Biology subjects

Bartacek, J.

Publications and source records attributed to Bartacek, J..

4 recordsLinked to original sources

bioRxiv2024

Mechanisms of Anammox Adaptation to High Temperatures: Increased Cyclization of Ladderane Lipids and Proteomic Insights

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=170 SRC="FIGDIR/small/604647v1_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@14c383borg.highwire.dtl.DTLVardef@ffdb64org.highwire.dtl.DTLVardef@19cacceorg.highwire.dtl.DTLVardef@115168b_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical abstractC_FLOATNO C_FIG Although anammox-based processes have been widely applied in mesophilic conditions of reject water and recently in mainstream conditions, the potential of their implementation in high-temperature wastewaters remains largely unexplored. Therefore, this study investigated the operation parameters for the successful adaptation of anammox bacteria and the mechanisms involved on the proteomic and cellular level including unique ladderane lipids. For this purpose, the enrichment of Candidatus Brocadia was cultivated in two fed-batch reactors (FBRs) at a lab scale. The temperature of one FBR was gradually increased from 30 to 40 {degrees}C while the other FBR was maintained at 30 {degrees}C with four consecutive replicates of this experiment. For this adaptation to be successful, the original loading rate had to be at least halved, or ideally maintained below half the value of the specific anammox activity at the time. The most notable adaptation mechanisms included: (1) upregulation of chaperones and (2) doubled ladderane cyclization via the replacement of non-ladderane fatty acid by a ladderane fatty acid in ladderane lipids (p-value 0.005). To our best knowledge, this is the first study to describe the novel mechanism of ladderane cyclization which together with other adaptation strategies presents crucial indicators in anammox adaptation to high-temperature wastewaters.

microbiology↗

bioRxiv2023

Influence of DNA extraction methods on microbiome and resistome analysis in activated sludge

Amplicon sequencing, metagenomics, and quantitative polymerase chain reaction (qPCR) are commonly used techniques to analyse microorganisms and antibiotic resistance genes (ARGs) in activated sludge from wastewater treatment plants (WWTPs). However, the lack of workflow harmonisation poses challenges in comparing measurements across studies and research groups. To address this issue, we examined the impact of DNA extraction procedures on 16S rRNA gene amplicon sequencing, shotgun metagenomics, and qPCR analyses of activated sludge by combining two widely used DNA extraction kits (PowerSoil and FastDNA) and two commonly employed disruption instruments (bead-beater and vortex) through a 2x2 factorial experimental design involving four groups of three analysts performing DNA extractions in triplicates. Our findings revealed significant differences in DNA yield, purity, and reproducibility of amplicon sequencing profiles among the extraction kits. Operator variability also influenced the results. We compared microbiome profiles obtained by amplicon sequencing and metagenomics and observed that bead-beating introduced more variability among triplicates compared to vortexing. The combinations of extraction kits and disruption instruments impacted the relative abundances of specific phyla such as Actinobacteriota, Bacteroidota, and Nitrospirota. For resistome analysis, we employed metagenomics for high-resolution profiling and qPCR for high-sensitivity detection of ARGs. The compositions and diversities of resistome datasets were not significantly affected by the choice of extraction kits and disruption instruments. Although using the same method is ideal for accurate comparisons, our results suggest that acceptable reproducibility can still be achieved when using different methods. This finding encourages the implementation of ARG monitoring in wastewater treatment processes. However, it is important to consider biases introduced by DNA extraction workflows when designing analytical studies, interpreting their results, and comparing their findings. Striving for more harmonised molecular workflows is crucial in the field of wastewater microbiology and engineering. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=153 SRC="FIGDIR/small/546617v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@caa36eorg.highwire.dtl.DTLVardef@1afabfdorg.highwire.dtl.DTLVardef@448b9aorg.highwire.dtl.DTLVardef@296404_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical abstractC_FLOATNO C_FIG

molecular biology↗

bioRxiv2021

Adaptation of anammox bacteria to low temperature via gradual acclimation and cold shocks: distinctions in protein expression, membrane composition and activities

