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Li L, Qin Y, Kong Z, Wu J, Kubota K, Li YY. Characterization of microbial community and main functional groups of prokaryotes in thermophilic anaerobic co-digestion of food waste and paper waste. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 652:709-717. [PMID: 30380478 DOI: 10.1016/j.scitotenv.2018.10.292] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Revised: 10/17/2018] [Accepted: 10/21/2018] [Indexed: 06/08/2023]
Abstract
The thermophilic anaerobic co-digestion of food waste and paper waste was successfully operated with a 0% to 70% fraction of paper waste. The variation of functional microbial community was investigated by 16S rRNA gene analysis. The results indicated that the hydrolyzing bacterial community changed from carbohydrate/protein-degrading bacteria to cellulose-degrading bacteria when the paper waste ratio was higher than 50%. Significant changes in the taxon responsible for cellulose degradation were found depending on the paper waste fraction. Cellulose-degrading bacteria outcompeted lactic acid bacteria in the degradation of monosaccharide, resulting in a decline in the proportion of lactic acid bacteria and the absence of an accumulation of lactic acid. At high paper waste ratios, because the cellulose-degrading bacteria, such as Defluviitoga tunisiensis, were more likely to degrade monosaccharides directly to acetate and hydrogen rather than to propionate and butyrate, the abundance of syntrophs was reduced. The variation of those bacteria with high H2-producing ability significantly influenced the proportion of hydrogenotrophic archaea. The change in the microbial community as the paper waste fraction increased was illustrated with regard to anaerobic degradation steps.
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Affiliation(s)
- Lu Li
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aza-Aoba, Aramaki, Aoba Ward, Sendai, Miyagi 980-8579, Japan
| | - Yu Qin
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aza-Aoba, Aramaki, Aoba Ward, Sendai, Miyagi 980-8579, Japan
| | - Zhe Kong
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aza-Aoba, Aramaki, Aoba Ward, Sendai, Miyagi 980-8579, Japan
| | - Jing Wu
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aza-Aoba, Aramaki, Aoba Ward, Sendai, Miyagi 980-8579, Japan
| | - Kengo Kubota
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aza-Aoba, Aramaki, Aoba Ward, Sendai, Miyagi 980-8579, Japan
| | - Yu-You Li
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aza-Aoba, Aramaki, Aoba Ward, Sendai, Miyagi 980-8579, Japan.
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52
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Lee YM, Hwang K, Lee JI, Kim M, Hwang CY, Noh HJ, Choi H, Lee HK, Chun J, Hong SG, Shin SC. Genomic Insight Into the Predominance of Candidate Phylum Atribacteria JS1 Lineage in Marine Sediments. Front Microbiol 2018; 9:2909. [PMID: 30555444 PMCID: PMC6281690 DOI: 10.3389/fmicb.2018.02909] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Accepted: 11/13/2018] [Indexed: 01/13/2023] Open
Abstract
Candidate phylum Atribacteria JS1 lineage is one of the predominant bacterial groups in anoxic subseafloor sediments, especially in organic-rich or gas hydrate-containing sediments. However, due to the lack of axenic culture representatives, metabolic potential and biogeochemical roles of this phylum have remained elusive. Here, we examined the microbial communities of marine sediments of the Ross Sea, Antarctica, and found candidate phylum Atribacteria JS1 lineage was the most abundant candidate phylum accounting for 9.8-40.8% of the bacterial communities with a single dominant operational taxonomic unit (OTU). To elucidate the metabolic potential and ecological function of this species, we applied a single-cell genomic approach and obtained 18 single-cell amplified genomes presumably from a single species that was consistent with the dominant OTU throughout the sediments. The composite genome constructed by co-assembly showed the highest genome completeness among available Atribacteria JS1 genomes. Metabolic reconstruction suggested fermentative potential using various substrates and syntrophic acetate oxidation coupled with hydrogen or formate scavenging methanogens. This metabolic potential supports the predominance of Atribacteria JS1 in anoxic environments expanding our knowledge of the ecological function of this uncultivated group.
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Affiliation(s)
- Yung Mi Lee
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon, South Korea
| | - Kyuin Hwang
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon, South Korea.,Department of Polar Science, University of Science and Technology, Daejeon, South Korea
| | - Jae Il Lee
- Division of Polar Paleoenvironment, Korea Polar Research Institute, Incheon, South Korea
| | - Mincheol Kim
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon, South Korea
| | - Chung Yeon Hwang
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon, South Korea
| | - Hyun-Ju Noh
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon, South Korea
| | - Hakkyum Choi
- Division of Polar Earth-System Sciences, Korea Polar Research Institute, Incheon, South Korea
| | - Hong Kum Lee
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon, South Korea
| | - Jongsik Chun
- School of Biological Sciences, College of Natural Sciences, Seoul National University, Seoul, South Korea
| | - Soon Gyu Hong
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon, South Korea
| | - Seung Chul Shin
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, South Korea
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53
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Ahrendt SR, Quandt CA, Ciobanu D, Clum A, Salamov A, Andreopoulos B, Cheng JF, Woyke T, Pelin A, Henrissat B, Reynolds NK, Benny GL, Smith ME, James TY, Grigoriev IV. Leveraging single-cell genomics to expand the fungal tree of life. Nat Microbiol 2018; 3:1417-1428. [PMID: 30297742 PMCID: PMC6784888 DOI: 10.1038/s41564-018-0261-0] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 09/03/2018] [Indexed: 11/09/2022]
Abstract
Environmental DNA surveys reveal that most fungal diversity represents uncultured species. We sequenced the genomes of eight uncultured species across the fungal tree of life using a new single-cell genomics pipeline. We show that, despite a large variation in genome and gene space recovery from each single amplified genome (SAG), ≥90% can be recovered by combining multiple SAGs. SAGs provide robust placement for early-diverging lineages and infer a diploid ancestor of fungi. Early-diverging fungi share metabolic deficiencies and show unique gene expansions correlated with parasitism and unculturability. Single-cell genomics holds great promise in exploring fungal diversity, life cycles and metabolic potential.
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Affiliation(s)
- Steven R Ahrendt
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA.,Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - C Alisha Quandt
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA.,Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, USA
| | - Doina Ciobanu
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Alicia Clum
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Asaf Salamov
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Bill Andreopoulos
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Jan-Fang Cheng
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Tanja Woyke
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Adrian Pelin
- Ottawa Hospital Research Institute, Centre for Innovative Cancer Research, Ottawa, Ontario, Canada
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, UMR 7857 CNRS, Aix-Marseille University, Marseille, France.,Institut National de la Recherche Agronomique, USC 1408 Architecture et Fonction des Macromolécules Biologiques, Marseille, France.,Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Nicole K Reynolds
- Department of Plant Pathology, University of Florida, Gainesville, FL, USA
| | - Gerald L Benny
- Department of Plant Pathology, University of Florida, Gainesville, FL, USA
| | - Matthew E Smith
- Department of Plant Pathology, University of Florida, Gainesville, FL, USA
| | - Timothy Y James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA.
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA. .,Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA.
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54
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Landry ZC, Vergin K, Mannenbach C, Block S, Yang Q, Blainey P, Carlson C, Giovannoni S. Optofluidic Single-Cell Genome Amplification of Sub-micron Bacteria in the Ocean Subsurface. Front Microbiol 2018; 9:1152. [PMID: 29937754 PMCID: PMC6003095 DOI: 10.3389/fmicb.2018.01152] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 05/14/2018] [Indexed: 12/03/2022] Open
Abstract
Optofluidic single-cell genome amplification was used to obtain genome sequences from sub-micron cells collected from the euphotic and mesopelagic zones of the northwestern Sargasso Sea. Plankton cells were visually selected and manually sorted with an optical trap, yielding 20 partial genome sequences representing seven bacterial phyla. Two organisms, E01-9C-26 (Gammaproteobacteria), represented by four single cell genomes, and Opi.OSU.00C, an uncharacterized Verrucomicrobia, were the first of their types retrieved by single cell genome sequencing and were studied in detail. Metagenomic data showed that E01-9C-26 is found throughout the dark ocean, while Opi.OSU.00C was observed to bloom transiently in the nutrient-depleted euphotic zone of the late spring and early summer. The E01-9C-26 genomes had an estimated size of 4.76-5.05 Mbps, and contained "O" and "W"-type monooxygenase genes related to methane and ammonium monooxygenases that were previously reported from ocean metagenomes. Metabolic reconstruction indicated E01-9C-26 are likely versatile methylotrophs capable of scavenging C1 compounds, methylated compounds, reduced sulfur compounds, and a wide range of amines, including D-amino acids. The genome sequences identified E01-9C-26 as a source of "O" and "W"-type monooxygenase genes related to methane and ammonium monooxygenases that were previously reported from ocean metagenomes, but are of unknown function. In contrast, Opi.OSU.00C genomes encode genes for catabolizing carbohydrate compounds normally associated with eukaryotic phytoplankton. This exploration of optofluidics showed that it was effective for retrieving diverse single-cell bacterioplankton genomes and has potential advantages in microbiology applications that require working with small sample volumes or targeting cells by their morphology.
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Affiliation(s)
- Zachary C. Landry
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
- Institut für Umweltingenieurwissenschaften, ETH Zurich, Zurich, Switzerland
| | - Kevin Vergin
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | | | - Stephen Block
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | - Qiao Yang
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
- East China Sea Fisheries Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Paul Blainey
- Department of Biological Engineering, Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Craig Carlson
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Stephen Giovannoni
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
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55
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Kong X, Yu S, Fang W, Liu J, Li H. Enhancing syntrophic associations among Clostridium butyricum, Syntrophomonas and two types of methanogen by zero valent iron in an anaerobic assay with a high organic loading. BIORESOURCE TECHNOLOGY 2018; 257:181-191. [PMID: 29501951 DOI: 10.1016/j.biortech.2018.02.088] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 02/15/2018] [Accepted: 02/16/2018] [Indexed: 05/28/2023]
Abstract
The impacts of ZVI on microbial community diversity in an anaerobic assay with high organic loading were investigated. The relative abundance of bacteria, archaea, and the functional methyl coenzyme-M reductase (mcrA) gene were investigated using high-throughput sequencing, and variations in their quantity were determined by qPCR. The results showed that ZVI significantly increased both the relative abundance and quantity of Methanobacteriales and Methanosarcinales during hydrogenotrophic and acetoclastic methanogenesis. The relative abundance of syntrophic Methanobacteriales at the hydrolysis and acidogenesis stages resulted in H2 partial pressure decrease through an interspecies hydrogen transfer (IHT) network, which further induced butyric conversion to acetic by Syntrophomonas. The primary microbial metabolism then converted to acetoclastic methanogensis in the assay with ZVI addition. The short duration of this process and high relative abundance of Syntrophomonas, Clostridium butyricum and Methanosarcinales potentially indicated the existence of a novelty syntrophic mechanism for extracellular electron transfer, which promoted CH4 generation.
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Affiliation(s)
- Xin Kong
- Key Laboratory for Solid Waste Management and Environment Safety, Ministry of Education of China, School of Environment, Tsinghua University, Beijing 10084, PR China; College of Environmental Science and Engineering, Taiyuan University of Technology, Taiyuan 030024, PR China
| | - Shuyao Yu
- Key Laboratory for Solid Waste Management and Environment Safety, Ministry of Education of China, School of Environment, Tsinghua University, Beijing 10084, PR China
| | - Wen Fang
- Key Laboratory for Solid Waste Management and Environment Safety, Ministry of Education of China, School of Environment, Tsinghua University, Beijing 10084, PR China
| | - Jianguo Liu
- Key Laboratory for Solid Waste Management and Environment Safety, Ministry of Education of China, School of Environment, Tsinghua University, Beijing 10084, PR China.
| | - Huan Li
- Shenzhen Environmental Microbial Application and Risk Control Key Laboratory, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, PR China
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56
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Isoprenoid Quinones Resolve the Stratification of Redox Processes in a Biogeochemical Continuum from the Photic Zone to Deep Anoxic Sediments of the Black Sea. Appl Environ Microbiol 2018. [PMID: 29523543 DOI: 10.1128/aem.02736-17] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The stratified water column of the Black Sea serves as a model ecosystem for studying the interactions of microorganisms with major biogeochemical cycles. Here, we provide detailed analysis of isoprenoid quinones to study microbial redox processes in the ocean. In a continuum from the photic zone through the chemocline into deep anoxic sediments of the southern Black Sea, diagnostic quinones and inorganic geochemical parameters indicate niche segregation between redox processes and corresponding shifts in microbial community composition. Quinones specific for oxygenic photosynthesis and aerobic respiration dominate oxic waters, while quinones associated with thaumarchaeal ammonia oxidation and bacterial methanotrophy, respectively, dominate a narrow interval in suboxic waters. Quinone distributions indicate highest metabolic diversity within the anoxic zone, with anoxygenic photosynthesis being a major process in its photic layer. In the dark anoxic layer, quinone profiles indicate the occurrence of bacterial sulfur and nitrogen cycling, archaeal methanogenesis, and archaeal methanotrophy. Multiple novel ubiquinone isomers, possibly originating from unidentified intra-aerobic anaerobes, occur in this zone. The respiration modes found in the anoxic zone continue into shallow subsurface sediments, but quinone abundances rapidly decrease within the upper 50 cm below the sea floor, reflecting the transition to lower energy availability. In the deep subseafloor sediments, quinone distributions and geochemical profiles indicate archaeal methanogenesis/methanotrophy and potentially bacterial fermentative metabolisms. We observed that sedimentary quinone distributions track lithology, which supports prior hypotheses that deep biosphere community composition and metabolisms are determined by environmental conditions during sediment deposition.IMPORTANCE Microorganisms play crucial roles in global biogeochemical cycles, yet we have only a fragmentary understanding of the diversity of microorganisms and their metabolisms, as the majority remains uncultured. Thus, culture-independent approaches are critical for determining microbial diversity and active metabolic processes. In order to resolve the stratification of microbial communities in the Black Sea, we comprehensively analyzed redox process-specific isoprenoid quinone biomarkers in a unique continuous record from the photic zone through the chemocline into anoxic subsurface sediments. We describe an unprecedented quinone diversity that allowed us to detect distinct biogeochemical processes, including oxygenic photosynthesis, archaeal ammonia oxidation, aerobic methanotrophy, and anoxygenic photosynthesis in defined geochemical zones.
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57
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Xu Y, Zhao F. Single-cell metagenomics: challenges and applications. Protein Cell 2018; 9:501-510. [PMID: 29696589 PMCID: PMC5960468 DOI: 10.1007/s13238-018-0544-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 04/18/2018] [Indexed: 02/01/2023] Open
Abstract
With the development of high throughput sequencing and single-cell genomics technologies, many uncultured bacterial communities have been dissected by combining these two techniques. Especially, by simultaneously leveraging of single-cell genomics and metagenomics, researchers can greatly improve the efficiency and accuracy of obtaining whole genome information from complex microbial communities, which not only allow us to identify microbes but also link function to species, identify subspecies variations, study host-virus interactions and etc. Here, we review recent developments and the challenges need to be addressed in single-cell metagenomics, including potential contamination, uneven sequence coverage, sequence chimera, genome assembly and annotation. With the development of sequencing and computational methods, single-cell metagenomics will undoubtedly broaden its application in various microbiome studies.
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Affiliation(s)
- Yuan Xu
- Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China
| | - Fangqing Zhao
- Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
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58
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Huang X, Dong W, Wang H, Feng Y. Role of acid/alkali-treatment in primary sludge anaerobic fermentation: Insights into microbial community structure, functional shifts and metabolic output by high-throughput sequencing. BIORESOURCE TECHNOLOGY 2018; 249:943-952. [PMID: 29145121 DOI: 10.1016/j.biortech.2017.10.104] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 10/30/2017] [Accepted: 10/31/2017] [Indexed: 06/07/2023]
Abstract
This study aimed to investigate the effect of acid- or alkali-treatment on volatile fatty acids (VFAs) production and microbiological mechanism during primary sludge anaerobic fermentation. Seven fermentation experiments were conducted at different pH (3-12). Results showed that the optimal pH was 10 for accumulation of VFAs. High-throughput sequencing results indicated that acid and alkali treatment could inhibit Erysipelotrichaceae_UCG-004 and norank_p_Aminicenantes, instead of promoting Pseudomonas and Tissierella at acidic and alkaline condition, respectively. Besides, molecular ecological networks (MENs) analysis and multivariate canonical correspondence analysis (CCA) revealed that the microbial community interactions are significant different between acid and alkali treatment groups, and acetic acid was the most vital factor in the distinct bacterial community assemblages. Predictive functional profiling using marker gene sequences found that amino acid transport and metabolism was the most abundant metabolic type with 8.43-9.41%, and acid- and alkali-treatment did not benefit Stickland reaction.
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Affiliation(s)
- Xiao Huang
- School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen 518055, China
| | - Wenyi Dong
- School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen 518055, China; Shenzhen Key Laboratory of Water Resource Utilization and Environmental Pollution Control, Shenzhen 518055, China
| | - Hongjie Wang
- School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen 518055, China; Shenzhen Key Laboratory of Water Resource Utilization and Environmental Pollution Control, Shenzhen 518055, China.
| | - Yangyang Feng
- School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen 518055, China
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59
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Obtaining high-quality draft genomes from uncultured microbes by cleaning and co-assembly of single-cell amplified genomes. Sci Rep 2018; 8:2059. [PMID: 29391438 PMCID: PMC5794965 DOI: 10.1038/s41598-018-20384-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 01/17/2018] [Indexed: 11/08/2022] Open
Abstract
Single-cell genomics is a straightforward approach to obtain genomes from uncultured microbes. However, sequence reads from a single-cell amplified genome (SAG) contain significant bias and chimeric sequences. Here, we describe Cleaning and Co-assembly of a Single-Cell Amplified Genome (ccSAG), a novel analytical workflow to obtain composite single-cell genomes with elimination of sequence errors. By the integration of ccSAG with a massively parallel single-cell genome amplification platform based on droplet microfluidics, we can generate multiple SAGs and effectively integrate them into the composite genomes quality equivalent to the data obtained from bulk DNA. We obtained two novel draft genomes from single gut microbial cells with high completeness (>96.6%) and extremely low contamination (<1.25%). Moreover, we revealed the presence of single nucleotide polymorphisms in the specific gene by sequence comparison at the single-cell level. Thus, the workflow yields near-complete genomes from uncultured microbes, and enables analyses of genetic heterogeneity within identical strains.
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60
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Mulat DG, Huerta SG, Kalyani D, Horn SJ. Enhancing methane production from lignocellulosic biomass by combined steam-explosion pretreatment and bioaugmentation with cellulolytic bacterium Caldicellulosiruptor bescii. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:19. [PMID: 29422947 PMCID: PMC5787918 DOI: 10.1186/s13068-018-1025-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 01/13/2018] [Indexed: 05/07/2023]
Abstract
BACKGROUND Biogas production from lignocellulosic biomass is generally considered to be challenging due to the recalcitrant nature of this biomass. In this study, the recalcitrance of birch was reduced by applying steam-explosion (SE) pretreatment (210 °C and 10 min). Moreover, bioaugmentation with the cellulolytic bacterium Caldicellulosiruptor bescii was applied to possibly enhance the methane production from steam-exploded birch in an anaerobic digestion (AD) process under thermophilic conditions (62 °C). RESULTS Overall, the combined SE and bioaugmentation enhanced the methane yield up to 140% compared to untreated birch, while SE alone contributed to the major share of methane enhancement by 118%. The best methane improvement of 140% on day 50 was observed in bottles fed with pretreated birch and bioaugmentation with lower dosages of C. bescii (2 and 5% of inoculum volume). The maximum methane production rate also increased from 4-mL CH4/g VS (volatile solids)/day for untreated birch to 9-14-mL CH4/g VS/day for steam-exploded birch with applied bioaugmentation. Bioaugmentation was particularly effective for increasing the initial methane production rate of the pretreated birch yielding 21-44% more methane than the pretreated birch without applied bioaugmentation. The extent of solubilization of the organic matter was increased by more than twofold when combined SE pretreatment and bioaugmentation was used in comparison with the methane production from untreated birch. The beneficial effects of SE and bioaugmentation on methane yield indicated that biomass recalcitrance and hydrolysis step are the limiting factors for efficient AD of lignocellulosic biomass. Microbial community analysis by 16S rRNA amplicon sequencing showed that the microbial community composition was altered by the pretreatment and bioaugmentation processes. Notably, the enhanced methane production by pretreatment and bioaugmentation was well correlated with the increase in abundance of key bacterial and archaeal communities, particularly the hydrolytic bacterium Caldicoprobacter, several members of syntrophic acetate oxidizing bacteria and the hydrogenotrophic Methanothermobacter. CONCLUSION Our findings demonstrate the potential of combined SE and bioaugmentation for enhancing methane production from lignocellulosic biomass.
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Affiliation(s)
- Daniel Girma Mulat
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P.O.Box 5003, 1432 Ås, Norway
| | - Silvia Greses Huerta
- Department of Chemical Engineering, University of Valencia, P.O.Box 46100, Valencia, Spain
| | - Dayanand Kalyani
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P.O.Box 5003, 1432 Ås, Norway
| | - Svein Jarle Horn
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P.O.Box 5003, 1432 Ås, Norway
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61
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Xie W, Luo H, Murugapiran SK, Dodsworth JA, Chen S, Sun Y, Hedlund BP, Wang P, Fang H, Deng M, Zhang CL. Localized high abundance of Marine Group II archaea in the subtropical Pearl River Estuary: implications for their niche adaptation. Environ Microbiol 2017; 20:734-754. [PMID: 29235710 DOI: 10.1111/1462-2920.14004] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 11/18/2017] [Accepted: 11/19/2017] [Indexed: 11/29/2022]
Abstract
Marine Group II archaea are widely distributed in global oceans and dominate the total archaeal community within the upper euphotic zone of temperate waters. However, factors controlling the distribution of MGII are poorly delineated and the physiology and ecological functions of these still-uncultured organisms remain elusive. In this study, we investigated the planktonic MGII associated with particles and in free-living forms in the Pearl River Estuary (PRE) over a 10-month period. We detected high abundance of particle-associated MGII in PRE (up to ∼108 16S rRNA gene copies/l), which was around 10-fold higher than the free-living MGII in the same region, and an order of magnitude higher than previously reported in other marine environments. 10‰ salinity appeared to be a threshold value for these MGII because MGII abundance decreased sharply below it. Above 10‰ salinity, the abundance of MGII on the particles was positively correlated with phototrophs and MGII in the surface water was negatively correlated with irradiance. However, the abundances of those free-living MGII showed positive correlations with salinity and temperature, suggesting the different physiological characteristics between particle-attached and free-living MGIIs. A nearly completely assembled metagenome, MGIIa_P, was recovered using metagenome binning methods. Compared with the other two MGII genomes from surface ocean, MGIIa_P contained higher proportions of glycoside hydrolases, indicating the ability of MGIIa_P to hydrolyse glycosidic bonds in complex sugars in PRE. MGIIa_P is the first assembled MGII metagenome containing a catalase gene, which might be involved in scavenging reactive oxygen species generated by the abundant phototrophs in the eutrophic PRE. Our study presented the widespread and high abundance of MGII in the water columns of PRE, and characterized the determinant abiotic factors affecting their distribution. Their association with heterotrophs, preference for particles and resourceful metabolic traits indicate MGII might play a significant role in metabolising organic matters in the PRE and other temperate estuarine systems.
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Affiliation(s)
- Wei Xie
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, 200092, China
| | - Haiwei Luo
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and Partner State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Senthil K Murugapiran
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV 89154, USA.,MetaGénoPolis, Institut National de la Recherche Agronomique (INRA), Université Paris-Saclay, Jouy-en-Josas, 78350, France
| | - Jeremy A Dodsworth
- Department of Biology, California State University, San Bernardino, CA 92407, USA
| | - Songze Chen
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, 200092, China
| | - Ying Sun
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and Partner State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV 89154, USA
| | - Peng Wang
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, 200092, China
| | - Huaying Fang
- School of Mathematical Sciences, Peking University, Beijing, 100871, China
| | - Minghua Deng
- School of Mathematical Sciences, Peking University, Beijing, 100871, China
| | - Chuanlun L Zhang
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
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62
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Lee J, Shin SG, Han G, Koo T, Hwang S. Bacteria and archaea communities in full-scale thermophilic and mesophilic anaerobic digesters treating food wastewater: Key process parameters and microbial indicators of process instability. BIORESOURCE TECHNOLOGY 2017; 245:689-697. [PMID: 28917104 DOI: 10.1016/j.biortech.2017.09.015] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 09/02/2017] [Accepted: 09/04/2017] [Indexed: 06/07/2023]
Abstract
In this study, four different mesophilic and thermophilic full-scale anaerobic digesters treating food wastewater (FWW) were monitored for 1-2years in order to investigate: 1) microbial communities underpinning anaerobic digestion of FWW, 2) significant factors shaping microbial community structures, and 3) potential microbial indicators of process instability. Twenty-seven bacterial genera were identified as abundant bacteria underpinning the anaerobic digestion of FWW. Methanosaeta harundinacea, M. concilii, Methanoculleus bourgensis, M. thermophilus, and Methanobacterium beijingense were revealed as dominant methanogens. Bacterial community structures were clearly differentiated by digesters; archaeal community structures of each digester were dominated by one or two methanogen species. Temperature, ammonia, propionate, Na+, and acetate in the digester were significant factors shaping microbial community structures. The total microbial populations, microbial diversity, and specific bacteria genera showed potential as indicators of process instability in the anaerobic digestion of FWW.
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Affiliation(s)
- Joonyeob Lee
- School of Environmental Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, Republic of Korea
| | - Seung Gu Shin
- Department of Energy Engineering, Gyeongnam National University of Science and Technology (GNTECH), Jinju, Gyeongnam, Republic of Korea
| | - Gyuseong Han
- School of Environmental Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, Republic of Korea
| | - Taewoan Koo
- School of Environmental Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, Republic of Korea
| | - Seokhwan Hwang
- School of Environmental Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, Republic of Korea.
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63
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Pampillón-González L, Ortiz-Cornejo NL, Luna-Guido M, Dendooven L, Navarro-Noya YE. Archaeal and Bacterial Community Structure in an Anaerobic Digestion Reactor (Lagoon Type) Used for Biogas Production at a Pig Farm. J Mol Microbiol Biotechnol 2017; 27:306-317. [DOI: 10.1159/000479108] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 07/03/2017] [Indexed: 01/02/2023] Open
Abstract
Biogas production from animal waste is an economically viable way to reduce environmental pollution and produce valuable products, i.e<i>.</i>, methane and a nutrient-rich organic waste product. An anaerobic digestion reactor for biogas production from pig waste was sampled at the entrance, middle (digestion chamber), and exit of a digester, while the bacterial and archaeal community structure was studied by 16S rRNA gene metagenomics. The number of bacterial operational taxonomic units (OTU)-97% was 3-7 times larger than that of archaeal ones. Bacteria and Archaea found in feces of animals (e.g., Clostridiaceae, Lachnospiraceae, Ruminococcaceae, <i>Methanosarcina</i>, <i>Methanolobus</i>, <i>Methanosaeta</i>, and <i>Methanospirillum</i>) dominated the entrance of the digester. The digestion chamber was dominated by anaerobic sugar-fermenting OP9 bacteria and the syntrophic bacteria <i>Candidatus</i> Cloacamonas (Waste Water of Evry 1; WWE1). The methanogens dominant in the digestion chamber were the acetoclastic <i>Methanosaeta</i> and the hydrogenothrophic <i>Methanoculleus</i> and <i>Methanospirillum</i>. Similar bacterial and archaeal groups that dominated in the middle of the digestion chamber were found in the waste that left the digester. Predicted functions associated with degradation of xenobiotic compounds were significantly different between the sampling locations. The microbial community found in an anaerobic digestion reactor loaded with pig manure contained microorganisms with biochemical capacities related to the 4 phases of methane production.
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64
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Depth Distribution and Assembly of Sulfate-Reducing Microbial Communities in Marine Sediments of Aarhus Bay. Appl Environ Microbiol 2017; 83:AEM.01547-17. [PMID: 28939599 DOI: 10.1128/aem.01547-17] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2017] [Accepted: 09/14/2017] [Indexed: 11/20/2022] Open
Abstract
Most sulfate-reducing microorganisms (SRMs) present in subsurface marine sediments belong to uncultured groups only distantly related to known SRMs, and it remains unclear how changing geochemical zones and sediment depth influence their community structure. We mapped the community composition and abundance of SRMs by amplicon sequencing and quantifying the dsrB gene, which encodes dissimilatory sulfite reductase subunit beta, in sediment samples covering different vertical geochemical zones ranging from the surface sediment to the deep sulfate-depleted subsurface at four locations in Aarhus Bay, Denmark. SRMs were present in all geochemical zones, including sulfate-depleted methanogenic sediment. The biggest shift in SRM community composition and abundance occurred across the transition from bioturbated surface sediments to nonbioturbated sediments below, where redox fluctuations and the input of fresh organic matter due to macrofaunal activity are absent. SRM abundance correlated with sulfate reduction rates determined for the same sediments. Sulfate availability showed a weaker correlation with SRM abundances and no significant correlation with the composition of the SRM community. The overall SRM species diversity decreased with depth, yet we identified a subset of highly abundant community members that persists across all vertical geochemical zones of all stations. We conclude that subsurface SRM communities assemble by the persistence of members of the surface community and that the transition from the bioturbated surface sediment to the unmixed sediment below is a main site of assembly of the subsurface SRM community.IMPORTANCE Sulfate-reducing microorganisms (SRMs) are key players in the marine carbon and sulfur cycles, especially in coastal sediments, yet little is understood about the environmental factors controlling their depth distribution. Our results suggest that macrofaunal activity is a key driver of SRM abundance and community structure in marine sediments and that a small subset of SRM species of high relative abundance in the subsurface SRM community persists from the sulfate-rich surface sediment to sulfate-depleted methanogenic subsurface sediment. More generally, we conclude that SRM communities inhabiting the subsurface seabed assemble by the selective survival of members of the surface community.
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65
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Diverse Marinimicrobia bacteria may mediate coupled biogeochemical cycles along eco-thermodynamic gradients. Nat Commun 2017; 8:1507. [PMID: 29142241 PMCID: PMC5688066 DOI: 10.1038/s41467-017-01376-9] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 09/11/2017] [Indexed: 12/22/2022] Open
Abstract
Microbial communities drive biogeochemical cycles through networks of metabolite exchange that are structured along energetic gradients. As energy yields become limiting, these networks favor co-metabolic interactions to maximize energy disequilibria. Here we apply single-cell genomics, metagenomics, and metatranscriptomics to study bacterial populations of the abundant "microbial dark matter" phylum Marinimicrobia along defined energy gradients. We show that evolutionary diversification of major Marinimicrobia clades appears to be closely related to energy yields, with increased co-metabolic interactions in more deeply branching clades. Several of these clades appear to participate in the biogeochemical cycling of sulfur and nitrogen, filling previously unassigned niches in the ocean. Notably, two Marinimicrobia clades, occupying different energetic niches, express nitrous oxide reductase, potentially acting as a global sink for the greenhouse gas nitrous oxide.
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66
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Becraft ED, Dodsworth JA, Murugapiran SK, Thomas SC, Ohlsson JI, Stepanauskas R, Hedlund BP, Swingley WD. Genomic Comparison of Two Family-Level Groups of the Uncultivated NAG1 Archaeal Lineage from Chemically and Geographically Disparate Hot Springs. Front Microbiol 2017; 8:2082. [PMID: 29163388 PMCID: PMC5671600 DOI: 10.3389/fmicb.2017.02082] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 10/11/2017] [Indexed: 11/13/2022] Open
Abstract
Recent progress based on single-cell genomics and metagenomic investigations of archaea in a variety of extreme environments has led to significant advances in our understanding of the diversity, evolution, and metabolic potential of archaea, yet the vast majority of archaeal diversity remains undersampled. In this work, we coordinated single-cell genomics with metagenomics in order to construct a near-complete genome from a deeply branching uncultivated archaeal lineage sampled from Great Boiling Spring (GBS) in the U.S. Great Basin, Nevada. This taxon is distantly related (distinct families) to an archaeal genome, designated "Novel Archaeal Group 1" (NAG1), which was extracted from a metagenome recovered from an acidic iron spring in Yellowstone National Park (YNP). We compared the metabolic predictions of the NAG1 lineage to better understand how these archaea could inhabit such chemically distinct environments. Similar to the NAG1 population previously studied in YNP, the NAG1 population from GBS is predicted to utilize proteins as a primary carbon source, ferment simple carbon sources, and use oxygen as a terminal electron acceptor under oxic conditions. However, GBS NAG1 populations contained distinct genes involved in central carbon metabolism and electron transfer, including nitrite reductase, which could confer the ability to reduce nitrite under anaerobic conditions. Despite inhabiting chemically distinct environments with large variations in pH, GBS NAG1 populations shared many core genomic and metabolic features with the archaeon identified from YNP, yet were able to carve out a distinct niche at GBS.
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Affiliation(s)
- Eric D Becraft
- Department of Biological Sciences, Northern Illinois University, DeKalb, IL, United States.,Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States
| | - Jeremy A Dodsworth
- Department of Biology, California State University, San Bernardino, San Bernardino, CA, United States.,School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States
| | - Senthil K Murugapiran
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States.,MetaGénoPolis, Institut National de la Recherche Agronomique (INRA), Université Paris-Saclay, Jouy-en-Josas, France
| | - Scott C Thomas
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States
| | - J Ingemar Ohlsson
- Department of Biological Sciences, Northern Illinois University, DeKalb, IL, United States
| | | | - Brian P Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States.,Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, Las Vegas, NV, United States
| | - Wesley D Swingley
- Department of Biological Sciences, Northern Illinois University, DeKalb, IL, United States
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67
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The trajectory of microbial single-cell sequencing. Nat Methods 2017; 14:1045-1054. [DOI: 10.1038/nmeth.4469] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 08/04/2017] [Indexed: 12/21/2022]
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68
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Carr SA, Schubotz F, Dunbar RB, Mills CT, Dias R, Summons RE, Mandernack KW. Acetoclastic Methanosaeta are dominant methanogens in organic-rich Antarctic marine sediments. ISME JOURNAL 2017; 12:330-342. [PMID: 29039843 PMCID: PMC5776447 DOI: 10.1038/ismej.2017.150] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 06/16/2017] [Accepted: 06/24/2017] [Indexed: 01/11/2023]
Abstract
Despite accounting for the majority of sedimentary methane, the physiology and relative abundance of subsurface methanogens remain poorly understood. We combined intact polar lipid and metagenome techniques to better constrain the presence and functions of methanogens within the highly reducing, organic-rich sediments of Antarctica's Adélie Basin. The assembly of metagenomic sequence data identified phylogenic and functional marker genes of methanogens and generated the first Methanosaeta sp. genome from a deep subsurface sedimentary environment. Based on structural and isotopic measurements, glycerol dialkyl glycerol tetraethers with diglycosyl phosphatidylglycerol head groups were classified as biomarkers for active methanogens. The stable carbon isotope (δ13C) values of these biomarkers and the Methanosaeta partial genome suggest that these organisms are acetoclastic methanogens and represent a relatively small (0.2%) but active population. Metagenomic and lipid analyses suggest that Thaumarchaeota and heterotrophic bacteria co-exist with Methanosaeta and together contribute to increasing concentrations and δ13C values of dissolved inorganic carbon with depth. This study presents the first functional insights of deep subsurface Methanosaeta organisms and highlights their role in methane production and overall carbon cycling within sedimentary environments.
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Affiliation(s)
| | - Florence Schubotz
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Robert B Dunbar
- Department of Environmental Earth Systems Science, Stanford University, Stanford, CA, USA
| | | | - Robert Dias
- US Geological Survey, Denver Federal Center, Denver, CO, USA
| | - Roger E Summons
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kevin W Mandernack
- Department of Earth Sciences, Indiana University - Purdue University Indianapolis, Indianapolis, IN, USA
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69
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Labonté JM, Lever MA, Edwards KJ, Orcutt BN. Influence of Igneous Basement on Deep Sediment Microbial Diversity on the Eastern Juan de Fuca Ridge Flank. Front Microbiol 2017; 8:1434. [PMID: 28824568 PMCID: PMC5539551 DOI: 10.3389/fmicb.2017.01434] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 07/14/2017] [Indexed: 12/18/2022] Open
Abstract
Microbial communities living in deeply buried sediment may be adapted to long-term energy limitation as they are removed from new detrital energy inputs for thousands to millions of years. However, sediment layers near the underlying oceanic crust may receive inputs from below that influence microbial community structure and/or activity. As part of the Census of Deep Life, we used 16S rRNA gene tag pyrosequencing on DNA extracted from a spectrum of deep sediment-basement interface samples from the subsurface of the Juan de Fuca Ridge flank (collected on IODP Expedition 327) to examine this possible basement influence on deep sediment communities. This area experiences rapid sedimentation, with an underlying basaltic crust that hosts a dynamic flux of hydrothermal fluids that diffuse into the sediment. Chloroflexi sequences dominated tag libraries in all sediment samples, with variation in the abundance of other bacterial groups (e.g., Actinobacteria, Aerophobetes, Atribacteria, Planctomycetes, and Nitrospirae). These variations occur in relation to the type of sediment (clays versus carbonate-rich) and the depth of sample origin, and show no clear connection to the distance from the discharge outcrop or to basement fluid microbial communities. Actinobacteria-related sequences dominated the basalt libraries, but these should be viewed cautiously due to possibilities for imprinting from contamination. Our results indicate that proximity to basement or areas of seawater recharge is not a primary driver of microbial community composition in basal sediment, even though fluids diffusing from basement into sediment may stimulate microbial activity.
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Affiliation(s)
- Jessica M Labonté
- Bigelow Laboratory for Ocean Sciences, East BoothbayME, United States.,Department of Marine Biology, Texas A&M University at Galveston, GalvestonTX, United States
| | - Mark A Lever
- Center for Geomicrobiology, Aarhus UniversityAarhus, Denmark.,Environmental Systems Science, ETH ZürichZurich, Switzerland
| | - Katrina J Edwards
- Department of Biological Sciences, University of Southern California, Los AngelesCA, United States
| | - Beth N Orcutt
- Bigelow Laboratory for Ocean Sciences, East BoothbayME, United States.,Center for Geomicrobiology, Aarhus UniversityAarhus, Denmark
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70
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Hosokawa M, Nishikawa Y, Kogawa M, Takeyama H. Massively parallel whole genome amplification for single-cell sequencing using droplet microfluidics. Sci Rep 2017; 7:5199. [PMID: 28701744 PMCID: PMC5507899 DOI: 10.1038/s41598-017-05436-4] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 05/30/2017] [Indexed: 11/17/2022] Open
Abstract
Massively parallel single-cell genome sequencing is required to further understand genetic diversities in complex biological systems. Whole genome amplification (WGA) is the first step for single-cell sequencing, but its throughput and accuracy are insufficient in conventional reaction platforms. Here, we introduce single droplet multiple displacement amplification (sd-MDA), a method that enables massively parallel amplification of single cell genomes while maintaining sequence accuracy and specificity. Tens of thousands of single cells are compartmentalized in millions of picoliter droplets and then subjected to lysis and WGA by passive droplet fusion in microfluidic channels. Because single cells are isolated in compartments, their genomes are amplified to saturation without contamination. This enables the high-throughput acquisition of contamination-free and cell specific sequence reads from single cells (21,000 single-cells/h), resulting in enhancement of the sequence data quality compared to conventional methods. This method allowed WGA of both single bacterial cells and human cancer cells. The obtained sequencing coverage rivals those of conventional techniques with superior sequence quality. In addition, we also demonstrate de novo assembly of uncultured soil bacteria and obtain draft genomes from single cell sequencing. This sd-MDA is promising for flexible and scalable use in single-cell sequencing.
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Affiliation(s)
- Masahito Hosokawa
- Research Organization for Nano & Life Innovation, Waseda University, 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo, 162-0041, Japan.,PRESTO, Japan Science and Technology Agency (JST), 5-3 Yonban-cho, Chiyoda-ku, Tokyo, 102-0075, Japan
| | - Yohei Nishikawa
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan
| | - Masato Kogawa
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan.,Computational Bio Big-Data Open Innovation Laboratory, AIST-Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-0072, Japan
| | - Haruko Takeyama
- Research Organization for Nano & Life Innovation, Waseda University, 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo, 162-0041, Japan. .,Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan. .,Computational Bio Big-Data Open Innovation Laboratory, AIST-Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-0072, Japan.
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71
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Fitamo T, Treu L, Boldrin A, Sartori C, Angelidaki I, Scheutz C. Microbial population dynamics in urban organic waste anaerobic co-digestion with mixed sludge during a change in feedstock composition and different hydraulic retention times. WATER RESEARCH 2017; 118:261-271. [PMID: 28456109 DOI: 10.1016/j.watres.2017.04.012] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 03/22/2017] [Accepted: 04/04/2017] [Indexed: 05/27/2023]
Abstract
Microbial communities play an essential role in the biochemical pathways of anaerobic digestion processes. The correlations between microorganisms' relative abundance and anaerobic digestion process parameters were investigated, by considering the effect of different feedstock compositions and hydraulic retention times (HRTs). Shifts in microbial diversity and changes in microbial community richness were observed by changing feedstock composition from mono-digestion of mixed sludge to co-digestion of food waste, grass clippings and garden waste with mixed sludge at HRT of 30, 20, 15 and 10 days. Syntrophic acetate oxidation along with hydrogenotrophic methanogenesis, mediated by Methanothermobacter, was found to be the most prevalent methane formation pathway, with the only exception of 10 days' HRT, in which Methanosarcina was the most dominant archaea. Significantly, the degradation of complex organic polymers was found to be the most active process, performed by members of S1 (Thermotogales), Thermonema and Lactobacillus in a reactor fed with a high share of food waste. Conversely, Thermacetogenium, Anaerobaculum, Ruminococcaceae, Porphyromonadaceae and the lignocellulosic-degrading Clostridium were the significantly more abundant bacteria in the reactor fed with an increased share of lignocellulosic biomass in the form of grass clippings and garden waste. Finally, microbes belonging to Coprothermobacter, Syntrophomonas and Clostridium were correlated significantly with the specific methane yield obtained in both reactors.
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Affiliation(s)
- Temesgen Fitamo
- Department of Environmental Engineering, Technical University of Denmark, Miljoevej, Building 115, DK-2800, Kongens Lyngby, Denmark.
| | - Laura Treu
- Department of Environmental Engineering, Technical University of Denmark, Miljoevej, Building 115, DK-2800, Kongens Lyngby, Denmark; Department of Agronomy, Food, Natural Resources, Animal and Environment (DAFNAE), viale dell'Università, 16, 35020, Legnaro, Padova, Italy
| | - Alessio Boldrin
- Department of Environmental Engineering, Technical University of Denmark, Miljoevej, Building 115, DK-2800, Kongens Lyngby, Denmark
| | - Cristina Sartori
- Department of Agronomy, Food, Natural Resources, Animal and Environment (DAFNAE), viale dell'Università, 16, 35020, Legnaro, Padova, Italy
| | - Irini Angelidaki
- Department of Environmental Engineering, Technical University of Denmark, Miljoevej, Building 115, DK-2800, Kongens Lyngby, Denmark
| | - Charlotte Scheutz
- Department of Environmental Engineering, Technical University of Denmark, Miljoevej, Building 115, DK-2800, Kongens Lyngby, Denmark
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72
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Thiel V, Hügler M, Ward DM, Bryant DA. The Dark Side of the Mushroom Spring Microbial Mat: Life in the Shadow of Chlorophototrophs. II. Metabolic Functions of Abundant Community Members Predicted from Metagenomic Analyses. Front Microbiol 2017. [PMID: 28634470 PMCID: PMC5459899 DOI: 10.3389/fmicb.2017.00943] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Microbial mat communities in the effluent channels of Octopus and Mushroom Springs within the Lower Geyser Basin of Yellowstone National Park have been extensively characterized. Previous studies have focused on the chlorophototrophic organisms of the phyla Cyanobacteria and Chloroflexi. However, the diversity and metabolic functions of the other portion of the community in the microoxic/anoxic region of the mat are poorly understood. We recently described the diverse but extremely uneven microbial assemblage in the undermat of Mushroom Spring based on 16S rRNA amplicon sequences, which was dominated by Roseiflexus members, filamentous anoxygenic chlorophototrophs. In this study, we analyzed the orange-colored undermat portion of the community of Mushroom Spring mats in a genome-centric approach and discuss the metabolic potentials of the major members. Metagenome binning recovered partial genomes of all abundant community members, ranging in completeness from ~28 to 96%, and allowed affiliation of function with taxonomic identity even for representatives of novel and Candidate phyla. Less complete metagenomic bins correlated with high microdiversity. The undermat portion of the community was found to be a mixture of phototrophic and chemotrophic organisms, which use bicarbonate as well as organic carbon sources derived from different cell components and fermentation products. The presence of rhodopsin genes in many taxa strengthens the hypothesis that light energy is of major importance. Evidence for the usage of all four bacterial carbon fixation pathways was found in the metagenome. Nitrogen fixation appears to be limited to Synechococcus spp. in the upper mat layer and Thermodesulfovibrio sp. in the undermat, and nitrate/nitrite metabolism was limited. A closed sulfur cycle is indicated by biological sulfate reduction combined with the presence of genes for sulfide oxidation mainly in phototrophs. Finally, a variety of undermat microorganisms have genes for hydrogen production and consumption, which leads to the observed diel hydrogen concentration patterns.
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Affiliation(s)
- Vera Thiel
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University ParkPA, United States
| | - Michael Hügler
- Department Microbiology and Molecular Biology, DVGW-Technologiezentrum WasserKarlsruhe, Germany
| | - David M Ward
- Department of Land Resources and Environmental Sciences, Montana State UniversityBozeman, MT, United States
| | - Donald A Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University ParkPA, United States.,Department of Chemistry and Biochemistry, Montana State UniversityBozeman, MT, United States
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73
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Deng Y, Huang Z, Zhao M, Ruan W, Miao H, Ren H. Effects of co-inoculating rice straw with ruminal microbiota and anaerobic sludge: digestion performance and spatial distribution of microbial communities. Appl Microbiol Biotechnol 2017; 101:5937-5948. [PMID: 28536735 DOI: 10.1007/s00253-017-8332-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 04/08/2017] [Accepted: 05/06/2017] [Indexed: 10/19/2022]
Abstract
Ruminal microbiota (RM) were co-inoculated with anaerobic sludge (AS) at different ratios to study the digestion of rice straw in batch experiments. The CH4 yield reached 273.64 mL/g volatile solid (VS) at a co-inoculum ratio of 1:1. The xylanase and cellulase activities were 198.88-212.88 and 24.51-29.08 U/mL in co-inoculated samples, respectively, and were significantly different compared to the results for single inoculum (p < 0.05). Higher ratios of AS enhanced acetoclastic methanogenesis, and propionate accumulation could be the main reason for the longer lag phase observed in samples with a higher RM ratio. The microbial compositions were clearly altered after digestion. Fibrobacter, Ruminococcus and Butyrivibrio from the rumen did not settle in the co-inoculated system, whereas Clostridiales members became the main polysaccharide degraders. Microbial interactions involving hydrolytic bacteria and acetoclastic methanogens in the residue were considered to be significant for hydrolysis activities and methane production. Syntrophy involving propionate oxidizers with associated methanogens occurred in the liquid phase. Our findings provide a better understanding of the anaerobic digestion of rice straw that is driven by specific microbial populations.
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Affiliation(s)
- Yuying Deng
- School of Environmental and Civil Engineering, Jiangnan University, Wuxi, 214122, China.,Changzhou Vocational Institute of Engineering, Changzhou, 213164, China
| | - Zhenxing Huang
- School of Environmental and Civil Engineering, Jiangnan University, Wuxi, 214122, China. .,Jiangsu Key Laboratory of Anaerobic Biotechnology, Wuxi, 214122, China. .,Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou, 215009, China.
| | - Mingxing Zhao
- School of Environmental and Civil Engineering, Jiangnan University, Wuxi, 214122, China.,Jiangsu Key Laboratory of Anaerobic Biotechnology, Wuxi, 214122, China
| | - Wenquan Ruan
- School of Environmental and Civil Engineering, Jiangnan University, Wuxi, 214122, China. .,Jiangsu Key Laboratory of Anaerobic Biotechnology, Wuxi, 214122, China. .,Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou, 215009, China.
| | - Hengfeng Miao
- School of Environmental and Civil Engineering, Jiangnan University, Wuxi, 214122, China.,Jiangsu Key Laboratory of Anaerobic Biotechnology, Wuxi, 214122, China
| | - Hongyan Ren
- School of Environmental and Civil Engineering, Jiangnan University, Wuxi, 214122, China.,Jiangsu Key Laboratory of Anaerobic Biotechnology, Wuxi, 214122, China
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74
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Waite DW, Vanwonterghem I, Rinke C, Parks DH, Zhang Y, Takai K, Sievert SM, Simon J, Campbell BJ, Hanson TE, Woyke T, Klotz MG, Hugenholtz P. Comparative Genomic Analysis of the Class Epsilonproteobacteria and Proposed Reclassification to Epsilonbacteraeota (phyl. nov.). Front Microbiol 2017; 8:682. [PMID: 28484436 PMCID: PMC5401914 DOI: 10.3389/fmicb.2017.00682] [Citation(s) in RCA: 218] [Impact Index Per Article: 31.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 04/04/2017] [Indexed: 12/25/2022] Open
Abstract
The Epsilonproteobacteria is the fifth validly described class of the phylum Proteobacteria, known primarily for clinical relevance and for chemolithotrophy in various terrestrial and marine environments, including deep-sea hydrothermal vents. As 16S rRNA gene repositories have expanded and protein marker analysis become more common, the phylogenetic placement of this class has become less certain. A number of recent analyses of the bacterial tree of life using both 16S rRNA and concatenated marker gene analyses have failed to recover the Epsilonproteobacteria as monophyletic with all other classes of Proteobacteria. In order to address this issue, we investigated the phylogenetic placement of this class in the bacterial domain using 16S and 23S rRNA genes, as well as 120 single-copy marker proteins. Single- and concatenated-marker trees were created using a data set of 4,170 bacterial representatives, including 98 Epsilonproteobacteria. Phylogenies were inferred under a variety of tree building methods, with sequential jackknifing of outgroup phyla to ensure robustness of phylogenetic affiliations under differing combinations of bacterial genomes. Based on the assessment of nearly 300 phylogenetic tree topologies, we conclude that the continued inclusion of Epsilonproteobacteria within the Proteobacteria is not warranted, and that this group should be reassigned to a novel phylum for which we propose the name Epsilonbacteraeota (phyl. nov.). We further recommend the reclassification of the order Desulfurellales (Deltaproteobacteria) to a novel class within this phylum and a number of subordinate changes to ensure consistency with the genome-based phylogeny. Phylogenomic analysis of 658 genomes belonging to the newly proposed Epsilonbacteraeota suggests that the ancestor of this phylum was an autotrophic, motile, thermophilic chemolithotroph that likely assimilated nitrogen from ammonium taken up from the environment or generated from environmental nitrate and nitrite by employing a variety of functional redox modules. The emergence of chemoorganoheterotrophic lifestyles in several Epsilonbacteraeota families is the result of multiple independent losses of various ancestral chemolithoautotrophic pathways. Our proposed reclassification of this group resolves an important anomaly in bacterial systematics and ensures that the taxonomy of Proteobacteria remains robust, specifically as genome-based taxonomies become more common.
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Affiliation(s)
- David W. Waite
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St LuciaQLD, Australia
| | - Inka Vanwonterghem
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St LuciaQLD, Australia
| | - Christian Rinke
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St LuciaQLD, Australia
| | - Donovan H. Parks
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St LuciaQLD, Australia
| | - Ying Zhang
- Department of Cell and Molecular Biology, College of the Environment and Life Sciences, University of Rhode Island, KingstonRI, USA
| | - Ken Takai
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and TechnologyYokosuka, Japan
| | - Stefan M. Sievert
- Department of Biology, Woods Hole Oceanographic Institution, Woods HoleMA, USA
| | - Jörg Simon
- Microbial Energy Conversion and Biotechnology, Department of Biology, Technische Universität DarmstadtDarmstadt, Germany
| | - Barbara J. Campbell
- Department of Biological Sciences, Life Science Facility, Clemson University, ClemsonSC, USA
| | - Thomas E. Hanson
- School of Marine Science and Policy, College of Earth, Ocean, and Environment, Delaware Biotechnology Institute, University of Delaware, NewarkDE, USA
| | - Tanja Woyke
- Department of Energy, Joint Genome Institute, Walnut CreekCA, USA
| | - Martin G. Klotz
- Department of Biology and School of Earth and Environmental Sciences, Queens College of the City University of New York, New YorkNY, USA
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen UniversityXiamen, China
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St LuciaQLD, Australia
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75
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Wang J, Song Y. Single cell sequencing: a distinct new field. Clin Transl Med 2017; 6:10. [PMID: 28220395 PMCID: PMC5318355 DOI: 10.1186/s40169-017-0139-4] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 02/11/2017] [Indexed: 12/12/2022] Open
Abstract
Single cell sequencing (SCS) has become a new approach to study biological heterogeneity. The advancement in technologies for single cell isolation, amplification of genome/transcriptome and next-generation sequencing enables SCS to reveal the inherent properties of a single cell from the large scale of the genome, transcriptome or epigenome at high resolution. Recently, SCS has been widely applied in various clinical and research fields, such as cancer biology and oncology, immunology, microbiology, neurobiology and prenatal diagnosis. In this review, we will discuss the development of SCS methods and focus on the latest clinical and research applications of SCS.
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Affiliation(s)
- Jian Wang
- Department of Pulmonary Medicine, Zhongshan Hospital, Fudan University, Shanghai, 200030, China
| | - Yuanlin Song
- Department of Pulmonary Medicine, Zhongshan Hospital, Fudan University, Shanghai, 200030, China.
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76
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Ji P, Zhang Y, Wang J, Zhao F. MetaSort untangles metagenome assembly by reducing microbial community complexity. Nat Commun 2017; 8:14306. [PMID: 28112173 PMCID: PMC5264255 DOI: 10.1038/ncomms14306] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 12/14/2016] [Indexed: 12/31/2022] Open
Abstract
Most current approaches to analyse metagenomic data rely on reference genomes. Novel microbial communities extend far beyond the coverage of reference databases and de novo metagenome assembly from complex microbial communities remains a great challenge. Here we present a novel experimental and bioinformatic framework, metaSort, for effective construction of bacterial genomes from metagenomic samples. MetaSort provides a sorted mini-metagenome approach based on flow cytometry and single-cell sequencing methodologies, and employs new computational algorithms to efficiently recover high-quality genomes from the sorted mini-metagenome by the complementary of the original metagenome. Through extensive evaluations, we demonstrated that metaSort has an excellent and unbiased performance on genome recovery and assembly. Furthermore, we applied metaSort to an unexplored microflora colonized on the surface of marine kelp and successfully recovered 75 high-quality genomes at one time. This approach will greatly improve access to microbial genomes from complex or novel communities.
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Affiliation(s)
- Peifeng Ji
- Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Yanming Zhang
- Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Jinfeng Wang
- Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Fangqing Zhao
- Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
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77
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Hagen LH, Frank JA, Zamanzadeh M, Eijsink VGH, Pope PB, Horn SJ, Arntzen MØ. Quantitative Metaproteomics Highlight the Metabolic Contributions of Uncultured Phylotypes in a Thermophilic Anaerobic Digester. Appl Environ Microbiol 2017; 83:e01955-16. [PMID: 27815274 PMCID: PMC5203625 DOI: 10.1128/aem.01955-16] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 10/31/2016] [Indexed: 01/23/2023] Open
Abstract
In this study, we used multiple meta-omic approaches to characterize the microbial community and the active metabolic pathways of a stable industrial biogas reactor with food waste as the dominant feedstock, operating at thermophilic temperatures (60°C) and elevated levels of free ammonia (367 mg/liter NH3-N). The microbial community was strongly dominated (76% of all 16S rRNA amplicon sequences) by populations closely related to the proteolytic bacterium Coprothermobacter proteolyticus. Multiple Coprothermobacter-affiliated strains were detected, introducing an additional level of complexity seldom explored in biogas studies. Genome reconstructions provided metabolic insight into the microbes that performed biomass deconstruction and fermentation, including the deeply branching phyla Dictyoglomi and Planctomycetes and the candidate phylum "Atribacteria" These biomass degraders were complemented by a synergistic network of microorganisms that convert key fermentation intermediates (fatty acids) via syntrophic interactions with hydrogenotrophic methanogens to ultimately produce methane. Interpretation of the proteomics data also suggested activity of a Methanosaeta phylotype acclimatized to high ammonia levels. In particular, we report multiple novel phylotypes proposed as syntrophic acetate oxidizers, which also exert expression of enzymes needed for both the Wood-Ljungdahl pathway and β-oxidation of fatty acids to acetyl coenzyme A. Such an arrangement differs from known syntrophic oxidizing bacteria and presents an interesting hypothesis for future studies. Collectively, these findings provide increased insight into active metabolic roles of uncultured phylotypes and presents new synergistic relationships, both of which may contribute to the stability of the biogas reactor. IMPORTANCE Biogas production through anaerobic digestion of organic waste provides an attractive source of renewable energy and a sustainable waste management strategy. A comprehensive understanding of the microbial community that drives anaerobic digesters is essential to ensure stable and efficient energy production. Here, we characterize the intricate microbial networks and metabolic pathways in a thermophilic biogas reactor. We discuss the impact of frequently encountered microbial populations as well as the metabolism of newly discovered novel phylotypes that seem to play distinct roles within key microbial stages of anaerobic digestion in this stable high-temperature system. In particular, we draft a metabolic scenario whereby multiple uncultured syntrophic acetate-oxidizing bacteria are capable of syntrophically oxidizing acetate as well as longer-chain fatty acids (via the β-oxidation and Wood-Ljundahl pathways) to hydrogen and carbon dioxide, which methanogens subsequently convert to methane.
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Affiliation(s)
- Live H Hagen
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Jeremy A Frank
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Mirzaman Zamanzadeh
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Vincent G H Eijsink
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Phillip B Pope
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Svein J Horn
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Magnus Ø Arntzen
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
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78
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Frank YA, Kadnikov VV, Gavrilov SN, Banks D, Gerasimchuk AL, Podosokorskaya OA, Merkel AY, Chernyh NA, Mardanov AV, Ravin NV, Karnachuk OV, Bonch-Osmolovskaya EA. Stable and Variable Parts of Microbial Community in Siberian Deep Subsurface Thermal Aquifer System Revealed in a Long-Term Monitoring Study. Front Microbiol 2016; 7:2101. [PMID: 28082967 PMCID: PMC5187383 DOI: 10.3389/fmicb.2016.02101] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 12/12/2016] [Indexed: 11/13/2022] Open
Abstract
The goal of this work was to study the diversity of microorganisms inhabiting a deep subsurface aquifer system in order to understand their functional roles and interspecies relations formed in the course of buried organic matter degradation. A microbial community of a deep subsurface thermal aquifer in the Tomsk Region, Western Siberia was monitored over the course of 5 years via a 2.7 km deep borehole 3P, drilled down to a Palaeozoic basement. The borehole water discharges with a temperature of ca. 50°C. Its chemical composition varies, but it steadily contains acetate, propionate, and traces of hydrocarbons and gives rise to microbial mats along the surface flow. Community analysis by PCR-DGGE 16S rRNA genes profiling, repeatedly performed within 5 years, revealed several dominating phylotypes consistently found in the borehole water, and highly variable diversity of prokaryotes, brought to the surface with the borehole outflow. The major planktonic components of the microbial community were Desulfovirgula thermocuniculi and Methanothermobacter spp. The composition of the minor part of the community was unstable, and molecular analysis did not reveal any regularity in its variations, except some predominance of uncultured Firmicutes. Batch cultures with complex organic substrates inoculated with water samples were set in order to enrich prokaryotes from the variable part of the community. PCR-DGGE analysis of these enrichments yielded uncultured Firmicutes, Chloroflexi, and Ignavibacteriae. A continuous-flow microaerophilic enrichment culture with a water sample amended with acetate contained Hydrogenophilus thermoluteolus, which was previously detected in the microbial mat developing at the outflow of the borehole. Cultivation results allowed us to assume that variable components of the 3P well community are hydrolytic organotrophs, degrading buried biopolymers, while the constant planktonic components of the community degrade dissolved fermentation products to methane and CO2, possibly via interspecies hydrogen transfer. Occasional washout of minor community components capable of oxygen respiration leads to the development of microbial mats at the outflow of the borehole where residual dissolved fermentation products are aerobically oxidized. Long-term community analysis with the combination of molecular and cultivation techniques allowed us to characterize stable and variable parts of the community and propose their environmental roles.
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Affiliation(s)
- Yulia A. Frank
- Department of Plant Physiology and Biotechnology, Tomsk State UniversityTomsk, Russia
| | - Vitaly V. Kadnikov
- Federal Research Centre (FRC) Biotechnology, Institute of BioengineeringMoscow, Russia
| | - Sergey N. Gavrilov
- Federal Research Centre (FRC) Biotechnology, Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences (RAS)Moscow, Russia
| | - David Banks
- Glasgow and Holymoor Consultancy Ltd., Glasgow UniversityChesterfield, UK
| | - Anna L. Gerasimchuk
- Department of Plant Physiology and Biotechnology, Tomsk State UniversityTomsk, Russia
| | - Olga A. Podosokorskaya
- Federal Research Centre (FRC) Biotechnology, Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences (RAS)Moscow, Russia
| | - Alexander Y. Merkel
- Federal Research Centre (FRC) Biotechnology, Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences (RAS)Moscow, Russia
| | - Nikolai A. Chernyh
- Federal Research Centre (FRC) Biotechnology, Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences (RAS)Moscow, Russia
| | - Andrey V. Mardanov
- Federal Research Centre (FRC) Biotechnology, Institute of BioengineeringMoscow, Russia
| | - Nikolai V. Ravin
- Federal Research Centre (FRC) Biotechnology, Institute of BioengineeringMoscow, Russia
| | - Olga V. Karnachuk
- Department of Plant Physiology and Biotechnology, Tomsk State UniversityTomsk, Russia
| | - Elizaveta A. Bonch-Osmolovskaya
- Federal Research Centre (FRC) Biotechnology, Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences (RAS)Moscow, Russia
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79
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Yokobori SI, Nakajima Y, Akanuma S, Yamagishi A. Birth of Archaeal Cells: Molecular Phylogenetic Analyses of G1P Dehydrogenase, G3P Dehydrogenases, and Glycerol Kinase Suggest Derived Features of Archaeal Membranes Having G1P Polar Lipids. ARCHAEA (VANCOUVER, B.C.) 2016; 2016:1802675. [PMID: 27774041 PMCID: PMC5059525 DOI: 10.1155/2016/1802675] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 08/08/2016] [Indexed: 01/25/2023]
Abstract
Bacteria and Eukarya have cell membranes with sn-glycerol-3-phosphate (G3P), whereas archaeal membranes contain sn-glycerol-1-phosphate (G1P). Determining the time at which cells with either G3P-lipid membranes or G1P-lipid membranes appeared is important for understanding the early evolution of terrestrial life. To clarify this issue, we reconstructed molecular phylogenetic trees of G1PDH (G1P dehydrogenase; EgsA/AraM) which is responsible for G1P synthesis and G3PDHs (G3P dehydrogenase; GpsA and GlpA/GlpD) and glycerol kinase (GlpK) which is responsible for G3P synthesis. Together with the distribution of these protein-encoding genes among archaeal and bacterial groups, our phylogenetic analyses suggested that GlpA/GlpD in the Commonote (the last universal common ancestor of all extant life with a cellular form, Commonote commonote) acquired EgsA (G1PDH) from the archaeal common ancestor (Commonote archaea) and acquired GpsA and GlpK from a bacterial common ancestor (Commonote bacteria). In our scenario based on this study, the Commonote probably possessed a G3P-lipid membrane synthesized enzymatically, after which the archaeal lineage acquired G1PDH followed by the replacement of a G3P-lipid membrane with a G1P-lipid membrane.
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Affiliation(s)
- Shin-ichi Yokobori
- Laboratory of Extremophiles, Department of Applied Life Sciences, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Yoshiki Nakajima
- Laboratory of Extremophiles, Department of Applied Life Sciences, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Satoshi Akanuma
- Faculty of Human Sciences, Waseda University, 2-579-15 Mikajima, Tokorozawa, Saitama 359-1192, Japan
| | - Akihiko Yamagishi
- Laboratory of Extremophiles, Department of Applied Life Sciences, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
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80
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Wang Y, Gao ZM, Li JT, Bougouffa S, Tian RM, Bajic VB, Qian PY. Draft genome of an Aerophobetes bacterium reveals a facultative lifestyle in deep-sea anaerobic sediments. Sci Bull (Beijing) 2016. [DOI: 10.1007/s11434-016-1135-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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81
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Virtual microfluidics for digital quantification and single-cell sequencing. Nat Methods 2016; 13:759-62. [PMID: 27479330 PMCID: PMC5007149 DOI: 10.1038/nmeth.3955] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 06/27/2016] [Indexed: 01/18/2023]
Abstract
Interest in highly parallelized analysis of single molecules and single cells is growing rapidly. Here we develop hydrogel-based virtual microfluidics as a simple alternative to complex engineered microfluidic systems for the compartmentalization of nucleic acid amplification reactions. We applied digital multiple displacement amplification (dMDA) to purified DNA templates, cultured bacterial cells, and human microbiome samples in the virtual microfluidics system and demonstrated recovery and whole-genome sequencing of single-cell MDA products. Our results from control samples showed excellent coverage uniformity and markedly reduced chimerism compared with single-cell data obtained from conventional liquid MDA reactions. We also demonstrate the applicability of the hydrogel method for genomic studies of naturally occurring microbes in human microbiome samples. The virtual microfluidics approach is a simple and robust method that will enable many laboratories to perform single-cell genomic analyses.
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82
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Thiel V, Wood JM, Olsen MT, Tank M, Klatt CG, Ward DM, Bryant DA. The Dark Side of the Mushroom Spring Microbial Mat: Life in the Shadow of Chlorophototrophs. I. Microbial Diversity Based on 16S rRNA Gene Amplicons and Metagenomic Sequencing. Front Microbiol 2016; 7:919. [PMID: 27379049 PMCID: PMC4911352 DOI: 10.3389/fmicb.2016.00919] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 05/27/2016] [Indexed: 11/13/2022] Open
Abstract
Microbial-mat communities in the effluent channels of Octopus and Mushroom Springs within the Lower Geyser Basin at Yellowstone National Park have been studied for nearly 50 years. The emphasis has mostly focused on the chlorophototrophic bacterial organisms of the phyla Cyanobacteria and Chloroflexi. In contrast, the diversity and metabolic functions of the heterotrophic community in the microoxic/anoxic region of the mat are not well understood. In this study we analyzed the orange-colored undermat of the microbial community of Mushroom Spring using metagenomic and rRNA-amplicon (iTag) analyses. Our analyses disclosed a highly diverse community exhibiting a high degree of unevenness, strongly dominated by a single taxon, the filamentous anoxygenic phototroph, Roseiflexus spp. The second most abundant organisms belonged to the Thermotogae, which have been hypothesized to be a major source of H2 from fermentation that could enable photomixotrophic metabolism by Chloroflexus and Roseiflexus spp. Other abundant organisms include two members of the Armatimonadetes (OP10); Thermocrinis sp.; and phototrophic and heterotrophic members of the Chloroflexi. Further, an Atribacteria (OP9/JS1) member; a sulfate-reducing Thermodesulfovibrio sp.; a Planctomycetes member; a member of the EM3 group tentatively affiliated with the Thermotogae, as well as a putative member of the Arminicenantes (OP8) represented ≥1% of the reads. Archaea were not abundant in the iTag analysis, and no metagenomic bin representing an archaeon was identified. A high microdiversity of 16S rRNA gene sequences was identified for the dominant taxon, Roseiflexus spp. Previous studies demonstrated that highly similar Synechococcus variants in the upper layer of the mats represent ecological species populations with specific ecological adaptations. This study suggests that similar putative ecotypes specifically adapted to different niches occur within the undermat community, particularly for Roseiflexus spp.
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Affiliation(s)
- Vera Thiel
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University University Park, PA, USA
| | - Jason M Wood
- Department of Land Resources and Environmental Sciences, Montana State University Bozeman, MT, USA
| | - Millie T Olsen
- Department of Land Resources and Environmental Sciences, Montana State University Bozeman, MT, USA
| | - Marcus Tank
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University University Park, PA, USA
| | - Christian G Klatt
- Department of Land Resources and Environmental Sciences, Montana State UniversityBozeman, MT, USA; Agricultural Research Service, United States Department of Agriculture, University of MinnesotaSaint Paul, MN, USA
| | - David M Ward
- Department of Land Resources and Environmental Sciences, Montana State University Bozeman, MT, USA
| | - Donald A Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State UniversityUniversity Park, PA, USA; Department of Chemistry and Biochemistry, Montana State UniversityBozeman, MT, USA
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83
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Saw JH, Spang A, Zaremba-Niedzwiedzka K, Juzokaite L, Dodsworth JA, Murugapiran SK, Colman DR, Takacs-Vesbach C, Hedlund BP, Guy L, Ettema TJG. Exploring microbial dark matter to resolve the deep archaeal ancestry of eukaryotes. Philos Trans R Soc Lond B Biol Sci 2016; 370:20140328. [PMID: 26323759 PMCID: PMC4571567 DOI: 10.1098/rstb.2014.0328] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The origin of eukaryotes represents an enigmatic puzzle, which is still lacking a number of essential pieces. Whereas it is currently accepted that the process of eukaryogenesis involved an interplay between a host cell and an alphaproteobacterial endosymbiont, we currently lack detailed information regarding the identity and nature of these players. A number of studies have provided increasing support for the emergence of the eukaryotic host cell from within the archaeal domain of life, displaying a specific affiliation with the archaeal TACK superphylum. Recent studies have shown that genomic exploration of yet-uncultivated archaea, the so-called archaeal ‘dark matter’, is able to provide unprecedented insights into the process of eukaryogenesis. Here, we provide an overview of state-of-the-art cultivation-independent approaches, and demonstrate how these methods were used to obtain draft genome sequences of several novel members of the TACK superphylum, including Lokiarchaeum, two representatives of the Miscellaneous Crenarchaeotal Group (Bathyarchaeota), and a Korarchaeum-related lineage. The maturation of cultivation-independent genomics approaches, as well as future developments in next-generation sequencing technologies, will revolutionize our current view of microbial evolution and diversity, and provide profound new insights into the early evolution of life, including the enigmatic origin of the eukaryotic cell.
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Affiliation(s)
- Jimmy H Saw
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Anja Spang
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | | | - Lina Juzokaite
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Jeremy A Dodsworth
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, USA
| | | | - Dan R Colman
- Department of Biology, University of New Mexico, Albuquerque, NM, USA
| | | | - Brian P Hedlund
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, USA
| | - Lionel Guy
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Thijs J G Ettema
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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84
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Bukin SV, Pavlova ON, Manakov AY, Kostyreva EA, Chernitsyna SM, Mamaeva EV, Pogodaeva TV, Zemskaya TI. The Ability of Microbial Community of Lake Baikal Bottom Sediments Associated with Gas Discharge to Carry Out the Transformation of Organic Matter under Thermobaric Conditions. Front Microbiol 2016; 7:690. [PMID: 27242716 PMCID: PMC4861714 DOI: 10.3389/fmicb.2016.00690] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 04/26/2016] [Indexed: 11/21/2022] Open
Abstract
The ability to compare the composition and metabolic potential of microbial communities inhabiting the subsurface sediment in geographically distinct locations is one of the keys to understanding the evolution and function of the subsurface biosphere. Prospective areas for study of the subsurface biosphere are the sites of hydrocarbon discharges on the bottom of the Lake Baikal rift, where ascending fluxes of gas-saturated fluids and oil from deep layers of bottom sediments seep into near-surface sediment. The samples of surface sediments collected in the area of the Posolskaya Bank methane seep were cultured for 17 months under thermobaric conditions (80°C, 5 MPa) with the addition of complementary organic substrate, and a different composition for the gas phase. After incubation, the presence of intact cells of microorganisms, organic matter transformation and the formation of oil biomarkers was confirmed in the samples, with the addition of Baikal diatom alga Synedra acus detritus, and gas mixture CH4:H2:CO2. Taxonomic assignment of the 16S rRNA sequence data indicates that the predominant sequences in the enrichment were Sphingomonas (55.3%), Solirubrobacter (27.5%) and Arthrobacter (16.6%). At the same time, in heat-killed sediment and in sediment without any additional substrates, which were cultivated in a CH4 atmosphere, no geochemical changes were detected, nor the presence of intact cells and 16S rRNA sequences of Bacteria and Archaea. This data may suggest that the decomposition of organic matter under culturing conditions could be performed by microorganisms from low-temperature sediment layers. One possible explanation of this phenomenon is migration of the representatives of the deep thermophilic community through fault zones in the near surface sediment layers, together with gas-bearing fluids.
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Affiliation(s)
- Sergei V Bukin
- Laboratory of Hydrocarbon Microbiology, Limnological Institute, Russian Academy of Science Irkutsk, Russia
| | - Olga N Pavlova
- Laboratory of Hydrocarbon Microbiology, Limnological Institute, Russian Academy of Science Irkutsk, Russia
| | - Andrei Y Manakov
- Laboratory of Clathrate Compounds, Nikolaev Institute of Inorganic Chemistry, Russian Academy of Science Novosibirsk, Russia
| | - Elena A Kostyreva
- Laboratory of Petroleum Geochemistry, Trofimuk Institute of Petroleum Geology and Geophysics, Russian Academy of Science Novosibirsk, Russia
| | - Svetlana M Chernitsyna
- Laboratory of Hydrocarbon Microbiology, Limnological Institute, Russian Academy of Science Irkutsk, Russia
| | - Elena V Mamaeva
- Laboratory of Hydrocarbon Microbiology, Limnological Institute, Russian Academy of Science Irkutsk, Russia
| | - Tatyana V Pogodaeva
- Laboratory of Hydrochemistry and Atmosphere Chemistry, Limnological Institute, