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Tedersoo L, Drenkhan R, Abarenkov K, Anslan S, Bahram M, Bitenieks K, Buegger F, Gohar D, Hagh‐Doust N, Klavina D, Makovskis K, Zusevica A, Pritsch K, Padari A, Põlme S, Rahimlou S, Rungis D, Mikryukov V. The influence of tree genus, phylogeny, and richness on the specificity, rarity, and diversity of ectomycorrhizal fungi. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13253. [PMID: 38575147 PMCID: PMC10994715 DOI: 10.1111/1758-2229.13253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 03/13/2024] [Indexed: 04/06/2024]
Abstract
Partner specificity is a well-documented phenomenon in biotic interactions, yet the factors that determine specificity in plant-fungal associations remain largely unknown. By utilizing composite soil samples, we identified the predictors that drive partner specificity in both plants and fungi, with a particular focus on ectomycorrhizal associations. Fungal guilds exhibited significant differences in overall partner preference and avoidance, richness, and specificity to specific tree genera. The highest level of specificity was observed in root endophytic and ectomycorrhizal associations, while the lowest was found in arbuscular mycorrhizal associations. The majority of ectomycorrhizal fungal species showed a preference for one of their partner trees, primarily at the plant genus level. Specialist ectomycorrhizal fungi were dominant in belowground communities in terms of species richness and relative abundance. Moreover, all tree genera (and occasionally species) demonstrated a preference for certain fungal groups. Partner specificity was not related to the rarity of fungi or plants or environmental conditions, except for soil pH. Depending on the partner tree genus, specific fungi became more prevalent and relatively more abundant with increasing stand age, tree dominance, and soil pH conditions optimal for the partner tree genus. The richness of partner tree species and increased evenness of ectomycorrhizal fungi in multi-host communities enhanced the species richness of ectomycorrhizal fungi. However, it was primarily the partner-generalist fungi that contributed to the high diversity of ectomycorrhizal fungi in mixed forests.
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Affiliation(s)
- Leho Tedersoo
- Mycology and Microbiology CenterUniversity of TartuTartuEstonia
- Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
- College of ScienceKing Saud UniversityRiyadhSaudi Arabia
| | - Rein Drenkhan
- Institute of Forestry and EngineeringEstonian University of Life SciencesTartuEstonia
| | | | - Sten Anslan
- Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
| | - Mohammad Bahram
- Mycology and Microbiology CenterUniversity of TartuTartuEstonia
- Department of EcologySwedish University of Agricultural SciencesUppsalaSweden
| | - Kriss Bitenieks
- Latvian State Forest Research Institute ‘Silava’ (LSFRI Silava)SalaspilsLatvia
| | - Franz Buegger
- Helmholtz Zentrum München – German Research Center for Environmental Health (GmbH), Research Unit Environmental SimulationNeuherbergGermany
| | - Daniyal Gohar
- Mycology and Microbiology CenterUniversity of TartuTartuEstonia
- Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
| | - Niloufar Hagh‐Doust
- Mycology and Microbiology CenterUniversity of TartuTartuEstonia
- Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
| | - Darta Klavina
- Latvian State Forest Research Institute ‘Silava’ (LSFRI Silava)SalaspilsLatvia
| | - Kristaps Makovskis
- Latvian State Forest Research Institute ‘Silava’ (LSFRI Silava)SalaspilsLatvia
| | - Austra Zusevica
- Latvian State Forest Research Institute ‘Silava’ (LSFRI Silava)SalaspilsLatvia
| | - Karin Pritsch
- Helmholtz Zentrum München – German Research Center for Environmental Health (GmbH), Research Unit Environmental SimulationNeuherbergGermany
| | - Allar Padari
- Institute of Forestry and EngineeringEstonian University of Life SciencesTartuEstonia
| | - Sergei Põlme
- Mycology and Microbiology CenterUniversity of TartuTartuEstonia
- Natural History MuseumUniversity of TartuTartuEstonia
| | - Saleh Rahimlou
- Mycology and Microbiology CenterUniversity of TartuTartuEstonia
| | - Dainis Rungis
- Latvian State Forest Research Institute ‘Silava’ (LSFRI Silava)SalaspilsLatvia
| | - Vladimir Mikryukov
- Mycology and Microbiology CenterUniversity of TartuTartuEstonia
- Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
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Rasmussen JA, Chua PYS. Genome-resolving metagenomics reveals wild western capercaillies (Tetrao urogallus) as avian hosts for antibiotic-resistance bacteria and their interactions with the gut-virome community. Microbiol Res 2023; 271:127372. [PMID: 37018898 DOI: 10.1016/j.micres.2023.127372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 03/29/2023] [Accepted: 03/31/2023] [Indexed: 04/04/2023]
Abstract
The gut microbiome is a critical component of avian health, influencing nutrient uptake and immune functions. While the gut microbiomes of agriculturally important birds have been studied, the microbiomes of wild birds still need to be explored. Filling this knowledge gap could have implications for the microbial rewilding of captive birds and managing avian hosts for antibiotic-resistant bacteria (ARB). Using genome-resolved metagenomics, we recovered 112 metagenome-assembled genomes (MAGs) from the faeces of wild and captive western capercaillies (Tetrao urogallus) (n = 8). Comparisons of bacterial diversity between the wild and captive capercaillies suggest that the reduced diversity in the captive individual could be due to differences in diet. This was further substantiated through the analyses of 517,657 clusters of orthologous groups (COGs), which revealed that gene functions related to amino acids and carbohydrate metabolisms were more abundant in wild capercaillies. Metagenomics mining of resistome identified 751 antibiotic resistance genes (ARGs), of which 40.7 % were specific to wild capercaillies suggesting that capercaillies could be potential reservoirs for hosting ARG-associated bacteria. Additionally, the core resistome shared between wild and captive capercaillies indicates that birds can acquire these ARG-associated bacteria naturally from the environment (43.1 % of ARGs). The association of 26 MAGs with 120 ARGs and 378 virus operational taxonomic units (vOTUs) also suggests a possible interplay between these elements, where putative phages could have roles in modulating the gut microbiota of avian hosts. These findings can have important implications for conservation and human health, such as avian gut microbiota rewilding, identifying the emerging threats or opportunities due to phage-microbe interactions, and monitoring the potential spread of ARG-associated bacteria from wild avian populations.
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Wang L, Zhang F, Li H, Yang S, Chen X, Long S, Yang S, Yang Y, Wang Z. Metabolic and inflammatory linkage of the chicken cecal microbiome to growth performance. Front Microbiol 2023; 14:1060458. [PMID: 36910194 PMCID: PMC9995838 DOI: 10.3389/fmicb.2023.1060458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 02/06/2023] [Indexed: 02/25/2023] Open
Abstract
Introduction Chinese indigenous chicken breeds are widely used as food in China but their slow growth rate and long farming cycle has limited their industrial production. Methods In the current study we examined whether the market weights of native chicken breeds were related to specific cecal bacteria, serum metabolites and inflammatory cytokines. We examined cecal bacterial taxa using 16S rDNA analysis along with untargeted serum metabolites and serum inflammatory cytokines. Results We found that the cecal microbiota could explain 10.1% of the individual differences in chicken weights and identified key cecal bacterial genera that influenced this phenotype. The presence of Sphaerochaeta spp. improved growth performance via bovinic acid metabolism. In contrast, Synergistes and norank_f_Desulfovibrionaceae had a negative effect on growth by inducing expression of the inflammatory cytokine IL-6. Discussion We were able to link specific bacterial genera with growth promotion in chickens and this study will allow further development of their use as probiotics in these animals.
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Affiliation(s)
- Liqi Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, Guizhou, China.,College of Animal Sciences, Guizhou University, Guiyang, Guizhou, China
| | - Fuping Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, Guizhou, China.,College of Animal Sciences, Guizhou University, Guiyang, Guizhou, China
| | - Hui Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, Guizhou, China.,College of Animal Sciences, Guizhou University, Guiyang, Guizhou, China
| | - Shenglin Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, Guizhou, China.,College of Animal Sciences, Guizhou University, Guiyang, Guizhou, China
| | - Xiang Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, Guizhou, China.,College of Animal Sciences, Guizhou University, Guiyang, Guizhou, China
| | - Shuihua Long
- School of Public Health, Xinyu University, Xinyu, Jiangxi, China
| | - Shenghong Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, Guizhou, China.,College of Animal Sciences, Guizhou University, Guiyang, Guizhou, China
| | - Yongxian Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, Guizhou, China.,College of Animal Sciences, Guizhou University, Guiyang, Guizhou, China
| | - Zhong Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, Guizhou, China.,College of Animal Sciences, Guizhou University, Guiyang, Guizhou, China
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Li LP, Qu L, Li T. Supplemental dietary Selenohomolanthionine affects growth and rumen bacterial population of Shaanbei white cashmere wether goats. Front Microbiol 2022; 13:942848. [PMID: 36338028 PMCID: PMC9632625 DOI: 10.3389/fmicb.2022.942848] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 09/28/2022] [Indexed: 11/27/2022] Open
Abstract
Selenium (Se) is an important trace element for all livestock growth. However, little is known about the dietary supplementation of Selenohomolanthionine (SeHLan) effect on growth and rumen microbiota of cashmere goats. In this study, thirty-two growing Shaanbei white cashmere wether goats with mean body weight (26.18 ± 2.71) kg were randomly assigned into 4 treatments, each with 8 replicates. The goats in 4 experimental groups were fed the basal diet (0.016 mg/kg Se) added with organic Se in the form of SeHLan, namely, control group (CG, added 0 mg/kg Se), low Se group (LSE, added 0.3 mg/kg Se), medium Se group (MSE, added 0.6 mg/kg Se), and high Se group (HSE, added 1.2 mg/kg Se). The feed experiment lasted for 70 days including 10-day adaptation, followed by 11 days digestibility trial including 7-day adaptation and 4-day collection period. On the last day of feeding experiment, rumen fluid was collected for microbial community analysis. The feed, orts, and fecal samples were collected for chemical analysis during digestibility trial. The results showed that average daily feed intake (ADFI) and the apparent digestibility of crude protein (CP) were both quadratic ally increased with increased SeHLan supply (Pquadratic < 0.05), while average daily gain (ADG) and feed conversion ratio (FCR) showed a linear response (Plinear < 0.05). The ADFI and ADG were all highest in the MSE group, which also had the lowest FCR (P < 0.05). Alpha diversity indices of the microbial community did not differ among four treatments. While principal coordinates analysis (PCoA) showed that rumen bacterial population differed among four groups. Taxonomic analysis revealed that Bacteroidetes, Firmicutes, and Euryarchaeota were the dominant phyla. The dominant families were Prevotellaceae, Selenomonadaceae, Methanobacteriaceae, and Bifidobacteriaceae. The significantly different rumen bacterial genera were found to be Methanobrevibacter, Quinella, Christensenellaceae_R-7_group, Veillonellaceae_UCG-001, and Succinivibrionaceae_UCG-002 (P < 0.05). In addition, Tax4fun analysis revealed that SeHLan supplemented groups enhanced the enrichment of genes related to energy metabolism, amino acid metabolism, carbohydrate metabolism, and enzymes. Twenty-eight pathways showed significant differences among four treatment groups (P < 0.05). In conclusion, dietary supplementation of medium SeHLan significantly affects rumen bacterial composition and ultimately promotes Shaanbei white cashmere wether goats nutrient digestibility and growth.
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Affiliation(s)
- Long-Ping Li
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin, China
- *Correspondence: Long-Ping Li,
| | - Lei Qu
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin, China
| | - Tuo Li
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin, China
- College of Life Sciences, Yulin University, Yulin, China
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Li C, Chen N, Zhang X, Shahzad K, Qi R, Zhang Z, Lu Z, Lu Y, Yu X, Zafar MH, Wang M, Liu W. Mixed silage with Chinese cabbage waste enhances antioxidant ability by increasing ascorbate and aldarate metabolism through rumen Prevotellaceae UCG-004 in Hu sheep. Front Microbiol 2022; 13:978940. [PMID: 36090065 PMCID: PMC9459383 DOI: 10.3389/fmicb.2022.978940] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 08/01/2022] [Indexed: 11/13/2022] Open
Abstract
Silage is rich in nutrients, which can make up for the lack of seasonal roughage, and has a certain promotion effect on the intensive feeding of ruminants. In addition, silage can maintain the rumen function of ruminants to a certain extent and reduce the risk of rumen acidosis and abomasum translocation. The purpose of this study was to investigate the effects of the mixed silage of Chinese cabbage waste and rice straw (mixed silage) on antioxidant performance, rumen microbial population, and fermentation metabolism of Hu sheep. The 16 healthy Hu sheep (eight rams and eight ewes, 39.11 ± 1.16 kg, 5.5 months) were randomly divided into two groups (the control group and the mixed silage group) with eight animals (four rams and four ewes) in each group. The control group was fed with farm roughage (peanut seedlings, corn husk, and high grain shell) as forage, and the mixed silage group was fed with the mixed silage as forage. The results showed that the mixed silage had no effect on the growth performance of Hu sheep (p > 0.05). Ruminal butyric acid, total volatile fatty acids (TVFA), and ammonia nitrogen (NH3-N) concentration in the mixed silage group were increased, whereas the pH was decreased (p < 0.05). The blood and rumen total antioxidants capacity (T-AOC) concentration in the mixed silage group was higher, and the malondialdehyde (MDA) content in rumen, serum, liver, and kidney was lower than that in the control group (p < 0.05). PCoA and ANOSIM results of Illumina sequencing indicated that the mixed silage affected the bacterial composition of the rumen microbes. The mixed silage increased the proportion of Prevotellaceae UCG-004 which was in a positive correlation with Vitamin C (Vc). In addition, PICRUSt functional prediction analysis showed that ascorbate and aldarate metabolism were up-regulated in the mixed silage group (p < 0.05). In conclusion, higher contents of VC and acid detergent fiber (ADF) in the mixed silage were beneficial to the growth and reproduction of Prevotellaceae UCG-004, resulting in increased production of the butyric acid significantly upregulated the metabolism of ascorbate and aldarate metabolism, thereby improving the antioxidant properties of Hu sheep.
