesis after four transfers (metagenome sequencing) and the only groups detected after 11 transfers (amplicon sequencing) on Fe0. Since abiotic H2 failed to explain the high metabolic rates on Fe0, we examined whether cell exudates (spent media filtrate) promoted the H2-evolving reaction on Fe0 above abiotic controls. Undeniably, spent media filtrate generated three- to four-fold more H2 than abiotic controls, which could be partly explained by thermolabile enzymes and partly by non-thermolabile constituents released by cells. Next, we examined the metagenome for candidate enzymes/shuttles that could catalyze H2 evolution from Fe0 and found candidate H2-evolving hydrogenases and an almost complete pathway for flavin biosynthesis in Clostridium. Clostridial ferredoxin-dependent [FeFe]-hydrogenases may be catalyzing the H2-evolving reaction on Fe0, explaining the significant H2 evolved by spent media exposed to Fe0. It is typical of Clostridia to secrete enzymes and other small molecules for lytic purposes. Here, they may secrete such molecules to enhance their own electron uptake from extracellular electron donors but indirectly make their H2-consuming neighbors—Methanobacterium—fare five times better in their presence. The particular enzymes and constituents promoting H2 evolution from Fe0 remain to be determined. However, we postulate that in a static environment like corrosive crust biofilms in lake sediments, less corrosive methanogens like Methanobacterium could extend corrosion long after acetogenesis ceased, by exploiting the constituents secreted by acetogens.

scholarly journals Reduced metagenome sequencing for strain-resolution taxonomic profiles

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Lars Snipen ◽  
Inga-Leena Angell ◽  
Torbjørn Rognes ◽  
Knut Rudi
Keyword(s):  
Microbial Community ◽  
Microbial Community Composition ◽  
Amplicon Sequencing ◽  
Good Alternative ◽  
Shotgun Sequencing ◽  
Least Square ◽  
Full Potential ◽  
Shotgun Metagenomics ◽  
Metagenome Sequencing ◽  
Reference Genomes

Abstract Background Studies of shifts in microbial community composition has many applications. For studies at species or subspecies levels, the 16S amplicon sequencing lacks resolution and is often replaced by full shotgun sequencing. Due to higher costs, this restricts the number of samples sequenced. As an alternative to a full shotgun sequencing we have investigated the use of Reduced Metagenome Sequencing (RMS) to estimate the composition of a microbial community. This involves the use of double-digested restriction-associated DNA sequencing, which means only a smaller fraction of the genomes are sequenced. The read sets obtained by this approach have properties different from both amplicon and shotgun data, and analysis pipelines for both can either not be used at all or not explore the full potential of RMS data. Results We suggest a procedure for analyzing such data, based on fragment clustering and the use of a constrained ordinary least square de-convolution for estimating the relative abundance of all community members. Mock community datasets show the potential to clearly separate strains even when the 16S is 100% identical, and genome-wide differences is < 0.02, indicating RMS has a very high resolution. From a simulation study, we compare RMS to shotgun sequencing and show that we get improved abundance estimates when the community has many very closely related genomes. From a real dataset of infant guts, we show that RMS is capable of detecting a strain diversity gradient for Escherichia coli across time. Conclusion We find that RMS is a good alternative to either metabarcoding or shotgun sequencing when it comes to resolving microbial communities at the strain level. Like shotgun metagenomics, it requires a good database of reference genomes and is well suited for studies of the human gut or other communities where many reference genomes exist. A data analysis pipeline is offered, as an R package at https://github.com/larssnip/microRMS.

scholarly journals Long-Read Amplicon Sequencing of Nitric Oxide Dismutase (nod) Genes Reveal Diverse Oxygenic Denitrifiers in Agricultural Soils and Lake Sediments

2020 ◽  
Vol 80 (1) ◽  
pp. 243-247 ◽  
Author(s):  
Baoli Zhu ◽  
Zhe Wang ◽  
Dheeraj Kanaparthi ◽  
Susanne Kublik ◽  
Tida Ge ◽  
...  
Keyword(s):  
Nitric Oxide ◽  
Lake Sediments ◽  
Agricultural Soils ◽  
Amplicon Sequencing ◽  
Nod Genes ◽  
Long Read

scholarly journals Combining whole genome shotgun sequencing and rDNA amplicon analyses to improve detection of microbe-microbe interaction networks in plant leaves

