Competition and coexistence of sulfate-reducing and methanogenic populations in anaerobic biofilms

Biofilm application for anaerobic digestion: a systematic review and an industrial scale case

Biofilm is a syntrophic community of microorganisms enveloped by extracellular polymeric substances and displays remarkable adaptability to dynamic environments. Implementing biofilm in anaerobic digestion has been widely investigated and applied as it promotes microbial retention time and enhances the efficiency. Previous studies on anaerobic biofilm primarily focused on application in wastewater treatment, while its role has been significantly extended to accelerate the degradation of lignocellulosic biomass, improve gas-liquid mass transfer for biogas upgrading, or enhance resistance to inhibitors or toxic pollutants. This work comprehensively reviewed the current applications of biofilm in anaerobic digestion and focused on impacting factors, optimization strategies, reactor set-up, and microbial communities. Moreover, a full-scale biofilm reactor case from Norway is also reported. This review provides a state of-the- art insight on the role of biofilm in anaerobic digestion.

Sulfide in engineered methanogenic systems - Friend or foe?

Sulfide ions are regarded to be toxic to microorganisms in engineered methanogenic systems (EMS), where organic substances are anaerobically converted to products such as methane, hydrogen, alcohols, and carboxylic acids. A vast body of research has addressed solutions to mitigate process disturbances associated with high sulfide levels, yet the established paradigm has drawn the attention away from the multifaceted sulfide interactions with minerals, organics, microbial interfaces and their implications for performance of EMS. This brief review brings forward sulfide-derived pathways other than toxicity and with potential significance for anaerobic organic matter degradation. Available evidence on sulfide reactions with organic matter, interventions with key microbial metabolisms, and interspecies electron transfer are critically synthesized as a guidance for comprehending the sulfide effects on EMS apart from the microbial toxicity. The outcomes identify existing knowledge gaps and specify future research needs as a step forward towards realizing the potential of sulfide-derived mechanisms in diversifying and optimizing EMS applications.

Bacteriophage-based biocontrol technology to enhance the efficiency of wastewater treatment and reduce targeted bacterial biofilms

Wastewater treatment is an essential process for public health and a sustainable ecosystem. Inadequate wastewater treatment can lead to the release of organic and inorganic pollutants and pathogenic bacteria into the receiving waters which could be further utilized for recreation purposes. The interaction between bacteriophage and bacteria in a wastewater treatment plant plays a major role in maintaining the treatment process. Phage therapy has been proposed as an alternative to conventional treatment methods as bacteriophages can be used on specific targets and leave useful bacteria unharmed. The bacterial species, which are responsible for bulking, foaming, and biofilm formation in a wastewater treatment plant (WWTP) have been identified and their respective phages are isolated to control their growth. Phages with lytic life cycles are preferred to lysogenic. Lytic phages can kill the specific target as they lyse the cell, infect most of the hosts, and have an immediate effect on controlling problems caused by bacteria in a WWTP. The bacteriophages such as T7, SPI1, GTE7, PhaxI, MAG1, MAG2, ϕPh_Se01, ϕPh_Se02, and Bxb1 have been investigated for the removal of bacterial biofilms from wastewater. Novel experimental setups have improved the efficiency of phage therapy in small-scale and pilot-scale experiments. Much more in-depth knowledge of the microbial community and their interaction would help promote the usage of phage therapy in large-scale wastewater treatments. This paper has covered the recent advancements in phage therapy as an effective biocontrol of pathogenic bacteria in the wastewater treatment process and has looked at certain shortcomings that have to be improved.

Treatment of acid rock drainage using a sulphate-reducing bioreactor with a limestone precolumn

Sulphate reducing bacteria (SRB) offer promise for the treatment of mine waste due to their effectiveness removing toxic heavy metals as highly insoluble metal sulphides and their ability to generate alkalinity. The main objective of this study was to develop a treatment composed of a sulphate-reducing bioreactor with a limestone precolumn for the removal of Cu(II) from a synthetic ARD. The purpose of the limestone column was to increase the pH values and decrease the level of Cu in the effluent to prevent SRB inhibition. The system was fed with a pH-2.7 synthetic ARD containing Cu(II) (10-40 mg/L), sulphate (2000 mg/L) and acetate (2.5 g COD/L) for 150 days. Copper removal efficiencies in the two-stage system were very high (95-99%), with a final concentration of 0.53 mg/L Cu, and almost complete removal occurred in the limestone precolumn. In the same manner, the acidity of the synthetic ARD was effectively reduced in the limestone precolumn to 7.3 and the pH was raised in the bioreactor (7.3-8.0). COD consumption by methanogens was predominant from day 0-118, but SRB dominated at the end of the experiment (day 150) when the average COD removal and sulphide production were 74.8% and 61.7%, respectively. Study of the microbial taxonomic composition in the bioreactor revealed that Methanosarcina and Methanosaeta were the most prevalent methanogens while the genera Desulfotomaculum and Syntrophobacter were the dominant SRB. Among the SRB identified Desulfotomaculum intricatum (99% identity) and Desulfotomaculum acetoxidans (96%) were the most abundant sequences of bacteria capable of using acetate.

Wastewater-derived biohydrogen: Critical analysis of related enzymatic processes at the research and large scales

Organic-rich wastewater is a feasible feedstock for biohydrogen production. Numerous review on the performance of microorganisms and the diversity of their communities during a biohydrogen process were published. However, there is still no in-depth overview of enzymes for biohydrogen production from wastewater and their scale-up applications. This review aims at providing an insightful exploration of critical discussion in terms of: (i) the roles and applications of enzymes in wastewater-based biohydrogen fermentation; (ii) systematical introduction to the enzymatic processes of photo fermentation and dark fermentation; (iii) parameters that affect enzymatic performances and measures for enzyme activity/ability enhancement; (iv) biohydrogen production bioreactors; as well as (v) enzymatic biohydrogen production systems and their larger scales application. Furthermore, to assess the best applications of enzymes in biohydrogen production from wastewater, existing problems and feasible future studies on the development of low-cost enzyme production methods and immobilized enzymes, the construction of multiple enzyme cooperation systems, the study of biohydrogen production mechanisms, more effective bioreactor exploration, larger scales enzymatic biohydrogen production, and the enhancement of enzyme activity or ability are also addressed.