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Affiliation(s)
- Chuang Li
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
- State Key Laboratory for Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
| | - Ning Chen
- State Key Laboratory for Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
- Institute of Animal Husbandry and Veterinary, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
| | - Xingxing Zhang
- State Key Laboratory for Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
- Institute of Animal Husbandry and Veterinary, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
| | - Khuram Shahzad
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Ruxin Qi
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Zhenbin Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Zhiqi Lu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Yue Lu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Xiang Yu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | | | - Mengzhi Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
- State Key Laboratory for Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
- Institute of Animal Husbandry and Veterinary, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
- *Correspondence: Mengzhi Wang,
| | - Wujun Liu
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
- Wujun Liu,
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Djemai K, Drancourt M, Tidjani Alou M. Bacteria and Methanogens in the Human Microbiome: a Review of Syntrophic Interactions. MICROBIAL ECOLOGY 2022; 83:536-554. [PMID: 34169332 DOI: 10.1007/s00248-021-01796-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 06/14/2021] [Indexed: 06/13/2023]
Abstract
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.
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Affiliation(s)
- Kenza Djemai
- IRD, MEPHI, IHU Méditerranée Infection, Aix-Marseille-University, 19-12 Bd Jean Moulin, 13005, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Michel Drancourt
- IRD, MEPHI, IHU Méditerranée Infection, Aix-Marseille-University, 19-12 Bd Jean Moulin, 13005, Marseille, France
| | - Maryam Tidjani Alou
- IRD, MEPHI, IHU Méditerranée Infection, Aix-Marseille-University, 19-12 Bd Jean Moulin, 13005, Marseille, France.
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Hardy J, Bonin P, Lazuka A, Gonidec E, Guasco S, Valette C, Lacroix S, Cabrol L. Similar Methanogenic Shift but Divergent Syntrophic Partners in Anaerobic Digesters Exposed to Direct versus Successive Ammonium Additions. Microbiol Spectr 2021; 9:e0080521. [PMID: 34612672 PMCID: PMC8510171 DOI: 10.1128/spectrum.00805-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 08/02/2021] [Indexed: 01/04/2023] Open
Abstract
During anaerobic digestion (AD) of protein-rich wastewater, ammonium (NH4+) is released by amino acid degradation. High NH4+ concentrations disturb the AD microbiome balance, leading to process impairments. The sensitivity of the AD microbiome to NH4+ and the inhibition threshold depend on multiple parameters, especially the previous microbial acclimation to ammonium stress. However, little is known about the effect of different NH4+ acclimation strategies on the differential expression of key active microbial taxa. Here, we applied NH4+ inputs of increasing intensity (from 1.7 to 15.2 g N-NH4+ liters-1) in batch assays fed with synthetic wastewater, according to two different strategies: (i) direct independent inputs at a unique target concentration and (ii) successive inputs in a stepwise manner. In both strategies, along the NH4+ gradient, the active methanogens shifted from acetoclastic Methanosaeta to Methanosarcina and eventually hydrogenotrophic Methanoculleus. Despite shorter latency times, the successive input modality led to lower methane production rate, lower soluble chemical oxygen demand (sCOD) removal efficiency, and lower half maximal inhibitory concentration, together with higher volatile fatty acid (VFA) accumulation, compared to the independent input modality. These differential performances were associated with a drastically distinct succession pattern of the active bacterial partners in both experiments. In particular, the direct exposure modality was characterized by a progressive enrichment of VFA producers (mainly Tepidimicrobium) and syntrophic VFA oxidizers (mainly Syntrophaceticus) with increasing NH4+ concentration, while the successive exposure modality was characterized by a more dynamic succession of VFA producers (mainly Clostridium, Sporanaerobacter, Terrisporobacter) and syntrophic VFA oxidizers (mainly Tepidanaerobacter, Syntrophomonas). These results bring relevant insights for improved process management through inoculum adaptation, bioaugmentation, or community-driven optimization. IMPORTANCE Anaerobic digestion (AD) is an attractive biotechnological process for wastewater bioremediation and bioenergy production in the form of methane-rich biogas. However, AD can be inhibited by ammonium generated by protein-rich effluent, commonly found in agro-industrial activities. Insights in the microbial community composition and identification of AD key players are crucial for anticipating process impairments in response to ammonium stress. They can also help in defining an optimal microbiome adapted to high ammonium levels. Here, we compared two strategies for acclimation of AD microbiome to increasing ammonium concentration to better understand the effect of this stress on the methanogens and their bacterial partners. Our results suggest that long-term cumulative exposure to ammonia disrupted the AD microbiome more strongly than direct (independent) ammonium additions. We identified bioindicators with different NH4+ tolerance capacity among VFA producers and syntrophic VFA oxidizers.
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Affiliation(s)
- Julie Hardy
- MIO, Aix Marseille University, University of Toulon, CNRS, IRD, Marseille, France
- Scientific & Technological Expertise Department, Veolia, Maisons-Laffitte, France
| | - Patricia Bonin
- MIO, Aix Marseille University, University of Toulon, CNRS, IRD, Marseille, France
| | - Adele Lazuka
- Scientific & Technological Expertise Department, Veolia, Maisons-Laffitte, France
| | - Estelle Gonidec
- Scientific & Technological Expertise Department, Veolia, Maisons-Laffitte, France
| | - Sophie Guasco
- MIO, Aix Marseille University, University of Toulon, CNRS, IRD, Marseille, France
| | - Corinne Valette
- MIO, Aix Marseille University, University of Toulon, CNRS, IRD, Marseille, France
| | - Sébastien Lacroix
- Scientific & Technological Expertise Department, Veolia, Maisons-Laffitte, France
| | - Léa Cabrol
- MIO, Aix Marseille University, University of Toulon, CNRS, IRD, Marseille, France
- Instituto de Ecologia y Biodiversidad (IEB) Facultad de Ciencias, Universidad de Chile Las Palmeras, Nunoa, Santiago, Chile
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Yang M, Li J, Lv XM, Dai LR, Wu KJ, Tu B, Lawson PA, Tang YQ, Cheng L. Thermosynergistes pyruvativorans gen. nov., sp. nov., an anaerobic, pyruvate-degrading bacterium from Shengli oilfield, and proposal of Thermosynergistaceae fam. nov. in the phylum Synergistetes. Int J Syst Evol Microbiol 2021; 71. [PMID: 34582328 DOI: 10.1099/ijsem.0.005031] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A strictly anaerobic, thermophilic, Gram-stain-negative bacterium, named as strain S15T, was isolated from oily sludge of Shengli oilfield in PR China. Cells of strain S15T were straight or slightly curved rods with 0.4-0.8 µm width × 1.4-3 µm length and occurred mostly in pairs or short chains. Endospore-formation was not observed. The strain grew optimally at 55 °C (range from 30-65 °C), pH 6.5 (pH 6.0-8.5) and 0-30 g l-1 NaCl (optimum with 10 g l-1 NaCl). Yeast extract was an essential growth factor for strain S15T. The major cellular fatty acid was iso-C15 : 0 (58.2 %), and the main polar lipids were amino phospholipid (APL), glycolipids (GLs) and phosphatidylethanolamine (PE). The G+C content of DNA of strain S15T was 52.2 mol%. Strain S15T shared 89.8 % 16S rRNA gene similarity with the most related organism Acetomicrobium hydrogeniformans DSM 22491T in the phylum Synergistetes. The paired genomic average amino acid identity (AAI) and percentage of conserved proteins (POCP) values showed relatedness of less than 58.0 and 39.7 % with type strains of the species in the phylum Synergistetes. On the basis of phenotypic, phylogenetic and phylogenomic evidences, strain S15T constitutes a novel species in a novel genus, for the name Thermosynergistes pyruvativorans gen. nov., sp. nov. is proposed. The type strain is S15T (=CCAM 583T=JCM 33159T). Thermosynergistaceae fam. nov. is also proposed.
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Affiliation(s)
- Min Yang
- Institute of New Energy and Low-Carbon Technology, Sichuan University, Chengdu, 610065, PR China.,Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
| | - Jiang Li
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
| | - Xiao-Meng Lv
- Institute of New Energy and Low-Carbon Technology, Sichuan University, Chengdu, 610065, PR China.,Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
| | - Li-Rong Dai
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
| | - Ke-Jia Wu
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
| | - Bo Tu
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
| | - Paul A Lawson
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Yue-Qin Tang
- Institute of New Energy and Low-Carbon Technology, Sichuan University, Chengdu, 610065, PR China
| | - Lei Cheng
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
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Cui X, Wang Z, Tan Y, Chang S, Zheng H, Wang H, Yan T, Guru T, Hou F. Selenium Yeast Dietary Supplement Affects Rumen Bacterial Population Dynamics and Fermentation Parameters of Tibetan Sheep ( Ovis aries) in Alpine Meadow. Front Microbiol 2021; 12:663945. [PMID: 34276597 PMCID: PMC8283570 DOI: 10.3389/fmicb.2021.663945] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 05/31/2021] [Indexed: 11/13/2022] Open
Abstract
Selenium (Se) deficiency is a widespread and seasonally chronic phenomenon observed in Tibetan sheep (Ovis aries) traditionally grazed on the Qinghai-Tibet Plateau (QTP). Effects of the dietary addition of Se-enriched yeast (SeY) on the bacterial community in sheep rumen and rumen fermentation were evaluated with the aim of gaining a better understanding of the rumen prokaryotic community. Twenty-four yearling Tibetan rams [initial average body weight (BW) of 31.0 ± 0.64 kg] were randomly divided into four treatment groups, namely, control (CK), low Se (L), medium Se (M), and high Se (H). Each group comprised six rams and was fed a basic diet of fresh forage cut from the alpine meadow, to which SeY was added at prescribed dose rates. This feed trial was conducted for over 35 days. On the final day, rumen fluid was collected using a transesophageal sampler for analyzing rumen pH, NH3-N content, volatile fatty acid (VFA) level, and the rumen microbial community. Our analyses showed that NH3-N, total VFA, and propionate concentrations in the M group were significantly higher than in the other groups (P < 0.05). Both the principal coordinates analysis (PCoA) and the analysis of similarities revealed that the bacterial population structure of rumen differed among the four groups. The predominant rumen bacterial phyla were found to be Bacteroidetes and Firmicutes, and the three dominant genera in all the samples across all treatments were Christensenellaceae R7 group, Rikenellaceae RC9 gut group, and Prevotella 1. The relative abundances of Prevotella 1, Rikenellaceae RC9 gut group, Ruminococcus 2, Lachnospiraceae XPB1014 group, Carnobacterium, and Hafnia-Obesumbacterium were found to differ significantly among the four treatment groups (P < 0.05). Moreover, Tax4fun metagenome estimation revealed that gene functions and metabolic pathways associated with carbohydrate and other amino acids were overexpressed in the rumen microbiota of SeY-supplemented sheep. To conclude, SeY significantly affects the abundance of rumen bacteria and ultimately affects the rumen microbial fermentation.
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Affiliation(s)
- Xiongxiong Cui
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Zhaofeng Wang
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Yuhui Tan
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Shenghua Chang
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Huiru Zheng
- School of Computing, Ulster University, Antrim, United Kingdom
| | - Haiying Wang
- School of Computing, Ulster University, Antrim, United Kingdom
| | - Tianhai Yan
- Sustainable Agri-Food Sciences Division, Agriculture Branch, Agri-Food and Biosciences Institute, Hillsborough, United Kingdom
| | - Tsedan Guru
- Animal Husbandry Science and Technology Demonstration Park of Maqu County, Gannan, China
| | - Fujiang Hou
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
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10
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Gomes MM, Sakamoto IK, Silva Rabelo CAB, Silva EL, Varesche MBA. Statistical optimization of methane production from brewery spent grain: Interaction effects of temperature and substrate concentration. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 288:112363. [PMID: 33756388 DOI: 10.1016/j.jenvman.2021.112363] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 02/16/2021] [Accepted: 03/07/2021] [Indexed: 06/12/2023]
Abstract
This study evaluated the effects of thermal pretreatment of brewery spent grain (BSG) (by autoclave 121 °C, 1.45 atm for 30 min) on methane production (CH4). Operation temperature (31-59 °C) and substrate concentration (8.3-19.7 g BSG.L-1) factors were investigated by Response Surface Methodology (RSM) and Central Composite Design (CCD). Values ranging from 81.1 ± 2.0 to 290.1 ± 3.5 mL CH4.g-1 TVS were obtained according to operation temperature and substrate concentration variation. The most adverse condition for methanogenesis (81.1 ± 2.0 mL CH4.g-1 TVS) was at 59 °C and 14 g BSG.L-1, in which there was increase in the organic matter concentration from 173.6 ± 4.94 to 3036 ± 7.78 mg.L-1) result of a higher final concentration of volatile fatty acids (VFA, 2662.7 mg.L-1). On the other hand, the optimum condition predicted by the statistical model was at 35 °C and 18 g BSG.L-1 (289.1 mL CH4.g-1 TVS), which showed decrease in the organic matter concentration of 78.6% and a lower final concentration of VFA (533.2 mg.L-1). Hydrogenospora and Methanosaeta were identified in this optimum CH4 production condition, where acetoclastic methanogenic pathway prevailed. The CH4 production enhancement was concomitant to acetic acid concentration decrease (from 578.9 to 135.7 mg.L-1).