2019 ◽  
Author(s):  
Julian Regalado ◽  
Derek S. Lundberg ◽  
Oliver Deusch ◽  
Sonja Kersten ◽  
Talia Karasov ◽  
...  
Keyword(s):  
16S Rdna ◽  
High Throughput Sequencing ◽  
Cost Effective ◽  
Amplicon Sequencing ◽  
Low Complexity ◽  
Shotgun Sequencing ◽  
Wild Plants ◽  
Hybrid Strategy ◽  
Domains Of Life ◽  
Metagenome Sequencing

AbstractMicroorganisms from all domains of life establish associations with plants. Although some harm the plant, others antagonize pathogens or prime the plant immune system, acquire nutrients, tune plant hormone levels, or perform additional services. Most culture-independent plant microbiome research has focused on amplicon sequencing of 16S rDNA and/or the internal transcribed spacer (ITS) of rDNA loci, but the decreasing cost of high-throughput sequencing has made shotgun metagenome sequencing increasingly accessible. Here, we describe shotgun sequencing of 275 wild Arabidopsis thaliana leaf microbiomes from southwest Germany, with additional bacterial 16S rDNA and eukaryotic ITS1 amplicon data from 176 of these samples. The shotgun data were dominated by bacterial sequences, with eukaryotes contributing only a minority of reads. For shotgun and amplicon data, microbial membership showed weak associations with both site of origin and plant genotype, both of which were highly confounded in this dataset. There was large variation among microbiomes, with one extreme comprising samples of low complexity and a high load of microorganisms typical of infected plants, and the other extreme being samples of high complexity and a low microbial load. We use the metagenome data, which captures the ratio of bacterial to plant DNA in leaves of wild plants, to scale the 16S rDNA amplicon data such that they reflect absolute bacterial abundance. We show that this cost-effective hybrid strategy overcomes compositionality problems in amplicon data and leads to fundamentally different conclusions about microbiome community assembly.

scholarly journals Non-native autoinducer analogs capable of modulating the SdiA quorum sensing receptor inSalmonella entericaserovar Typhimurium

2018 ◽  
Vol 14 ◽  
pp. 2651-2664 ◽  
Author(s):  
Matthew J Styles ◽  
Helen E Blackwell
Keyword(s):  
Quorum Sensing ◽  
Small Molecules ◽  
Homoserine Lactone ◽  
Interspecies Interactions ◽  
Host Colonization ◽  
Serovar Typhimurium ◽  
Coordinate Group ◽  
A Cell ◽  
Production Host

Quorum sensing (QS) allows many common bacterial pathogens to coordinate group behaviors such as virulence factor production, host colonization, and biofilm formation at high population densities. This cell–cell signaling process is regulated byN-acyl L-homoserine lactone (AHL) signals, or autoinducers, and LuxR-type receptors in Gram-negative bacteria. SdiA is an orphan LuxR-type receptor found inEscherichia, Salmonella, Klebsiella, and Enterobactergenera that responds to AHL signals produced by other species and regulates genes involved in several aspects of host colonization. The inhibition of QS using non-native small molecules that target LuxR-type receptors offers a non-biocidal approach for studying, and potentially controlling, virulence in these bacteria. To date, few studies have characterized the features of AHLs and other small molecules capable of SdiA agonism, and no SdiA antagonists have been reported. Herein, we report the screening of a set of AHL analogs to both uncover agonists and antagonists of SdiA and to start to delineate structure–activity relationships (SARs) for SdiA:AHL interactions. Using a cell-based reporter of SdiA inSalmonella entericaserovar Typhimurium, several non-natural SdiA agonists and the first set of SdiA antagonists were identified and characterized. These compounds represent new chemical probes for exploring the mechanisms by which SdiA functions during infection and its role in interspecies interactions. Moreover, as SdiA is highly stable when produced in vitro, these compounds could advance fundamental studies of LuxR-type receptor:ligand interactions that engender both agonism and antagonism.