Influence of cysteine, serine, sulfate, and sulfide on anaerobic conversion of unsaturated long-chain fatty acid, oleate, to methane

This study aims to elucidate the role of sulfide and its precursors in anaerobic digestion (i.e., cysteine, representing sulfur-containing amino acids, and sulfate) on microbial oleate conversion to methane. Serine, with a similar structure to cysteine but with a hydroxyl group instead of a thiol, was included as a control to assess potential effects on methane formation that were not related to sulfur functionalities. The results showed that copresence of sulfide and oleate in anaerobic batch assays accelerated the methane formation compared to assays with only oleate and mitigated negative effect on methane formation caused by increased sulfide level. Nuclear magnetic resonance spectroscopy of sulfide-exposed oleate suggested that sulfide reaction with oleate double bonds likely contributed to negation of the negative effect on the methanogenic activity. Methane formation from oleate was also accelerated in the presence of cysteine or serine, while sulfate decreased the cumulative methane formation from oleate. Neither cysteine nor serine was converted to methane, and their accelerating effects was associated to different mechanisms due to establishment of microbial communities with different structures, as evidenced by high-throughput sequencing of 16S rRNA gene. These outcomes contribute with new knowledge to develop strategies for optimum use of sulfur- and lipid-rich wastes in anaerobic digestion processes.

Lytics broadcasting system: A novel approach to disseminate bacteriophages for disinfection and biogenic hydrogen sulphide removal tested in synthetic sewage

Owing to their selective nature, bacteriophages are prospective in targeted wastewater disinfection. Other potential applications include the removal of biogenic malodour and the mitigation of corrosion in sewerage pipelines. Nevertheless, its applications are ridden with challenges, the most prominent of which is scaling up. Towards that end, effective methodologies are required for dispersing phages into wastewater. The study describes a device arbitrarily named Lytics Broadcasting System. In principle, the device contains phages that can be continuously dispersed into wastewater. The modified version is called Bacteriophage Amplification Reactor, which operates with both phages and their respective hosts, ensuring continual production and dissemination of phages. Both prototypes utilize 0.22 μm cellulose membranes as an interface through which phage diffuse passively and selectively owing to its smaller size and established through membrane-overlay method. In the study, previously reported bacteriophage φPh_Se01 and Salmonella enterica were used. A reduction of 3-4 log was achieved with both the prototypes after 48 h of operation in 1 L of augmented synthetic sewage. Subsequently, the biogenic H₂S produced by Salmonella enterica was reduced by 64-74% indicating its utility for targeted disinfection and malodour mitigation of wastewater. This study aims to provide a framework for the development of scalable prototypes of Lytic Broadcasting Systems for real-world wastewater applications.

Metatranscriptomics reveals different features of methanogenic archaea among global vegetated coastal ecosystems

Vegetated coastal ecosystems (VCEs; i.e., mangroves, saltmarshes, and seagrasses) represent important sources of natural methane emission. Despite recent advances in the understanding of novel taxa and pathways associated with methanogenesis in these ecosystems, the key methanogenic players and the contribution of different substrates to methane formation remain elusive. Here, we systematically investigate the community and activity of methanogens using publicly available metatranscriptomes at a global scale together with our in-house metatranscriptomic dataset. Taxonomic profiling reveals that 13 groups of methanogenic archaea were transcribed in the investigated VCEs, and they were predominated by Methanosarcinales. Among these VCEs, methanogens exhibited all the three known methanogenic pathways in some mangrove sediments, where methylotrophic methanogens Methanosarcinales/Methanomassiliicoccales grew on diverse methyl compounds and coexisted with hydrogenotrophic (mainly Methanomicrobiales) and acetoclastic (mainly Methanothrix) methanogens. Contrastingly, the predominant methanogenic pathway in saltmarshes and seagrasses was constrained to methylotrophic methanogenesis. These findings reveal different archaeal methanogens in VCEs and suggest the potentially distinct methanogenesis contributions in these VCEs to the global warming.

Comparison of Metabolic Kinetics during High and Low Solids Anaerobic Digestion of Fecal Sludge

High solids anaerobic digestion (HS-AD) is an attractive energy producing technology; however, high total solids (TS) content may inhibit methanogens due to high volatile fatty acid (VFA) and total ammonia nitrogen (TAN) concentrations. The objective of this paper is to quantify rate limiting metabolic kinetic parameters to determine the influence of TS content during anaerobic digestion of fecal sludge. Two TS content; 11 and 17% microcosms were analyzed. Good performance was observed in both systems, with VS removals greater than 50%, CH₄ yield between 0.44-0.56 m³ CH₄ /g VS added and cumulative CH₄ production between 1.78-2.03 m³ CH₄ / m³ digester-day. At 11% TS VFA consumption and VS removal had a positive correlation to CH₄ production while the 17% TS microcosm had a negative correlation with both. This is the first study to determine the kinetic parameters for hydrolysis, VFA consumption and methanogenesis during digestion of fecal sludge. These kinetic parameters are necessary in the design and operation of anaerobic digestion systems treating fecal sludge. This article is protected by copyright. All rights reserved.

When anaerobes encounter oxygen: mechanisms of oxygen toxicity, tolerance and defence

The defining trait of obligate anaerobes is that oxygen blocks their growth, yet the underlying mechanisms are unclear. A popular hypothesis was that these microorganisms failed to evolve defences to protect themselves from reactive oxygen species (ROS) such as superoxide and hydrogen peroxide, and that this failure is what prevents their expansion to oxic habitats. However, studies reveal that anaerobes actually wield most of the same defences that aerobes possess, and many of them have the capacity to tolerate substantial levels of oxygen. Therefore, to understand the structures and real-world dynamics of microbial communities, investigators have examined how anaerobes such as Bacteroides, Desulfovibrio, Pyrococcus and Clostridium spp. struggle and cope with oxygen. The hypoxic environments in which these organisms dwell - including the mammalian gut, sulfur vents and deep sediments - experience episodic oxygenation. In this Review, we explore the molecular mechanisms by which oxygen impairs anaerobes and the degree to which bacteria protect their metabolic pathways from it. The emergent view of anaerobiosis is that optimal strategies of anaerobic metabolism depend upon radical chemistry and low-potential metal centres. Such catalytic sites are intrinsically vulnerable to direct poisoning by molecular oxygen and ROS. Observations suggest that anaerobes have evolved tactics that either minimize the extent to which oxygen disrupts their metabolism or restore function shortly after the stress has dissipated.

Ecogenomics Reveals Microbial Metabolic Networks in a Psychrophilic Methanogenic Bioreactor Treating Soy Sauce Production Wastewater

An ecogenomic analysis of the methanogenic microbial community in a laboratory-scale up-flow anaerobic sludge blanket (UASB) reactor treating soy sauce-processing wastewater revealed a synergistic metabolic network. Granular sludge samples were collected from the UASB reactor operated under psychrophilic (20°C) conditions with a COD removal rate >75%. A 16S rRNA gene amplicon sequencing-based microbial community analysis classified the major microbial taxa as Methanothrix, Methanobacterium, Pelotomaculaceae, Syntrophomonadaceae, Solidesulfovibrio, and members of the phyla Synergistota and Bacteroidota. Draft genomes of dominant microbial populations were recovered by metagenomic shotgun sequencing. Metagenomic- and metatranscriptomic-assisted metabolic reconstructions indicated that Synergistota- and Bacteroidota-related organisms play major roles in the degradation of amino acids. A metagenomic bin of the uncultured Bacteroidales 4484-276 clade encodes genes for proteins that may function in the catabolism of phenylalanine and tyrosine under microaerobic conditions. Syntrophomonadaceae and Pelotomaculaceae oxidize fatty acid byproducts presumably derived from the degradation of amino acids in syntrophic association with aceticlastic and hydrogenotrophic methanogen populations. Solidesulfovibrio organisms are responsible for the reduction of sulfite and may support the activity of hydrogenotrophic methanogens and other microbial populations by providing hydrogen and ammonia using nitrogen fixation-related proteins. Overall, functionally diverse anaerobic organisms unite to form a metabolic network that performs the complete degradation of amino acids in the psychrophilic methanogenic microbiota.

