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Anaerobic digestion (AD) is a well-established technology used for the treatment of wastes and wastewaters with high organic content. During AD organic matter is converted stepwise to methane-containing biogasa renewable energy carrier. Methane production occurs in the last AD step and relies on methanogens, which are rather sensitive to some contaminants commonly found in wastewaters (e.g. heavy metals), or easily outcompeted by other groups of microorganisms (e.g. sulphate reducing bacteria, SRB). This review gives an overview of previous research and pilot-scale studies that shed some light on the effects of sulphate and heavy metals on methanogenesis. Despite the numerous studies on this subject, comparison is not always possible due to differences in the experimental conditions used and parameters explained. An overview of the possible benefits of methanogens and SRB co-habitation is also covered. Small amounts of sulphide produced by SRB can precipitate with metals, neutralising the negative effects of sulphide accumulation and free heavy metals on methanogenesis. Knowledge on how to untangle and balance sulphate reduction and methanogenesis is crucial to take advantage of the potential for the utilisation of biogenic sulphide as a metal detoxification agent with minimal loss in methane production in anaerobic digesters. ; The research was financially supported by the People Program (Marie Curie Actions) of the European Union's Seventh Framework Programme FP7/2007-2013 under REA agreement ...

Biological treatment of wastewaters depends on microbial processes, usually carried out by mixed microbial communities. Environmental and operational factors can affect microorganisms and/or impact microbial community function, and this has repercussion in bioreactor performance. Novel high-throughput molecular methods (metagenomics, metatranscriptomics, metaproteomics, metabolomics) are providing detailed knowledge on the microorganisms governing wastewater treatment systems and on their metabolic capabilities. The genomes of uncultured microbes with key roles in wastewater treatment plants (WWTP), such as the polyphosphate-accumulating microorganism Candidatus Accumulibacter phosphatis, the nitrite oxidizer Candidatus Nitrospira defluvii or the anammox bacterium Candidatus Kuenenia stuttgartiensis are now available through metagenomic studies. Metagenomics allows to genetically characterize full-scale WWTP and provides information on the lifestyles and physiology of key microorganisms for wastewater treatment. Integrating metagenomic data of microorganisms with metatranscriptomic, metaproteomic and metabolomic information provides a better understanding of the microbial responses to perturbations or environmental variations. Data integration may allow the creation of predictive behavior models of wastewater ecosystems, which could help in an improved exploitation of microbial processes. This review discusses the impact of meta-omic approaches on the understanding of wastewater treatment processes, and the implications of these methods for the optimization and design of wastewater treatment bioreactors. ; Research was supported by the Spanish Ministry of Education and Science (Contract Project CTQ2007-64324 and CONSOLIDER-CSD 2007-00055) and the Regional Government of Castilla y Leon (Ref. VA038A07). Research of AJMS is supported by the European Research Council (Grant ...

Organic and inorganic chlorine compounds are formed by a broad range of natural geochemical, photochemical and biological processes. In addition, chlorine compounds are produced in large quantities for industrial, agricultural and pharmaceutical purposes, which has led to widespread environmental pollution. Abiotic transformations and microbial metabolism of inorganic and organic chlorine compounds combined with human activities constitute the chlorine cycle on Earth. Naturally occurring organochlorines compounds are synthesized and transformed by diverse groups of (micro)organisms in the presence or absence of oxygen. In turn, anthropogenic chlorine contaminants may be degraded under natural or stimulated conditions. Here, we review phylogeny, biochemistry and ecology of microorganisms mediating chlorination and dechlorination processes. In addition, the co-occurrence and potential interdependency of catabolic and anabolic transformations of natural and synthetic chlorine compounds are discussed for selected microorganisms and particular ecosystems. ; The authors thank METAEXPLORE, funded by the European Union Seventh Framework Program (Grant No. 222625), BEBASIC-FES funds from the Dutch Ministry of Economic Affairs (Projects F07.001.05 and F08.004.01), Shell Global Solutions International BV, the ERC Advanced grant "Novel Anaerobes" (Project 323009), the SIAM Gravitation grant "Microbes for Health and the Environment" (Project 024.002.002) of the Netherlands Ministry of Education, Culture and Science, and the Netherlands Science Foundation (NWO) for funding. ...

