Syntrophic Process Research Articles

Polyhydroxybutyrate Production from Methane and Carbon Dioxide by a Syntrophic Consortium of Methanotrophs with Oxygenic Photogranules without an External Oxygen Supply.

Here, a syntrophic process was developed to produce polyhydroxy-β-butyrate (PHB) from a gas stream containing CH4 and CO2 without an external oxygen supply using a combination of methanotrophs with the community of oxygenic photogranules (OPGs). The co-culture features of Methylomonas sp. DH-1 and Methylosinus trichosporium OB3b were evaluated under carbon-rich and carbon-lean conditions. The critical role of O2 in the syntrophy was confirmed through the sequencing of 16S rRNA gene fragments. Based on their carbon consumption rates and the adaptation to a poor environment, M. trichosporium OB3b with OPGs was selected for methane conversion and PHB production. Nitrogen limitation stimulated PHB accumulation in the methanotroph but hindered the growth of the syntrophic consortium. At 2.9 mM of the nitrogen source, 1.13 g/L of biomass and 83.0 mg/L of PHB could be obtained from simulated biogas. These results demonstrate that syntrophy has the potential to convert greenhouse gases into valuable products efficiently.

The biological and abiotic effects of powdered activated carbon on the anaerobic digestion performance of cornstalk

To comprehensively evaluate the biological and abiotic influence of powdered activated carbon (PAC) on the anaerobic digestion of cornstalk, mesophilic and thermophilic digestion were conducted. Adding PAC (10 g/L) under thermophilic system obtained the maximum cellulose degradation rate and methane yield (MY), which were 57.47% and 128.19 L/kg VS. However, adding same dose of PAC at mesophilic system decreased the MY by 8.16% while increased the cellulose degradation rate and methane production rate by 6.48% and 17.92%. Under mesophilic conditions, the enhancement of PAC was owing to the enrichment of cellulolytic microorganisms, improvement of the syntrophic process and direct interspecies electron transfer. The lower methane yield was attributed to the adsorption of carbon source by PAC and CH4 consumption by Norank_c_Bathyarchaeia. The good performance of thermophilic system was owing to the lower adsorption capability of PAC, absence of Norank_c_Bathyarchaeia, and concentrated carbon flow to methane.

Syntrophy of Crypthecodinium cohnii and immobilized Zymomonas mobilis for docosahexaenoic acid production from sucrose-containing substrates

Marine heterotrophic dinoflagellate Crypthecodinium cohnii is an aerobic oleaginous microorganism that accumulates intracellular lipid with high content of 4,7,10,13,16,19-docosahexaenoic acid (DHA), a polyunsaturated ω−3 (22:6) fatty acid with multiple health benefits. C. cohnii can grow on glucose and ethanol, but not on sucrose or fructose. For conversion of sucrose-containing renewables to C. cohnii DHA, we investigated a syntrophic process, involving immobilized cells of ethanologenic bacterium Zymomonas mobilis for fermenting sucrose to ethanol. The non-respiring, NADH dehydrogenase-deficient Z. mobilis strain Zm6-ndh, with high ethanol yield both under anaerobic and aerobic conditions, was taken as the genetic background for inactivation of levansucrase (sacB). SacB mutation eliminated the levan-forming activity on sucrose. The double mutant Zm6-ndh-sacB cells were immobilized in Ca alginate, and applied for syntrophic conversion of sucrose to DHA of C. cohnii, either taking the ethanol-containing fermentation medium from the immobilized Z. mobilis for feeding to the C. cohnii fed-batch culture, or directly coculturing the immobilized Zm6-ndh-sacB with C. cohnii on sucrose. Both modes of cultivation produced C. cohnii CCMP 316 biomass with DHA content around 2–3 % of cell dry weight, corresponding to previously reported results for this strain on glucose.

Bacteria and Methanogens in the Human Microbiome: a Review of Syntrophic Interactions.