Saline mine-water alters the structure and function of prokaryote communities in shallow groundwater below a tropical stream

Bacteria and archaea (prokaryotes) are vital components for maintaining healthy function of groundwater ecosystems. The prokaryotic community composition and associated putative functional processes were examined in a shallow sandy aquifer in a wet-dry tropical environment. The aquifer had a contaminated gradient of saline mine-water, which primarily consisted of elevated magnesium (Mg²⁺) and sulfate (SO₄^2-), although other major ions and trace metals were also present. Groundwaters were sampled from piezometers, approximately 2 m in depth, located in the creek channel upstream and downstream of the mine-water influence. Sampling occurred during the dry-season when only subsurface water flow was present. Next generation sequencing was used to analyse the prokaryote assemblages using 16S rDNA and metabolic functions were predicted with FAPROTAX. Significant changes in community composition and functional processes were observed with exposure to mine-waters. Communities in the exposed sites had significantly lower relative abundance of methanotrophs such as Methylococcaceae and methanogens (Methanobacteriaceae), but higher abundance in Nitrososphaeraceae, associated with nitrification, indicating potentially important changes in the biogeochemistry of the exposed sites. The changes were most strongly correlated with concentrations of SO₄^2-, Mg²⁺ and Na⁺. This knowledge allows an assessment of the risk of mine-water contamination to groundwater ecosystem function and aids mine-water management.

Microbial sulfur metabolism and environmental implications

Sulfur as a macroelement plays an important role in biochemistry in both natural environments and engineering biosystems, which can be further linked to other important element cycles, e.g. carbon, nitrogen and iron. Consequently, the sulfur cycling primarily mediated by sulfur compounds oxidizing microorganisms and sulfur compounds reducing microorganisms has enormous environmental implications, particularly in wastewater treatment and pollution bioremediation. In this review, to connect the knowledge in microbial sulfur metabolism to environmental applications, we first comprehensively review recent advances in understanding microbial sulfur metabolisms at molecular-, cellular- and ecosystem-levels, together with their energetics. We then discuss the environmental implications to fight against soil and water pollution, with four foci: (1) acid mine drainage, (2) water blackening and odorization in urban rivers, (3) SANI® and DS-EBPR processes for sewage treatment, and (4) bioremediation of persistent organic pollutants. In addition, major challenges and further developments toward elucidation of microbial sulfur metabolisms and their environmental applications are identified and discussed.

Emission characteristics of odorous volatile sulfur compound from a full-scale sequencing batch reactor wastewater treatment plant

Volatile sulfur compounds (VSCs) generated and discharged as air pollutants from wastewater treatment plants (WWTPs) pose a threat to human health and the environment. This study characterized VSC emissions from a full-scale sequencing batch reactor (SBR) WWTP at the water-air interface for one year. Results demonstrated that higher ambient temperatures and aeration contributed significantly to VSC emissions as the highest emissions occurred over summer during the feeding synchronous aeration period. VSC emissions were related to chemical oxygen demand and sulfate concentrations in wastewater, and empirical formulas based on these values were proposed that can be used to model VSC emission fluxes from SBR WWTP. VSC emission factors (μg·ton^-1 wastewater) throughout the SBR treatment process were: 361 ± 101 hydrogen sulfide (H₂S), 82 ± 76 methyl mercaptan (MT), 61 ± 31 dimethyl sulfide, 17 ± 5 carbon disulfide, and 46 ± 24 dimethyl disulfide. H₂S and MT were the dominant odors released. Findings from this study may be applicable for calculating VSC emissions during SBR wastewater treatment stages, and may be beneficial for determining methods and strategies to reduce VSCs.

Microbial Diversity Dynamics in a Methanogenic-Sulfidogenic UASB Reactor

In this study, the long-term performance and microbial dynamics of an Upflow Anaerobic Sludge Blanket (UASB) reactor targeting sulfate reduction in a SOx emissions treatment system were assessed using crude glycerol as organic carbon source and electron donor under constant S and C loading rates. The reactor was inoculated with granular sludge obtained from a pulp and paper industry and fed at a constant inlet sulfate concentration of 250 mg S-SO₄²⁻L⁻¹ and a constant C/S ratio of 1.5 ± 0.3 g Cg⁻¹ S for over 500 days. Apart from the regular analysis of chemical species, Illumina analyses of the 16S rRNA gene were used to study the dynamics of the bacterial community along with the whole operation. The reactor was sampled along the operation to monitor its diversity and the changes in targeted species to gain insight into the performance of the sulfidogenic UASB. Moreover, studies on the stratification of the sludge bed were performed by sampling at different reactor heights. Shifts in the UASB performance correlated well with the main shifts in microbial communities of interest. A progressive loss of the methanogenic capacity towards a fully sulfidogenic UASB was explained by a progressive wash-out of methanogenic Archaea, which were outcompeted by sulfate-reducing bacteria. Desulfovibrio was found as the main sulfate-reducing genus in the reactor along time. A progressive reduction in the sulfidogenic capacity of the UASB was found in the long run due to the accumulation of a slime-like substance in the UASB.

Phage cocktail strategies for the suppression of a pathogen in a cross-feeding coculture

Cocktail combinations of bacteria-infecting viruses (bacteriophages) can suppress pathogenic bacterial growth. However, predicting how phage cocktails influence microbial communities with complex ecological interactions, specifically cross-feeding interactions in which bacteria exchange nutrients, remains challenging. Here, we used experiments and mathematical simulations to determine how to best suppress a model pathogen, E. coli, when obligately cross-feeding with S. enterica. We tested whether the duration of pathogen suppression caused by a two-lytic phage cocktail was maximized when both phages targeted E. coli, or when one phage targeted E. coli and the other its cross-feeding partner, S. enterica. Experimentally, we observed that cocktails targeting both cross-feeders suppressed E. coli growth longer than cocktails targeting only E. coli. Two non-mutually exclusive mechanisms could explain these results: (i) we found that treatment with two E. coli phage led to the evolution of a mucoid phenotype that provided cross-resistance against both phages, and (ii) S. enterica set the growth rate of the coculture, and therefore, targeting S. enterica had a stronger effect on pathogen suppression. Simulations suggested that cross-resistance and the relative growth rates of cross-feeders modulated the duration of E. coli suppression. More broadly, we describe a novel bacteriophage cocktail strategy for pathogens that cross-feed.

