Methane production from protozoan endosymbionts following stimulation of microbial metabolism within subsurface sediments
TL;DR: Results suggest that, following the stimulation of subsurface microbial growth with acetate, protozoa harboring methanogenic endosymbionts become important members of the microbial community, feeding on moribund biomass and producing methane.
Abstract: Previous studies have suggested that protozoa prey on Fe(III)- and sulfate-reducing bacteria that are enriched when acetate is added to uranium contaminated subsurface sediments to stimulate U(VI) reduction. In order to determine whether protozoa continue to impact subsurface biogeochemistry after these acetate amendments have stopped, 18S rRNA and s-tubulin sequences from this phase of an in situ uranium bioremediation field experiment were analyzed. Sequences most similar to Metopus species predominated, with the majority of sequences most closely related to M. palaeformis, a cilitated protozoan known to harbor methanogenic symbionts. Quantification of mcrA mRNA transcripts in the groundwater suggested that methanogens closely related to Metopus endosymbionts were metabolically active at this time. There was a strong correlation between the number of mcrA transcripts from the putative endosymbiotic methanogen and Metopus s-tubulin mRNA transcripts during the course of the field experiment, suggesting that the activity of the methanogens was dependent upon the activity of the Metopus species. Addition of the eukaryotic inhibitors cyclohexamide and colchicine to laboratory incubations of acetate-amended subsurface sediments significantly inhibited methane production and there was a direct correlation between methane concentration and Metopus s-tubulin and putative symbiont mcrA gene copies. These results suggest that, following the stimulation of subsurface microbial growth with acetate, protozoa harboring methanogenic endosymbionts become important members of the microbial community, feeding on moribund biomass and producing methane.
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TL;DR: This study sequenced DNA from complex sediment and planktonic consortia from an aquifer adjacent to the Colorado River and reconstructed the first complete genomes for Archaea using cultivation-independent methods, which dramatically expand genomic sampling of the domain Archaea and clarify taxonomic designations within a major superphylum.
463 citations
Cites background from "Methane production from protozoan e..."
...Although evidence for their activity has been detected during in situ acetate amendment [27], methanogenic Archaea did not appear to be abundant in the filtrate....
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TL;DR: The results suggest that the reason that Geobacter species are repeatedly found to be among the most metabolically active microorganisms in methanogenic soils is that they grow syntrophically in cooperation with Methanothrix spp.
Abstract: The possibility that Methanothrix (formerly Methanosaeta) and Geobacter species cooperate via direct interspecies electron transfer (DIET) in terrestrial methanogenic environments was investigated in rice paddy soils. Genes with high sequence similarity to the gene for the PilA pilin monomer of the electrically conductive pili (e-pili) of Geobacter sulfurreducens accounted for over half of the PilA gene sequences in metagenomic libraries and 42% of the mRNA transcripts in RNA sequencing (RNA-seq) libraries. This abundance of e-pilin genes and transcripts is significant because e-pili can serve as conduits for DIET. Most of the e-pilin genes and transcripts were affiliated with Geobacter species, but sequences most closely related to putative e-pilin genes from genera such as Desulfobacterium, Deferribacter, Geoalkalibacter, and Desulfobacula, were also detected. Approximately 17% of all metagenomic and metatranscriptomic bacterial sequences clustered with Geobacter species, and the finding that Geobacter spp. were actively transcribing growth-related genes indicated that they were metabolically active in the soils. Genes coding for e-pilin were among the most highly transcribed Geobacter genes. In addition, homologs of genes encoding OmcS, a c-type cytochrome associated with the e-pili of G. sulfurreducens and required for DIET, were also highly expressed in the soils. Methanothrix species in the soils highly expressed genes for enzymes involved in the reduction of carbon dioxide to methane. DIET is the only electron donor known to support CO2 reduction in Methanothrix Thus, these results are consistent with a model in which Geobacter species were providing electrons to Methanothrix species for methane production through electrical connections of e-pili.IMPORTANCEMethanothrix species are some of the most important microbial contributors to global methane production, but surprisingly little is known about their physiology and ecology. The possibility that DIET is a source of electrons for Methanothrix in methanogenic rice paddy soils is important because it demonstrates that the contribution that Methanothrix makes to methane production in terrestrial environments may extend beyond the conversion of acetate to methane. Furthermore, defined coculture studies have suggested that when Methanothrix species receive some of their energy from DIET, they grow faster than when acetate is their sole energy source. Thus, Methanothrix growth and metabolism in methanogenic soils may be faster and more robust than generally considered. The results also suggest that the reason that Geobacter species are repeatedly found to be among the most metabolically active microorganisms in methanogenic soils is that they grow syntrophically in cooperation with Methanothrix spp., and possibly other methanogens, via DIET.
