Growth and activity of ANME clades with different sulfate and sulfide concentrations in presence of methane

Extensive geochemical data showed that significant methane oxidation activity exists in marine sediments. The organisms responsible for this activity are anaerobic methane-oxidizing archaea (ANME) that occur in consortia with sulfate-reducing bacteria. A distinct zonation of different clades of ANME (ANME-1, ANME-2a/b and ANME-2c) exists in marine sediments, which could be related to the localized concentrations of methane, sulfate and sulfide. In order to test this hypothesis we performed long-term incubation of marine sediments under defined conditions with methane as a headspace gas: low or high sulfate (?4 and ?21 mM, respectively) in combination with low or high sulfide (?0.1 and ?4 mM, respectively) concentrations. Control incubations were also performed, with only methane, high sulfate or high sulfide. Methane oxidation was monitored and growth of subtypes ANME-1, ANME-2a/b, and ANME-2c assessed using qPCR analysis. A preliminary archaeal community analysis was performed to gain insight into the ecological and taxonomic diversity. Almost all of the incubations with methane had methane oxidation activity, with the exception of the incubations with combined low sulfate and high sulfide concentrations. Sulfide inhibition occurred only with low sulfate concentrations, which could be due to the lower Gibbs free energy available as well as sulfide toxicity. ANME-2a/b appear to mainly grow in incubations which had high sulfate levels and methane oxidation activity, whereas ANME-1 did not show this distinction. ANME-2c only grew in incubations with only sulfate addition. These findings are consistent with previously published in situ profiling analysis of ANME subclusters in different marine sediments. Interestingly, since all ANME subtypes also grew in incubations with only methane or sulfate addition, ANME may also be able to perform anaerobic methane oxidation under substrate limited conditions or alternatively perform additional metabolic processes.We want to thank all reviewers for constructive comments, Joan Edwards (Laboratory of Microbiology, WUR) for extensive proof-reading, Bartholomeus van den Bogert (Laboratory of Microbiology, WUR) for help with the MiSeq sequencing and Diego A. Suarez-Zuluaga (Environmental Technology, WUR) for help with carbon dioxide calculations. This research is supported by the Dutch Technology Foundation STW (project 10711), which is part of the Netherlands Organization for Scientific Research (NWO), and which is partly funded by the Ministry of Economic Affairs. Research of AJMS is supported by ERC grant (project 323009) and the Gravitation grant (project 024.002.002) of the Netherlands Ministry of Education, Culture and Science and the Netherlands Science Foundation (NWO)

Development of quantitative PCR for the detection of Alkalilimnicola ehrlichii, Thioalkalivibrio sulfidiphilus and Thioalkalibacter halophilus in gas biodesulfurization processes

Chemolithoautotrophic sulfur-oxidizing bacteria (SOB) are crucial key players in biotechnological processes to remove hydrogen sulfide from sour gas streams. Several different haloalkaliphilic SOB have been detected and isolated from lab- and full-scale facilities, which all performed differently considering end product yields (sulfur and sulfate) and conversion rates. Understanding and regulating bacterial community dynamics in biodesulfurization processes will enable optimization of the process operation. We developed quantitative PCR (qPCR) assays to quantify haloalkaliphilic sulfur-oxidizing gammaproteobacterial species Alkalilimnicola ehrlichii, Thioalkalivibrio sulfidiphilus, and Thioalkalibacter halophilus that dominate bacterial communities of biodesulfurization lab- and full-scale installations at haloalkaline conditions. The specificity and PCR efficiency of novel primer sets were evaluated using pure cultures of these target species. We further validated the qPCR assays by quantification of target organisms in five globally distributed full-scale biodesulfurization installations. The qPCR assays perform a sensitive and accurate quantification of Alkalilimnicola ehrlichii, Thioalkalivibrio sulfidiphilus and Thioalkalibacter halophilus, thus providing rapid and valuable insights into process performance and SOB growth dynamics in gas biodesulfurization systems.</p

Effect of methanethiol on process performance, selectivity and diversity of sulfur-oxidizing bacteria in a dual bioreactor gas biodesulfurization system