Effect of Sub-Stoichiometric Fe(III) Amounts on LCFA Degradation by Methanogenic Communities

Long-chain fatty acids (LCFA) are common contaminants in municipal and industrial wastewater that can be converted anaerobically to methane. A low hydrogen partial pressure is required for LCFA degradation by anaerobic bacteria, requiring the establishment of syntrophic relationships with hydrogenotrophic methanogens. However, high LCFA loads can inhibit methanogens, hindering biodegradation. Because it has been suggested that anaerobic degradation of these compounds may be enhanced by the presence of alternative electron acceptors, such as iron, we investigated the effect of sub-stoichiometric amounts of Fe(III) on oleate (C18:1 LCFA) degradation by suspended and granular methanogenic sludge. Fe(III) accelerated oleate biodegradation and hydrogenotrophic methanogenesis in the assays with suspended sludge, with H₂-consuming methanogens coexisting with iron-reducing bacteria. On the other hand, acetoclastic methanogenesis was delayed by Fe(III). These effects were less evident with granular sludge, possibly due to its higher initial methanogenic activity relative to suspended sludge. Enrichments with close-to-stoichiometric amounts of Fe(III) resulted in a microbial community mainly composed of Geobacter, Syntrophomonas, and Methanobacterium genera, with relative abundances of 83-89%, 3-6%, and 0.2-10%, respectively. In these enrichments, oleate was biodegraded to acetate and coupled to iron-reduction and methane production, revealing novel microbial interactions between syntrophic LCFA-degrading bacteria, iron-reducing bacteria, and methanogens.

Key syntrophic partnerships identified in a granular activated carbon amended UASB treating municipal sewage under low temperature conditions

Two laboratory-scale up-flow anaerobic sludge blankets (UASB) reactors, one with and one without granular activated carbon (GAC), were operated for municipal sewage treatment at low temperatures (16.5 ± 2.0 °C). During the 120-day operation, the GAC-amended reactor significantly enhanced COD removal (from 62% to 75%, P < 0.05) and methane production (from 87 to 218 mg CH₄-COD/reactor/d) than the non-GAC reactor. Bacterial communities were significantly different between the two reactors (P < 0.05). Geobacter, a key indicator for direct interspecies electron transfer (DIET), had the highest differential score (LEfSe analysis), showing significantly higher abundances in the GAC-amended reactor (3.7-8.8%) than the non-GAC reactor (0.9-4.0%). GAC also enriched syntrophic bacteria, Syntrophomonas, Syntrophus and sulfate reducing bacteria. Methanobacterium dominated the archaeal community in the GAC-amended reactor sludge (35.7%) and GAC-biofilm (75.3%), and was less abundant in the non-GAC reactor (9.9%). It indicates that GAC enriched microbial syntrophic partners with potential electro-activities in the anaerobic digestion process.

Design, application, and microbiome of sulfate-reducing bioreactors for treatment of mining-influenced water

Sulfate-reducing bioreactors, also called biochemical reactors, represent a promising option for passive treatment of mining-influenced water (MIW) based on similar technology to aerobic/anaerobic-constructed wetlands and vertical-flow wetlands. MIW from each mine site has a variety of site-specific properties related to its treatment; therefore, design factors, including the organic substrates and inorganic materials packed into the bioreactor, must be tested and evaluated before installation of full-scale sulfate-reducing bioreactors. Several full-scale sulfate-reducing bioreactors operating at mine sites provide examples, but holistic understanding of the complex treatment processes occurring inside the bioreactors is lacking. With the recent introduction of high-throughput DNA sequencing technologies, microbial processes within bioreactors may be clarified based on the relationships between operational parameters and key microorganisms identified using high-resolution microbiome data. In this review, the test design procedures and precedents of full-scale bioreactor application for MIW treatment are briefly summarized, and recent knowledge on the sulfate-reducing microbial communities of field-based bioreactors from fine-scale monitoring is presented.Key points• Sulfate-reducing bioreactors are promising for treatment of mining-influenced water.• Various design factors should be tested for application of full-scale bioreactors.• Introduction of several full-scale passive bioreactor systems at mine sites.• Desulfosporosinus spp. can be one of the key bacteria within field-based bioreactors.

Increasing sulfate levels show a differential impact on synthetic communities comprising different methanogens and a sulfate reducer

Methane-producing microbial communities are of ecological and biotechnological interest. Syntrophic interactions among sulfate reducers and aceto/hydrogenotrophic and obligate hydrogenotrophic methanogens form a key component of these communities, yet, the impact of these different syntrophic routes on methane production and their stability against sulfate availability are not well understood. Here, we construct model synthetic communities using a sulfate reducer and two types of methanogens representing different methanogenesis routes. We find that tri-cultures with both routes increase methane production by almost twofold compared to co-cultures and are stable in the absence of sulfate. With increasing sulfate, system stability and productivity decreases and does so faster in communities with aceto/hydrogenotrophic methanogens despite the continued presence of acetate. We show that this is due to a shift in the metabolism of these methanogens towards co-utilization of hydrogen with acetate. These findings indicate the important role of hydrogen dynamics in the stability and productivity of syntrophic communities.

Alleviating sulfide toxicity using biochar during anaerobic treatment of sulfate-laden wastewater

This study examined the use of biochar to alleviate sulfide toxicity to methane producing archaea (MPA) and sulfate-reducing bacteria (SRB) during anaerobic treatment of sulfate-rich wastewater with concomitant sulfur recovery. At the sulfate concentration of 6000 mg SO₄^2-/L, the dissolved sulfide (DS) of 131 mg S/L resulted in total volatile fatty acids concentration of 3500 mg/L as acetic acid (HAc) and the reactors were on the verge of failure. Biochar removed >98% of H₂S_(g), 94% of DS, and 89% of unionized sulfide (H₂S_aq). 16S rRNA analysis revealed that after sulfide removal the relative abundance of MPA (Methanobacterium and Methanosaeta) increased from 0.7% to 3.7%, while the relative abundance of SRB (Desulfovibrio) decreased from 9.3% to 0.5% indicating that the reactor recovered to stable state. This study showed that biochar could effectively remove H₂S from biogas, alleviate sulfide toxicity to MPA and SRB, and promote stability of the anaerobic process.

