Publications by authors named "A Loy"

215 Publications

Genomic insights into diverse bacterial taxa that degrade extracellular DNA in marine sediments.

Nat Microbiol 2021 Jun 14. Epub 2021 Jun 14.

Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.

Extracellular DNA is a major macromolecule in global element cycles, and is a particularly crucial phosphorus, nitrogen and carbon source for microorganisms in the seafloor. Nevertheless, the identities, ecophysiology and genetic features of DNA-foraging microorganisms in marine sediments are largely unknown. Here, we combined microcosm experiments, DNA stable isotope probing (SIP), single-cell SIP using nano-scale secondary isotope mass spectrometry (NanoSIMS) and genome-centric metagenomics to study microbial catabolism of DNA and its subcomponents in marine sediments. C-DNA added to sediment microcosms was largely degraded within 10 d and mineralized to CO. SIP probing of DNA revealed diverse 'Candidatus Izemoplasma', Lutibacter, Shewanella and Fusibacteraceae incorporated DNA-derived C-carbon. NanoSIMS confirmed incorporation of C into individual bacterial cells of Fusibacteraceae sorted from microcosms. Genomes of the C-labelled taxa all encoded enzymatic repertoires for catabolism of DNA or subcomponents of DNA. Comparative genomics indicated that diverse 'Candidatus Izemoplasmatales' (former Tenericutes) are exceptional because they encode multiple (up to five) predicted extracellular nucleases and are probably specialized DNA-degraders. Analyses of additional sediment metagenomes revealed extracellular nuclease genes are prevalent among Bacteroidota at diverse sites. Together, our results reveal the identities and functional properties of microorganisms that may contribute to the key ecosystem function of degrading and recycling DNA in the seabed.
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http://dx.doi.org/10.1038/s41564-021-00917-9DOI Listing
June 2021

An Economical and Flexible Dual Barcoding, Two-Step PCR Approach for Highly Multiplexed Amplicon Sequencing.

Front Microbiol 2021 20;12:669776. Epub 2021 May 20.

Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria.

In microbiome research, phylogenetic and functional marker gene amplicon sequencing is the most commonly-used community profiling approach. Consequently, a plethora of protocols for the preparation and multiplexing of samples for amplicon sequencing have been developed. Here, we present two economical high-throughput gene amplification and sequencing workflows that are implemented as standard operating procedures at the Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna. These workflows are based on a previously-published two-step PCR approach, but have been updated to either increase the accuracy of results, or alternatively to achieve orders of magnitude higher numbers of samples to be multiplexed in a single sequencing run. The high-accuracy workflow relies on unique dual sample barcoding. It allows the same level of sample multiplexing as the previously-published two-step PCR approach, but effectively eliminates residual read missasignments between samples (crosstalk) which are inherent to single barcoding approaches. The high-multiplexing workflow is based on combinatorial dual sample barcoding, which theoretically allows for multiplexing up to 299,756 amplicon libraries of the same target gene in a single massively-parallelized amplicon sequencing run. Both workflows presented here are highly economical, easy to implement, and can, without significant modifications or cost, be applied to any target gene of interest.
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http://dx.doi.org/10.3389/fmicb.2021.669776DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8173057PMC
May 2021

Novel taxa of Acidobacteriota implicated in seafloor sulfur cycling.

ISME J 2021 May 12. Epub 2021 May 12.

Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.

