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Hallberg ZF, Nicolas AM, Alvarez-Aponte ZI, Mok KC, Sieradzki ET, Pett-Ridge J, Banfield JF, Carlson HK, Firestone MK, Taga ME. Vitamin B 12 variants structure soil microbial communities despite soil's vast reservoir of B 12. bioRxiv 2024:2024.02.12.580003. [PMID: 38405713 PMCID: PMC10888822 DOI: 10.1101/2024.02.12.580003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Soil microbial communities perform critical ecosystem services through the collective metabolic activities of numerous individual organisms. Most microbes use corrinoids, a structurally diverse family of cofactors related to vitamin B12. Corrinoid structure influences the growth of individual microbes, yet how these growth responses scale to the community level remains unknown. Analysis of metagenome-assembled genomes suggests corrinoids are supplied to the community by members of the archaeal and bacterial phyla Thermoproteota, Actinobacteria, and Proteobacteria. Corrinoids were found largely adhered to the soil matrix in a grassland soil, at levels exceeding those required by cultured bacteria. Enrichment cultures and soil microcosms seeded with different corrinoids show distinct shifts in bacterial 16S composition, supporting the hypothesis that corrinoid structure can shape communities. Environmental context influenced both community and taxon-specific responses to specific corrinoids. These results implicate corrinoids as key determinants of soil microbiome structure and suggest that environmental micronutrient reservoirs promote community stability.
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Affiliation(s)
- Zachary F. Hallberg
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, 94720 USA
| | - Alexa M. Nicolas
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, 94720 USA
| | - Zoila I. Alvarez-Aponte
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, 94720 USA
| | - Kenny C. Mok
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, 94720 USA
| | - Ella T. Sieradzki
- Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA, 94720 USA
| | - Jennifer Pett-Ridge
- Lawrence Livermore National Laboratory, Livermore, CA USA
- Innovative Genomics Institute, Berkeley, CA, 94720 USA
| | - Jillian F. Banfield
- Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA, 94720 USA
- Lawrence Berkeley National Laboratory, Berkeley, CA USA
- Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, 94720 USA
- Innovative Genomics Institute, Berkeley, CA, 94720 USA
| | | | - Mary K. Firestone
- Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA, 94720 USA
- Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Michiko E. Taga
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, 94720 USA
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2
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Kim Y, Flinkstrom Z, Candry P, Winkler MKH, Myung J. Resource availability governs polyhydroxyalkanoate (PHA) accumulation and diversity of methanotrophic enrichments from wetlands. Front Bioeng Biotechnol 2023; 11:1210392. [PMID: 37588137 PMCID: PMC10425282 DOI: 10.3389/fbioe.2023.1210392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 07/12/2023] [Indexed: 08/18/2023] Open
Abstract
Aquatic environments account for half of global CH4 emissions, with freshwater wetlands being the most significant contributors. These CH4 fluxes can be partially offset by aerobic CH4 oxidation driven by methanotrophs. Additionally, some methanotrophs can convert CH4 into polyhydroxyalkanoate (PHA), an energy storage molecule as well as a promising bioplastic polymer. In this study, we investigate how PHA-accumulating methanotrophic communities enriched from wetlands were shaped by varying resource availability (i.e., C and N concentrations) at a fixed C/N ratio. Cell yields, PHA accumulation, and community composition were evaluated in high (20% CH4 and 10 mM NH4 +) and low resource (0.2% CH4 and 0.1 mM NH4 +) conditions simulating engineered and environmental settings, respectively. High resource availability decreased C-based cell yields, while N-based cell yields remained stable, suggesting nutrient exchange patterns differed between methanotrophic communities at different resource concentrations. PHA accumulation was only observed in high resource enrichments, producing approximately 12.6% ± 2.4% (m/m) PHA, while PHA in low resource enrichments remained below detection. High resource enrichments were dominated by Methylocystis methanotrophs, while low resource enrichments remained significantly more diverse and contained only a minor population of methanotrophs. This study demonstrates that resource concentration shapes PHA-accumulating methanotrophic communities. Together, this provides useful information to leverage such communities in engineering settings as well as to begin understanding their role in the environment.
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Affiliation(s)
- Yujin Kim
- Department of Civil and Environmental Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Zachary Flinkstrom
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, United States
| | - Pieter Candry
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, United States
| | - Mari-Karoliina H. Winkler
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, United States
| | - Jaewook Myung
- Department of Civil and Environmental Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
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3
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Alig BN, Malheiros RD, Anderson KE. Evaluation of Physical Egg Quality Parameters of Commercial Brown Laying Hens Housed in Five Production Systems. Animals (Basel) 2023; 13:ani13040716. [PMID: 36830504 PMCID: PMC9951926 DOI: 10.3390/ani13040716] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 02/14/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
This study evaluates the effect of housing environment on the egg quality characteristics of brown egg layers as many different environments are currently used in the industry. Battery cages, barren colony cages, enriched colony cages, cage-free, and free-range environments were evaluated. Overall, all egg quality measurements were affected by housing environment (p < 0.01) except for vitelline membrane strength, elasticity, and egg solids. Eggshells and yolks were lightest in barren colony cages and darkest from free-range hens (p < 0.0001). Free-range eggs were heavier than eggs from all other environments (p < 0.0001). Cage-free eggs had lower albumen height and Haugh units than other environments (p < 0.0001). Lastly, cage-free and free-range eggs had stronger eggshells than the other environments (p < 0.0001), and free-range eggs had more elastic eggshells than eggs from conventional battery cages and barren colony cages (p < 0.01). Access to the range seemed to give free-range hens different nutritional advantages, which allowed for the darker yolks and shells. Furthermore, eggs from barren colony cages seemed to exhibit more negative characteristics. Simply adding enrichments to colony cages did not improve or detract from egg quality. From this research, it appears that, as the industry moves toward extensive environments, the egg quality of brown egg layers will improve.
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4
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Iacono R, Strazzulli A, Giglio R, Bitetti F, Cobucci-Ponzano B, Moracci M. Valorization of Biomasses from Energy Crops for the Discovery of Novel Thermophilic Glycoside Hydrolases through Metagenomic Analysis. Int J Mol Sci 2022; 23:10505. [PMID: 36142415 DOI: 10.3390/ijms231810505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 09/06/2022] [Accepted: 09/08/2022] [Indexed: 11/16/2022] Open
Abstract
The increasing interest for environmentally friendly technologies is driving the transition from fossil-based economy to bioeconomy. A key enabler for circular bioeconomy is to valorize renewable biomasses as feedstock to extract high value-added chemicals. Within this transition the discovery and the use of robust biocatalysts to replace toxic chemical catalysts play a significant role as technology drivers. To meet both the demands, we performed microbial enrichments on two energy crops, used as low-cost feed for extremophilic consortia. A culture-dependent approach coupled to metagenomic analysis led to the discovery of more than 300 glycoside hydrolases and to characterize a new α-glucosidase from an unknown hyperthermophilic archaeon. Aglu1 demonstrated to be the most active archaeal GH31 on 4Np-α-Glc and it showed unexpected specificity vs. kojibiose, revealing to be a promising candidate for biotechnological applications such as the liquefaction/saccharification of starch.
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5
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Stouten GR, Hamers K, van Tatenhove-Pel RJ, van der Knaap E, Kleerebezem R. Seemingly trivial secondary factors may determine microbial competition: a cautionary tale on the impact of iron supplementation through corrosion. FEMS Microbiol Ecol 2021; 97:6081106. [PMID: 33428722 PMCID: PMC7878175 DOI: 10.1093/femsec/fiab002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 01/08/2021] [Indexed: 11/13/2022] Open
Abstract
Microbial community engineering aims for enrichment of a specific microbial trait by imposing specific cultivation conditions. This work demonstrates that things may be more complicated than typically presumed and that microbial competition can be affected by seemingly insignificant variables, like in this case the type of acid used for pH control. Aerobic bioreactors pulse fed with acetate operated with hydrochloric acid resulted in the enrichment of Plasticicumulans acidivorans, and changing the pH controlling agent to sulfuric acid shifted the community towards Zoogloea sp. Further research demonstrated that the change in community structure was not directly caused by the change in acid used for pH control, but resulted from the difference in corrosive strength of both acids and the related iron leaching from the bioreactor piping. Neither system was iron deficient, suggesting that the biological availability of iron is affected by the leaching process. Our results demonstrate that microbial competition and process development can be affected dramatically by secondary factors related to nutrient supply and bioavailability, and is way more complex than generally assumed in a single carbon substrate limited process.
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Affiliation(s)
- Gerben R Stouten
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Kelly Hamers
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Rinke J van Tatenhove-Pel
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, The Netherlands.,Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - Eline van der Knaap
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Robbert Kleerebezem
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, The Netherlands
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6
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Moote PE, Zaytsoff SJM, Ortega Polo R, Abbott DW, Uwiera RRE, Inglis GD. Application of culturomics to characterize diverse anaerobic bacteria from the gastrointestinal tract of broiler chickens in relation to environmental reservoirs. Can J Microbiol 2020; 66:288-302. [PMID: 31986063 DOI: 10.1139/cjm-2019-0469] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Characterization of the microbiota of chickens is of current interest. The goals of the current study were to apply anaerobic isolation methods to comprehensively isolate and identify bacteria from the gastrointestinal tract of chickens and their environment. Bacterial communities within the drinking water were dominated by Escherichia, whereas communities in litter were more representative of the cecum. The crop and small intestine (jejunum and ileum) were dominated by Lactobacillus and Enterococcus spp., and the cecum was dominated by Proteus spp. The collection of bacteria isolated was dominated by Enterococcus spp., Escherichia/Shigella spp., Lactobacillus spp., and Proteus spp.; however, many rare taxa were observed. These included members of the Clostridiales and Clostridium spp., which were commonly isolated from the ileum and cecum. Bacteria isolated by enrichment and direct plating differed. The selective de Man-Rogosa-Sharpe agar was commonly associated with the isolation of Lactobacillus spp. and yielded the lowest diversity of all methods utilized. Increased diversity and frequency of Clostridium spp. was observed in enrichments of blood and mucus or by plating on Columbia agar supplemented with 10% blood and gentamicin. The bacteria isolated from this study provide source material for genomic and functional studies in chicken hosts.
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Affiliation(s)
- Paul E Moote
- Agriculture and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, AB T1J 4B1, Canada.,Department of Agricultural, Food and Nutritional Science, 410 Agriculture/Forestry Centre, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Sarah J M Zaytsoff
- Agriculture and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, AB T1J 4B1, Canada.,Department of Agricultural, Food and Nutritional Science, 410 Agriculture/Forestry Centre, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Rodrigo Ortega Polo
- Agriculture and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, AB T1J 4B1, Canada
| | - D Wade Abbott
- Agriculture and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, AB T1J 4B1, Canada
| | - Richard R E Uwiera
- Department of Agricultural, Food and Nutritional Science, 410 Agriculture/Forestry Centre, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - G Douglas Inglis
- Agriculture and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, AB T1J 4B1, Canada
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7
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Wen ZL, Yang MK, Du MH, Zhong ZZ, Lu YT, Wang GH, Hua XM, Fazal A, Mu CH, Yan SF, Zhen Y, Yang RW, Qi JL, Hong Z, Lu GH, Yang YH. Enrichments/Derichments of Root-Associated Bacteria Related to Plant Growth and Nutrition Caused by the Growth of an EPSPS-Transgenic Maize Line in the Field. Front Microbiol 2019; 10:1335. [PMID: 31275269 PMCID: PMC6591461 DOI: 10.3389/fmicb.2019.01335] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 05/29/2019] [Indexed: 11/13/2022] Open
Abstract
During the past decades, the effects of the transgenic crops on soil microbial communities have aroused widespread interest of scientists, which was mainly related to the health and growth of plants. In this study, the maize root-associated bacterial communities of 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) transgenic glyphosate-tolerant (GT) maize line CC-2 (CC2) and its recipient variety Zhengdan958 (Z958) were compared at the tasseling and flowering stages by high-throughput sequencing of V3-V4 hypervariable regions of 16S rRNA gene (16S rDNA) amplicons via Illumina MiSeq. In addition, real-time quantitative PCR (qPCR) was also performed to analyze the nifH gene abundance between CC2 and Z958. Our results showed no significant difference in alpha/beta diversity of root-associated bacterial communities at the tasseling or flowering stage between CC2 and Z958 under field growth conditions. The relative abundances of the genera Bradyrhizobium and Bacillus including species B. cereus and B. muralis were significantly lower in the roots of CC2 than that of Z985 under field conditions. Both these species are regarded as plant growth promoting bacteria (PGPB), as they belong to both nitrogen-fixing and phosphate-solubilizing bacterial genera. The comparison of the relative abundance of nitrogen-fixing/phosphate-solubilizing bacteria at the class, order or family levels indicated that only one class Bacilli, one order Bacillales and one family Bacillaceae were found to be significantly lower in the roots of CC2 than that of Z985. These bacteria were also enriched in the roots and rhizospheric soil than in the surrounding soil at both two stages. Furthermore, the class Betaproteobacteria, the order Burkholderiales, the family Comamonadaceae, and the genus Acidovorax were significantly higher in the roots of CC2 than that of Z985 at the tasseling stage, meanwhile the order Burkholderiales and the family Comamonadaceae were also enriched in the roots than in the rhizospheric soil at both stages. Additionally, the nifH gene abundance at the tasseling stage in the rhizosphere soil also showed significant difference. The relative abundance of nifH gene was higher in the root samples and lower in the surrounding soil, which implicated that the roots of maize tend to be enriched in nitrogen-fixing bacteria.
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Affiliation(s)
- Zhong-Ling Wen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Institute for Plant Molecular Biology, Nanjing University, Nanjing, China.,Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Min-Kai Yang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Institute for Plant Molecular Biology, Nanjing University, Nanjing, China.,Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Mei-Hang Du
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Institute for Plant Molecular Biology, Nanjing University, Nanjing, China.,Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Zhao-Zhao Zhong
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Institute for Plant Molecular Biology, Nanjing University, Nanjing, China
| | - Yun-Ting Lu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Institute for Plant Molecular Biology, Nanjing University, Nanjing, China.,Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Gu-Hao Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Institute for Plant Molecular Biology, Nanjing University, Nanjing, China
| | - Xiao-Mei Hua
- Research Center for Soil Pollution Prevention and Control, Nanjing Institute of Environmental Sciences, MEE, Nanjing, China
| | - Aliya Fazal
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Institute for Plant Molecular Biology, Nanjing University, Nanjing, China
| | - Chun-Hua Mu
- Shandong Academy of Agriculture Sciences, Jinan, China
| | - Shu-Feng Yan
- Henan Academy of Agriculture Sciences, Zhengzhou, China
| | - Yan Zhen
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Rong-Wu Yang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Institute for Plant Molecular Biology, Nanjing University, Nanjing, China
| | - Jin-Liang Qi
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Institute for Plant Molecular Biology, Nanjing University, Nanjing, China.,Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Zhi Hong
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Institute for Plant Molecular Biology, Nanjing University, Nanjing, China
| | - Gui-Hua Lu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Institute for Plant Molecular Biology, Nanjing University, Nanjing, China.,Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Yong-Hua Yang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Institute for Plant Molecular Biology, Nanjing University, Nanjing, China.,Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
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8
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Söllinger A, Schwab C, Weinmaier T, Loy A, Tveit AT, Schleper C, Urich T. Phylogenetic and genomic analysis of Methanomassiliicoccales in wetlands and animal intestinal tracts reveals clade-specific habitat preferences. FEMS Microbiol Ecol 2016; 92:fiv149. [PMID: 26613748 DOI: 10.1093/femsec/fiv149] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/24/2015] [Indexed: 01/30/2023] Open
Abstract
Methanogenic Thermoplasmata of the novel order Methanomassiliicoccales were recently discovered in human and animal gastro-intestinal tracts (GITs). However, their distribution in other methanogenic environments has not been addressed systematically. Here, we surveyed Methanomassiliicoccales presence in wetland soils, a globally important source of methane emissions to the atmosphere, and in the GITs of different animals by PCR targeting their 16S rRNA and methyl:coenzyme M reductase (α-subunit) genes. We detected Methanomassiliicoccales in all 16 peat soils investigated, indicating their wide distribution in these habitats. Additionally, we detected their genes in various animal faeces. Methanomassiliicoccales were subdivided in two broad phylogenetic clades designated 'environmental' and 'GIT' clades based on differential, although non-exclusive, habitat preferences of their members. A well-supported cluster within the environmental clade comprised more than 80% of all wetland 16S rRNA gene sequences. Metagenome assembly from bovine rumen fluid enrichments resulted in two almost complete genomes of both Methanomassiliicoccales clades. Comparative genomics revealed that members of the environmental clade contain larger genomes and a higher number of genes encoding anti-oxidative enzymes than animal GIT clade representatives. This study highlights the wide distribution of Methanomassiliicoccales in wetlands, which suggests that they contribute to methane emissions from these climate-relevant ecosystems.
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Affiliation(s)
- Andrea Söllinger
- Department of Ecogenomics and Systems Biology, University of Vienna, 1090 Vienna, Austria
| | - Clarissa Schwab
- Institute of Food, Nutrition and Health, ETH Zürich, 8092 Zurich, Switzerland
| | - Thomas Weinmaier
- Department of Microbiology and Ecosystem Science, University of Vienna, 1090 Vienna, Austria
| | - Alexander Loy
- Department of Microbiology and Ecosystem Science, University of Vienna, 1090 Vienna, Austria
| | - Alexander T Tveit
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | - Christa Schleper
- Department of Ecogenomics and Systems Biology, University of Vienna, 1090 Vienna, Austria
| | - Tim Urich
- Department of Ecogenomics and Systems Biology, University of Vienna, 1090 Vienna, Austria Institute for Microbiology, Ernst-Moritz-Arndt University Greifswald, 17489 Greifswald, Germany
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9
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Unal B, Perry VR, Sheth M, Gomez-Alvarez V, Chin KJ, Nüsslein K. Trace elements affect methanogenic activity and diversity in enrichments from subsurface coal bed produced water. Front Microbiol 2012; 3:175. [PMID: 22590465 PMCID: PMC3349271 DOI: 10.3389/fmicb.2012.00175] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Accepted: 04/20/2012] [Indexed: 12/01/2022] Open
Abstract
Microbial methane from coal beds accounts for a significant and growing percentage of natural gas worldwide. Our knowledge of physical and geochemical factors regulating methanogenesis is still in its infancy. We hypothesized that in these closed systems, trace elements (as micronutrients) are a limiting factor for methanogenic growth and activity. Trace elements are essential components of enzymes or cofactors of metabolic pathways associated with methanogenesis. This study examined the effects of eight trace elements (iron, nickel, cobalt, molybdenum, zinc, manganese, boron, and copper) on methane production, on mcrA transcript levels, and on methanogenic community structure in enrichment cultures obtained from coal bed methane (CBM) well produced water samples from the Powder River Basin, Wyoming. Methane production was shown to be limited both by a lack of additional trace elements as well as by the addition of an overly concentrated trace element mixture. Addition of trace elements at concentrations optimized for standard media enhanced methane production by 37%. After 7 days of incubation, the levels of mcrA transcripts in enrichment cultures with trace element amendment were much higher than in cultures without amendment. Transcript levels of mcrA correlated positively with elevated rates of methane production in supplemented enrichments (R2 = 0.95). Metabolically active methanogens, identified by clone sequences of mcrA mRNA retrieved from enrichment cultures, were closely related to Methanobacterium subterraneum and Methanobacterium formicicum. Enrichment cultures were dominated by M. subterraneum and had slightly higher predicted methanogenic richness, but less diversity than enrichment cultures without amendments. These results suggest that varying concentrations of trace elements in produced water from different subsurface coal wells may cause changing levels of CBM production and alter the composition of the active methanogenic community.
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Affiliation(s)
- Burcu Unal
- Department of Microbiology, University of Massachusetts Amherst, MA, USA
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10
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Ramakrishnan R, Ramakrishnan JD. A state space transformation can yield identifiable models for tracer kinetic studies with enrichment data. Bull Math Biol 2010; 72:2019-46. [PMID: 20195911 PMCID: PMC3275642 DOI: 10.1007/s11538-010-9522-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2009] [Accepted: 02/09/2010] [Indexed: 10/19/2022]
Abstract
Tracer studies are analyzed almost universally by multicompartmental models where the state variables are tracer amounts or activities in the different pools. The model parameters are rate constants, defined naturally by expressing fluxes as fractions of the source pools. We consider an alternative state space with tracer enrichments or specific activities as the state variables, with the rate constants redefined by expressing fluxes as fractions of the destination pools. Although the redefinition may seem unphysiological, the commonly computed fractional synthetic rate actually expresses synthetic flux as a fraction of the product mass (destination pool). We show that, for a variety of structures, provided the structure is linear and stationary, the model in the enrichment state space has fewer parameters than that in the activities state space, and is hence better both to study identifiability and to estimate parameters. The superiority of enrichment modeling is shown for structures where activity model unidentifiability is caused by multiple exit pathways; on the other hand, with a single exit pathway but with multiple untraced entry pathways, activity modeling is shown to be superior. With the present-day emphasis on mass isotopes, the tracer in human studies is often of a precursor, labeling most or all entry pathways. It is shown that for these tracer studies, models in the activities state space are always unidentifiable when there are multiple exit pathways, even if the enrichment in every pool is observed; on the other hand, the corresponding models in the enrichment state space have fewer parameters and are more often identifiable. Our results suggest that studies with labeled precursors are modeled best with enrichments.
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Affiliation(s)
- Rajasekhar Ramakrishnan
- Department of Pediatrics, Columbia University College of Physicians and Surgeons, New York, NY 10032, USA.
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