Complementary DNA/RNA-Based Profiling: Characterization of Corrosive Microbial Communities and Their Functional Profiles in an Oil Production Facility

DNA and RNA-based sequencing of the 16S rRNA gene and transcripts were used to assess the phylogenetic diversity of microbial communities at assets experiencing corrosion in an oil production facility. The complementary methodological approach, coupled with extensive bioinformatics analysis, allowed to visualize differences between the total and potentially active communities present in several locations of the production facility. According to the results, taxa indicative for thermophiles and oil-degrading microorganisms decreased their relative abundances in the active communities, whereas sulfate reducing bacteria and methanogens had the opposite pattern. The differences in the diversity profile between total and active communities had an effect on the microbial functional capability predicted from the 16S rRNA sequences. Primarily, genes involved in methane metabolism were enriched in the RNA-based sequencing approach. Comparative analysis of microbial communities in the produced water, injection water and deposits in the pipelines showed that deposits host more individual species than other sample sources in the facility. Similarities in the number of cells and microbial profiles of active communities in biocide treated and untreated sampling locations suggested that the treatment was ineffective at controlling the growth of microbial populations with a known corrosive metabolism. Differences in the results between DNA and RNA-based profiling demonstrated that DNA results alone can lead to the underestimation of active members in the community, highlighting the importance of using a complementary approach to obtain a broad general overview not only of total and active members but also in the predicted functionality.

Exploring the performance limits of a sulfidogenic UASB during the long-term use of crude glycerol as electron donor

SOx contained in flue gases and S-rich liquid effluents can be valorized to recover elemental sulfur in a two-stage bioscrubbing process. The reduction of sulfate to sulfide is the most crucial stage to be optimized. In this study, the long-term performance of an up-flow anaerobic sludge blanket (UASB) reactor using crude glycerol as electron donor was assessed. The UASB was operated for 400 days with different sulfate and organic loading rates (SLR and OLR, respectively) and a COD/S-SO₄^2- ratio ranging from 3.8 g O₂ g^-1 S to 5.4 g O₂ g^-1 S. After inoculation with methanogenic, granular biomass, the competition between sulfate-reducing and methanogenic microorganisms determined to what extent dissolved sulfide and methane were produced. After the complete washout of methanogens, which was revealed by next-generation sequencing analysis, the highest S-EC was reached in the system. The highest average sulfate elimination capacity (S-EC = 4.3 kg S m^-3d^-1) was obtained at a COD/S-SO₄^2- ratio of 5.4 g O₂ g^-1 S and an OLR of 24.4 kg O₂ m^-3d^-1 with a sulfate removal efficiency of 94%. The conversion of influent COD to methane decreased from 12% to 2.5% as the SLR increased while a large fraction of acetate (35% of the initial COD) was accumulated. Our data indicate that crude glycerol can promote sulfidogenesis. However, the disappearance of methanogens in the long-term due to the out competition by sulfate reducing bacteria, lead to such large accumulation of acetate.

Vulnerability of seagrass blue carbon to microbial attack following exposure to warming and oxygen

Seagrass meadows store globally-significant quantities of organic 'blue' carbon. These blue carbon stocks are potentially vulnerable to anthropogenic stressors (e.g. coastal development, climate change). Here, we tested the impact of oxygen exposure and warming (major consequences of human disturbance) on rates of microbial carbon break-down in seagrass sediments. Active microbes occurred throughout seagrass sediment profiles, but deep, ancient sediments (~5000 yrs. old) contained only 3% of the abundance of active microbes as young, surface sediments (<2 yrs. old). Metagenomic analysis revealed that microbial community structure and function changed with depth, with a shift from proteobacteria and high levels of genes involved in sulfur cycling in the near surface samples, to a higher proportion of firmicutes and euraracheota and genes involved in methanogenesis at depth. Ancient carbon consisted almost entirely (97%) of carbon considered 'thermally recalcitrant', and therefore presumably inaccessible to microbial attack. Experimental warming had little impact on carbon; however, exposure of ancient sediments to oxygen increased microbial abundance, carbon uptake and sediment carbon turnover (34-38 fold). Overall, this study provides detailed characterization of seagrass blue carbon (chemical stability, age, associated microbes) and suggests that environmental disturbances that expose coastal sediments to oxygen (e.g. dredging) have the capacity to diminish seagrass sediment carbon stocks by facilitating microbial remineralisation.

A conceptual method to simultaneously inhibit methane and hydrogen sulfide production in sewers: The carbon metabolic pathway and microbial community shift

In this study, the impact of COD/SO₄^2- ratio in sewage on methane and hydrogen sulfide production in sewer biofilms was investigated by using three identical lab-scale gravity sewer systems. The results showed that the COD/SO₄^2- played a key role in the competition between methanogenic archaea (MA) and sulfate reducing bacteria (SRB). Both the lowest methane and hydrogen sulfide production were obtained at COD/SO₄^2- ratio of 6. The carbon transformation revealed that the activity of both MA and SRB was inhibited at this COD/SO₄^2- ratio. Methanosarcina and Methanobacterium were the two dominant MA, while Desulfonema, Desulfotomaculum and Desulfovibrio were the dominant SRB in this case. The specific SRB activity measured by batch tests proved that acetate was mainly degraded by the MA, while propionate was the preferred substrate for the SRB.

Microbial community evolution and fate of antibiotic resistance genes during sludge treatment in two full-scale anaerobic digestion plants with thermal hydrolysis pretreatment

Anaerobic digestion (AD) with thermal hydrolysis pretreatment is widely used as an efficient sludge treatment nowadays. However, the evolution of microbial community (especially for the archaea community), the fate of antibiotic resistance genes (ARGs), and their associations during such process in full-scale sludge treatment plants are rarely reported. Therefore, these scientific questions were explored at two full-scale sludge treatment plants through high-throughput sequencing and quantitative PCR. Results showed that Methanobacterium and Methanosphaera were the dominant archaea in thermal hydrolyzed sludge. The predominant bacteria in the sludge first shifted from nutrients removal functional bacteria to spore-forming bacteria after thermal hydrolysis, and then shifted to fermentative bacteria after AD. The full-scale plants could select ermB, ermF, mefA/E, qnrS and tetM. Though the bacteria and archaea biomass and community largely influenced the fate of ARGs, multiple linear regression analysis showed that the total ARGs were mainly affected by mobile genetic elements (MGEs).

COD/sulfate ratio does not affect the methane yield and microbial diversity in anaerobic digesters

Anaerobic digestion of organic matter is the major route of biomethane production. However, in the presence of sulfate, sulfate-reducing bacteria (SRB) typically outcompete methanogens, which may reduce or even preclude methane production from sulfate-containing wastewaters. Although sulfate-reduction and methanogenesis can occur simultaneously, our limited understanding of the microbiology of anaerobic digesters treating sulfate-containing wastewaters constrains improvements in the production of methane from these systems. This study tested the effects of carbon sources and chemical oxygen demand-to-sulfate ratio (COD/SO₄^2-) on the diversity and interactions of SRB and methanogens in an anaerobic digester treating a high-sulfate waste stream. Overall, the data showed that sulfate removal and methane generation occurred in varying efficiencies and the carbon source had limited effect on the methane yield. Importantly, the results demonstrated that methanogenic and SRB diversities were only affected by the carbon source and not by the COD/SO₄^2- ratio.