Acidobacteriota are widespread and often abundant in marine sediments, yet their metabolic and ecological properties are poorly understood. Here, we examined metabolisms and distributions of Acidobacteriota in marine sediments of Svalbard by functional predictions from metagenome-assembled genomes (MAGs), amplicon sequencing of 16S rRNA and dissimilatory sulfite reductase (dsrB) genes and transcripts, and gene expression analyses of tetrathionate-amended microcosms. Acidobacteriota were the second most abundant dsrB-harboring (averaging 13%) phylum after Desulfobacterota in Svalbard sediments, and represented 4% of dsrB transcripts on average. Meta-analysis of dsrAB datasets also showed Acidobacteriota dsrAB sequences are prominent in marine sediments worldwide, averaging 15% of all sequences analysed, and represent most of the previously unclassified dsrAB in marine sediments. We propose two new Acidobacteriota genera, Candidatus Sulfomarinibacter (class Thermoanaerobaculia, "subdivision 23") and Ca. Polarisedimenticola ("subdivision 22"), with distinct genetic properties that may explain their distributions in biogeochemically distinct sediments. Ca. Sulfomarinibacter encode flexible respiratory routes, with potential for oxygen, nitrous oxide, metal-oxide, tetrathionate, sulfur and sulfite/sulfate respiration, and possibly sulfur disproportionation. Potential nutrients and energy include cellulose, proteins, cyanophycin, hydrogen, and acetate. A Ca. Polarisedimenticola MAG encodes various enzymes to degrade proteins, and to reduce oxygen, nitrate, sulfur/polysulfide and metal-oxides. 16S rRNA gene and transcript profiling of Svalbard sediments showed Ca. Sulfomarinibacter members were relatively abundant and transcriptionally active in sulfidic fjord sediments, while Ca. Polarisedimenticola members were more relatively abundant in metal-rich fjord sediments. Overall, we reveal various physiological features of uncultured marine Acidobacteriota that indicate fundamental roles in seafloor biogeochemical cycling.
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http://dx.doi.org/10.1038/s41396-021-00992-0DOI Listing
May 2021

Recent advances in green solvents for lignocellulosic biomass pretreatment: Potential of choline chloride (ChCl) based solvents.

Bioresour Technol 2021 Aug 23;333:125195. Epub 2021 Apr 23.

PETRONAS Research Sdn. Bhd. (PRSB), Lot 3288 & 3289, Off Jalan Ayer Itam, Kawasan Institusi Bangi, 43000 Kajang, Selangor, Malaysia. Electronic address:

Biomass wastes exhibit a great potential to be used as a source of non-depleting renewable energy and synthesis of value-added products. The key to the valorization of excess lignocellulosic biomass wastes in the world lies on the pretreatment process to recalcitrant barrier of the lignocellulosic material for the access to useful substrates. A wide range of pretreatment techniques are available and advances in this field is continuously happening, in search for cheap, effective, and environmentally friendly methods. This review starts with an introduction to conventional approaches and green solvents for pretreatment of lignocellulosic biomass. Subsequently, the mechanism of actions along with the advantages and disadvantages of pretreatment techniques were reviewed. The roles of choline chloride (ChCl) in green solvents and their potential applications were also comprehensively reviewed. The collection of ideas in this review serve as an insight for future works or interest on biomass-to-energy conversion using green solvents.
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http://dx.doi.org/10.1016/j.biortech.2021.125195DOI Listing
August 2021

Developmental instability and phenotypic evolution in a small and isolated bear population.

Biol Lett 2021 04 21;17(4):20200729. Epub 2021 Apr 21.

Research Institute on Terrestrial Ecosystems, National Research Council, 00015 Montelibretti, Rome, Italy.

We explored fluctuating asymmetry (FA) and morphological integration (MI) in the skull of the small, highly inbred and divergent Apennine bear (), to explore its uniqueness and investigate any potential effects of inbreeding depression. We used 3D geometric morphometrics contrasting Apennine bears with other two large outbred bear populations from Scandinavia and Kamchatka as controls. Shape divergence and variability were explored by a principal component analysis on aligned coordinates of 39 landmarks. Procrustes ANOVA, morphological disparity and the global integration index were used to explore FA, shape variance and MI. By remarking Apennine bears as a highly divergent phenotype, we recorded the highest FA and deviation from self-similarity compared with the other two control populations. We conclude that Apennine bears are likely facing developmental instability as a consequence of inbreeding depression, whereas the divergent trait covariance pattern may represent a potential source of evolutionary novelties. We discuss the implications for the conservation and management of this imperiled taxon.
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http://dx.doi.org/10.1098/rsbl.2020.0729DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8086926PMC
April 2021