Methanogens are microorganisms belonging to the Archaea domain and represent the primary source of biotic methane. Methanogens encode a series of enzymes which can convert secondary substrates into methane following three major methanogenesis pathways. Initially recognized as environmental microorganisms, methanogens have more recently been acknowledged as host-associated microorganisms after their detection and initial isolation in ruminants in the 1950s. Methanogens have also been co-detected with bacteria in various pathological situations, bringing their role as pathogens into question. Here, we review reported associations between methanogens and bacteria in physiological and pathological situations in order to understand the metabolic interactions explaining these associations. To do so, we describe the origin of the metabolites used for methanogenesis and highlight the central role of methanogens in the syntrophic process during carbon cycling. We then focus on the metabolic abilities of co-detected bacterial species described in the literature and infer from their genomes the probable mechanisms of their association with methanogens. The syntrophic interactions between bacteria and methanogens are paramount to gut homeostasis. Therefore, any dysbiosis affecting methanogens might impact human health. Thus, the monitoring of methanogens may be used as a bio-indicator of dysbiosis. Moreover, new therapeutic approaches can be developed based on their administration as probiotics. We thus insist on the importance of investigating methanogens in clinical microbiology.

Taxonomic and functional diversity of the microbiome in a jet fuel contaminated site as revealed by combined application of in situ microcosms with metagenomic analysis

Natural attenuation represents all processes that govern contaminant mass removal, which mainly occurs via microbial degradation in the environment. Although this process is intrinsic its rate and efficiency depend on multiple factors. This study aimed to characterize the microbial taxonomic and functional diversity in different aquifer sediments collected in the saturated zone and in situ microcosms (BACTRAP®s) amended with hydrocarbons (13C-labeled and non-labeled benzene, toluene and naphthalene) using 16S rRNA gene and “shotgun” Illumina high throughput sequencing at a jet-fuel contaminated site. The BACTRAP®s were installed to assess hydrocarbon metabolism by native bacteria. Results indicated that Proteobacteria, Actinobacteria and Firmicutes were the most dominant phyla (~98%) in the aquifer sediment samples. Meanwhile, in the benzene- and toluene-amended BACTRAP®s the phyla Firmicutes and Proteobacteria accounted for about 90% of total community. In the naphthalene-amended BACTRAP®, members of the SR-FBR-L83 family (Order Ignavibacteriales) accounted for almost 80% of bacterial community. Functional annotation of metagenomes showed that only the sediment sample located at the source zone border and with the lowest BTEX concentration, has metabolic potential to degrade hydrocarbons aerobically. On the other hand, in situ BACTRAP®s allowed enrichment of hydrocarbon-degrading bacteria. Metagenomic data suggest that fumarate addition is the main mechanism for hydrocarbon activation of toluene. Also, indications for methylation, hydroxylation and carboxylation as activation mechanisms for benzene anaerobic conversion were found. After 120 days of exposure in the contaminated groundwater, the isotopic analysis of fatty acids extracted from BACTRAP®s demonstrated the assimilation of isotopic labeled compounds in the cells of microbes expressed by strong isotopic enrichment. We propose that the microbiota in this jet-fuel contaminated site has metabolic potential to degrade benzene and toluene by a syntrophic process, between members of the families Geobacteraceae and Peptococcaceae (genus Pelotomaculum), coupled to nitrate, iron and/or sulfate reduction.

The role of conductive materials in the start-up period of thermophilic anaerobic system

The major obstacle for thermophilic anaerobic digestion (TAD) is the inhibited microorganism activity and process instability during the start-up period. This study proposed a strategy to accelerate and stabilize the thermophilic reactors start-up via adding conductive materials. The results show that methane production rate in conductive materials supplemented (CMS) reactors was almost two times higher than the control reactors. Caloramator sp., a candidate of electroactive bacteria, was significantly enriched in the carbon nano-tube (CNT) supplemented groups (12.89%) as compared to control groups (1.26% only). Together with the doubled abundance of Methanosaeta and Methanosarcina methanogens in CMS groups, it is highly possible Caloramator sp. and Methanosaeta/Methanosarcina have established syntrophic direct interspecies electron transfer (DIET), via adopting conductive materials as electron conduit. Microbial community analysis indicates DIET was likely to be an unstable condition triggered syntrophic process. This study demonstrated that conductive materials could promote microbial activity and shorten start-up period for thermophilic anaerobic system.