229 citations
Cites methods from "Methane production from protozoan e..."
...Sulfate reduction was monitored with an ion chromatograph (ICS-2100; Dionex, CA) equipped with an AS18 column under isocratic elution with 32 mM KOH as the eluent (57)....
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TL;DR: The current understanding of the archaeome in humans, the specific adaptations involved in interaction with the resident microbial community as well as with the host, and the roles of the archaeological community in both health and disease are presented.
Abstract: Host-associated microbial communities have an important role in shaping the health and fitness of plants and animals. Most studies have focused on the bacterial, fungal or viral communities, but often the archaeal component has been neglected. The archaeal community, the so-called archaeome, is now increasingly recognized as an important component of host-associated microbiomes. It is composed of various lineages, including mainly Methanobacteriales and Methanomassiliicoccales (Euryarchaeota), as well as representatives of the Thaumarchaeota. Host–archaeome interactions have mostly been delineated from methanogenic archaea in the gastrointestinal tract, where they contribute to substantial methane production and are potentially also involved in disease-relevant processes. In this Review, we discuss the diversity and potential roles of the archaea associated with protists, plants and animals. We also present the current understanding of the archaeome in humans, the specific adaptations involved in interaction with the resident microbial community as well as with the host, and the roles of the archaeome in both health and disease. The archaeal community, the archaeome, is now increasingly recognized as an important component of host-associated microbiomes. In this Review, Moissl-Eichinger and colleagues discuss the diversity and potential roles of the archaea associated with protists, plants and animals, highlighting the potential roles of archaea in human health and disease.
106 citations
12 Feb 2019
TL;DR: Fermentation in a semi-continuous in-vitro rumen system suggests that A. taxiformis can reduce methane production from enteric fermentation in dairy cattle by 95% when added at a 5% OM inclusion rate without any obvious negative impacts on volatile fatty acid production.
Abstract: Recent studies using batch-fermentation suggest that the red macroalgae Asparagopsis taxiformis has the potential to reduce methane (CH4) production from beef cattle by up to ~ 99% when added to Rhodes grass hay; a common feed in the Australian beef industry. These experiments have shown significant reductions in CH4 without compromising other fermentation parameters (i.e. volatile fatty acid production) with A. taxiformis organic matter (OM) inclusion rates of up to 5%. In the study presented here, A. taxiformis was evaluated for its ability to reduce methane production from dairy cattle fed a mixed ration widely utilized in California, the largest milk producing state in the US. Fermentation in a semi-continuous in-vitro rumen system suggests that A. taxiformis can reduce methane production from enteric fermentation in dairy cattle by 95% when added at a 5% OM inclusion rate without any obvious negative impacts on volatile fatty acid production. High-throughput 16S ribosomal RNA (rRNA) gene amplicon sequencing showed that seaweed amendment effects rumen microbiome consistent with the Anna Karenina hypothesis, with increased β-diversity, over time scales of approximately 3 days. The relative abundance of methanogens in the fermentation vessels amended with A. taxiformis decreased significantly compared to control vessels, but this reduction in methanogen abundance was only significant when averaged over the course of the experiment. Alternatively, significant reductions of CH4 in the A. taxiformis amended vessels was measured in the early stages of the experiment. This suggests that A. taxiformis has an immediate effect on the metabolic functionality of rumen methanogens whereas its impact on microbiome assemblage, specifically methanogen abundance, is delayed. The methane reducing effect of A. taxiformis during rumen fermentation makes this macroalgae a promising candidate as a biotic methane mitigation strategy for dairy cattle. But its effect in-vivo (i.e. in dairy cattle) remains to be investigated in animal trials. Furthermore, to obtain a holistic understanding of the biochemistry responsible for the significant reduction of methane, gene expression profiles of the rumen microbiome and the host animal are warranted.