Inhibition of methanogens by long chain fatty acids (LCFA) and the low numbers of LCFA-degrading bacteria are limitations to exploit biogas production from fat-rich wastewaters. Generally reactors fail due to excessive LCFA accumulation onto the sludge. Here, long-term acclimation and bioaugmentation with a LCFA-degrading coculture were hypothesized as strategies to enhance methanogenic conversion of these compounds. Anaerobic sludges previously exposed to LCFA for more than 100 days converted a specific biomass-associated substrate of (3.2 ± 0.1) kg·kg−1 with very short lag phases (<1 day), whereas non-acclimated sludges showed lag phases of 11–15 days for metabolizing (1.6–1.8) kg·kg−1. Addition of a coculture of Syntrophomonas zehnderi and Methanobacterium formicicum to sludges previously loaded with LCFA and containing different amounts of biomass-associated substrate (from (0.5–3.2) kg·kg−1) did not improve methane production neither lag phases were shortened, indicating that the endogenous microbiota are not a limiting factor. Clearly, we show that long-term sludge acclimation to LCFA is essential for high rate methanogenesis from LCFA. ; The authors acknowledge the financial support by the European Regional Development Fund - ERDF, through the Operational Program Thematic Factors of Competitiveness - COMPETE, and by Portuguese funds, through the Portuguese Foundation for Science and Technology (FCT), in the frame of the project FCOMP-01-0124-FEDER-014784. FCT Strategic Project PEst-OE/EQB/LA0023/2013 is also acknowledged. A.J. Cavaleiro thanks FCT for the post-doctoral fellowship ref. SFRH/BPD/75247/2010. A.J.M. Stams has received funding from the European Research Council under the European Union's Seventh Framework Programme (FP/2007-2013)/ERC Grant Agreement n. ...

Many questions regarding proteins involved in microbial sulfur metabolism remain unsolved. For sulfur respiration at low pH, the terminal electron acceptor is still unclear. Desulfurella amilsii is a sulfur-reducing bacterium that respires elemental sulfur (S0) or thiosulfate, and grows by S0 disproportionation. Due to its versatility, comparative studies on D. amilsii may shed light on microbial sulfur metabolism. Requirement of physical contact between cells and S0 was analyzed. Sulfide production decreased by around 50\% when S0 was trapped in dialysis membranes, suggesting that contact between cells and S0 is beneficial, but not strictly needed. Proteome analysis was performed under the aforementioned conditions. A Mo-oxidoreductase suggested from genome analysis to act as sulfur reductase was not detected in any growth condition. Thiosulfate and sulfite reductases showed increased abundance in thiosulfate-reducing cultures, while rhodanese-like sulfurtransferases were highly abundant in all conditions. DsrE and DsrL were abundantly detected during thiosulfate reduction, suggesting a modified mechanism of sulfite reduction. Proteogenomics suggest a different disproportionation pathway from what has been reported. This work points to an important role of rhodaneses in sulfur processes and these proteins should be considered in searches for sulfur metabolism in broader fields like meta-omics. ; This research was supported by the organization of the Brazilian Government for the development of Science and Technology CNPq (Conselho Nacional de Desenvolvimento Científico e Tecnológico), by ERC project 323009 and a Gravitation project from the Netherlands Ministry of Education, Culture and Science (024.002.002). The authors thank Monika Jarzembowska (WUR, Wageningen, The Netherlands) for the support with the scanning electron microscopy analysis ...

Haloalkaliphilic microorganisms that grow optimally at high-pH and high-salinity conditions can be found in natural environments such as soda lakes. These globally spread lakes harbour interesting anaerobic microorganisms that have the potential of being applied in existing technologies or create new opportunities. In this review, we discuss the potential application of haloalkaliphilic anaerobic microbial communities in the fermentation of lignocellulosic feedstocks material subjected to an alkaline pre-treatment, methane production and sulfur removal technology. Also, the general advantages of operation at haloalkaline conditions, such as low volatile fatty acid and sulfide toxicity, are addressed. Finally, an outlook into the main challenges like ammonia toxicity and lack of aggregation is provided. ; This work was performed in the TTIW- cooperation framework of Wetsus, European Centre of Excel- lence for Sustainable Water Technology (www.wetsus.nl). Wetsus is funded by the Dutch Ministry of Economic Affairs, the European Union Regional Development Fund, the Province of Fryslân, the City of Leeuwarden and the EZ/Kompas program of the" Samenwerkingsverband Noord-Nederland". The authors would like to thank the participants of the research theme "Sulfur", namely Paqell, for fruitful discussions and financial ...