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Affiliation(s)
- Marina Mauro Gomes
- Laboratory of Biological Processes, Department of Hydraulics and Sanitation, São Carlos School of Engineering, University of São Paulo, Campus II, São Carlos, SP CEP, 13563-120, Brazil.
| | - Isabel Kimiko Sakamoto
- Laboratory of Biological Processes, Department of Hydraulics and Sanitation, São Carlos School of Engineering, University of São Paulo, Campus II, São Carlos, SP CEP, 13563-120, Brazil
| | - Camila Abreu B Silva Rabelo
- Laboratory of Biological Processes, Department of Hydraulics and Sanitation, São Carlos School of Engineering, University of São Paulo, Campus II, São Carlos, SP CEP, 13563-120, Brazil
| | - Edson Luiz Silva
- Center of Exact Sciences and Technology, Department of Chemical Engineering, Federal University of São Carlos, São Carlos, SP CEP, 13565-905, Brazil
| | - Maria Bernadete Amâncio Varesche
- Laboratory of Biological Processes, Department of Hydraulics and Sanitation, São Carlos School of Engineering, University of São Paulo, Campus II, São Carlos, SP CEP, 13563-120, Brazil.
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11
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Kang S, Khan S, Webb R, Denman S, McSweeney C. Characterization and survey in cattle of a rumen Pyrimadobacter sp. which degrades the plant toxin fluoroacetate. FEMS Microbiol Ecol 2020; 96:5827530. [PMID: 32353874 DOI: 10.1093/femsec/fiaa077] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 04/29/2020] [Indexed: 11/14/2022] Open
Abstract
Among the natural halogenic compounds, the plant toxin fluoroacetate (FA) causes livestock fatalities in southern hemisphere countries. Here, we report on the isolation of a rumen bacterium, strain C12-8 that degrades FA under anaerobic conditions. 16S rRNA gene sequence analysis showed this bacterium belonged to the Pyramidobacter genus within the Synergistetes phylum and was 98% similar to Pyramidobacter piscolens W5455 isolated from the human oral cavity. Transmission electron microscopy showed the cell envelope to be unusual, with only one membrane and no obvious external wall. Growth and FA degradation were enhanced by peptide-rich protein hydrolysates but not carbohydrates. End products of metabolism were mainly acetate, propionate/isovalerate and isobutyrate. Strain C12-8 preferentially used peptide-bound amino acids rather than free amino acids. Glycine, serine, threonine, leucine, histidine and isoleucine were utilized as free and peptide-bound amino acids, but there was minimal utilization of alanine, proline, methionine, aspartic acid, lysine and arginine in either form. A survey of several cattle properties in northern Australia showed that strain C12-8 and other FA degrading bacteria affiliated with Cloacibacillus porcorum strain MFA1 were endemic to cattle in the northern beef herd and may help to reduce toxicity.
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Affiliation(s)
- Seungha Kang
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, St. Lucia, QLD, Australia
| | - Shahjalal Khan
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, St. Lucia, QLD, Australia
| | - Rick Webb
- Centre for Microscopy and Microanalysis, University of Queensland, QLD, Australia
| | - Stuart Denman
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, St. Lucia, QLD, Australia
| | - Chris McSweeney
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, St. Lucia, QLD, Australia
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12
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McCracken BA, Nathalia Garcia M. Phylum Synergistetes in the oral cavity: A possible contributor to periodontal disease. Anaerobe 2020; 68:102250. [PMID: 32791127 DOI: 10.1016/j.anaerobe.2020.102250] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 07/27/2020] [Accepted: 07/28/2020] [Indexed: 12/13/2022]
Abstract
Microbial contributions to periodontal disease have been under renewed scrutiny with the advent of newer technologies to identify their presence and gene expression at the molecular level. Members of the phylum Synergistetes are some of the more recent bacteria to be associated with periodontal disease. Bacteria classified in this phylum can be found in a wide variety of habitats including both inside and outside of a mammalian host. Members of this phylum have been identified as part of the human microbiome. Indeed, many of the identified phylotypes have yet to be cultivated. Here we consider contributions of three named and formally described species to the oral microbial community and to pathogenesis of periodontal disease.
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Affiliation(s)
- Barbara Anne McCracken
- Section of Microbiology, Department of Growth, Development And Structure, 2800 College Ave., Alton, IL, 62002, USA.
| | - M Nathalia Garcia
- Southern Illinois University School of Dental Medicine, Alton, IL, 62002, USA
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13
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Assessment of the microbial interplay during anaerobic co-digestion of wastewater sludge using common components analysis. PLoS One 2020; 15:e0232324. [PMID: 32357180 PMCID: PMC7194399 DOI: 10.1371/journal.pone.0232324] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 04/12/2020] [Indexed: 12/29/2022] Open
Abstract
Anaerobic digestion (AD) is used to minimize solid waste while producing biogas by the action of microorganisms. To give an insight into the underlying microbial dynamics in anaerobic digesters, we investigated two different AD systems (wastewater sludge mixed with either fish or grass waste). The microbial activity was characterized by 16S RNA sequencing. 16S data is sparse and dispersed, and existent data analysis methods do not take into account this complexity nor the potential microbial interactions. In this line, we proposed a data pre-processing pipeline addressing these issues while not restricting only to the most abundant microorganisms. The data were analyzed by Common Components Analysis (CCA) to decipher the effect of substrate composition on the microorganisms. CCA results hinted the relationships between the microorganisms responding similarly to the AD physicochemical parameters. Thus, in overall, CCA allowed a better understanding of the inter-species interactions within microbial communities.
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14
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Shamurad B, Gray N, Petropoulos E, Tabraiz S, Sallis P. Improving the methane productivity of anaerobic digestion using aqueous extracts from municipal solid waste incinerator ash. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2020; 260:110160. [PMID: 32090847 DOI: 10.1016/j.jenvman.2020.110160] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 01/10/2020] [Accepted: 01/17/2020] [Indexed: 06/10/2023]
Abstract
This study investigated the effects of mineral waste extracts (MWE) on laboratory-scale two-stage anaerobic digesters treating synthetic organic waste. MWE was prepared as aqueous extracts from different ash samples (incineration bottom ash (IBA), fly ash (FA) and boiler ash (BA) taken from a municipal solid waste incineration plant. At 20 days hydraulic retention time, all three MWE stimulated hydrogen production in their respective acidogenic reactor by around 35% (c.f. control acidogenic reactor), whilst no difference was seen in the methane productivity of the linked methanogenic reactors (average 527 ± 45 mL CH4/g VS, including control methanogenic reactor). Following a step reduction in hydraulic retention time from 20 to 10 days and a doubling of the organic loading rate from 2.5 g to 5 g VS/L. d, no significant change was seen in hydrogen production (p > 0.05) in the acidogenic reactor amended with MWE from IBA and BA, or the control acidogenic reactor. However, the acidogenic reactor receiving MWE from FA had 45% lower hydrogen productivity. The step change in hydraulic retention time and organic loading rates led to the failure of most methanogenic reactors (≤100 mL CH4/g VS), however, the one receiving feed containing MWE from IBA showed stable performance without signs of failure, and had higher volumetric methane productivity, albeit at lower methane yields (370 ± 20 mL CH4/g VS). 16S rRNA analysis using the Illumina sequencing platform revealed acidogenesis by Lactobacillaceae in the acidogenic reactor and syntrophic acetate oxidation by Synergistaceae linked to enrichment of the candidatus genus Methanofastidiosum, in the stable methanogenic reactor receiving MWE from IBA.
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Affiliation(s)
- Burhan Shamurad
- School of Engineering, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK.
| | - Neil Gray
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | | | - Shamas Tabraiz
- School of Engineering, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Paul Sallis
- School of Engineering, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
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15
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Comparative Analysis of Bacterial and Archaeal Community Structure in Microwave Pretreated Thermophilic and Mesophilic Anaerobic Digesters Utilizing Mixed Sludge under Organic Overloading. WATER 2020. [DOI: 10.3390/w12030887] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The effects of microwave (MW) pretreatment were investigated by six anaerobic digesters operated under thermophilic and mesophilic conditions at high organic loading rates (4.9–5.7 g volatile solids/L/d). The experiments and analyses were mainly designed to reveal the impact of MW pretreatment and digester temperatures on the process stability and microbial community structure by correlating the composition of microbial populations with volatile fatty acid (VFA) concentrations. A slight shift from biogas production (with a reasonable methane content) to VFA accumulation was observed in the thermophilic digesters, especially in the MW-irradiated reactors. Microbial population structure was assessed using a high-throughput sequencing of 16S rRNA gene on the MiSeq platform. Microbial community structure was slightly affected by different MW pretreatment conditions, while substantially affected by the digester temperature. The phylum Bacteroidetes proliferated in the MW-irradiated mesophilic digesters by resisting high-temperature MW (at 160 °C). Hydrogenotrophic methanogenesis (mostly the genus of Methanothermobacter) was found to be a key route of methane production in the thermophilic digesters, whereas aceticlastic methanogenesis (mostly the genus of Methanosaeta) was the main pathway in the mesophilic digesters.
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16
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Han R, Zhu D, Xing J, Li Q, Li Y, Chen L. The effect of temperature fluctuation on the microbial diversity and community structure of rural household biogas digesters at Qinghai Plateau. Arch Microbiol 2019; 202:525-538. [PMID: 31712862 DOI: 10.1007/s00203-019-01767-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 10/27/2019] [Accepted: 10/31/2019] [Indexed: 01/04/2023]
Abstract
Seasonal temperature-fluctuation has been regarded as a key environmental factor affecting rural biogas fermentation yields. The present study investigated the impact of seasonal temperature-fluctuation on operating-temperatures and biogas production in rural household digesters at Qinghai Plateau and revealed the related changes in microbial diversity and community structure by 16S rRNA gene high-throughput sequencing (HTS) analysis. Our results showed closely positive correlation between operating-temperatures and biogas production. HTS analysis indicated the highest diversity for bacteria community in autumn (at highest operating-temperatures) and late winter (at lowest operating-temperatures) and for archaea community only in autumn. HTS analysis classified bacteria into 21 phyla and 346 genera with the most predominant phyla Firmicutes, Bacteroidetes and Proteobacteria (> 72.4% in total) and the most predominant genera Proteiniphilum, Clostridium sensustricto 1, Petrimonas, Pseudomonas and Fastidiosipila (37.09-38.61% in total). HTS analysis also revealed two main archaea orders (Methanomicrobiales and Methanobacteriales) and one predominant genus Methanogenium to support plateau biogas fermentation. Especially, a remarkable impact of temperature on the community abundances of bacteria phyla Synergistetes and archaea genera Methanogenium and Thermogymnomonas was observed, and such microbial community structure changes were positively consistent with the biogas production. The present work provided the first set of evidences to link temperature-controlled modulation of microbial community structure with rural household biogas production at Qinghai Plateau.
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Affiliation(s)
- Rui Han
- Qinghai Key Laboratory of Vegetable Genetics and Physiology, Academy of Agriculture and Forestry, Qinghai University, Ningda Road 253, Xining, Qinghai, 810016, China
| | - Derui Zhu
- Research Center of Basic Medical Sciences, Qinghai University Medical College, Xining, Qinghai, 810006, China.
| | - Jiangwa Xing
- Research Center of Basic Medical Sciences, Qinghai University Medical College, Xining, Qinghai, 810006, China
| | - Quanhui Li
- Qinghai Key Laboratory of Vegetable Genetics and Physiology, Academy of Agriculture and Forestry, Qinghai University, Ningda Road 253, Xining, Qinghai, 810016, China
| | - Yi Li
- Qinghai Key Laboratory of Vegetable Genetics and Physiology, Academy of Agriculture and Forestry, Qinghai University, Ningda Road 253, Xining, Qinghai, 810016, China
| | - Laisheng Chen
- Qinghai Key Laboratory of Vegetable Genetics and Physiology, Academy of Agriculture and Forestry, Qinghai University, Ningda Road 253, Xining, Qinghai, 810016, China.