Fate of Neptunium in an Anaerobic, Ethanogenic Microcosm

1999 ◽  
Vol 556 ◽  
Author(s):  
J. E. Banaszak ◽  
S. M. Webb ◽  
B. E. Rittmann ◽  
J.-F. Gaillard ◽  
D. T. Reed
Keyword(s):  
Methane Production ◽  
Analytical Techniques ◽  
Electron Donors ◽  
Natural Systems ◽  
Sulfate Reducing ◽  
Exogenous Substrate ◽  
Nir Absorption ◽  
Abiotic Controls ◽  
Control Samples ◽  
Substrate Addition

AbstractNeptunium is found predominantly as Np(IV) in reducing environments, but as Np(V) in aerobic environments. Currently, it is not known how the interplay between biotic and abiotic processes affects Np redox speciation in the environment. To evaluate the effect of anaerobic microbial activity on the fate of Np in natural systems, Np(V) was added to a microcosm inoculated with anaerobic sediments from a metal-contaminated freshwater lake. The consortium included metal-reducing, sulfate-reducing, and methanogenic microorganisms, and acetate was supplied as the only exogenous substrate. Addition of more than 10−5M Np did not inhibit methane production. Total Np solubility in the active microcosm, as well as in sterilized control samples, decreased by nearly two orders of magnitude. A combination of analytical techniques, including VIS-NIR absorption spectroscopy and XANES, identified Np(IV) as the oxidation state associated with the sediments. The similar results from the active microcosm and the abiotic controls suggest that microbially produced Mn(II/III) and Fe(II) may serve as electron donors for Np reduction.

scholarly journals Kelpie: generating full-length ‘amplicons’ from whole-metagenome datasets

PeerJ ◽  
2019 ◽  
Vol 6 ◽  
pp. e6174 ◽  
Author(s):  
Paul Greenfield ◽  
Nai Tran-Dinh ◽  
David Midgley
Keyword(s):  
Marker Gene ◽  
Amplicon Sequencing ◽  
Genomic Region ◽  
Full Length ◽  
Rrna Gene ◽  
Multiple Regions ◽  
Metagenome Sequencing ◽  
And Function ◽  
Genomic Regions ◽  
Metagenomic Assembly

Introduction Whole-metagenome sequencing can be a rich source of information about the structure and function of entire metagenomic communities, but getting accurate and reliable results from these datasets can be challenging. Analysis of these datasets is founded on the mapping of sequencing reads onto known genomic regions from known organisms, but short reads will often map equally well to multiple regions, and to multiple reference organisms. Assembling metagenomic datasets prior to mapping can generate much longer and more precisely mappable sequences but the presence of closely related organisms and highly conserved regions makes metagenomic assembly challenging, and some regions of particular interest can assemble poorly. One solution to these problems is to use specialised tools, such as Kelpie, that can accurately extract and assemble full-length sequences for defined genomic regions from whole-metagenome datasets. Methods Kelpie is a kMer-based tool that generates full-length amplicon-like sequences from whole-metagenome datasets. It takes a pair of primer sequences and a set of metagenomic reads, and uses a combination of kMer filtering, error correction and assembly techniques to construct sets of full-length inter-primer sequences. Results The effectiveness of Kelpie is demonstrated here through the extraction and assembly of full-length ribosomal marker gene regions, as this allows comparisons with conventional amplicon sequencing and published metagenomic benchmarks. The results show that the Kelpie-generated sequences and community profiles closely match those produced by amplicon sequencing, down to low abundance levels, and running Kelpie on the synthetic CAMI metagenomic benchmarking datasets shows similar high levels of both precision and recall. Conclusions Kelpie can be thought of as being somewhat like an in-silico PCR tool, taking a primer pair and producing the resulting ‘amplicons’ from a whole-metagenome dataset. Marker regions from the 16S rRNA gene were used here as an example because this allowed the overall accuracy of Kelpie to be evaluated through comparisons with other datasets, approaches and benchmarks. Kelpie is not limited to this application though, and can be used to extract and assemble any genomic region present in a whole metagenome dataset, as long as it is bound by a pairs of highly conserved primer sequences.

scholarly journals Inference based PICRUSt accuracy varies across sample types and functional categories

2019 ◽  
Author(s):  
Shan Sun ◽  
Roshonda B. Jones ◽  
Anthony A. Fodor
Keyword(s):  
16S Rrna ◽  
Gene Prediction ◽  
Amplicon Sequencing ◽  
Taxonomic Composition ◽  
Inference Models ◽  
16S Rrna Amplicon Sequencing ◽  
Gene Profiles ◽  
Metagenome Sequencing ◽  
The Cost ◽  
Functional Profiles