Succession of lignocellulolytic bacterial consortia bred anaerobically from lake sediment.

Anaerobic bacteria degrade lignocellulose in various anoxic and organically rich environments, often in a syntrophic process. Anaerobic enrichments of bacterial communities on a recalcitrant lignocellulose source were studied combining polymerase chain reaction-denaturing gradient gel electrophoresis, amplicon sequencing of the 16S rRNA gene and culturing. Three consortia were constructed using the microbiota of lake sediment as the starting inoculum and untreated switchgrass (Panicum virgatum) (acid or heat) or treated (with either acid or heat) as the sole source of carbonaceous compounds. Additionally, nitrate was used in order to limit sulfate reduction and methanogenesis. Bacterial growth took place, as evidenced from 3 to 4 log unit increases in the 16S rRNA gene copy numbers as well as direct cell counts through three transfers on cleaned and reused substrate placed in fresh mineral medium. After 2 days, Aeromonas bestiarum-like organisms dominated the enrichments, irrespective of the substrate type. One month later, each substrate revealed major enrichments of organisms affiliated with different species of Clostridium. Moreover, only the heat-treated substrate selected Dysgonomonas capnocytophagoides-affiliated bacteria (Bacteroidetes). Towards the end of the experiment, members of the Proteobacteria (Aeromonas, Rhizobium and/or Serratia) became dominant in all three types of substrates. A total of 160 strains was isolated from the enrichments. Most of the strains tested (78%) were able to grow anaerobically on carboxymethyl cellulose and xylan. The final consortia yield attractive biological tools for the depolymerization of recalcitrant lignocellulosic materials and are proposed for the production of precursors of biofuels.

Detection of Metabolic Key Enzymes of Methane Turnover Processes in Cold Seep Microbial Biofilms

In anoxic environments, methane oxidation is conducted in a syntrophic process between methanotrophic archaea (ANME) and sulfate reducing bacteria (SRB). Microbial mats consisting of ANME, SRB and other microorganisms form methane seep-related carbonate buildups in the anoxic bottom waters of the Black Sea Crimean shelf. To shed light on the localization of the biochemical processes at the level of single cells in the Black Sea microbial mats, we applied antibody-based markers for key enzymes of the relevant metabolic pathways. The dissimilatory adenosine-5′-phosphosulfate (APS) reductase, methyl-coenzyme M reductase (MCR) and methanol dehydrogenase (MDH) were selected to localize sulfate respiration, reverse methanogenesis and aerobic methane oxidation, respectively. The key enzymes could be localized by double immunofluorescence and immunocytochemistry at light- and electron microscopic levels. In this study we show that sulfate reduction is conducted synchronized and in direct proximity to reverse methanogenesis of ANME archaea. Microcolonies in interspaces between ANME/SRB express methanol dehydrogenase, which is indicative for oxidation of C1 compounds by methylotrophic or methanotrophic bacteria. Thus, in addition to syntrophic AOM, oxygen-dependent processes are also conducted by a small proportion of the microbial population.

Zero-valent sulphur and marine methane oxidation

In marine sediments, anaerobic oxidation of methane (AOM) coupled to sulphate reduction was thought to be carried out by a consortium of methanotrophic archaea (ANME) and co-occurring sulphate-reducing deltaproteobacteria, but the mechanistic details of this partnership had not been resolved. Now, Milucka et al. show that ANME carry out AOM as well as dissimilatory sulphate reduction to form disulphide and other zero-valent sulphur compounds. Instead of carrying out the coupled sulphate reduction processes, as previously expected, the deltaproteobacteria in the culture took up the disulphide produced by ANME, and this disulphide was then disproportionated to sulphide and sulphate, the latter of which could feed back to ANME for further rounds of AOM. These studies provide the first evidence for the direct formation of zero-valent sulphur compounds during sulphate reduction and reveal that AOM is not necessarily an obligate syntrophic process between ANME and deltaproteobacteria. The precise details of the enzymatic pathways involved in dissimilatory sulphate reduction by ANME remain to be determined.