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17
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Hupfauf S, Plattner P, Wagner AO, Kaufmann R, Insam H, Podmirseg SM. Temperature shapes the microbiota in anaerobic digestion and drives efficiency to a maximum at 45 °C. BIORESOURCE TECHNOLOGY 2018; 269:309-318. [PMID: 30195223 DOI: 10.1016/j.biortech.2018.08.106] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 08/24/2018] [Accepted: 08/25/2018] [Indexed: 06/08/2023]
Abstract
Throwing longstanding habits over the pile may be necessary to improve biogas production, in particular when it comes to the process temperature. Its effect on biogas production was investigated with lab-scale reactors operated in fed-batch mode (cattle slurry and maize straw) at 10-55 °C over six months. Biochemical and microbial changes were comprehensively investigated. Production was highest and most efficient at 45 °C with an average methane yield of 166 NL kg-1 VS, and thus 12.8% and 9.6% higher than at 37 and 55 °C. Temperature significantly affected the microbiota and higher temperature provoked a shift from Bacteroidetes/Proteobacteria to Firmicutes. A transition from hydrogenotrophic to acetoclastic methanogenesis was observed from 10 to 45 °C, while the trend was reversed at 55 °C. The results contest the textbook notion of preferred and most efficient temperatures for AD and suggest reconsideration of the temperature range around 45 °C for efficient manure-based co-fermentation.
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Affiliation(s)
- Sebastian Hupfauf
- Institut für Mikrobiologie, Universität Innsbruck, Technikerstraße 25d, 6020 Innsbruck, Austria.
| | - Pia Plattner
- Institut für Mikrobiologie, Universität Innsbruck, Technikerstraße 25d, 6020 Innsbruck, Austria
| | - Andreas Otto Wagner
- Institut für Mikrobiologie, Universität Innsbruck, Technikerstraße 25d, 6020 Innsbruck, Austria
| | - Rüdiger Kaufmann
- Institut für Ökologie, Universität Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria
| | - Heribert Insam
- Institut für Mikrobiologie, Universität Innsbruck, Technikerstraße 25d, 6020 Innsbruck, Austria
| | - Sabine Marie Podmirseg
- Institut für Mikrobiologie, Universität Innsbruck, Technikerstraße 25d, 6020 Innsbruck, Austria
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18
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Keating C, Hughes D, Mahony T, Cysneiros D, Ijaz UZ, Smith CJ, O'Flaherty V. Cold adaptation and replicable microbial community development during long-term low-temperature anaerobic digestion treatment of synthetic sewage. FEMS Microbiol Ecol 2018; 94:5004848. [PMID: 29846574 PMCID: PMC5995215 DOI: 10.1093/femsec/fiy095] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 05/24/2018] [Indexed: 11/12/2022] Open
Abstract
The development and activity of a cold-adapting microbial community was monitored during low-temperature anaerobic digestion (LtAD) treatment of wastewater. Two replicate hybrid anaerobic sludge bed-fixed-film reactors treated a synthetic sewage wastewater at 12°C, at organic loading rates of 0.25-1.0 kg chemical oxygen demand (COD) m-3 d-1, over 889 days. The inoculum was obtained from a full-scale anaerobic digestion reactor, which was operated at 37°C. Both LtAD reactors readily degraded the influent with COD removal efficiencies regularly exceeding 78% for both the total and soluble COD fractions. The biomass from both reactors was sampled temporally and tested for activity against hydrolytic and methanogenic substrates at 12°C and 37°C. Data indicated that significantly enhanced low-temperature hydrolytic and methanogenic activity developed in both systems. For example, the hydrolysis rate constant (k) at 12°C had increased 20-30-fold by comparison to the inoculum by day 500. Substrate affinity also increased for hydrolytic substrates at low temperature. Next generation sequencing demonstrated that a shift in a community structure occurred over the trial, involving a 1-log-fold change in 25 SEQS (OTU-free approach) from the inoculum. Microbial community structure changes and process performance were replicable in the LtAD reactors.
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Affiliation(s)
- C Keating
- Microbiology, School of Natural Sciences and Ryan Institute, National University of Ireland, Galway, Ireland
| | - D Hughes
- Microbiology, School of Natural Sciences and Ryan Institute, National University of Ireland, Galway, Ireland
| | - T Mahony
- Microbiology, School of Natural Sciences and Ryan Institute, National University of Ireland, Galway, Ireland
| | - D Cysneiros
- Microbiology, School of Natural Sciences and Ryan Institute, National University of Ireland, Galway, Ireland
| | - U Z Ijaz
- Infrastructure and Environment, School of Engineering, University of Glasgow, Rankine Building, 79-85 Oakfield Avenue, Glasgow, G12 8LT, UK
| | - C J Smith
- Microbiology, School of Natural Sciences and Ryan Institute, National University of Ireland, Galway, Ireland
| | - V O'Flaherty
- Microbiology, School of Natural Sciences and Ryan Institute, National University of Ireland, Galway, Ireland
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19
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Durán F, Zamorano-López N, Barat R, Ferrer J, Aguado D. Understanding the performance of an AnMBR treating urban wastewater and food waste via model simulation and characterization of the microbial population dynamics. Process Biochem 2018. [DOI: 10.1016/j.procbio.2018.02.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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20
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de Lima e Silva MR, Correa RC, Sakamoto IK, Varesche MBA. Microbial Characterization of Methanogenic and Iron-reducing Consortium in Reactors with Polychlorinated Biphenyls. Curr Microbiol 2018; 75:666-676. [DOI: 10.1007/s00284-018-1431-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 01/03/2018] [Indexed: 10/18/2022]
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21
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Díaz-Cárdenas C, López G, Alzate-Ocampo JD, González LN, Shapiro N, Woyke T, Kyrpides NC, Restrepo S, Baena S. Draft genome sequence of Dethiosulfovibrio salsuginis DSM 21565 T an anaerobic, slightly halophilic bacterium isolated from a Colombian saline spring. Stand Genomic Sci 2017; 12:86. [PMID: 29276571 PMCID: PMC5738826 DOI: 10.1186/s40793-017-0303-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 12/05/2017] [Indexed: 11/10/2022] Open
Abstract
A bacterium belonging to the phylum Synergistetes, genus Dethiosulfovibrio was isolated in 2007 from a saline spring in Colombia. Dethiosulfovibrio salsuginis USBA 82T (DSM 21565T= KCTC 5659T) is a mesophilic, strictly anaerobic, slightly halophilic, Gram negative bacterium with a diderm cell envelope. The strain ferments peptides, amino acids and a few organic acids. Here we present the description of the complete genome sequencing and annotation of the type species Dethiosulfovibrio salsuginis USBA 82T. The genome consisted of 2.68 Mbp with a 53.7% G + C. A total of 2609 genes were predicted and of those, 2543 were protein coding genes and 66 were RNA genes. We detected in USBA 82T genome six Synergistetes conserved signature indels (CSIs), specific for Jonquetella, Pyramidobacter and Dethiosulfovibrio. The genome of D. salsuginis contained, as expected, genes related to amino acid transport, amino acid metabolism and thiosulfate reduction. These genes represent the major gene groups of Synergistetes, related with their phenotypic traits, and interestingly, 11.8% of the genes in the genome belonged to the amino acid fermentation COG category. In addition, we identified in the genome some ammonification genes such as nitrate reductase genes. The presence of proline operon genes could be related to de novo synthesis of proline to protect the cell in response to high osmolarity. Our bioinformatics workflow included antiSMASH and BAGEL3 which allowed us to identify bacteriocins genes in the genome.
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Affiliation(s)
- Carolina Díaz-Cárdenas
- Unidad de Saneamiento y Biotecnología Ambiental, Departamento de Biología, Pontificia Universidad Javeriana, POB 56710, Bogotá, DC Colombia
| | - Gina López
- Unidad de Saneamiento y Biotecnología Ambiental, Departamento de Biología, Pontificia Universidad Javeriana, POB 56710, Bogotá, DC Colombia
| | | | - Laura N González
- Biological Sciences Department, Universidad de los Andes, Cra 1 No. 18A-12, Bogotá, DC Colombia
| | - Nicole Shapiro
- Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - Tanja Woyke
- Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - Nikos C Kyrpides
- Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - Silvia Restrepo
- Biological Sciences Department, Universidad de los Andes, Cra 1 No. 18A-12, Bogotá, DC Colombia
| | - Sandra Baena
- Unidad de Saneamiento y Biotecnología Ambiental, Departamento de Biología, Pontificia Universidad Javeriana, POB 56710, Bogotá, DC Colombia
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22
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Shiffman ME, Soo RM, Dennis PG, Morrison M, Tyson GW, Hugenholtz P. Gene and genome-centric analyses of koala and wombat fecal microbiomes point to metabolic specialization for Eucalyptus digestion. PeerJ 2017; 5:e4075. [PMID: 29177117 PMCID: PMC5697889 DOI: 10.7717/peerj.4075] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 10/31/2017] [Indexed: 01/09/2023] Open
Abstract
The koala has evolved to become a specialist Eucalyptus herbivore since diverging from its closest relative, the wombat, a generalist herbivore. This niche adaptation involves, in part, changes in the gut microbiota. The goal of this study was to compare koala and wombat fecal microbiomes using metagenomics to identify potential differences attributable to dietary specialization. Several populations discriminated between the koala and wombat fecal communities, most notably S24-7 and Synergistaceae in the koala, and Christensenellaceae and RF39 in the wombat. As expected for herbivores, both communities contained the genes necessary for lignocellulose degradation and urea recycling partitioned and redundantly encoded across multiple populations. Secondary metabolism was overrepresented in the koala fecal samples, consistent with the need to process Eucalyptus secondary metabolites. The Synergistaceae population encodes multiple pathways potentially relevant to Eucalyptus compound metabolism, and is predicted to be a key player in detoxification of the koala's diet. Notably, characterized microbial isolates from the koala gut appear to be minor constituents of this habitat, and the metagenomes provide the opportunity for genome-directed isolation of more representative populations. Metagenomic analysis of other obligate and facultative Eucalyptus folivores will reveal whether putatively detoxifying bacteria identified in the koala are shared across these marsupials.
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Affiliation(s)
- Miriam E. Shiffman
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Rochelle M. Soo
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Paul G. Dennis
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, Australia
| | - Mark Morrison
- The University of Queensland Diamantina Institute, Translational Research Institute, The University of Queensland, Brisbane, Australia
| | - Gene W. Tyson
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
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23
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Zhang L, Chung J, Jiang Q, Sun R, Zhang J, Zhong Y, Ren N. Characteristics of rumen microorganisms involved in anaerobic degradation of cellulose at various pH values. RSC Adv 2017. [DOI: 10.1039/c7ra06588d] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Microbial degradation of straw, the main by-product of agricultural production, has proved to be the most economical and effective means of producing hydrogen.
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Affiliation(s)
- Lu Zhang
- State Key Laboratory of Urban Water Resource and Environment
- School of Municipal and Environmental Engineering
- Harbin Institute of Technology
- Harbin 150090
- China
| | - Jongshik Chung
- State Key Laboratory of Urban Water Resource and Environment
- School of Municipal and Environmental Engineering
- Harbin Institute of Technology
- Harbin 150090
- China
| | - Qingqing Jiang
- State Key Laboratory of Urban Water Resource and Environment
- School of Municipal and Environmental Engineering
- Harbin Institute of Technology
- Harbin 150090
- China
| | - Rui Sun
- State Key Laboratory of Urban Water Resource and Environment
- School of Municipal and Environmental Engineering
- Harbin Institute of Technology
- Harbin 150090
- China
| | - Jian Zhang
- Shenzhen Greenster Environmental Technology Co., Ltd
- Shenzhen 518055
- China
| | - Yingjuan Zhong
- Shenzhen Greenster Environmental Technology Co., Ltd
- Shenzhen 518055
- China
| | - Nanqi Ren
- State Key Laboratory of Urban Water Resource and Environment
- School of Municipal and Environmental Engineering
- Harbin Institute of Technology
- Harbin 150090
- China
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24
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Motteran F, Braga JK, Silva EL, Varesche MBA. Kinetics of methane production and biodegradation of linear alkylbenzene sulfonate from laundry wastewater. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART A, TOXIC/HAZARDOUS SUBSTANCES & ENVIRONMENTAL ENGINEERING 2016; 51:1288-1302. [PMID: 27533507 DOI: 10.1080/10934529.2016.1215197] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
This study evaluates the kinetics of methane production and degradation of standard linear alkylbenzene sulfonate (LAS) (50 ± 3.5 mg/L) and LAS from laundry wastewater (85 ± 2.1 mg/L) in anaerobic batch reactors at 30°C with different sources of inoculum. The inocula were obtained by auto-fermentation (AFM) and UASB reactors from wastewater treatment of poultry slaughterhouse (SGH), swine production (SWT) and wastewater treatment thermophilic of sugarcane industry (THR). The study was divided into three phases: synthetic substrate (Phase I), standard LAS (Phase II) and LAS from laundry wastewater (Phase III). For SGH, the highest values for cumulative methane productions (1,844.8 ± 149 µmol-Phase II), methane production rate (70.8 ± 88 µmol/h-Phase II and 4.01 ± 07 µmol/h-Phase III) were observed. The use of thermophilic biomass (THR) incubated at 30°C was not favorable for methane production and LAS biodegradation, but the highest kinetic coefficient degradation (k1app) was obtained for LAS (0.33 ± 0.3 h) compared with mesophilic biomass (SGH and SWT) (0.13 ± 0.02 h). Therefore, both LAS sources influenced the kinetics of methane production and organic matter degradation. For SGH, inoculum obtained the highest LAS degradation. In the SGH inoculum sequenced by MiSeq-Illumina was identified genera (VadinCA02, Candidatus Cloacamonas, VadinHB04, PD-UASB-13) related to degrade toxic compounds. Therefore, it recommended the reactor mesophilic inoculum UASB (SGH) for the LAS degradation.