AbstractBackgroundDespite recent decreases in the cost of sequencing, shotgun metagenome sequencing remains more expensive compared with 16S rRNA amplicon sequencing. Methods have been developed to predict the functional profiles of microbial communities based on their taxonomic composition, and PICRUSt is the most widely used of these techniques. In this study, we evaluated the performance of PICRUSt by comparing the significance of the differential abundance of functional gene profiles predicted with PICRUSt to those from shotgun metagenome sequencing across different environments.ResultsWe selected 7 datasets of human, non-human animal and environmental (soil) samples that have publicly available 16S rRNA and shotgun metagenome sequences. As we would expect based on previous literature, strong Spearman correlations were observed between gene compositions predicted with PICRUSt and measured with shotgun metagenome sequencing. However, these strong correlations were preserved even when the sample labels were shuffled. This suggests that simple correlation coefficient is a highly unreliable measure for the performance of algorithms like PICRUSt. As an alternative, we compared the performance of PICRUSt predicted genes to metagenome genes in inference models associated with metadata within each dataset. With this method, we found reasonable performance for human datasets, with PICRUSt performing better for inference on genes related to “house-keeping” functions. However, the performance of PICRUSt degraded sharply outside of human datasets when used for inference.ConclusionWe conclude that the utility of PICRUSt for inference with the default database is likely limited outside of human samples and that development of tools for gene prediction specific to different non-human and environmental samples is warranted.

scholarly journals Selecting the best electron donor and operational temperature for the rapid biotransformation of the insensitive munitions compound 2,4-dinitroanisole (DNAN) by anaerobic sludge

2021 ◽  
Author(s):  
Natanna Melo ◽  
Osmar Menezes ◽  
Matheus Paraiso ◽  
Lourdinha Florêncio ◽  
Mário T. Kato ◽  
...  
Keyword(s):  
Reduction Rate ◽  
Anaerobic Treatment ◽  
Electron Donors ◽  
Anaerobic Sludge ◽  
Amino Groups ◽  
Manufacturing Plants ◽  
Insensitive Munitions ◽  
Operational Temperature ◽  
Abiotic Controls ◽  
The Military

Abstract 2,4-Dinitroanisole (DNAN) is a toxic compound increasingly used by the military that can be released to the environment on the soil of training fields and in the wastewater of manufacturing plants. DNAN's nitro groups are anaerobically reduced to amino groups by microorganisms when electron donors are available. Using anaerobic sludge as inoculum, we tested different electron donors for DNAN bioreduction at 20 and 30 °C: acetate, ethanol, pyruvate, hydrogen, and hydrogen + pyruvate. Biotic controls without external electron donors and abiotic controls with heat-killed sludge were also assayed. No DNAN conversion was observed in the abiotic controls. In all biotic treatments, DNAN was reduced to 2-methoxy-5-nitroaniline (MENA), which was further reduced to 2,4-diaminoanisole (DAAN). Ethanol or acetate did not increase DNAN reduction rate compared to the endogenous control. The electron donors that caused the fastest DNAN reductions were (rates at 30 °C): H2 and pyruvate combined (311.28 ± 10.02 μM·d−1·gSSV−1), followed by H2 only (207.19 ± 5.95 μM·d−1·gSSV−1), and pyruvate only (36.35 ± 2.95 μM·d−1·gSSV−1). Raising the temperature to 30 °C improved DNAN reduction rates when pyruvate, H2, or H2 + pyruvate were used as electrons donors. Our results can be applied to optimize the anaerobic treatment of DNAN-containing wastewater.

Solution-processed new porphyrin-based small molecules as electron donors for highly efficient organic photovoltaics

2015 ◽  
Vol 51 (77) ◽  
pp. 14439-14442 ◽  
Author(s):  
Song Chen ◽  
Liangang Xiao ◽  
Xunjin Zhu ◽  
Xiaobing Peng ◽  
Wai-Kwok Wong ◽  
...  
Keyword(s):  
Solar Cells ◽  
Small Molecules ◽  
Power Conversion Efficiency ◽  
Conversion Efficiency ◽  
Organic Photovoltaics ◽  
Organic Solar Cells ◽  
Bulk Heterojunction ◽  
Power Conversion ◽  
Electron Donors ◽  
Solution Processed

A series of new A–D–A structural 5,15-dialkylated porphyrin-cored small molecules have been developed as donors in bulk heterojunction organic solar cells, and the highest power conversion efficiency of 6.49% has been achieved.

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