Zero-valent sulphur is a key intermediate in marine methane oxidation

Emissions of methane, a potent greenhouse gas, from marine sediments are controlled by anaerobic oxidation of methane coupled primarily to sulphate reduction (AOM). Sulphate-coupled AOM is believed to be mediated by a consortium of methanotrophic archaea (ANME) and sulphate-reducing Deltaproteobacteria but the underlying mechanism has not yet been resolved. Here we show that zero-valent sulphur compounds (S(0)) are formed during AOM through a new pathway for dissimilatory sulphate reduction performed by the methanotrophic archaea. Hence, AOM might not be an obligate syntrophic process but may be carried out by the ANME alone. Furthermore, we show that the produced S(0)--in the form of disulphide--is disproportionated by the Deltaproteobacteria associated with the ANME. Our observations expand the diversity of known microbially mediated sulphur transformations and have significant implications for our understanding of the biogeochemical carbon and sulphur cycles.

Anaerobic benzene degradation under denitrifying conditions: Peptococcaceae as dominant benzene degraders and evidence for a syntrophic process

An anaerobic microbial community was enriched in a chemostat that was operated for more than 8 years with benzene and nitrate as electron acceptor. The coexistence of multiple species in the chemostat and the presence of a biofilm, led to the hypothesis that benzene-degrading species coexist in a syntrophic interaction, and that benzene can be degraded in syntrophy by consortia with various electron acceptors in the same culture. The benzene-degrading microorganisms were identified by DNA-stable isotope probing with [U-(13) C]-labelled benzene, and the effect of different electron donors and acceptors on benzene degradation was investigated. The degradation rate constant of benzene with nitrate (0.7 day(-1) ) was higher than reported previously. In the absence of nitrate, the microbial community was able to use sulfate, chlorate or ferric iron as electron acceptor. Bacteria belonging to the Peptococcaceae were identified as dominant benzene consumers, but also those related to Rhodocyclaceae and Burkholderiaceae were found to be associated with the anaerobic benzene degradation process. The benzene degradation activity in the chemostat was associated with microbial growth in biofilms. This, together with the inhibiting effect of hydrogen and the ability to degrade benzene with different electron acceptors, suggests that benzene was degraded via a syntrophic process.

Mercury Speciation in Marine Sediments under Sulfate-Limited Conditions

Sediment profiles of total mercury (Hg) and monomethylmercury (MMHg) were determined from a 30-m drill hole located north of Venice, Italy. While the sediment profile of total Hg concentration was fairly constant between 1 and 10 m, that of the MMHg concentration showed an unexpected peak at a depth of 6 m. Due to the limited sulfate content (<1 mM) at the depth of 6 m, we hypothesized that the methylation of inorganic Hg(II) at this depth is associated with the syntrophic processes occurring between methanogens and sulfidogens. To test this hypothesis, anoxic sediment slurries were prepared using buried Venice Lagoon sediments amended with HgCl(2), and we monitored MMHg concentration in sediment slurries over time under two geochemical conditions: high sulfate (1-16 mM) and limited sulfate concentrations (<100 microM). After day 52 and onward from the addition of inorganic Hg(II), the MMHg concentrations were higher in sulfate-limited slurries compared to high sulfate slurries, along with methane production in both slurries. On the basis of these results, we argue that active methylation of inorganic Hg(II) occurs under sulfate-limited conditions possibly by syntrophic processes occurring between methanogens and sulfidogens. The environmental significance of syntrophic Hg(II) methylation should be further studied.