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Affiliation(s)
- Fabrício Motteran
- a Department of Hydraulics and Sanitation , School of Engineering of São Carlos, University of São Paulo , São Carlos, São Paulo , Brazil
| | - Juliana K Braga
- a Department of Hydraulics and Sanitation , School of Engineering of São Carlos, University of São Paulo , São Carlos, São Paulo , Brazil
| | - Edson L Silva
- b Department of Chemical Engineering , Federal University of São Carlos , São Carlos, São Paulo , Brazil
| | - Maria Bernadete A Varesche
- a Department of Hydraulics and Sanitation , School of Engineering of São Carlos, University of São Paulo , São Carlos, São Paulo , Brazil
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25
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Weiß S, Somitsch W, Klymiuk I, Trajanoski S, Guebitz GM. Comparison of biogas sludge and raw crop material as source of hydrolytic cultures for anaerobic digestion. BIORESOURCE TECHNOLOGY 2016; 207:244-251. [PMID: 26894564 DOI: 10.1016/j.biortech.2016.01.137] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 01/29/2016] [Accepted: 01/31/2016] [Indexed: 06/05/2023]
Abstract
Mixed fermentative/hydrolytic bacteria were enriched on lignocellulose substrates in minimal medium under semi-anaerobic mesophilic conditions in the presence or absence of natural zeolite as growth supporter to ultimately bioaugment non-adapted sludge and thereby enhance the overall anaerobic digestion (AD) of recalcitrant plant material. Desired enzyme activities, i.e. xylanases and cellulase were monitored during subsequent cultivation cycles. Furthermore, enriched microbial communities were characterized by 16S rRNA-based 454-Pyrosequencing, revealing Firmicutes, Bacteriodetes, Proteobacteria and Spirochaetes to be the predominant bacterial groups in cultures derived from anaerobic sludge and raw crop material, i.e. maple green cut and wheat straw as well. Enriched populations relevant for biopolymer hydrolysis were then compared in biological methane potential tests to demonstrate positive effects on the biogasification of renewable plant substrate material. A significant impact on methane productivity was observed with adapted mixed cultures when used in combination with clinoptilolite to augment and supplement non-adapted bioreactor sludge.
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Affiliation(s)
- Stefan Weiß
- Austrian Centre of Industrial Biotechnology, Petersgasse 14/5, A-8010 Graz, Austria.
| | - Walter Somitsch
- Engineering Consultant, Wiedner Hauptstrasse 90/2/19, A-1050 Vienna, Austria; IPUS Mineral- und Umwelttechnologie GmbH, Werksgasse 281, A-8786 Rottenmann, Austria
| | - Ingeborg Klymiuk
- Medical University of Graz, Centre for Medical Research, Core Facility Molecular Biology, Stiftingtalstraße 24, A-8010 Graz, Austria
| | - Slave Trajanoski
- Medical University of Graz, Centre for Medical Research, Core Facility Computational Bioanalytics, Bioinformatics, Stiftingtalstraße 24, A-8010 Graz, Austria
| | - Georg M Guebitz
- Austrian Centre of Industrial Biotechnology, Petersgasse 14/5, A-8010 Graz, Austria; University of Natural Resources and Life Sciences, Institute of Environmental Biotechnology, Konrad Lorenz Strasse 20, A-3430 Tulln, Austria
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26
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Leong LEX, Denman SE, Hugenholtz P, McSweeney CS. Amino Acid and Peptide Utilization Profiles of the Fluoroacetate-Degrading Bacterium Synergistetes Strain MFA1 Under Varying Conditions. MICROBIAL ECOLOGY 2016; 71:494-504. [PMID: 26111963 DOI: 10.1007/s00248-015-0641-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2015] [Accepted: 06/10/2015] [Indexed: 05/08/2023]
Abstract
Synergistetes strain MFA1 is an asaccharolytic ruminal bacterium isolated based on its ability to degrade fluoroacetate, a plant toxin. The amino acid and peptide requirements of the bacterium were investigated under different culturing conditions. The growth of strain MFA1 and its fluoroacetate degradation rate were enhanced by peptide-rich protein hydrolysates (tryptone and yeast extract) compared to casamino acid, an amino acid-rich protein hydrolysate. Complete utilization and preference for arginine, asparagine, glutamate, glycine, and histidine as free amino acids from yeast extract were observed, while the utilization of serine, threonine, and lysine in free form and peptide-bound glutamate was stimulated during growth on fluoroacetate. A predominant peptide in yeast extract preferentially utilized by strain MFA1 was partially characterized by high-liquid performance chromatography-mass spectrometry as a hepta-glutamate oligopeptide. Similar utilization profiles of amino acids were observed between the co-culture of strain MFA1 with Methanobrevibacter smithii without fluoroacetate and pure strain MFA1 culture with fluoroacetate. This suggests that growth of strain MFA1 could be enhanced by a reduction of hydrogen partial pressure as a result of hydrogen removal by a methanogen or reduction of fluoroacetate.
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Affiliation(s)
- Lex E X Leong
- CSIRO Agriculture, St Lucia, QLD, 4067, Australia
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, 4072, Australia
- Infection and Immunity, South Australian Health and Medical Research Institute, Flinders University, Bedford Park, SA, 5042, Australia
| | | | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, 4072, Australia
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27
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Luo F, Devine CE, Edwards EA. Cultivating microbial dark matter in benzene-degrading methanogenic consortia. Environ Microbiol 2015; 18:2923-36. [PMID: 26549712 DOI: 10.1111/1462-2920.13121] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 10/26/2015] [Accepted: 11/02/2015] [Indexed: 11/27/2022]
Abstract
The microbes responsible for anaerobic benzene biodegradation remain poorly characterized. In this study, we identified and quantified microbial populations in a series of 16 distinct methanogenic, benzene-degrading enrichment cultures using a combination of traditional 16S rRNA clone libraries (four cultures), pyrotag 16S rRNA amplicon sequencing (11 cultures), metagenome sequencing (1 culture) and quantitative polymerase chain reaction (qPCR; 12 cultures). An operational taxonomic unit (OTU) from the Deltaproteobacteria designated ORM2 that is only 84% to 86% similar to Syntrophus or Desulfobacterium spp. was consistently identified in all enrichment cultures, and typically comprised more than half of the bacterial sequences. In addition to ORM2, a sequence belonging to Parcubacteria (candidate division OD1) identified from the metagenome data was the only other OTU common to all the cultures surveyed. Culture transfers (1% and 0.1%) were made in the presence and absence of benzene, and the abundance of ORM2, OD1 and other OTUs was tracked over 415 days using qPCR. ORM2 sequence abundance increased only when benzene was present, while the abundance of OD1 and other OTUs increased even in the absence of benzene. Deltaproteobacterium ORM2 is unequivocally the benzene-metabolizing population. This study also hints at laboratory cultivation conditions for a member of the widely distributed yet uncultivated Parcubacteria (OD1).
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Affiliation(s)
- Fei Luo
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON, M5S 3E5, Canada
| | - Cheryl E Devine
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON, M5S 3E5, Canada
| | - Elizabeth A Edwards
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON, M5S 3E5, Canada. .,Department of Cell and System Biology, University of Toronto, 26 Harbord Street, Toronto, ON, M5S 3G5, Canada.
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28
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Militon C, Hamdi O, Michotey V, Fardeau ML, Ollivier B, Bouallagui H, Hamdi M, Bonin P. Ecological significance of Synergistetes in the biological treatment of tuna cooking wastewater by an anaerobic sequencing batch reactor. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:18230-18238. [PMID: 26194235 DOI: 10.1007/s11356-015-4973-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 06/29/2015] [Indexed: 06/04/2023]
Abstract
Lab-scale 2L-anaerobic sequencing batch reactor was operated under mesothermic conditions. The degradation of protein-rich organic matter was determined by chemical oxygen demand, biogas production, and protein-removal activity over the operation. The structure of the microbial community was determined by qPCR and next-generation sequencing on 16S rRNA genes. At the steady state, a very efficient removal of protein (92%) was observed. Our results demonstrate a decrease of archaeal and bacterial abundance over time. Members of the phylum Synergistetes, with a peculiar emphasis for those pertaining to families Dethiosulfovibrionaceae and Aminiphilaceae, are of major ecological significance regarding the treatment of this industrial wastewater. The prominent role to be played by members of the phylum Synergistetes regarding protein and/or amino acid degradation is discussed.
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Affiliation(s)
- Cécile Militon
- Aix Marseille Université, CNRS, Université de Toulon, IRD, MIO UM 110, 13288, Marseille, France
| | - Olfa Hamdi
- Aix Marseille Université, CNRS, Université de Toulon, IRD, MIO UM 110, 13288, Marseille, France
- Laboratoire d'écologie et biotechnologie microbienne, Institut National des Sciences Appliquées, Université de Carthage, Centre Urbain Nord, BP 676, 1080, Tunis Cedex, Tunisie
| | - Valerie Michotey
- Aix Marseille Université, CNRS, Université de Toulon, IRD, MIO UM 110, 13288, Marseille, France
| | - Marie-Laure Fardeau
- Aix Marseille Université, CNRS, Université de Toulon, IRD, MIO UM 110, 13288, Marseille, France
| | - Bernard Ollivier
- Aix Marseille Université, CNRS, Université de Toulon, IRD, MIO UM 110, 13288, Marseille, France
| | - Hassib Bouallagui
- Laboratoire d'écologie et biotechnologie microbienne, Institut National des Sciences Appliquées, Université de Carthage, Centre Urbain Nord, BP 676, 1080, Tunis Cedex, Tunisie
| | - Moktar Hamdi
- Laboratoire d'écologie et biotechnologie microbienne, Institut National des Sciences Appliquées, Université de Carthage, Centre Urbain Nord, BP 676, 1080, Tunis Cedex, Tunisie
| | - Patricia Bonin
- Aix Marseille Université, CNRS, Université de Toulon, IRD, MIO UM 110, 13288, Marseille, France.
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29
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Suzuki S, Shintani M, Sanchez ZK, Kimura K, Numata M, Yamazoe A, Kimbara K. Effects of phosphate addition on methane fermentation in the batch and upflow anaerobic sludge blanket (UASB) reactors. Appl Microbiol Biotechnol 2015; 99:10457-66. [PMID: 26350145 DOI: 10.1007/s00253-015-6942-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 08/15/2015] [Indexed: 11/28/2022]
Abstract
Ammonia inhibition of methane fermentation is one of the leading causes of failure of anaerobic digestion reactors. In a batch anaerobic digestion reactor with 429 mM NH3-N/L of ammonia, the addition of 25 mM phosphate resulted in an increase in methane production rate. Similar results were obtained with the addition of disodium phosphate in continuous anaerobic digestion using an upflow anaerobic sludge blanket (UASB) reactor. While methane content and production rate decreased in the presence of more than 143 mM NH3-N/L of ammonium chloride in UASB, the addition of 5 mM disodium phosphate suppressed ammonia inhibition at 214 mM NH3-N/L of ammonium chloride. The addition prevented acetate/propionate accumulation, which might be one of the effects of the phosphate on the ammonia inhibition. The effects on the microbial community in the UASB reactor was also assessed, which was composed of Bacteria involved in hydrolysis, acidogenesis, acetogenesis, and dehydrogenation, as well as Archaea carrying out methanogenesis. The change in the microbial community was observed by ammonia inhibition and the addition of phosphate. The change indicates that the suppression of ammonia inhibition by disodium phosphate addition could stimulate the activity of methanogens, reduce shift in bacterial community, and enhance hydrogen-producing bacteria. The addition of phosphate will be an important treatment for future studies of methane fermentation.
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Affiliation(s)
- Sho Suzuki
- Applied Chemistry and Biochemical Engineering Course, Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu, 432-8561, Shizuoka, Japan
| | - Masaki Shintani
- Applied Chemistry and Biochemical Engineering Course, Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu, 432-8561, Shizuoka, Japan
| | - Zoe Kuizon Sanchez
- Applied Chemistry and Biochemical Engineering Course, Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu, 432-8561, Shizuoka, Japan
| | - Kohei Kimura
- Applied Chemistry and Biochemical Engineering Course, Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu, 432-8561, Shizuoka, Japan
| | - Mitsuru Numata
- NITE Biological Resource Center, National Institute of Technology and Evaluation, 2-49-10, Nishihara, Shibuya-ku, Tokyo, 151-0066, Japan
| | - Atsushi Yamazoe
- NITE Biological Resource Center, National Institute of Technology and Evaluation, 2-49-10, Nishihara, Shibuya-ku, Tokyo, 151-0066, Japan
| | - Kazuhide Kimbara
- Applied Chemistry and Biochemical Engineering Course, Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu, 432-8561, Shizuoka, Japan.