Anammox bacteria enable an efficient removal of nitrogen from sewage in processes involving partial nitritation and anammox (PN/A) or nitrification, partial denitrification, and anammox (N-PdN/A). In mild climates, anammox bacteria must be adapted to [≤]15 {degrees}C, typically by gradual temperature decrease; however, this takes months or years. To reduce the time necessary for the adaptation, an unconventional method of cold shocks is promising, involving hours-long exposure of anammox biomass to extremely low temperatures. We compared the efficacies of gradual temperature decrease and cold shocks to increase the metabolic activity of anammox (fed batch reactor, planktonic "Ca. Kuenenia"). We assessed the cold shock mechanism on the level of protein expression (quantitative shot-gun proteomics, LC-HRMS/MS) and structure of membrane lipids (UPLC-HRMS/MS). The shocked culture was more active (0.66{+/-}0.06 vs 0.48{+/-}0.06 kg-N/kg-VSS/d) and maintained the relative content of N-respiration proteins at levels consistent levels with the initial state, whereas the content of these proteins decreased in gradually acclimated culture. Cold shocks also induced a more efficient up-regulation of cold shock proteins (e.g. CspB, TypA, ppiD). Ladderane lipids characteristic for anammox evolved to a similar end-point in both cultures which confirms their role in anammox bacteria adaptation to cold and indicates a three-pronged adaptation mechanism involving ladderane lipids (ladderane alkyl length, introduction of shorter non-ladderane alkyls, polar headgroup). Overall, we show the outstanding potential of cold shocks for low-temperature adaptation of anammox bacteria and provide yet unreported detailed mechanisms of anammox adaptation to low temperatures. HighlightsO_LIAnammox bacteria were adapted to low T by gradual acclimation and cold shocks C_LIO_LIThe shocked culture was more active (0.66{+/-}0.06 vs 0.48{+/-}0.06 kg-N/kg-VSS/d) C_LIO_LIN-respiration proteins content decreased in gradually acclimated bacteria C_LIO_LISeveral cold shock proteins were upregulated more efficiently by cold shocks C_LIO_LIAt {downarrow}T, anammox adjusted ladderane membrane lipid composition in three aspects C_LI Graphical abstract O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY

bioengineering↗

bioRxiv2019

On anammox activity at low temperature: effect of ladderane composition, process conditions and dominant anammox population

The application of partial nitritation-anammox (PN/A) under mainstream conditions can enable substantial cost savings at wastewater treatment plants (WWTPs), but how process conditions and cell physiology affect anammox performance at psychrophilic temperatures below 15 {degrees}C remains poorly understood. We tested 14 anammox communities, including 8 from globally-installed PN/A processes, for (i) specific activity at 10-30 {degrees}C (batch assays), (ii) composition of membrane lipids (U-HPLC-HRMS/MS), and (iii) microbial community structure (16S rRNA gene amplicon sequencing). Crucially, the key parameters impacting anammox activity were the membrane lipid composition and cultivation temperature. The size of ladderane lipids and the content of bacteriohopanoids were key physiological drivers of anammox performance at low temperatures. Higher contents of (i) short C18 [3]-ladderane alkyl and (ii) large phosphatidylcholine headgroup were determined in anammox more active at 15-30 {degrees}C and 10-15 {degrees}C, respectively. At below 15 {degrees}C, the activation energies of most mesophilic cultures severely increased while those of the psychrophilic cultures remained stable; this indicates that the adaptation of mesophilic cultures to psychrophilic regime necessitates months, but in some cases can take up to 5 years. Interestingly, biomass enriched in the marine genus "Candidatus Scalindua" displayed exceptionally highest activity at 10-20 {degrees}C (0.50 kg-N.kg-VSS-1.d-1 at 10 {degrees}C, Ea10-30 {degrees}C = 51{+/-}16 kJ.mol-1), indicating outstanding potential for nitrogen removal from cold streams. Collectively, our comprehensive study provides essential knowledge of cold adaptation mechanism, will enable more accurate modelling and suggests highly promising target anammox genera for inoculation and set-up of anammox reactors, in particular for mainstream WWTPs. HighlightsO_LILadderane size and cold exposure affected anammox activation energy (Ea). C_LIO_LIEa improved with more C18 [3]-ladderanes over C20 and larger polar headgroup. C_LIO_LILong-term cold exposure reduced Ea at 10-15 {degrees}C, not activity per se. C_LIO_LIMarine "Ca. Scalindua" was exceptionally suitable for cold streams. C_LIO_LIAnammox Ea at 15-30 {degrees}C was 79{+/-}18 kJ.mol-1. C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=121 SRC="FIGDIR/small/873869v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@1c5c3aborg.highwire.dtl.DTLVardef@b11ed2org.highwire.dtl.DTLVardef@5e7ec9org.highwire.dtl.DTLVardef@1d5cba5_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