This study provides important new insights on how to achieve high sulfur selectivities and stable gas biodesulfurization process operation in the presence of both methanethiol and H2S in the feed gas. On the basis of previous research, we hypothesized that a dual bioreactor lineup (with an added anaerobic bioreactor) would favor sulfur-oxidizing bacteria (SOB) that yield a higher sulfur selectivity. Therefore, the focus of the present study was to enrich thiol-resistant SOB that can withstand methanethiol, the most prevalent and toxic thiol in sulfur-containing industrial off gases. In addition, the effect of process conditions on the SOB population dynamics was investigated. The results confirmed that thiol-resistant SOB became dominant with a concomitant increase of the sulfur selectivity from 75 mol% to 90 mol% at a loading rate of 2 mM S methanethiol day−1. The abundant SOB in the inoculum – Thioalkalivibrio sulfidiphilus – was first outcompeted by Alkalilimnicola ehrlichii after which Thioalkalibacter halophilus eventually became the most abundant species. Furthermore, we found that the actual electron donor in our lab-scale biodesulfurization system was polysulfide, and not the primarily supplied sulfide.</p

Identifying Eukaryotes and Factors Influencing Their Biogeography in Drinking Water Metagenomes

The biogeography of eukaryotes in drinking water systems is poorly understood relative to that of prokaryotes or viruses, limiting the understanding of their role and management. A challenge with studying complex eukaryotic communities is that metagenomic analysis workflows are currently not as mature as those that focus on prokaryotes or viruses. In this study, we benchmarked different strategies to recover eukaryotic sequences and genomes from metagenomic data and applied the best-performing workflow to explore the factors affecting the relative abundance and diversity of eukaryotic communities in drinking water distribution systems (DWDSs). We developed an ensemble approach exploiting k-mer- and reference-based strategies to improve eukaryotic sequence identification and identified MetaBAT2 as the best-performing binning approach for their clustering. Applying this workflow to the DWDS metagenomes showed that eukaryotic sequences typically constituted small proportions (i.e., <1%) of the overall metagenomic data with higher relative abundances in surface water-fed or chlorinated systems with high residuals. The α and β diversities of eukaryotes were correlated with those of prokaryotic and viral communities, highlighting the common role of environmental/management factors. Finally, a co-occurrence analysis highlighted clusters of eukaryotes whose members’ presence and abundance in DWDSs were affected by disinfection strategies, climate conditions, and source water types

Isolation and characterization of Sphingomonadaceae from fouled membranes

Membrane filtration systems are widely applied for the production of clean drinking water. However, the accumulation of particles on synthetic membranes leads to fouling. Biological fouling (i.e., biofouling) of reverse osmosis and nanofiltration membranes is difficult to control by existing cleaning procedures. Improved strategies are therefore needed. The bacterial diversity on fouled membranes has been studied, especially to identify bacteria with specialized functions and to develop targeted approaches against these microbes. Previous studies have shown that Sphingomonadaceae are initial membrane colonizers that remain dominant while the biofilm develops. Here, we characterized 21 Sphingomonadaceae isolates, obtained from six different fouled membranes, to determine which physiological traits could contribute to colonization of membrane surfaces. Their growth conditions ranged from temperatures between 8 and 42 oC, salinity between 0.0 and 5.0% w/v NaCl, pH from 4 and 10, and all isolates were able to metabolize a wide range of substrates. The results presented here show that Sphingomonadaceae membrane isolates share many features that are uncommon for other members of the Sphingomonadaceae family: all membrane isolates are motile and their tolerance for different temperatures, salt concentrations, and pH is high. Although relative abundance is an indicator of fitness for a whole group, for the Sphingomonadaceae it does not reveal the specific physiological traits that are required for membrane colonization. This study, therefore, adds to more fundamental insights in membrane biofouling.</p

Effect of methanethiol on process performance, selectivity and diversity of sulfur-oxidizing bacteria in a dual bioreactor gas biodesulfurization system