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30
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Jumas-Bilak E, Bouvet P, Allen-Vercoe E, Aujoulat F, Lawson PA, Jean-Pierre H, Marchandin H. Rarimicrobium hominis gen. nov., sp. nov., representing the fifth genus in the phylum Synergistetes that includes human clinical isolates. Int J Syst Evol Microbiol 2015; 65:3965-3970. [PMID: 26320053 DOI: 10.1099/ijsem.0.000520] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Five human clinical isolates of an unknown, strictly anaerobic, slow-growing, Gram-stain-negative, rod-shaped micro-organism were subjected to a polyphasic taxonomic study. Comparative 16S rRNA gene sequence-based phylogeny showed that the isolates grouped in a clade that included members of the genera Pyramidobacter, Jonquetella, and Dethiosulfovibrio; the type strain of Pyramidobacter piscolens was the closest relative with 91.5-91.7 % 16S rRNA gene sequence similarity. The novel strains were mainly asaccharolytic and unreactive in most conventional biochemical tests. Major metabolic end products in trypticase/glucose/yeast extract broth were acetic acid and propionic acid and the major cellular fatty acids were C13 : 0 and C16 : 0, each of which could be used to differentiate the strains from P. piscolens. The DNA G+C content based on whole genome sequencing for the reference strain 22-5-S 12D6FAA was 57 mol%. Based on these data, a new genus, Rarimicrobium gen. nov., is proposed with one novel species, Rarimicrobium hominis sp. nov., named after the exclusive and rare finding of the taxon in human samples. Rarimicrobium is the fifth genus of the 14 currently characterized in the phylum Synergistetes and the third one in subdivision B that includes human isolates. The type strain of Rarimicrobium hominis is ADV70T ( = LMG 28163T = CCUG 65426T).
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Affiliation(s)
- Estelle Jumas-Bilak
- Université de Montpellier, Unité Mixte de Recherche 5569 - Hydrosciences Montpellier, Equipe Pathogènes Hydriques Santé Environnements, Unité de Bactériologie, Faculté de Pharmacie, 15, Avenue Charles Flahault, BP 14491, 34093 Montpellier Cedex 5, France.,Centre Hospitalier Universitaire de Montpellier, Laboratoire d'Hygiène Hospitalière, 778 rue de la croix verte, 34295 Montpellier Cedex 5, France
| | - Philippe Bouvet
- Institut Pasteur, Centre National de Référence des Bactéries Anaérobies et du Botulisme, 25 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Emma Allen-Vercoe
- Molecular and Cellular Biology, University of Guelph, 50 Stone Road East, Guelph, Ontario, N1G 2W1, Canada
| | - Fabien Aujoulat
- Université de Montpellier, Unité Mixte de Recherche 5569 - Hydrosciences Montpellier, Equipe Pathogènes Hydriques Santé Environnements, Unité de Bactériologie, Faculté de Pharmacie, 15, Avenue Charles Flahault, BP 14491, 34093 Montpellier Cedex 5, France
| | - Paul A Lawson
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Hélène Jean-Pierre
- Université de Montpellier, Unité Mixte de Recherche 5569 - Hydrosciences Montpellier, Equipe Pathogènes Hydriques Santé Environnements, Unité de Bactériologie, Faculté de Pharmacie, 15, Avenue Charles Flahault, BP 14491, 34093 Montpellier Cedex 5, France.,Centre Hospitalier Universitaire de Montpellier, Hôpital Arnaud de Villeneuve, Laboratoire de Bactériologie, 371 Avenue du Doyen Gaston Giraud, 34295 Montpellier Cedex 5, France
| | - Hélène Marchandin
- Centre Hospitalier Universitaire de Montpellier, Hôpital Arnaud de Villeneuve, Laboratoire de Bactériologie, 371 Avenue du Doyen Gaston Giraud, 34295 Montpellier Cedex 5, France.,Université de Montpellier, Unité Mixte de Recherche 5569 - Hydrosciences Montpellier, Equipe Pathogènes Hydriques Santé Environnements, Unité de Bactériologie, Faculté de Pharmacie, 15, Avenue Charles Flahault, BP 14491, 34093 Montpellier Cedex 5, France
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31
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Cloacibacillus sp., a Potential Human Pathogen Associated with Bacteremia in Quebec and New Brunswick. J Clin Microbiol 2015. [PMID: 26224843 DOI: 10.1128/jcm.01137-15] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacteremia due to Cloacibacillus species is poorly described. We present three cases involving either Cloacibacillus evryensis or Cloacibacillus porcorum. The isolates were identified by 16S rRNA gene sequencing and were susceptible to antibiotics commonly used for anaerobic infections. The clinical significance of these organisms as potential emerging pathogens is discussed.
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32
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Braun F, Hamelin J, Bonnafous A, Delgenès N, Steyer JP, Patureau D. Similar PAH fate in anaerobic digesters inoculated with three microbial communities accumulating either volatile fatty acids or methane. PLoS One 2015; 10:e0125552. [PMID: 25874750 PMCID: PMC4398385 DOI: 10.1371/journal.pone.0125552] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 03/25/2015] [Indexed: 02/01/2023] Open
Abstract
Urban sludge produced on wastewater treatment plants are often contaminated by organic pollutants such as polycyclic aromatic hydrocarbons (PAH). Their removal under methanogenic conditions was already reported, but the factors influencing this removal remain unclear. Here, we determined the influence of microbial communities on PAH removal under controlled physico-chemical conditions. Twelve mesophilic anaerobic digesters were inoculated with three microbial communities extracted from ecosystems with contrasting pollution histories: a PAH contaminated soil, a PCB contaminated sediment and a low contaminated anaerobic sludge. These anaerobic digesters were operated during 100 days in continuous mode. A sterilised activated sludge, spiked with 13 PAH at concentrations usually encountered in full-scale wastewater treatment plants, was used as substrate. The dry matter and volatile solid degradation, the biogas production rate and composition, the volatile fatty acids (VFA) production and the PAH removals were monitored. Bacterial and archaeal communities were compared in abundance (qPCR), in community structure (SSCP fingerprinting) and in dominant microbial species (454-pyrosequencing). The bioreactors inoculated with the community extracted from low contaminated anaerobic sludge showed the greater methane production. The PAH removals ranged from 10 % to 30 %, respectively, for high and low molecular weight PAH, whatever the inoculums tested, and were highly correlated with the dry matter and volatile solid removals. The microbial community structure and diversity differed with the inoculum source; this difference was maintained after the 100 days of digestion. However, the PAH removal was not correlated to these diverse structures and diversities. We hence obtained three functional stable consortia with two contrasted metabolic activities, and three different pictures of microbial diversity, but similar PAH and matter removals. These results confirm that PAH removal depends on the molecule type and on the solid matter removal. But, as PAH elimination is similar whether the solid substrate is degraded into VFA or into methane, it seems that the fermentative communities are responsible for their elimination.
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Affiliation(s)
- Florence Braun
- INRA, UR0050, Laboratoire de Biotechnologie de l’Environnement, Avenue des Etangs, Narbonne, F-11100, France
- ADEME, French Environment and Energy Management Agency, 20 avenue du Grésillé-BP 90406, F-49004, Angers, Cedex 01, France
| | - Jérôme Hamelin
- INRA, UR0050, Laboratoire de Biotechnologie de l’Environnement, Avenue des Etangs, Narbonne, F-11100, France
| | - Anaïs Bonnafous
- INRA, UR0050, Laboratoire de Biotechnologie de l’Environnement, Avenue des Etangs, Narbonne, F-11100, France
| | - Nadine Delgenès
- INRA, UR0050, Laboratoire de Biotechnologie de l’Environnement, Avenue des Etangs, Narbonne, F-11100, France
| | - Jean-Philippe Steyer
- INRA, UR0050, Laboratoire de Biotechnologie de l’Environnement, Avenue des Etangs, Narbonne, F-11100, France
| | - Dominique Patureau
- INRA, UR0050, Laboratoire de Biotechnologie de l’Environnement, Avenue des Etangs, Narbonne, F-11100, France
- * E-mail:
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Hamdi O, Ben Hania W, Postec A, Bouallagui H, Hamdi M, Bonin P, Ollivier B, Fardeau ML. Aminobacterium thunnarium sp. nov., a mesophilic, amino acid-degrading bacterium isolated from an anaerobic sludge digester, pertaining to the phylum Synergistetes. Int J Syst Evol Microbiol 2015; 65:609-614. [DOI: 10.1099/ijs.0.068965-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A new Gram-staining-positive, non-sporulating, mesophilic, amino acid-degrading anaerobic bacterium, designated strain OTA 102T, was isolated from an anaerobic sequencing batch reactor treating wastewater from cooking tuna. The cells were curved rods (0.6–2.5×0.5 µm) and occurred singly or in pairs. The strain was motile by means of one lateral flagellum. Strain OTA 102T grew at temperatures between 30 and 45 °C (optimum 40 °C), between pH 6.0 and 8.4 (optimum pH 7.2) and NaCl concentrations between 1 and 5 % (optimum 2 %, w/v). Strain OTA 102T required yeast extract for growth. Serine, threonine, glycine, cysteine, citrate, fumarate, α-ketoglutarate and pyruvate were fermented. When co-cultured with
Methanobacterium formicicum
as the hydrogen scavenger, strain OTA 102T oxidized alanine, valine, leucine, isoleucine, aspartate, tyrosine, methionine, histidine and asparagine. The genomic DNA G+C content of strain OTA 102T was 41.7 mol%. The main fatty acid was iso-C15 : 0. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain OTA 102T was related to
Aminobacterium colombiense
and
Aminobacterium mobile
(95.5 and 95.2 % similarity, respectively), of the phylum
Synergistetes
. On the basis of phylogenetic, genetic and physiological characteristics, strain OTA 102T is proposed to represent a novel species of the genus
Aminobacterium
, Aminobacterium thunnarium sp. nov. The type strain is OTA 102T ( = DSM 27500T = JCM 19320T).
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Affiliation(s)
- Olfa Hamdi
- Laboratoire d’Ecologie et de Technologie Microbienne, Institut National des Sciences Appliquées et de Technologie, Centre Urbain Nord, BP 676, 1080 Tunis, Université de Carthage, Tunisia
- Aix Marseille Université, CNRS, Université de Toulon, IRD, Mediterranean Institute of Oceanography (MIO), UM 110, 13288 Marseille, France
| | - Wajdi Ben Hania
- Aix Marseille Université, CNRS, Université de Toulon, IRD, Mediterranean Institute of Oceanography (MIO), UM 110, 13288 Marseille, France
| | - Anne Postec
- Aix Marseille Université, CNRS, Université de Toulon, IRD, Mediterranean Institute of Oceanography (MIO), UM 110, 13288 Marseille, France
| | - Hassib Bouallagui
- Laboratoire d’Ecologie et de Technologie Microbienne, Institut National des Sciences Appliquées et de Technologie, Centre Urbain Nord, BP 676, 1080 Tunis, Université de Carthage, Tunisia
| | - Moktar Hamdi
- Laboratoire d’Ecologie et de Technologie Microbienne, Institut National des Sciences Appliquées et de Technologie, Centre Urbain Nord, BP 676, 1080 Tunis, Université de Carthage, Tunisia
| | - Patricia Bonin
- Aix Marseille Université, CNRS, Université de Toulon, IRD, Mediterranean Institute of Oceanography (MIO), UM 110, 13288 Marseille, France
| | - Bernard Ollivier
- Aix Marseille Université, CNRS, Université de Toulon, IRD, Mediterranean Institute of Oceanography (MIO), UM 110, 13288 Marseille, France
| | - Marie-Laure Fardeau
- Aix Marseille Université, CNRS, Université de Toulon, IRD, Mediterranean Institute of Oceanography (MIO), UM 110, 13288 Marseille, France
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Evidence of in situ microbial activity and sulphidogenesis in perennially sub-0 °C and hypersaline sediments of a high Arctic permafrost spring. Extremophiles 2014; 19:1-15. [DOI: 10.1007/s00792-014-0703-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Accepted: 10/14/2014] [Indexed: 10/24/2022]
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Qiu YL, Hanada S, Kamagata Y, Guo RB, Sekiguchi Y. Lactivibrio alcoholicus gen. nov., sp. nov., an anaerobic, mesophilic, lactate-, alcohol-, carbohydrate- and amino-acid-degrading bacterium in the phylum Synergistetes. Int J Syst Evol Microbiol 2014; 64:2137-2145. [DOI: 10.1099/ijs.0.060681-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A mesophilic, obligately anaerobic, lactate-, alcohol-, carbohydrate- and amino-acid- degrading bacterium, designated strain 7WAY-8-7T, was isolated from an upflow anaerobic sludge blanket reactor treating high-strength organic wastewater from isomerized sugar production processes. Cells of strain 7WAY-8-7T were motile, curved rods (0.7–1.0×5.0–8.0 µm). Spore formation was not observed. The strain grew optimally at 37 °C (range for growth was 25–40 °C) and pH 7.0 (pH 6.0–7.5), and could grow fermentatively on yeast extract, glucose, ribose, xylose, malate, tryptone, pyruvate, fumarate, Casamino acids, serine and cysteine. The main end-products of glucose fermentation were acetate and hydrogen. In co-culture with the hydrogenotrophic methanogen
Methanospirillum hungatei
DSM 864T, strain 7WAY-8-7T could utilize lactate, glycerol, ethanol, 1-propanol, 1-butanol, l-glutamate, alanine, leucine, isoleucine, valine, histidine, asparagine, glutamine, arginine, lysine, threonine, 2-oxoglutarate, aspartate and methionine. A Stickland reaction was not observed with some pairs of amino acids. Yeast extract was required for growth. Nitrate, sulfate, thiosulfate, elemental sulfur, sulfite and Fe (III) were not used as terminal electron acceptors. The G+C content of the genomic DNA was 61.4 mol%. 16S rRNA gene sequence analysis revealed that the isolate belongs to the uncultured environmental clone clade (called ‘PD-UASB-13’ in the Greengenes database) in the bacterial phylum
Synergistetes
, showing less than 90 % sequence similarity with closely related described species such as
Aminivibrio pyruvatiphilus
and
Aminobacterium colombiense
(89.7 % and 88.7 %, respectively). The major cellular fatty acids were iso-C13 : 0, iso-C15 : 0, anteiso-C15 : 0, C18 : 1, C19 : 1, C20 : 1 and C21 : 1. A novel genus and species, Lactivibrio alcoholicus gen. nov., sp. nov. is proposed to accommodate strain 7WAY-8-7T ( = JCM 17151T = DSM 24196T = CGMCC 1.5159T).