Fat, oils, and grease present in complex wastewater can be readily converted to methane, but the energy potential of these compounds is not always recyclable, due to incomplete degradation of long chain fatty acids (LCFA) released during lipids hydrolysis. Oleate (C18:1) is generally the dominant LCFA in lipid-containing wastewater, and its conversion in anaerobic bioreactors results in palmitate (C16:0) accumulation. The reason why oleate is continuously converted to palmitate without further degradation via β-oxidation is still unknown. In this work, the influence of methanogenic activity in the initial conversion steps of unsaturated LCFA was studied in 10 bioreactors continuously operated with saturated or unsaturated C16- and C18-LCFA, in the presence or absence of the methanogenic inhibitor bromoethanesulfonate (BrES). Saturated Cn-2-LCFA accumulated both in the presence and absence of BrES during the degradation of unsaturated Cn-LCFA, and represented more than 50\% of total LCFA. In the presence of BrES further conversion of saturated intermediates did not proceed, not even when prolonged batch incubation was applied. As the initial steps of unsaturated LCFA degradation proceed uncoupled from methanogenesis, accumulation of saturated LCFA can be expected. Analysis of the active microbial communities suggests a role for facultative anaerobic bacteria in the initial steps of unsaturated LCFA biodegradation. Understanding this role is now imperative to optimize methane production from LCFA. ; European Research Council under the European Union's Seventh Framework Programme (FP/2007-2013)/ERC Grant Agreement No 323009, and the Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of UID/BIO/04469/2013 unit and COMPETE 2020 (POCI-01-0145-FEDER-006684), and Project RECI/BBB-EBI/0179/2012 (FCOMP-01-0124-FEDER-027462). We also thank the Gravitation grant (project 024.002.002) of the Netherlands Ministry of Education, Culture and Science and the Netherlands Science ...

Long-chain fatty acids (LCFA) can inhibit methane production by methanogenic archaea. The effect of oleate and palmitate on pure cultures of Methanosaeta concilii and Methanosarcina mazei was assessed by comparing methane production rates from acetate before and after LCFA addition. For both methanogens, a sharp decrease in methane production (> 50%) was observed at 0.5 mmol L1 oleate, and no methane was formed at concentrations higher than 2 mmol L1 oleate. Palmitate was less inhibitory than oleate, and M. concilii was more tolerant to palmitate than M. mazei, with 2 mmol L1 palmitate causing 11% and 64% methanogenic inhibition respectively. This study indicates that M. concilii and M. mazei tolerate LCFA concentrations similar to those previously described for hydrogenotrophic methanogens. In particular, the robustness of M. concilii might contribute to the observed prevalence of Methanosaeta species in anaerobic bioreactors used to treat LCFA-rich wastewater. ; The authors thank the European Research Council under the European Union's Seventh Framework Programme (FP/2007-2013)/ERC Grant Agreement no. 323009 and the Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of UID/BIO/04469/2013 unit and COMPETE 2020 (POCI-01-0145-FEDER-006684), and Project RECI/BBBEBI/0179/2012 ...

Carbon materials have been reported to facilitate direct interspecies electron transfer (DIET) between bacteria and methanogens improving methane production in anaerobic processes. In this work, the effect of increasing concentrations of carbon nanotubes (CNT) on the activity of pure cultures of methanogens and on typical fatty acid-degrading syntrophic methanogenic coculture was evaluated. CNT affected methane production by methanogenic cultures, although acceleration was higher for hydrogenotrophic methanogens than for acetoclastic methanogens or syntrophic coculture. Interestingly, the initial methane production rate (IMPR) by Methanobacterium formicicum cultures increased 17 times with 5 g·L1 CNT. Butyrate conversion to methane by Syntrophomonas wolfei and Methanospirillum hungatei was enhanced (1.5 times) in the presence of CNT (5 g·L1), but indications of DIET were not obtained. Increasing CNT concentrations resulted in more negative redox potentials in the anaerobic microcosms. Remarkably, without a reducing agent but in the presence of CNT, the IMPR was higher than in incubations with reducing agent. No growth was observed without reducing agent and without CNT. This finding is important to re-frame discussions and re-interpret data on the role of conductive materials as mediators of DIET in anaerobic communities. It also opens new challenges to improve methane production in engineered methanogenic processes. This article is protected by copyright. All rights reserved. ; This study was supported by the European Research Council under the European Union's Seventh Framework Programme (FP/2007-2013)/ERC Grant Agreement no. 323009 and by the Portuguese Foundation for Science and Technology (FCT) under the scope of the following programs: strategic funding of UID/BIO/04469/2013 unit, funded by COMPETE 2020 (POCI-01-0145-FEDER-006684), Project RECI/BBBEBI/0179/2012 (FCOMP-01-0124-FEDER-027462), Project UID/CTM/50011/2013 (POCI-01-0145-FEDER-007679), fellowship awarded to Gilberto Martins (SFRH/BPD/80528/ 2011) ...