Physicochemical and microbiological monitoring of anaerobic digestion at laboratory and low cost tubular digester

The aim of this work was to use an inexpensive technique, such as the most probable number, MPN to quantitatively and qualitatively examine microbial groups in anaerobic digestion, AD of cattle manure, CM. Different diluents and mixing ratios were evaluated in 100 mL reactors using biomethane potential, BMP, as output variable. MPN tests were performed to samples from a 23 L tank and 6.5 m³ low-cost tubular digester, LCTD. To monitor LCTD stability, volatile solids, VS, specific methanogenic activity, SMA, pH, volatile fatty acids, VFA, and chemical oxygen demand, COD were measured. Microbial characterization highlighted the optimal population essential to initiate the anaerobic digestion process. Bacteria domain were predominant over Archaea, with average abundance values of 78% and 22%, respectively. SMA of 0.0486 g COD g^-1 SV d^-1 was obtained at laboratory-scale and LCTD reached 83% of this value. Conditions selected are cost-effective to establish a biodigester in rural areas.

Effects of mercury addition on microbial community composition and nitrate removal inside permeable reactive barriers

Permeable reactive barriers (PRBs) remove nitrogen from groundwater by enhancing microbial denitrification. The PRBs consist of woodchips that provide carbon for denitrifiers, but these woodchips also support other anaerobic microbes, including sulfate-reducing bacteria. Some of these anaerobes have the ability to methylate inorganic mercury present in groundwater. Methylmercury is hazardous to human health, so it is essential to understand whether PRBs promote mercury methylation. We examined microbial communities and geochemistry in fresh water and sulfate-enriched PRB flow-through columns by spiking replicates of both treatments with mercuric chloride. We hypothesized that mercury addition could alter bacterial community composition to favor higher abundances of genera containing known methylating taxa and that the sulfate-rich columns would produce more methylmercury after mercury addition, due mainly to an increase in abundance of sulfate reducing bacteria (SRB). However, methylmercury output at the end of the experiment was not different from output at the beginning, due in part to coupled Hg methylation and demethylation. There was a transient reduction in nitrate removal after mercury addition in the sulfate enriched columns, but nitrate removal returned to initial rates after two weeks, demonstrating resilience of the denitrifying community. Since methylmercury output did not increase and nitrate removal was not permanently affected, PRBs could be a low cost approach to combat eutrophication.

Electron carriers increase electricity production in methane microbial fuel cells that reverse methanogenesis

BACKGROUND

We previously reversed methanogenesis in microbial fuel cells (MFCs) to produce electricity for the first time from methane by combining an engineered archaeal strain that produces methyl-coenzyme M reductase from unculturable anaerobic methanotrophs (to capture methane and secrete acetate) with Geobacter sulfurreducens (to produce electrons from the generated acetate) and methane-acclimated sludge (to provide electron shuttles).

RESULTS

Here, the power density in MFCs was increased 77-fold to 5216 mW/m² and the current density in MFCs was increased 73-fold to 7.3 A/m² by reducing the surface area of the cathode (to make reasonable comparisons to other MFCs), by changing the order the strains of the consortium were added to the anode compartment, and by adding additional electron carriers (e.g., humic acids and cytochrome C).

CONCLUSIONS

This power density and current density are comparable to the best for any MFC, including those with Shewanella and Geobacter spp. that utilize non-gaseous substrates. In addition, we demonstrate the methane MFC may be used to power a fan by storing the energy in a capacitor. Hence, MFCs that convert methane to electricity are limited by electron carriers.

Core Sulphate-Reducing Microorganisms in Metal-Removing Semi-Passive Biochemical Reactors and the Co-Occurrence of Methanogens

Biochemical reactors (BCRs) based on the stimulation of sulphate-reducing microorganisms (SRM) are emerging semi-passive remediation technologies for treatment of mine-influenced water. Their successful removal of metals and sulphate has been proven at the pilot-scale, but little is known about the types of SRM that grow in these systems and whether they are diverse or restricted to particular phylogenetic or taxonomic groups. A phylogenetic study of four established pilot-scale BCRs on three different mine sites compared the diversity of SRM growing in them. The mine sites were geographically distant from each other, nevertheless the BCRs selected for similar SRM types. Clostridia SRM related to Desulfosporosinus spp. known to be tolerant to high concentrations of copper were members of the core microbial community. Members of the SRM family Desulfobacteraceae were dominant, particularly those related to Desulfatirhabdium butyrativorans. Methanogens were dominant archaea and possibly were present at higher relative abundances than SRM in some BCRs. Both hydrogenotrophic and acetoclastic types were present. There were no strong negative or positive co-occurrence correlations of methanogen and SRM taxa. Knowing which SRM inhabit successfully operating BCRs allows practitioners to target these phylogenetic groups when selecting inoculum for future operations.

Modelling the long-term effect of wastewater compositions on maximum sulfide and methane production rates of sewer biofilm

Reliable modelling of sulfide and methane production in sewer systems is required for efficient sewer emission management. Wastewater compositions affect sulfide and methane production kinetics through both its short-term variation influencing the substrate availability to sewer biofilms, and its long-term variation affecting the sewer biofilm structure. While the short-term effect is well considered in existing sewer models with the use of Monod or half-order equations, the long-term effect has not been explicitly considered in current sewer models suitable for network modelling. In this study, the long-term effect of wastewater compositions on sulfide and methane production activities in rising main sewers was investigated. A detailed biofilm model was firstly developed, and then calibrated and validated using experimental data measured during the entire biofilm development period of a laboratory sewer reactor. Based on scenario simulations using the detailed biofilm model, empirical equations describing the long-term effect of sulfate and sCOD (soluble chemical oxygen demand) concentrations on k_H2S (the maximum sulfide production rate of sewer biofilm) and k_CH4 (the maximum methane production rate of sewer biofilm) were proposed. These equations require further verification in future studies before their potential integration into network-wide sewer models.

Do microbial communities in an anaerobic bioreactor change with continuous feeding sludge into a full-scale anaerobic digestion system?

Microbial communities of sludge samples from a full-scale anaerobic digestion (AD) fed with primary sludge (PS) and excess sludge (ES) were analyzed using qPCR and MiSeq. The results showed that the microbial composition of digested sludge remained relatively stable but was partially changed by microbial immigration from feeding sludge. The dominant archaea in the digested sludge were largely the same as those in the feeding sludge, but their abundances differed markedly. The dominant fungal genera in the digested sludge were different from those in PS but were similar to those in ES. Various differences in bacterial community differences between digested sludge and PS/ES were observed. Notably, this study is the first to suggest Verrucomicrobia is the predominant bacterial phylum in the digested sludge, and that numerous unreported microorganisms belonging to the order LD1-PB3 existed in this AD system and potentially played roles in the processes of hydrolysis, fermentation, and acetogenesis.