86 citations
Cites background from "Methane production from protozoan e..."
...It is well known that there is a mutualistic relationship between protozoa and methanogens [33, 34], and it has been shown before that the removal of rumen protozoa results in a reduction of the methanogen population and methanogenesis during enteric fermentation [35, 36]....
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TL;DR: These studies with Methanosarcina acetivorans provide the first genetic evidence for cytochrome-based extracellular electron transfer in Archaea, and suggest parallels with Gram-negative bacteria, such as Shewanella and Geobacter species, in which multiheme outer-surface c-type cytochromes are an essential component for electrical communication with the ext racellular environment.
Abstract: Extracellular electron exchange in Methanosarcina species and closely related Archaea plays an important role in the global carbon cycle and enhances the speed and stability of anaerobic digestion by facilitating efficient syntrophic interactions. Here, we grew Methanosarcina acetivorans with methanol provided as the electron donor and the humic analogue, anthraquione-2,6-disulfonate (AQDS), provided as the electron acceptor when methane production was inhibited with bromoethanesulfonate. AQDS was reduced with simultaneous methane production in the absence of bromoethanesulfonate. Transcriptomics revealed that expression of the gene for the transmembrane, multiheme, c-type cytochrome MmcA was higher in AQDS-respiring cells than in cells performing methylotrophic methanogenesis. A strain in which the gene for MmcA was deleted failed to grow via AQDS reduction but grew with the conversion of methanol or acetate to methane, suggesting that MmcA has a specialized role as a conduit for extracellular electron transfer. Enhanced expression of genes for methanol conversion to methyl-coenzyme M and the Rnf complex suggested that methanol is oxidized to carbon dioxide in AQDS-respiring cells through a pathway that is similar to methyl-coenzyme M oxidation in methanogenic cells. However, during AQDS respiration the Rnf complex and reduced methanophenazine probably transfer electrons to MmcA, which functions as the terminal reductase for AQDS reduction. Extracellular electron transfer may enable the survival of methanogens in dynamic environments in which oxidized humic substances and Fe(III) oxides are intermittently available. The availability of tools for genetic manipulation of M. acetivorans makes it an excellent model microbe for evaluating c-type cytochrome-dependent extracellular electron transfer in Archaea. IMPORTANCE The discovery of a methanogen that can conserve energy to support growth solely from the oxidation of organic carbon coupled to the reduction of an extracellular electron acceptor expands the possible environments in which methanogens might thrive. The potential importance of c-type cytochromes for extracellular electron transfer to syntrophic bacterial partners and/or Fe(III) minerals in some Archaea was previously proposed, but these studies with Methanosarcina acetivorans provide the first genetic evidence for cytochrome-based extracellular electron transfer in Archaea. The results suggest parallels with Gram-negative bacteria, such as Shewanella and Geobacter species, in which multiheme outer-surface c-type cytochromes are an essential component for electrical communication with the extracellular environment. M. acetivorans offers an unprecedented opportunity to study mechanisms for energy conservation from the anaerobic oxidation of one-carbon organic compounds coupled to extracellular electron transfer in Archaea with implications not only for methanogens but possibly also for Archaea that anaerobically oxidize methane.
63 citations
Cites methods from "Methane production from protozoan e..."
...Methane in the headspace was measured by gas chromatography with a flame ionization detector (Shimadzu, GC-8A) as previously described (85)....
