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Gut Microbes Dec 2023Methanogens, reductive acetogens and sulfate-reducing bacteria play an important role in disposing of hydrogen in gut ecosystems. However, how they interact with each...
Methanogens, reductive acetogens and sulfate-reducing bacteria play an important role in disposing of hydrogen in gut ecosystems. However, how they interact with each other remains largely unknown. This study cocultured (reductive acetogen), (sulfate reducer) and (methanogen). Results revealed that these three species coexisted and did not compete for hydrogen in the early phase of incubations. Sulfate reduction was not affected by and . inhibited the growth of and after 10 h incubations, and the inhibition on was associated with increased sulfide concentration. Remarkably, growth lag phase was shortened by coculturing with and . Formate was rapidly used by under high acetate concentration. Overall, these findings indicated that the interactions of the hydrogenotrophic microbes are condition-dependent, suggesting their interactions may vary in gut ecosystems.
Topics: Methanobrevibacter; Ecosystem; Gastrointestinal Microbiome; Hydrogen; Sulfates
PubMed: 37753963
DOI: 10.1080/19490976.2023.2261784 -
Nature Communications Sep 2023Hybrid cluster proteins (HCPs) are Fe-S-O cluster-containing metalloenzymes in three distinct classes (class I and II: monomer, III: homodimer), all of which...
Hybrid cluster proteins (HCPs) are Fe-S-O cluster-containing metalloenzymes in three distinct classes (class I and II: monomer, III: homodimer), all of which structurally related to homodimeric Ni, Fe-carbon monoxide dehydrogenases (CODHs). Here we show X-ray crystal structure of class III HCP from Methanothermobacter marburgensis (Mm HCP), demonstrating its homodimeric architecture structurally resembles those of CODHs. Also, despite the different architectures of class III and I/II HCPs, [4Fe-4S] and hybrid clusters are found in equivalent positions in all HCPs. Structural comparison of Mm HCP and CODHs unveils some distinct features such as the environments of their homodimeric interfaces and the active site metalloclusters. Furthermore, structural analysis of Mm HCP C67Y and characterization of several Mm HCP variants with a Cys67 mutation reveal the significance of Cys67 in protein structure, metallocluster binding and hydroxylamine reductase activity. Structure-based bioinformatics analysis of HCPs and CODHs provides insights into the structural evolution of the HCP/CODH superfamily.
Topics: Carbon Monoxide; Computational Biology; Metalloproteins; Methanobacteriaceae; Mutation; Synapsins
PubMed: 37709776
DOI: 10.1038/s41467-023-41289-4 -
The ISME Journal Nov 2023Propionate is a key intermediate in anaerobic digestion processes and often accumulates in association with perturbations, such as elevated levels of ammonia. Under such...
Propionate is a key intermediate in anaerobic digestion processes and often accumulates in association with perturbations, such as elevated levels of ammonia. Under such conditions, syntrophic ammonia-tolerant microorganisms play a key role in propionate degradation. Despite their importance, little is known about these syntrophic microorganisms and their cross-species interactions. Here, we present metagenomes and metatranscriptomic data for novel thermophilic and ammonia-tolerant syntrophic bacteria and the partner methanogens enriched in propionate-fed reactors. A metagenome for a novel bacterium for which we propose the provisional name 'Candidatus Thermosyntrophopropionicum ammoniitolerans' was recovered, together with mapping of its highly expressed methylmalonyl-CoA pathway for syntrophic propionate degradation. Acetate was degraded by a novel thermophilic syntrophic acetate-oxidising candidate bacterium. Electron removal associated with syntrophic propionate and acetate oxidation was mediated by the hydrogen/formate-utilising methanogens Methanoculleus sp. and Methanothermobacter sp., with the latter observed to be critical for efficient propionate degradation. Similar dependence on Methanothermobacter was not seen for acetate degradation. Expression-based analyses indicated use of both H and formate for electron transfer, including cross-species reciprocation with sulphuric compounds and microbial nanotube-mediated interspecies interactions. Batch cultivation demonstrated degradation rates of up to 0.16 g propionate L day at hydrogen partial pressure 4-30 Pa and available energy was around -20 mol propionate. These observations outline the multiple syntrophic interactions required for propionate oxidation and represent a first step in increasing knowledge of acid accumulation in high-ammonia biogas production systems.