Parallelized, Aerobic, Single Carbon-Source Enrichments from Different Natural Environments Contain Divergent Microbial Communities

Microbial communities that inhabit environments such as soil can contain thousands of distinct taxa, yet little is known about how this diversity is maintained in response to environmental perturbations such as changes in the availability of carbon. By utilizing aerobic substrate arrays to examine the effect of carbon amendment on microbial communities taken from six distinct environments (soil from a temperate prairie and forest, tropical forest soil, subalpine forest soil, and surface water and soil from a palustrine emergent wetland), we examined how carbon amendment and inoculum source shape the composition of the community in each enrichment. Dilute subsamples from each environment were used to inoculate 96-well microtiter plates containing triplicate wells amended with one of 31 carbon sources from six different classes of organic compounds (phenols, polymers, carbohydrates, carboxylic acids, amines, amino acids). After incubating each well aerobically in the dark for 72 h, we analyzed the composition of the microbial communities on the substrate arrays as well as the initial inocula by sequencing 16S rRNA gene amplicons using the Illumina MiSeq platform. Comparisons of alpha and beta diversity in these systems showed that, while the composition of the communities that grow to inhabit the wells in each substrate array diverges sharply from that of the original community in the inoculum, these enrichment communities are still strongly affected by the inoculum source. We found most enrichments were dominated by one or several OTUs most closely related to aerobes or facultative anaerobes from the Proteobacteria (e.g., Pseudomonas, Burkholderia, and Ralstonia) or Bacteroidetes (e.g., Chryseobacterium). Comparisons within each substrate array based on the class of carbon source further show that the communities inhabiting wells amended with a carbohydrate differ significantly from those enriched with a phenolic compound. Selection therefore seems to play a role in shaping the communities in the substrate arrays, although some stochasticity is also seen whereby several replicate wells within a single substrate array display strongly divergent community compositions. Overall, the use of highly parallel substrate arrays offers a promising path forward to study the response of microbial communities to perturbations in a changing environment.

Unraveling the Microbial Interactions and Metabolic Potentials in Pre- and Post-treated Sludge from a Wastewater Treatment Plant Using Metagenomic Studies

Sewage waste represents an ecosystem of complex and interactive microbial consortia which proliferate with different kinetics according to their individual genetic as well as metabolic potential. We performed metagenomic shotgun sequencing on Ion-Torrent platform, to explore the microbial community structure, their biological interactions and associated functional capacity of pre-treated/raw sludge (RS) and post-treated/dried sludge (DS) of wastewater treatment plant. Bacterial phylotypes belonging to Epsilonproteobacteria (∼45.80%) dominated the RS with relatively few Archaea (∼1.94%) whereas DS has the dominance of beta- (30.23%) and delta- (13.38%) classes of Proteobacteria with relatively greater abundance of Archaea (∼7.18%). In particular, Epsilonproteobacteria appears as a primary energy source in RS and sulfur-reducing bacteria with methanogens seems to be in the potential syntrophic association in DS. These interactions could be ultimately responsible for carrying out amino-acid degradation, aromatic compound degradation and degradation of propionate and butyrate in DS. Our data also reveal the presence of key genes in the sludge microbial community responsible for degradation of polycyclic aromatic hydrocarbons. Potential pathogenic microbes and genes for the virulence factors were found to be relatively abundant in RS which clearly reflect the necessity of treatment of RS. After treatment, potential pathogens load was reduced, indicating the sludge hygienisation in DS. Additionally, the interactions found in this study would reveal the biological and environmental cooperation among microbial communities for domestic wastewater treatment.

Robustness of a model microbial community emerges from population structure among single cells of a clonal population

Microbial populations can withstand, overcome and persist in the face of environmental fluctuation. Previously, we demonstrated how conditional gene regulation in a fluctuating environment drives dilution of condition-specific transcripts, causing a population of Desulfovibrio vulgaris Hildenborough (DvH) to collapse after repeatedly transitioning from sulfate respiration to syntrophic conditions with the methanogen Methanococcus maripaludis. Failure of the DvH to successfully transition contributed to the collapse of this model community. We investigated the mechanistic basis for loss of robustness by examining whether conditional gene regulation altered heterogeneity in gene expression across individual DvH cells. We discovered that robustness of a microbial population across environmental transitions was attributable to the retention of cells in two states that exhibited different condition-specific gene expression patterns. In our experiments, a population with disrupted conditional regulation successfully alternated between cell states. Meanwhile, a population with intact conditional regulation successfully switched between cell states initially, but collapsed after repeated transitions, possibly due to the high energy requirements of regulation. These results demonstrate that the survival of this entire model microbial community is dependent on the regulatory system's influence on the distribution of distinct cell states among individual cells within a clonal population.

Ca2+ in Hybridization Solutions for Fluorescence in situ Hybridization Facilitates the Detection of Enterobacteriaceae

Fluorescence in situ hybridization (FISH) has been employed to identify microorganisms at the single cell level under a microscope. Extensive efforts have been made to improve and extend the FISH technique; however, the development of a widely applicable protocol is a continuing challenge. The present study evaluated the effects of divalent cations in the hybridization solution on the FISH-based detection of various species of bacteria and archaea with rRNA-targeted probes. A flow cytometric analysis after FISH with a standard hybridization buffer detected positive signals from less than 30% of Escherichia coli IAM 1264 cells. However, the number of cells with positive signals increased to more than 90% after the addition of calcium chloride to the hybridization buffer. Mn²⁺ also had positive effects, whereas Mg²⁺ did not. The positive effects of Ca²⁺ were similarly observed for bacteria belonging to Enterobacteriaceae, including Enterobacter sakazakii IAM 12660^T, E. aerogenes IAM 12348, Klebsiella planticola IAM 14202, and Salmonella enterica subsp. enterica serovar Typhimurium strain LT2. These results indicate that the supplementation of Ca²⁺ to the hybridization buffer for FISH contributes to the efficient detection of Enterobacteriaceae cells.

Methanogenic biodegradation of paraffinic solvent hydrocarbons in two different oil sands tailings

Microbial communities drive many biogeochemical processes in oil sands tailings and cause greenhouse gas emissions from tailings ponds. Paraffinic solvent (primarily C₅-C₆; n- and iso-alkanes) is used by some oil sands companies to aid bitumen extraction from oil sands ores. Residues of unrecovered solvent escape to tailings ponds during tailings deposition and sustain microbial metabolism. To investigate biodegradation of hydrocarbons in paraffinic solvent, mature fine tailings (MFT) collected from Albian and CNRL ponds were amended with paraffinic solvent at ~0.1wt% (final concentration: ~1000mgL^-1) and incubated under methanogenic conditions for ~1600d. Albian and CNRL MFTs exhibited ~400 and ~800d lag phases, respectively after which n-alkanes (n-pentane and n-hexane) in the solvent were preferentially metabolized to methane over iso-alkanes in both MFTs. Among iso-alkanes, only 2-methylpentane was completely biodegraded whereas 2-methylbutane and 3-methylpentane were partially biodegraded probably through cometabolism. 16S rRNA gene pyrosequencing showed dominance of Anaerolineaceae and Methanosaetaceae in Albian MFT and Peptococcaceae and co-domination of "Candidatus Methanoregula" and Methanosaetaceae in CNRL MFT bacterial and archaeal communities, respectively, during active biodegradation of paraffinic solvent. The results are important for developing future strategies for tailings reclamation and management of greenhouse gas emissions.