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Affiliation(s)
- Yan-Ling Qiu
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8566, Japan
- Shandong Industrial Engineering Laboratory of Biogas Production & Utilization, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong Province 266101, PR China
| | - Satoshi Hanada
- Bioprocess Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8566, Japan
| | - Yoichi Kamagata
- Bioprocess Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Hokkaido 062-8517, Japan
| | - Rong-Bo Guo
- Shandong Industrial Engineering Laboratory of Biogas Production & Utilization, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong Province 266101, PR China
| | - Yuji Sekiguchi
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8566, Japan
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Briones A, Coats E, Brinkman C. Should we build "obese" or "lean" anaerobic digesters? PLoS One 2014; 9:e97252. [PMID: 24831948 PMCID: PMC4022501 DOI: 10.1371/journal.pone.0097252] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2014] [Accepted: 04/16/2014] [Indexed: 01/04/2023] Open
Abstract
Conventional anaerobic digesters (ADs) treating dairy manure are fed with raw or fermented manure rich in volatile fatty acids (VFAs). In contrast, pre-fermented AD (PF-AD) is fed with the more recalcitrant, fiber-rich fraction of manure that has been pre-fermented and depleted of VFAs. Thus, the substrate of PF-AD may be likened to a lean diet rich in fibers while the pre-fermentation stage fermenter is fed a relatively rich diet containing labile organic substances. Previous results have shown that conventional and pre-fermented ADs fed with raw or pre-fermented manure, respectively, produced comparable methane yields. The primary objective of this study was to characterize, using next-generation DNA sequencing, the bacterial communities in various bioreactors (pre-fermentation stage fermenter; various operational arrangements PF-AD; conventional single-stage AD; and a full scale AD) and compare the Firmicutes to Bacteroidetes (F/B) ratios in these different systems. Firmicutes and Bacteroidetes constituted the two most abundant phyla in all AD samples analyzed, as well as most of the samples analyzed in the fermenters and manure samples. Higher relative abundance of Bacteroidetes, ranging from 26% to 51% of bacteria, tended to be associated with PF-AD samples, while the highest relative abundance of Firmicutes occurred in the fermenter (maximum of 76% of bacteria) and manure (maximum of 66% of bacteria) samples. On average, primary stage fermenters exhibited microbiological traits linked to obesity: higher F/B ratios and a ‘diet’ that is less fibrous and more labile compared to that fed to PF-AD. On the other hand, microbial characteristics associated with leanness (lower F/B ratios combined with fibrous substrate) were associated with PF-AD. We propose that bacterial communities in AD shift depending on the quality of substrate, which ultimately results in maintaining VFA yields in PF-AD, similar to the role of bacterial communities and a high fiber diet in lean mice.
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Affiliation(s)
- Aurelio Briones
- Department of Plant, Soil and Entomological Sciences, University of Idaho, Moscow, Idaho, United States of America
- * E-mail:
| | - Erik Coats
- Department of Civil Engineering, University of Idaho, Moscow, Idaho, United States of America
| | - Cynthia Brinkman
- Department of Civil Engineering, University of Idaho, Moscow, Idaho, United States of America
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Honda T, Fujita T, Tonouchi A. Aminivibrio pyruvatiphilus gen. nov., sp. nov., an anaerobic, amino-acid-degrading bacterium from soil of a Japanese rice field. Int J Syst Evol Microbiol 2013; 63:3679-3686. [DOI: 10.1099/ijs.0.052225-0] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel anaerobic bacterium that could ferment amino acids and organic acids was isolated from an anaerobic, propionate-oxidizing enrichment culture originating from soil of a rice field in Japan. Cells of the isolate, designated strain 4F6ET, were Gram-staining-negative, oxidase- and catalase-negative, non-spore-forming, vibrio-shaped, motile rods (0.8×2.0–2.5 µm) with two or three lateral flagella. Growth occurred at 20–42 °C (optimum at 37–40 °C), at pH 6.4–8.4 (optimum at pH 7.3) and at 0–1.5 % (w/v) NaCl (optimum at 0–0.5 %). Good growth occurred on glycine, serine, cysteine, pyruvate and citrate, whereas poor growth was observed on threonine, glutamine, l-malate, α-ketoglutarate, peptone and Casamino acids. In co-culture with the hydrogen-utilizing methanogen
Methanobacterium formicicum
JCM 10132T, strain 4F6ET oxidized alanine, valine, leucine, isoleucine, methionine, aspartate, glutamate, histidine, asparagine and fumarate. Yeast extract was required for growth. The G+C content of genomic DNA was 61.9 mol%. A phylogenetic analysis based on comparison of the 16S rRNA gene sequence showed that the type strains of
Fretibacterium fastidiosum
,
Aminobacterium colombiense
and
Aminobacterium mobile
, members of the family
Synergistaceae
, were the closest relatives of strain 4F6ET, with low sequence similarities (89.3, 89.5 and 86.2 %, respectively). Strain 4F6ET contained iso-C13 : 0 (24.43 %), iso-C15 : 0 (16.47 %) and C19 : 1ω11c/C19 : 1ω9c (16.32 %) as the major fatty acids, which differed from those of
F. fastidiosum
,
Aminobacterium colombiense
and
Aminobacterium mobile
. On the basis of phenotypic, chemotaxonomic and phylogenetic differences between strain 4F6ET and the type strains of
F. fastidiosum
and
Aminobacterium
species, we propose that strain 4F6ET represents a novel genus and species, Aminivibrio pyruvatiphilus gen. nov., sp. nov. The type strain of Aminivibrio pyruvatiphilus is strain 4F6ET ( = JCM 18417T = DSM 25964T).
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Affiliation(s)
- Takuya Honda
- Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori 036-8561, Japan
| | - Takashi Fujita
- Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori 036-8561, Japan
| | - Akio Tonouchi
- Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori 036-8561, Japan
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Microbial community analysis of swine wastewater anaerobic lagoons by next-generation DNA sequencing. Anaerobe 2013; 21:50-7. [PMID: 23538056 DOI: 10.1016/j.anaerobe.2013.03.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Revised: 03/01/2013] [Accepted: 03/10/2013] [Indexed: 11/24/2022]
Abstract
Anaerobic lagoons are a standard practice for the treatment of swine wastewater. This practice relies heavily on microbiological processes to reduce concentrated organic material and nutrients. Despite this reliance on microbiological processes, research has only recently begun to identify and enumerate the myriad and complex interactions that occur in this microbial ecosystem. To further this line of study, we utilized a next-generation sequencing (NGS) technology to gain a deeper insight into the microbial communities along the water column of four anaerobic swine wastewater lagoons. Analysis of roughly one million 16S rDNA sequences revealed a predominance of operational taxonomic units (OTUs) classified as belonging to the phyla Firmicutes (54.1%) and Proteobacteria (15.8%). At the family level, 33 bacterial families were found in all 12 lagoon sites and accounted for between 30% and 50% of each lagoon's OTUs. Analysis by nonmetric multidimensional scaling (NMS) revealed that TKN, COD, ORP, TSS, and DO were the major environmental variables in affecting microbial community structure. Overall, 839 individual genera were classified, with 223 found in all four lagoons. An additional 321 genera were identified in sole lagoons. The top 25 genera accounted for approximately 20% of the OTUs identified in the study, and the low abundances of most of the genera suggests that most OTUs are present at low levels. Overall, these results demonstrate that anaerobic lagoons have distinct microbial communities which are strongly controlled by the environmental conditions present in each individual lagoon.
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Belibasakis GN, Öztürk VÖ, Emingil G, Bostanci N. Synergistetes
cluster A in saliva is associated with periodontitis. J Periodontal Res 2013; 48:727-32. [DOI: 10.1111/jre.12061] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/15/2013] [Indexed: 10/27/2022]
Affiliation(s)
- G. N. Belibasakis
- Oral Microbiology and Immunology; Institute of Oral Biology; Center of Dental Medicine; University of Zürich; Zürich Switzerland
| | - V.-Ö. Öztürk
- Oral Translational Research; Institute of Oral Biology; Center of Dental Medicine; University of Zürich; Zürich Switzerland
- Department of Periodontology; School of Dentistry; Ege University; İzmir Turkey
| | - G. Emingil
- Department of Periodontology; School of Dentistry; Ege University; İzmir Turkey
| | - N. Bostanci
- Oral Translational Research; Institute of Oral Biology; Center of Dental Medicine; University of Zürich; Zürich Switzerland
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Baumgartner A, Thurnheer T, Lüthi-Schaller H, Gmür R, Belibasakis GN. The phylum Synergistetes in gingivitis and necrotizing ulcerative gingivitis. J Med Microbiol 2012; 61:1600-1609. [PMID: 22878253 DOI: 10.1099/jmm.0.047456-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The clinical manifestation of necrotizing ulcerative gingivitis (NUG) is distinct from that of common gingivitis in that it is characterized by local necrosis of the gingival tissues, rapid onset, pain and extensive bleeding. The phylum Synergistetes is a novel bacterial phylum consisting of Gram-negative anaerobes, with evidence of presence in biofilms associated with periodontal and endodontic infections. To date, the involvement of members of this phylum in NUG has not been investigated. This study aimed to evaluate the presence and levels of known human oral Synergistetes bacterial clusters in dental plaque from patients with NUG and compare them with those found in gingivitis. Marginal dental plaque samples from 21 NUG and 21 gingivitis patients were analysed quantitatively by fluorescent in situ hybridization and microscopy for members of two oral Synergistetes clusters (A and B) and for Jonquetella anthropi. Synergistetes cluster A bacteria were detected in all samples but at higher levels (9.4-fold) and proportions (2.5-fold) in NUG patients than in gingivitis patients. However, with regard to Synergistetes cluster B bacteria, there were no differences between NUG and gingivitis patients. J. anthropi was detected in only half of the samples and at lower levels than the other taxa. In conclusion, these data demonstrate that Synergistetes cluster A bacteria, but not cluster B bacteria or J. anthropi, are more strongly associated with NUG than with gingivitis.
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Affiliation(s)
- Angelica Baumgartner
- Oral Microbiology and Immunology, Institute of Oral Biology, Center of Dental Medicine, University of Zurich, Plattenstrasse 11, 8032 Zurich, Switzerland
| | - Thomas Thurnheer
- Oral Microbiology and Immunology, Institute of Oral Biology, Center of Dental Medicine, University of Zurich, Plattenstrasse 11, 8032 Zurich, Switzerland
| | - Helga Lüthi-Schaller
- Oral Microbiology and Immunology, Institute of Oral Biology, Center of Dental Medicine, University of Zurich, Plattenstrasse 11, 8032 Zurich, Switzerland
| | - Rudolf Gmür
- Oral Microbiology and Immunology, Institute of Oral Biology, Center of Dental Medicine, University of Zurich, Plattenstrasse 11, 8032 Zurich, Switzerland
| | - Georgios N Belibasakis
- Oral Microbiology and Immunology, Institute of Oral Biology, Center of Dental Medicine, University of Zurich, Plattenstrasse 11, 8032 Zurich, Switzerland
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You M, Mo S, Watt RM, Leung WK. Prevalence and diversity of Synergistetes taxa in periodontal health and disease. J Periodontal Res 2012; 48:159-68. [PMID: 22881378 DOI: 10.1111/j.1600-0765.2012.01516.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/26/2012] [Indexed: 11/28/2022]
Abstract
BACKGROUND AND OBJECTIVE Members of the phylum Synergistetes have previously been identified within periodontitis subgingival plaque and are considered putative periodontopathogens. This study compared the diversity of subginigval Synergistetes in a cohort of subjects with periodontitis (n = 10) vs. periodontitis-free controls (n = 10). MATERIAL AND METHODS Pooled subgingival plaque samples from all deep periodontal pockets or all sulci were collected from the periodontitis and periodontitis-free subjects, respectively. Bacterial 16S rRNA genes were PCR-amplified from purified subgingival plaque DNA using a Synergistetes 'selective' primer set. PCR products were cloned and sequenced to analyze the prevalence and diversity of Synergistetes operational taxonomic units (OTUs) present in plaque samples of both subject groups. RESULTS A total of 1030 non-chimeric 16S rRNA clones were obtained, of which 162 corresponded to members of the phylum Synergistetes. A significantly larger number of Synergistetes clones were obtained from periodontitis subgingival plaque than from periodontitis-free controls (25.4% vs. 5.9%, p < 0.001). All Synergistetes clones corresponded to cluster A oral Synergistetes, and fell into 31 OTUs (99% sequence identity cut-off). Twenty-nine Synergistetes OTUs were detected in the periodontitis group while eight were detected in the periodontitis-free group (p < 0.001). Five Synergistetes OTUs; including one OTU corresponding to the recently-characterized species Fretibacterium fastidiosum, were more prevalent in the periodontitis subjects (p < 0.05). CONCLUSION OTUs belonging to oral Synergistetes cluster A were more readily detectable and were more diverse in subgingival plaque from periodontitis subjects compared with periodontitis-free controls. Specific Synergistetes OTUs appear to be associated with periodontitis.