This study provides important new insights on how to achieve high sulfur selectivities and stable gas biodesulfurization process operation in the presence of both methanethiol and H2S in the feed gas. On the basis of previous research, we hypothesized that a dual bioreactor lineup (with an added anaerobic bioreactor) would favor sulfur-oxidizing bacteria (SOB) that yield a higher sulfur selectivity. Therefore, the focus of the present study was to enrich thiol-resistant SOB that can withstand methanethiol, the most prevalent and toxic thiol in sulfur-containing industrial off gases. In addition, the effect of process conditions on the SOB population dynamics was investigated. The results confirmed that thiol-resistant SOB became dominant with a concomitant increase of the sulfur selectivity from 75 mol% to 90 mol% at a loading rate of 2 mM S methanethiol day−1. The abundant SOB in the inoculum – Thioalkalivibrio sulfidiphilus – was first outcompeted by Alkalilimnicola ehrlichii after which Thioalkalibacter halophilus eventually became the most abundant species. Furthermore, we found that the actual electron donor in our lab-scale biodesulfurization system was polysulfide, and not the primarily supplied sulfide.BT/Environmental Biotechnolog

Isolation and characterization of Sphingomonadaceae from fouled membranes

Membrane filtration systems are widely applied for the production of clean drinking water. However, the accumulation of particles on synthetic membranes leads to fouling. Biological fouling (i.e., biofouling) of reverse osmosis and nanofiltration membranes is difficult to control by existing cleaning procedures. Improved strategies are therefore needed. The bacterial diversity on fouled membranes has been studied, especially to identify bacteria with specialized functions and to develop targeted approaches against these microbes. Previous studies have shown that Sphingomonadaceae are initial membrane colonizers that remain dominant while the biofilm develops. Here, we characterized 21 Sphingomonadaceae isolates, obtained from six different fouled membranes, to determine which physiological traits could contribute to colonization of membrane surfaces. Their growth conditions ranged from temperatures between 8 and 42 oC, salinity between 0.0 and 5.0% w/v NaCl, pH from 4 and 10, and all isolates were able to metabolize a wide range of substrates. The results presented here show that Sphingomonadaceae membrane isolates share many features that are uncommon for other members of the Sphingomonadaceae family: all membrane isolates are motile and their tolerance for different temperatures, salt concentrations, and pH is high. Although relative abundance is an indicator of fitness for a whole group, for the Sphingomonadaceae it does not reveal the specific physiological traits that are required for membrane colonization. This study, therefore, adds to more fundamental insights in membrane biofouling.</p

Improved drinking water quality after adding advanced oxidation for organic micropollutant removal to pretreatment of river water undergoing dune infiltration near The Hague, Netherlands

AOP decreases the number and concentration of OMP and chances of negative impact on ecology and groundwater quality.AOP decreased OMP concentrations in drinking water with no measurable negative effect on water quality parameters.MARR produces water with a highly stable chemical and microbiological composition and levels out seasonal peak fluctuations.There is redundancy in OMP removal by MARR and AOP, but AOP is able to remove certain OMP that MARR is not, and vice versa

Controlling Ethanol Use in Chain Elongation by CO₂ Loading Rate

Chain elongation is an open-culture biotechnological process which converts volatile fatty acids (VFAs) into medium chain fatty acids (MCFAs) using ethanol and other reduced substrates. The objective of this study was to investigate the quantitative effect of CO₂ loading rate on ethanol usages in a chain elongation process. We supplied different rates of CO₂ to a continuously stirred anaerobic reactor, fed with ethanol and propionate. Ethanol was used to upgrade ethanol itself into caproate and to upgrade the supplied VFA (propionate) into heptanoate. A high CO₂ loading rate (2.5 L_CO2·L^–1·d^–1) stimulated excessive ethanol oxidation (EEO; up to 29%) which resulted in a high caproate production (10.8 g·L^–1·d^–1). A low CO₂ loading rate (0.5 L_CO2·L^–1·d^–1) reduced EEO (16%) and caproate production (2.9 g·L^–1·d^–1). Heptanoate production by VFA upgrading remained constant (∼1.8 g·L^–1·d^–1) at CO₂ loading rates higher than or equal to 1 L_CO2·L^–1·d^–1. CO₂ was likely essential for growth of chain elongating microorganisms while it also stimulated syntrophic ethanol oxidation. A high CO₂ loading rate must be selected to upgrade ethanol (e.g., from lignocellulosic bioethanol) into MCFAs whereas lower CO₂ loading rates must be selected to upgrade VFAs (e.g., from acidified organic residues) into MCFAs while minimizing use of costly ethanol