Importance of sulfide interaction with iron as regulator of the microbial community in biogas reactors and its effect on methanogenesis, volatile fatty acids turnover, and syntrophic long-chain fatty acids degradation

The inhibitory effects of sulfide on microbial processes during anaerobic digestion have been widely addressed. However, other effects of sulfide are less explored, given that sulfide is a potential sulfur source for microorganisms and its high reactivity triggers a suit of abiotic reactions. We demonstrated that sulfide interaction with Fe regulates the dynamics and activities of microbial community during anaerobic digestion. This was manifested by the S:Fe molar ratio, whose increase adversely influenced the acetoclastic methanogens, Methanosaeta, and turnover of acetate. Dynamics of hydrogenotrophic methanogens, Methanoculleus and Methanobrevibacter, were presumably influenced by sulfide-induced changes in the partial pressure of hydrogen. Interestingly, conversion of the long-chain fatty acid (LCFA), oleate, to methane was enhanced together with the abundance of LCFA-degrading, β-oxidizing Syntrophomonas at an elevated S:Fe molar ratio. The results suggested that sulfur chemical speciation is a controlling factor for microbial community functions in anaerobic digestion processes.

Modelling Methane Production and Sulfate Reduction in Anaerobic Granular Sludge Reactor with Ethanol as Electron Donor

In this work, a mathematical model based on growth kinetics of microorganisms and substrates transportation through biofilms was developed to describe methane production and sulfate reduction with ethanol being a key electron donor. The model was calibrated and validated using experimental data from two case studies conducted in granule-based Upflow Anaerobic Sludge Blanket reactors. The results suggest that the developed model could satisfactorily describe methane and sulfide productions as well as ethanol and sulfate removals in both systems. The modeling results reveal a stratified distribution of methanogenic archaea, sulfate-reducing bacteria and fermentative bacteria in the anaerobic granular sludge and the relative abundances of these microorganisms vary with substrate concentrations. It also indicates sulfate-reducing bacteria can successfully outcompete fermentative bacteria for ethanol utilization when COD/SO₄²⁻ ratio reaches 0.5. Model simulation suggests that an optimal granule diameter for the maximum methane production efficiency can be achieved while the sulfate reduction efficiency is not significantly affected by variation in granule size. It also indicates that the methane production and sulfate reduction can be affected by ethanol and sulfate loading rates, and the microbial community development stage in the reactor, which provided comprehensive insights into the system for its practical operation.

Dynamic of sulphate-reducing microorganisms in petroleum-contaminated marine sediments inhabited by the polychaete Hediste diversicolor

The behaviour of sulphate-reducing microbial community was investigated at the oxic-anoxic interface (0-2 cm) of marine sediments when submitted to oil and enhanced bioturbation activities by the addition of Hediste diversicolor. Although total hydrocarbon removal was not improved by the addition of H. diversicolor, terminal restriction fragment length polymorphism (T-RFLP) analyses based on dsrAB (dissimilatory sulphite reductase) genes and transcripts showed different patterns according to the presence of H. diversicolor which favoured the abundance of dsrB genes during the early stages of incubation. Complementary DNA (cDNA) dsrAB libraries revealed that in presence of H. diversicolor, most dsrAB sequences belonged to hydrocarbonoclastic Desulfobacteraceae, suggesting that sulphate-reducing microorganisms (SRMs) may play an active role in hydrocarbon biodegradation in sediments where the reworking activity is enhanced. Furthermore, the presence of dsrAB sequences related to sequences found associated to environments with high dinitrogen fixation activity suggested potential N2 fixation by SRMs in bioturbated-polluted sediments.

Metabolic associations with archaea drive shifts in hydrogen isotope fractionation in sulfate-reducing bacterial lipids in cocultures and methane seeps

Correlation between hydrogen isotope fractionation in fatty acids and carbon metabolism in pure cultures of bacteria indicates the potential of biomarker D/H analysis as a tool for diagnosing carbon substrate usage in environmental samples. However, most environments, in particular anaerobic habitats, are built from metabolic networks of micro-organisms rather than a single organism. The effect of these networks on D/H of lipids has not been explored and may complicate the interpretation of these analyses. Syntrophy represents an extreme example of metabolic interdependence. Here, we analyzed the effect of metabolic interactions on the D/H biosignatures of sulfate-reducing bacteria (SRB) using both laboratory maintained cocultures of the methanogen Methanosarcina acetivorans and the SRB Desulfococcus multivorans in addition to environmental samples harboring uncultured syntrophic consortia of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing Deltaproteobacteria (SRB) recovered from deep-sea methane seeps. Consistent with previously reported trends, we observed a ~80‰ range in hydrogen isotope fractionation (ε(lipid-water)) for D. multivorans grown under different carbon assimilation conditions, with more D-enriched values associated with heterotrophic growth. In contrast, for cocultures of D. multivorans with M. acetivorans, we observed a reduced range of ε(lipid-water) values (~36‰) across substrates with shifts of up to 61‰ compared to monocultures. Sediment cores from methane seep settings in Hydrate Ridge (offshore Oregon, USA) showed similar D-enrichment in diagnostic SRB fatty acids coinciding with peaks in ANME/SRB consortia concentration suggesting that metabolic associations are connected to the observed shifts in ε(lipid-water) values.

Biogas Production from Sugarcane Waste: Assessment on Kinetic Challenges for Process Designing

Biogas production from sugarcane waste has large potential for energy generation, however, to enable the optimization of the anaerobic digestion (AD) process each substrate characteristic should be carefully evaluated. In this study, the kinetic challenges for biogas production from different types of sugarcane waste were assessed. Samples of vinasse, filter cake, bagasse, and straw were analyzed in terms of total and volatile solids, chemical oxygen demand, macronutrients, trace elements, and nutritional value. Biochemical methane potential assays were performed to evaluate the energy potential of the substrates according to different types of sugarcane plants. Methane yields varied considerably (5-181 Nm³·tonFM(-1)), mainly due to the different substrate characteristics and sugar and/or ethanol production processes. Therefore, for the optimization of AD on a large-scale, continuous stirred-tank reactor with long hydraulic retention times (>35 days) should be used for biogas production from bagasse and straw, coupled with pre-treatment process to enhance the degradation of the fibrous carbohydrates. Biomass immobilization systems are recommended in case vinasse is used as substrate, due to its low solid content, while filter cake could complement the biogas production from vinasse during the sugarcane offseason, providing a higher utilization of the biogas system during the entire year.