Under methanogenic conditions, short-chain fatty acids are common byproducts from degradation of organic compounds and conversion of these acids is an important component of the global carbon cycle. Due to the thermodynamic difficulty of propionate degradation, this process requires syntrophic interaction between a bacterium and partner methanogen; however, the metabolic strategies and behavior involved are not fully understood. In this study, the first genome analysis of obligately syntrophic propionate degraders (Pelotomaculum schinkii HH and P. propionicicum MGP) and comparison with other syntrophic propionate degrader genomes elucidated novel components of energy metabolism behind Pelotomaculum propionate oxidation. Combined with transcriptomic examination of P. schinkii behavior in co-culture with Methanospirillum hungatei, we found that formate may be the preferred electron carrier for P. schinkii syntrophy. Propionate-derived menaquinol may be primarily re-oxidized to formate, and energy was conserved during formate generation through newly proposed proton-pumping formate extrusion. P. schinkii did not overexpress conventional energy metabolism associated with a model syntrophic propionate degrader Syntrophobacter fumaroxidans MPOB (i.e., CoA transferase, Fix, and Rnf). We also found that P. schinkii and the partner methanogen may also interact through flagellar contact and amino acid and fructose exchange. These findings provide new understanding of syntrophic energy acquisition and interactions. This article is protected by copyright. All rights reserved. ; We thank Steven Aalvink for scanning electron microscopy analysis and WEMC for making the system available. The research leading to these results has received funding from the European Research Council under the European Union's Seventh Framework Programme (FP/2007-2013) / ERC Grant Agreement n. [323009] and a Gravitation Grant (Project 024.002.002) of the Netherlands Ministry of Education, Culture and Science and the Netherlands Organisation for ...

The online version of this article (doi:10.1007/s00253-017-8212-x) contains supplementary material, which is available to authorized users. ; The surfactant sodium lauryl ether sulfate (SLES) is widely used in the composition of detergents and frequently ends up in wastewater treatment plants (WWTPs). While aerobic SLES degradation is well studied, little is known about the fate of this compound in anoxic environments, such as denitrification tanks of WWTPs, nor about the bacteria involved in the anoxic biodegradation. Here, we used SLES as sole carbon and energy source, at concentrations ranging from 50 to 1000 mg L1, to enrich and isolate nitrate-reducing bacteria from activated sludge of a WWTP with the anaerobic-anoxic-oxic (A2/O) concept. In the 50 mg L1 enrichment, Comamonas (50%), Pseudomonas (24%), and Alicycliphilus (12%) were present at higher relative abundance, while Pseudomonas (53%) became dominant in the 1000 mg L1 enrichment. Aeromonas hydrophila strain S7, Pseudomonas stutzeri strain S8, and Pseudomonas nitroreducens strain S11 were isolated from the enriched cultures. Under denitrifying conditions, strains S8 and S11 degraded 500 mg L1 SLES in less than 1 day, while strain S7 required more than 6 days. Strains S8 and S11 also showed a remarkable resistance to SLES, being able to grow and reduce nitrate with SLES concentrations up to 40 g L1. Strain S11 turned out to be the best anoxic SLES degrader, degrading up to 41% of 500 mg L1. The comparison between SLES anoxic and oxic degradation by strain S11 revealed differences in SLES cleavage, degradation, and sulfate accumulation; both ester and ether cleavage were probably employed in SLES anoxic degradation by strain S11. ; This research was supported by the Spanish Ministry of Education and Science (contract project CTQ2007-64324 and 447 CONSOLIDER-CSD 2007-00055). The Regional Government of Castilla y Leon (Ref. GR76) is also gratefully acknowledged. MRD is supported by the WIMEK graduate school (project BAdaptive capacity and functionality of ...