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References
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TL;DR: It is concluded that the ML and MCR primers had better amplification ranges than the ME set, but the use of MCR with peat samples was problematic due to poor amplification, Consequently, the ML primers were best suited for mcrA analysis of peatland methanogen communities.
109 citations
"Methane production from protozoan e..." refers background in this paper
...Gene fragments from the bacterial 16S rRNA gene were amplified with 8F (Eden et al., 1991) and 519R (Lane et al., 1985); 344F and 915R (Casamayor et al., 2002) amplified archaeal 16S rRNA gene fragments; 515F (Giovannoni et al., 1988) and 1209R (Reysenbach et al., 1992) amplified eukaryotic 18S rRNA gene fragments; BT107F and BT261R (Baker et al., 2004) amplified protozoan ß-tubulin gene fragments; and MLf (Luton et al., 2002) and ME2 (Juottonen et al., 2006) amplified mcrA gene fragments (See Supplementary Material, Table S1)....
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...…and 1209R (Reysenbach et al., 1992) amplified eukaryotic 18S rRNA gene fragments; BT107F and BT261R (Baker et al., 2004) amplified protozoan ß-tubulin gene fragments; and MLf (Luton et al., 2002) and ME2 (Juottonen et al., 2006) amplified mcrA gene fragments (See Supplementary Material, Table S1)....
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01 Jan 2009
TL;DR: In this article, an integrated analysis of the major chemical properties of NOM, based on the mean and median results of the statistical summaries, is used to demonstrate consistency (or the lack thereof) among reported properties.
Abstract: Scientists and engineers specialized in geochemistry, chemistry, biology, and ecology of natural waters have collectively contributed thousands of published works dealing with natural organic matter (NOM). That body of scientific information is dispersed across a wide range of disciplinary journals and books, and it ranges in quality from the mundane to the exceptional. This review includes quantitative estimates of the global riverine transport of NOM from the continents to the oceans and the corresponding average concentration of total organic carbon in rivers, methods of isolation and characterization of NOM from inland waters, and simple statistical summaries of the most commonly reported chemical properties of NOM. The chemical properties of NOM are compared and contrasted with those of the major components of biomass to highlight the most distinctive traits of NOM – its high degree of oxidation, its high level of unsaturation, and its high concentration of carboxylic acid functional groups. An integrated analysis of the major chemical properties of NOM, based on the mean and median results of the statistical summaries, is used to demonstrate consistency (or the lack thereof) among reported properties of NOM.
91 citations
TL;DR: Results demonstrate that subsurface Geobacter species can tightly regulate their physiological response to changes in groundwater arsenic concentrations, and should be useful for the study of a diversity of other environments in which Geobacteria species are considered to have an important influence on arsenic biogeochemistry.
Abstract: The possibility of arsenic release and the potential role of Geobacter in arsenic biogeochemistry during in situ uranium bioremediation was investigated because increased availability of organic matter has been associated with substantial releases of arsenic in other subsurface environments. In a field experiment conducted at the Rifle, CO study site, groundwater arsenic concentrations increased when acetate was added. The number of transcripts from arrA, which codes for the α-subunit of dissimilatory As(V) reductase, and acr3, which codes for the arsenic pump protein Acr3, were determined with quantitative reverse transcription-PCR. Most of the arrA (>60%) and acr3-1 (>90%) sequences that were recovered were most similar to Geobacter species, while the majority of acr3-2 (>50%) sequences were most closely related to Rhodoferax ferrireducens. Analysis of transcript abundance demonstrated that transcription of acr3-1 by the subsurface Geobacter community was correlated with arsenic concentrations in the groundwater. In contrast, Geobacter arrA transcript numbers lagged behind the major arsenic release and remained high even after arsenic concentrations declined. This suggested that factors other than As(V) availability regulated the transcription of arrA in situ, even though the presence of As(V) increased the transcription of arrA in cultures of Geobacter lovleyi, which was capable of As(V) reduction. These results demonstrate that subsurface Geobacter species can tightly regulate their physiological response to changes in groundwater arsenic concentrations. The transcriptomic approach developed here should be useful for the study of a diversity of other environments in which Geobacter species are considered to have an important influence on arsenic biogeochemistry.