Effect of methanogenic substrates on anaerobic oxidation of methane and sulfate reduction by an anaerobic methanotrophic enrichment

Anaerobic oxidation of methane (AOM) coupled to sulfate reduction (SR) is assumed to be a syntrophic process, in which methanotrophic archaea produce an interspecies electron carrier (IEC), which is subsequently utilized by sulfate-reducing bacteria. In this paper, six methanogenic substrates are tested as candidate-IECs by assessing their effect on AOM and SR by an anaerobic methanotrophic enrichment. The presence of acetate, formate or hydrogen enhanced SR, but did not inhibit AOM, nor did these substrates trigger methanogenesis. Carbon monoxide also enhanced SR but slightly inhibited AOM. Methanol did not enhance SR nor did it inhibit AOM, and methanethiol inhibited both SR and AOM completely. Subsequently, it was calculated at which candidate-IEC concentrations no more Gibbs free energy can be conserved from their production from methane at the applied conditions. These concentrations were at least 1,000 times lower can the final candidate-IEC concentration in the bulk liquid. Therefore, the tested candidate-IECs could not have been produced from methane during the incubations. Hence, acetate, formate, methanol, carbon monoxide, and hydrogen can be excluded as sole IEC in AOM coupled to SR. Methanethiol did inhibit AOM and can therefore not be excluded as IEC by this study.

Syntrophic Processes Drive the Conversion of Glucose in Microbial Fuel Cell Anodes

Microbial fuel cell (MFC) anodes are anaerobic bioreactors. Processes such as fermentations and methanogenesis are likely competitors to electricity generation. This work studied the pathway of glucose conversion in continuous microbial fuel cell anodes with an adapted bacterial community. The study revealed that the majority of glucose is first fermented to hydrogen and acetate. Both are then used as substrates for bacterial electricity generation. When methanogens are present methane production occurs at a rate that slightly increases with the current. Methanogenesis and electricity generation compete for hydrogen, causing increased fermentation rates. In a rather young anodic biofilm on granular graphite, methanogenesis can be suppressed by aerating the anode compartment for one hour. Only short-term inhibition can be achieved applying the same technique on a well established biofilm on granular graphite. This study shows that fermentative processes are not detrimental to current generation, and that direct oxidation of glucose does not play a major role in mixed population conversions in a MFC anode.

Phylogenetic diversity and activity of anaerobic microorganisms of high-temperature horizons of the Dagang oil field (P. R. China)

The number of microorganisms of major metabolic groups and the rates of sulfate-reducing and methanogenic processes in the formation waters of the high-temperature horizons of Dagang oilfield have been determined. Using cultural methods, it was shown that the microbial community contained aerobic bacteria oxidizing crude oil, anaerobic fermentative bacteria, sulfate-reducing bacteria, and methanogenic bacteria. Using cultural methods, the possibility of methane production from a mixture of hydrogen and carbon dioxide (H2 + CO2) and from acetate was established, and this result was confirmed by radioassays involving NaH14CO3 and 14CH3COONa. Analysis of 16S rDNA of enrichment cultures of methanogens demonstrated that these microorganisms belong to Methanothermobacter sp. (M. thermoautotrophicus), which consumes hydrogen and carbon dioxide as basic substrates. The genes of acetate-utilizing bacteria were not identified. Phylotypes of the representatives of Thermococcus spp. were found among 16S rDNAs of archaea. 16S rRNA genes of bacterial clones belong to the orders Thermoanaerobacteriales (Thermoanaerobacter, Thermovenabulum, Thermacetogenium, and Coprothermobacter spp.), Thermotogales, Nitrospirales (Thermodesulfovibrio sp.) and Planctomycetales. 16S rDNA of a bacterium capable of oxidizing acetate in the course of syntrophic growth with H2-utilizing methanogens was found at high-temperature petroleum reservoirs for the first time. These results provide further insight into the composition of microbial communities of high-temperature petroleum reservoirs, indicating that syntrophic processes play an important part in acetate degradation accompanied by methane production.