Background: Exploring different microbial sources for biotechnological production of organic acids is important. Dutch and Thai cow rumen samples were used as inocula to produce organic acid from starch waste in anaerobic reactors. Organic acid production profiles were determined and microbial communities were compared using 16S ribosomal ribonucleic acid gene amplicon pyrosequencing. Results In both reactors, lactate was the main initial product and was associated with growth of Streptococcus spp. (86% average relative abundance). Subsequently, lactate served as a substrate for secondary fermentations. In the reactor inoculated with rumen fluid from the Dutch cow, the relative abundance of Bacillus and Streptococcus increased from the start, and lactate, acetate, formate and ethanol were produced. From day 1.33 to 2, lactate and acetate were degraded, resulting in butyrate production. Butyrate production coincided with a decrease in relative abundance of Streptococcus spp. and increased relative abundances of bacteria of other groups, including Parabacteroides, Sporanaerobacter, Helicobacteraceae, Peptostreptococcaceae and Porphyromonadaceae. In the reactor with the Thai cow inoculum, Streptococcus spp. also increased from the start. When lactate was consumed, acetate, propionate and butyrate were produced (day 34). After day 3, bacteria belonging to five dominant groups, Bacteroides, Pseudoramibacter_Eubacterium, Dysgonomonas, Enterobacteriaceae and Porphyromonadaceae, were detected and these showed significant positive correlations with acetate, propionate and butyrate levels. Conclusions The complexity of rumen microorganisms with high adaptation capacity makes rumen fluid a suitable source to convert organic waste into valuable products without the addition of hydrolytic enzymes. Starch waste is a source for organic acid production, especially lactate. ; Susakul Palakawong Na Ayudthaya was financially supported by a Royal Thai Government Scholarship, Thailand. We thank Stang Pumisutapon at The Charoen ...

The data from this study are available in the manuscript and additional file. Genomic data are deposited in public databases (accession numbers are provided in Additional File 1: Table S1). The genomic sequence data of Trichococcus strain ES5 that supports the findings of this study have been deposited in GenBank with accession codes GCA_900067165.1, GCF_900067165.1. Supplementary information accompanies this paper at https://doi.org/10. 1186/s12864-019-6410-x. ; The genus Trichococcus currently contains nine species: T. flocculiformis, T. pasteurii, T. palustris, T. collinsii, T. patagoniensis, T. ilyis, T. paludicola, T. alkaliphilus, and T. shcherbakoviae. In general, Trichococcus species can degrade a wide range of carbohydrates. However, only T. pasteurii and a non-characterized strain of Trichococcus, strain ES5, have the capacity of converting glycerol to mainly 1,3-propanediol. Comparative genomic analysis of Trichococcus species provides the opportunity to further explore the physiological potential and uncover novel properties of this genus. ; This research was supported by the European Research Council under the European Union's Seventh Framework Programme / ERC Grant Agreement (323009) and by the Gravitation grant (024.002.002) of the Netherlands Ministry of Education, Culture and Science. The work conducted by the U.S. Department of Energy Joint Genome Institute (DOE-JGI), a DOE Office of Science User Facility, was supported by the Office of Science of the DOE under Contract No. DE-AC02-05CH11231. The funding bodies played no role in the design of the study and collection, analysis, and interpretation of data and in writing the manuscript. ...

Lipid-rich wastewaters are ideal sources for methane production, but lipids are generally separated and removed prior to anaerobic treatment to avoid sludge flotation and microbial inhibition. In this work, we review the major technological and microbiological advances in the anaerobic digestion (AD) of lipids, while highlighting the most important breakthroughs in the field and identifying the future perspectives. In the past decades, several treatment processes have been developed for lipidrich wastewaters, moving from the upflow granular sludge based reactor designs to anaerobic membrane bioreactors and in situ flotation based bioreactors all now commercially available. Knowledge on the complexity of microbial communities and microbial interactions has increased greatly, allowing a better interpretation of lipids anaerobic biodegradation. However, there are still knowledge gaps and bottlenecks in lipids AD that need to be overcome to improve industrial applications. A multi-faceted approach with industrial and academic partners will provide a unique strategy for future widespread usage of waste-lipids as valuable resource for AD. ; The authors acknowledge the funding from EPA Research (Ireland), the Irish Dairy Processing Technology Centre, The Irish Research Council (EBPS2012) and the Microbiology Society; the Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of UID/BIO/04469/2013 unit and COMPETE 2020 (POCI-01-0145-FEDER-006684), of Project RECI/BBB-EBI/0179/2012 (FCOMP-01-0124-FEDER-027462), POCI-01-0145-FEDER-007679 (UID/CTM/50011/2013), and by BioTecNorte operation (NORTE-01-0145-FEDER-000004) funded by the European Regional Development Fund under the scope of Norte2020 - Programa Operacional Regional do Norte. The authors also acknowledge the financial support of the European Research Council under the European Union's Seventh Framework Programme (FP/2007-2013)/ERC Grant Agreement no. 323009 and the funding of ANII-Uruguay, UNESCO-IHE and LATU (Uruguay). ...