89 citations
"Methane production from protozoan e..." refers background or methods in this paper
...For example, as U(VI) was reductively precipitated from the groundwater, arsenic was also released (Giloteaux et al., 2013), presumably as the result of microbial reduction of Fe(III) minerals that adsorb arsenic in the subsurface (Dowdle et al., 1996; Redman et al., 2002; Islam et al., 2004;…...
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...…groundwater, arsenic was also released (Giloteaux et al., 2013), presumably as the result of microbial reduction of Fe(III) minerals that adsorb arsenic in the subsurface (Dowdle et al., 1996; Redman et al., 2002; Islam et al., 2004; Rowland et al., 2007; Hery et al., 2010; Giloteaux et al., 2013)....
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...In 2011, a small-scale in situ bioremediation experiment was conducted on the grounds of a former uranium ore processing facility in Rifle, Colorado (USA) during the months of August-October as previously described (Giloteaux et al., 2013)....
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TL;DR: The results suggest that both aceticlastic and CO2-type substrate-consuming methanogens are likely involved in the terminal step of hydrocarbon degradation, while methanogenesis from methanol plays a minor role.
Abstract: Methanogenic activity was investigated in a petroleum hydrocarbon-contaminated aquifer by using a series of four push-pull tests with acetate, formate, H2 plus CO2, or methanol to target different groups of methanogenic Archaea. Furthermore, the community composition of methanogens in water and aquifer material was explored by molecular analyses, i.e., fluorescence in situ hybridization (FISH), denaturing gradient gel electrophoresis (DGGE) of 16S rRNA genes amplified with the Archaea-specific primer set ARCH915 and UNI-b-rev, and sequencing of DNA from dominant DGGE bands. Molecular analyses were subsequently compared with push-pull test data. Methane was produced in all tests except for a separate test where 2-bromoethanesulfonate, a specific inhibitor of methanogens, was added. Substrate consumption rates were 0.11 mM day−1 for methanol, 0.38 mM day−1 for acetate, 0.90 mM day−1 for H2, and 1.85 mM day−1 for formate. Substrate consumption and CH4 production during all tests suggested that at least three different physiologic types of methanogens were present: H2 plus CO2 or formate, acetate, and methanol utilizers. The presence of 15 to 20 bands in DGGE profiles indicated a diverse archaeal population. High H2 and formate consumption rates agreed with a high diversity of methanogenic Archaea consuming these substrates (16S rRNA gene sequences related to several members of the Methanomicrobiaceae) and the detection of Methanomicrobiaceae by using FISH (1.4% of total DAPI [4′,6-diamidino-2-phenylindole]-stained microorganisms in one water sample; probe MG1200). Considerable acetate consumption agreed with the presence of sequences related to the obligate acetate degrader Methanosaeata concilii and the detection of this species by FISH (5 to 22% of total microorganisms; probe Rotcl1). The results suggest that both aceticlastic and CO2-type substrate-consuming methanogens are likely involved in the terminal step of hydrocarbon degradation, while methanogenesis from methanol plays a minor role. DGGE profiles further indicate similar archaeal community compositions in water and aquifer material. The combination of hydrogeological and molecular methods employed in this study provide improved information on the community and the potential activity of methanogens in a petroleum hydrocarbon-contaminated aquifer.
83 citations
"Methane production from protozoan e..." refers background in this paper
...It has already been shown that high levels of organic contaminants in groundwater can promote methanogenesis (Lovley, 1997; Bekins et al., 2001; Kleikemper et al., 2005)....
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TL;DR: This is a taxonomic revision of anaerobic free-living ciliates in the genus Metopus that includes a rationalization of all nominal species described in the literature, and the allocation of the survivors to “morphospecies“.
64 citations
"Methane production from protozoan e..." refers background in this paper
...Metopus species are known to feed both on detritus as well as intact bacterial cells (Esteban et al., 1995; Dewdney, 2010)....
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