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Affiliation(s)
- M You
- Oral Diagnosis and Polyclinics, Prince Philip Dental Hospital, The University of Hong Kong, Hong Kong SAR, China
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Molecular signatures for the phylum Synergistetes and some of its subclades. Antonie Van Leeuwenhoek 2012; 102:517-40. [DOI: 10.1007/s10482-012-9759-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Accepted: 05/30/2012] [Indexed: 10/28/2022]
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Segata N, Haake SK, Mannon P, Lemon KP, Waldron L, Gevers D, Huttenhower C, Izard J. Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples. Genome Biol 2012; 13:R42. [PMID: 22698087 PMCID: PMC3446314 DOI: 10.1186/gb-2012-13-6-r42] [Citation(s) in RCA: 662] [Impact Index Per Article: 55.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Revised: 03/12/2012] [Accepted: 06/14/2012] [Indexed: 02/06/2023] Open
Abstract
Background To understand the relationship between our bacterial microbiome and health, it is essential to define the microbiome in the absence of disease. The digestive tract includes diverse habitats and hosts the human body's greatest bacterial density. We describe the bacterial community composition of ten digestive tract sites from more than 200 normal adults enrolled in the Human Microbiome Project, and metagenomically determined metabolic potentials of four representative sites. Results The microbiota of these diverse habitats formed four groups based on similar community compositions: buccal mucosa, keratinized gingiva, hard palate; saliva, tongue, tonsils, throat; sub- and supra-gingival plaques; and stool. Phyla initially identified from environmental samples were detected throughout this population, primarily TM7, SR1, and Synergistetes. Genera with pathogenic members were well-represented among this disease-free cohort. Tooth-associated communities were distinct, but not entirely dissimilar, from other oral surfaces. The Porphyromonadaceae, Veillonellaceae and Lachnospiraceae families were common to all sites, but the distributions of their genera varied significantly. Most metabolic processes were distributed widely throughout the digestive tract microbiota, with variations in metagenomic abundance between body habitats. These included shifts in sugar transporter types between the supragingival plaque, other oral surfaces, and stool; hydrogen and hydrogen sulfide production were also differentially distributed. Conclusions The microbiomes of ten digestive tract sites separated into four types based on composition. A core set of metabolic pathways was present across these diverse digestive tract habitats. These data provide a critical baseline for future studies investigating local and systemic diseases affecting human health.
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Affiliation(s)
- Nicola Segata
- Department of Molecular Genetics, The Forsyth Institute, Cambridge, MA 02142, USA
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44
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Davis CK, Webb RI, Sly LI, Denman SE, McSweeney CS. Isolation and survey of novel fluoroacetate-degrading bacteria belonging to the phylum Synergistetes. FEMS Microbiol Ecol 2012; 80:671-84. [PMID: 22372434 DOI: 10.1111/j.1574-6941.2012.01338.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2011] [Revised: 01/16/2012] [Accepted: 02/12/2012] [Indexed: 11/29/2022] Open
Abstract
Microbial dehalogenation of chlorinated compounds in anaerobic environments is well known, but the degradation of fluorinated compounds under similar conditions has rarely been described. Here, we report on the isolation of a bovine rumen bacterium that metabolizes fluoroacetate under anaerobic conditions, the mode of degradation and its presence in gut ecosystems. The bacterium was identified using 16S rRNA gene sequence analysis as belonging to the phylum Synergistetes and was designated strain MFA1. Growth was stimulated by amino acids with greater quantities of amino acids metabolized in the presence of fluoroacetate, but sugars were not fermented. Acetate, formate, propionate, isobutryate, isovalerate, ornithine and H(2) were end products of amino acid metabolism. Acetate was the primary end product of fluoroacetate dehalogenation, and the amount produced correlated with the stoichiometric release of fluoride which was confirmed using fluorine nuclear magnetic resonance ((19) F NMR) spectroscopy. Hydrogen and formate produced in situ were consumed during dehalogenation. The growth characteristics of strain MFA1 indicated that the bacterium may gain energy via reductive dehalogenation. This is the first study to identify a bacterium that can anaerobically dehalogenate fluoroacetate. Nested 16S rRNA gene-specific PCR assays detected the bacterium at low numbers in the gut of several herbivore species.
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Affiliation(s)
- Carl K Davis
- CSIRO Livestock Industries, Queensland Bioscience Precinct, St Lucia, Qld, Australia
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45
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The bacterial microbiota in the ceca of Capercaillie (Tetrao urogallus) differs between wild and captive birds. Syst Appl Microbiol 2011; 34:542-51. [DOI: 10.1016/j.syapm.2011.06.003] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2011] [Revised: 05/30/2011] [Accepted: 06/01/2011] [Indexed: 11/21/2022]
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46
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Segata N, Izard J, Waldron L, Gevers D, Miropolsky L, Garrett WS, Huttenhower C. Metagenomic biomarker discovery and explanation. Genome Biol 2011; 12:R60. [PMID: 21702898 PMCID: PMC3218848 DOI: 10.1186/gb-2011-12-6-r60] [Citation(s) in RCA: 9055] [Impact Index Per Article: 696.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2011] [Revised: 05/31/2011] [Accepted: 06/24/2011] [Indexed: 12/11/2022] Open
Abstract
This study describes and validates a new method for metagenomic biomarker discovery by way of class comparison, tests of biological consistency and effect size estimation. This addresses the challenge of finding organisms, genes, or pathways that consistently explain the differences between two or more microbial communities, which is a central problem to the study of metagenomics. We extensively validate our method on several microbiomes and a convenient online interface for the method is provided at http://huttenhower.sph.harvard.edu/lefse/.
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Affiliation(s)
- Nicola Segata
- Department of Biostatistics, 677 Huntington Avenue, Harvard School of Public Health, Boston, MA 02115, USA
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47
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Maune MW, Tanner RS. Description of Anaerobaculum hydrogeniformans sp. nov., an anaerobe that produces hydrogen from glucose, and emended description of the genus Anaerobaculum. Int J Syst Evol Microbiol 2011; 62:832-838. [PMID: 21602364 DOI: 10.1099/ijs.0.024349-0] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel anaerobic, moderately thermophilic, NaCl-requiring fermentative bacterium, strain OS1T, was isolated from oil production water collected from Alaska, USA. Cells were Gram-negative, non-motile, non-spore-forming rods (1.7-2.7×0.4-0.5 µm). The G+C content of the genomic DNA of strain OS1T was 46.6 mol%. The optimum temperature, pH and NaCl concentration for growth of strain OS1T were 55 °C, pH 7 and 10 g l(-1), respectively. The bacterium fermented D-fructose, D-glucose, maltose, D-mannose, α-ketoglutarate, L-glutamate, malonate, pyruvate, L-tartrate, L-asparagine, Casamino acids, L-cysteine, L-histidine, L-leucine, L-phenylalanine, L-serine, L-threonine, L-valine, inositol, inulin, tryptone and yeast extract. When grown on D-glucose, 3.86 mol hydrogen and 1.4 mol acetate were produced per mol substrate. Thiosulfate, sulfur and L-cystine were reduced to sulfide, and crotonate was reduced to butyrate with glucose as the electron donor. 16S rRNA gene sequence analysis indicated that strain OS1T was related to Anaerobaculum thermoterrenum (99.7 % similarity to the type strain), a member of the phylum Synergistetes. DNA-DNA hybridization between strain OS1T and A. thermoterrenum DSM 13490T yielded 68 % relatedness. Unlike A. thermoterrenum, strain OS1T fermented malonate, maltose, tryptone, L-leucine and L-phenylalanine, but not citrate, fumarate, lactate, L-malate, glycerol, pectin or starch. The major cellular fatty acid of strain OS1T was iso-C15:0 (91 % of the total). Strain OS1T also contained iso-C13:0 3-OH (3 %), which was absent from A. thermoterrenum, and iso-C13:0 (2 %), which was absent from Anaerobaculum mobile. On the basis of these results, strain OS1T represents a novel species of the genus Anaerobaculum, for which the name Anaerobaculum hydrogeniformans sp. nov. is proposed. The type strain is OS1T (=DSM 22491T=ATCC BAA-1850T). An emended description of the genus Anaerobaculum is also given.
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Affiliation(s)
- Matthew W Maune
- Department of Botany and Microbiology, University of Oklahoma, Norman, OK 73019, USA
| | - Ralph S Tanner
- Department of Botany and Microbiology, University of Oklahoma, Norman, OK 73019, USA
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Identification of a novel acetate-utilizing bacterium belonging to Synergistes group 4 in anaerobic digester sludge. ISME JOURNAL 2011; 5:1844-56. [PMID: 21562600 DOI: 10.1038/ismej.2011.59] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Major acetate-utilizing bacterial and archaeal populations in methanogenic anaerobic digester sludge were identified and quantified by radioisotope- and stable-isotope-based functional analyses, microautoradiography-fluorescence in situ hybridization (MAR-FISH) and stable-isotope probing of 16S rRNA (RNA-SIP) that can directly link 16S rRNA phylogeny with in situ metabolic function. First, MAR-FISH with (14)C-acetate indicated the significant utilization of acetate by only two major groups, unidentified bacterial cells and Methanosaeta-like filamentous archaeal cells, in the digester sludge. To identify the acetate-utilizing unidentified bacteria, RNA-SIP was conducted with (13)C(6)-glucose and (13)C(3)-propionate as sole carbon source, which were followed by phylogenetic analysis of 16S rRNA. We found that bacteria belonging to Synergistes group 4 were commonly detected in both 16S rRNA clone libraries derived from the sludge incubated with (13)C-glucose and (13)C-propionate. To confirm that this bacterial group can utilize acetate, specific FISH probe targeting for Synergistes group 4 was newly designed and applied to the sludge incubated with (14)C-acetate for MAR-FISH. The MAR-FISH result showed that bacteria belonging to Synergistes group 4 significantly took up acetate and their active population size was comparable to that of Methanosaeta in this sludge. In addition, as bacteria belonging to Synergistes group 4 had high K(m) for acetate and maximum utilization rate, they are more competitive for acetate over Methanosaeta at high acetate concentrations (2.5-10 mM). To our knowledge, it is the first time to report the acetate-utilizing activity of uncultured bacteria belonging to Synergistes group 4 and its competitive significance to acetoclastic methanogen, Methanosaeta.
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Aquino ARL, Lima KC, Paiva MS, Rôças IN, Siqueira JF. Molecular survey of atheromatous plaques for the presence of DNA from periodontal bacterial pathogens, archaea and fungi. J Periodontal Res 2011; 46:303-9. [PMID: 21261623 DOI: 10.1111/j.1600-0765.2010.01343.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
BACKGROUND AND OBJECTIVE Chronic infections, such as periodontitis, have been associated with the development and progression of atherosclerosis. The mechanisms through which this occurs have yet to be elucidated. This study was carried out to detect periodontopathic bacteria as well as archaea and fungi in atheromatous plaques and search for factors associated with their occurrence in atheromas. MATERIAL AND METHODS A cross-sectional study was carried out including 30 patients diagnosed with atherosclerosis in the carotid, coronary or femoral arteries. Plaques were collected during surgery and analysed using PCR to detect Aggregatibacter actinomycetemcomitans, Porphyromonas gingivalis, Treponema denticola and members of the Synergistetes group. Samples were also surveyed with universal primers for bacterial, archaeal and fungal DNA. Patients responded to a questionnaire to determine factors associated with PCR results. RESULTS All dentate individuals (66.7%) had periodontal disease, 95% of which was severe and 65% extensive. None of the targeted periodontopathic bacteria was found in the atheromas. No sample yielded positive results for fungal and archaeal DNA. Four samples (13%) were positive for the presence of bacterial DNA. Of these, three participants were dentate (two with severely chronic generalized periodontitis and one with severely chronic localized periodontitis). CONCLUSION This study did not confirm previous findings of periodontal pathogens in atheromas, making it impossible to establish factors associated with their presence in plaques. Presence of bacterial DNA in some samples indicates that periodontal or nonoral bacterial species other than the ones targeted in this study may be involved with some cases of atherosclerosis.
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Affiliation(s)
- A R L Aquino
- Departments of Preventive Dentistry, Federal University of Rio Grande do Norte, Natal, RN, Brazil.
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Ziganshin AM, Schmidt T, Scholwin F, Il’inskaya ON, Harms H, Kleinsteuber S. Bacteria and archaea involved in anaerobic digestion of distillers grains with solubles. Appl Microbiol Biotechnol 2010; 89:2039-52. [DOI: 10.1007/s00253-010-2981-9] [Citation(s) in RCA: 119] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2010] [Revised: 10/20/2010] [Accepted: 10/20/2010] [Indexed: 02/02/2023]
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