Topics: Propionates; Ammonia; Anaerobiosis; Bacteria; Acetates; Methanobacteriaceae; Euryarchaeota; Formates; Hydrogen; Methane
PubMed: 37679429
DOI: 10.1038/s41396-023-01504-y -
Scientific Reports Jun 2023This study investigated the effects of 67 species of macroalgae on methanogenesis and rumen fermentation in vitro. Specimens were analyzed for their effect on ruminal...
This study investigated the effects of 67 species of macroalgae on methanogenesis and rumen fermentation in vitro. Specimens were analyzed for their effect on ruminal fermentation and microbial community profiles. Incubations were carried out in an automated gas production system for 24-h and macroalgae were tested at 2% (feed dry matter basis) inclusion rate. Methane yield was decreased 99% by Asparagopsis taxiformis (AT) when compared with the control. Colpomenia peregrina also decreased methane yield 14% compared with control; no other species influenced methane yield. Total gas production was decreased 14 and 10% by AT and Sargassum horneri compared with control, respectively. Total volatile fatty acid (VFA) concentration was decreased between 5 and 8% by 3 macroalgae, whereas AT reduced it by 10%. Molar proportion of acetate was decreased 9% by AT, along with an increase in propionate by 14%. Asparagopsis taxiformis also increased butyrate and valerate molar proportions by 7 and 24%, respectively, whereas 3 macroalgae species decreased molar proportion of butyrate 3 to 5%. Vertebrata lanosa increased ammonia concentration, whereas 3 other species decreased it. Inclusion of AT decreased relative abundance of Prevotella, Bacteroidales, Firmicutes and Methanobacteriaceae, whereas Clostridium, Anaerovibrio and Methanobrevibacter were increased. Specific gene activities for Methanosphaera stadtmane and Methanobrevibacter ruminantium were decreased by AT inclusion. In this in vitro study, Asparagopsis taxiformis was most effective in decreasing methane concentration and yield, but also decreased total gas production and VFA concentration which indicates overall inhibition of ruminal fermentation. No other macroalgae were identified as potential mitigants of enteric methane.
Topics: Animals; Seaweed; Methane; Rumen; Fatty Acids, Volatile; Butyrates; Fermentation; Diet; Animal Feed; Digestion
PubMed: 37330586
DOI: 10.1038/s41598-023-36359-y -
Applied and Environmental Microbiology Jul 2023This study is a continuation by the Environmental Biotechnology Group of the University of Tübingen in memoriam to Reinhard Wirth, who initiated the work on Mth60...
This study is a continuation by the Environmental Biotechnology Group of the University of Tübingen in memoriam to Reinhard Wirth, who initiated the work on Mth60 fimbriae at the University of Regensburg. Growth in biofilms or biofilm-like structures is the prevailing lifestyle for most microbes in nature. The first crucial step to initiate biofilms is the adherence of microbes to biotic and abiotic surfaces. Therefore, it is crucial to elucidate the initial step of biofilm formation, which is generally established through cell-surface structures (i.e., cell appendages), such as fimbriae or pili, that adhere to biotic and abiotic surfaces. The Mth60 fimbriae of Methanothermobacter thermautotrophicus ΔH are one of only a few known archaeal cell appendages that do not assemble via the type IV pili assembly mechanism. Here, we report the constitutive expression of Mth60 fimbria-encoding genes from a shuttle-vector construct and the deletion of the Mth60 fimbria-encoding genes from the genomic DNA of ΔH. For this, we expanded our system for genetic modification of ΔH using an allelic-exchange method. While overexpression of the respective genes increased the number of Mth60 fimbriae, deletion of the Mth60 fimbria-encoding genes led to a loss of Mth60 fimbriae in planktonic cells of ΔH compared to the wild-type strain. This, either increased or decreased, number of Mth60 fimbriae correlated with a significant increase or decrease of biotic cell-cell connections in the respective ΔH strains compared to the wild-type strain. spp. have been studied for the biochemistry of hydrogenotrophic methanogenesis for many years. However, a detailed investigation of certain aspects, such as regulatory processes, was impossible due to the lack of genetic tools. Here, we amend our genetic toolbox for ΔH with an allelic exchange method. We report the deletion of genes that encode the Mth60 fimbriae. Our findings provide the first genetic evidence of whether the expression of these genes underlies regulation and reveal a role of the Mth60 fimbriae in the formation of cell-cell connections of ΔH.
Topics: Fimbriae, Bacterial; Biofilms; Methanobacteriaceae
PubMed: 37310347
DOI: 10.1128/aem.00575-23 -
Frontiers in Microbiology 2023Wetlands are an important source of atmospheric methane (CH) and are sensitive to global climate change. Alpine swamp meadows, accounting for ~50% of the natural...
Response of methanogenic community and their activity to temperature rise in alpine swamp meadow at different water level of the permafrost wetland on Qinghai-Tibet Plateau.
Wetlands are an important source of atmospheric methane (CH) and are sensitive to global climate change. Alpine swamp meadows, accounting for ~50% of the natural wetlands on the Qinghai-Tibet Plateau, were considered one of the most important ecosystems. Methanogens are important functional microbes that perform the methane producing process. However, the response of methanogenic community and the main pathways of CH production to temperature rise remains unknown in alpine swamp meadow at different water level in permafrost wetlands. In this study, we investigated the response of soil CH production and the shift of methanogenic community to temperature rise in the alpine swamp meadow soil samples with different water levels collected from the Qinghai-Tibet Plateau through anaerobic incubation at 5°C, 15°C and 25°C. The results showed that the CH contents increased with increasing incubation temperature, and were 5-10 times higher at the high water level sites (GHM1 and GHM2) than that at the low water level site (GHM3). For the high water level sites (GHM1 and GHM2), the change of incubation temperatures had little effect on the methanogenic community structure. (32.44-65.46%), (19.30-58.86%) and (3.22-21.24%) were the dominant methanogen groups, with the abundance of and having a significant positive correlation with CH production ( < 0.01). For the low water level site (GHM3), the methanogenic community structure changed greatly at 25°C. The (59.65-77.33%) was the dominant methanogen group at 5°C and 15°C; In contrast, the (69.29%) dominated at 25°C, and its abundance showed a significant positive correlation with CH production ( < 0.05). Collectively, these findings enhance the understanding of methanogenic community structures and CH production in permafrost wetlands with different water levels during the warming process.
PubMed: 37213493
DOI: 10.3389/fmicb.2023.1181658 -
Archives of Microbiology Apr 2023A novel interdomain consortium composed of a methanogenic Archaeon and a sulfate-reducing bacterium was isolated from a microbial biofilm in an oil well in Cahuita...
A novel interdomain consortium composed of a methanogenic Archaeon and a sulfate-reducing bacterium was isolated from a microbial biofilm in an oil well in Cahuita National Park, Costa Rica. Both organisms can be grown in pure culture or as stable co-culture. The methanogenic cells were non-motile rods producing CH exclusively from H/CO. Cells of the sulfate-reducing partner were motile rods forming cell aggregates. They utilized hydrogen, lactate, formate, and pyruvate as electron donors. Electron acceptors were sulfate, thiosulfate, and sulfite. 16S rRNA sequencing revealed 99% gene sequence similarity of strain CaP3V-M-L2A to Methanobacterium subterraneum and 98.5% of strain CaP3V-S-L1A to Desulfomicrobium baculatum. Both strains grew from 20 to 42 °C, pH 5.0-7.5, and 0-4% NaCl. Based on our data, type strains CaP3V-M-L2A (= DSM 113354 = JCM 39174) and CaP3V-S-L1A (= DSM 113299 = JCM 39179) represent novel species which we name Methanobacterium cahuitense sp. nov. and Desulfomicrobium aggregans sp. nov.
Topics: Methanobacterium; Costa Rica; Oil and Gas Fields; RNA, Ribosomal, 16S; Sulfates; Phylogeny; DNA, Bacterial; Sequence Analysis, DNA; Fatty Acids
PubMed: 37055657
DOI: 10.1007/s00203-023-03533-9 -
Journal of Microbiological Methods Apr 2023Methanobrevibacter smithii (M. smithii), the most prevalent and abundant gut methanogen, detoxifies hydrogen into methane and is, therefore, of paramount importance for...
Methanobrevibacter smithii (M. smithii), the most prevalent and abundant gut methanogen, detoxifies hydrogen into methane and is, therefore, of paramount importance for the equilibrium of the gut microbiota. The isolation by culture of M. smithii has routinely relied upon hydrogen‑carbon dioxide-enriched, oxygen-deprived atmospheres. In this study, we developed a medium referred to as "GG", which allowed for M. smithii growth and isolation by culture in an oxygen-deprived atmosphere, with no supply of either hydrogen or carbon dioxide, making it easier to detect M. smithii by culture in clinical microbiology laboratories.
Topics: Methanobrevibacter; Carbon Dioxide; Bacteria, Anaerobic; Gastrointestinal Microbiome; Hydrogen
PubMed: 36907565
DOI: 10.1016/j.mimet.2023.106704 -
Ecology and Evolution Feb 2023Numerous gut microbial studies have focused on bacteria. However, archaea, viruses, fungi, protists, and nematodes are also regular residents of the gut ecosystem....
Numerous gut microbial studies have focused on bacteria. However, archaea, viruses, fungi, protists, and nematodes are also regular residents of the gut ecosystem. Little is known about the composition and potential interactions among these six kingdoms in the same samples. Here, we unraveled the complex connection among them using approximately 123 gut metagenomes from 42 mammalian species (including carnivores, omnivores, and herbivores). We observed high variation in bacterial and fungal families and relatively low variation in archaea, viruses, protists, and nematodes. We found that some fungi in the mammalian intestine might come from environmental sources (e.g., soil and dietary plants), and some might be native to the intestine (e.g., the occurrence of ). The and families (archaea and protozoa, respectively) were predominant in these metagenomes, whereas and were the two most common nematodes, and and the two most common virus families in these mammalian gut metagenomes. Interestingly, most of the pairwise co-occurrence patterns were significantly positive among these six kingdoms, and significantly negative networks mainly occurred between fungi and prokaryotes (both bacteria and archaea). Our study revealed some inconvenient characteristics in the mammalian gut microorganism ecosystem: (1) the community formed by members of the analyzed kingdoms reflects the life history of the host and the potential threat posed by pathogenic protists and nematodes in mammals; and (2) the networks suggest the existence of predicted mutualism among members of these six kingdoms and of the predicted competition, mainly among fungi and other kingdoms.
PubMed: 36844675
DOI: 10.1002/ece3.9829 -
Animals : An Open Access Journal From... Feb 2023The aim of this study was to assess if molasses could modify VFA production and the rumen microbial community in vitro. Three beet (treatment Beet) and three cane...
The aim of this study was to assess if molasses could modify VFA production and the rumen microbial community in vitro. Three beet (treatment Beet) and three cane (treatment Cane) molasses preparations were randomly selected from a variety of samples collected worldwide and incubated in vitro with rumen fluid along with a control sample (treatment CTR, in which no molasses was used). Flasks for VFA analysis were sampled at 0, 1, 2, 3, 4, 6, 8, and 24 h of each incubation. For microbiota analysis, samples from each fermentation flask after 12 and 24 h were subjected to microbial DNA extraction and V3-V4 16S rRNA gene sequencing on an Illumina MiSeq platform. Total net VFA production was higher in the beet and cane preparations than in the control (CTR) group at 24 h (33 mmol/L, 34 mmol/L, and 24.8 mmol/L, respectively), and the composition of VFAs was affected by the inclusion of molasses: acetic acid increased in the CTR group (73.5 mol%), while propionic acid increased in the beet and cane molasses (19.6 mol% and 18.6 mol%, respectively), and butyric acid increased, especially in the cane group (23.2 mol%). Molasses even influenced the composition of the rumen microbiota, and particularly the relative abundance of the most dominant family in the rumen, Prevotellaceae, which decreased compared to CTR (37.13%, 28.88%, and 49.6%, respectively). In contrast, Streptococcaceae (19.62% and 28.10% in molasses compared to 6.23% in CTR), Veillonellaceae (6.48% and 8.67% in molasses compared to 4.54% in CTR), and Fibrobacteraceae (0.90% and 0.88% in molasses compared to 0.62% in CTR) increased in the beet and cane groups compared to the CTR group. Another important finding is the lower proportion of Methanobacteriaceae following the addition of molasses compared to CTR (0.26%, 0.28%, and 0.43%, respectively). This study showed the impact of molasses in influencing VFA production and composition as a result of a modified rumen microbial composition.
PubMed: 36830515
DOI: 10.3390/ani13040728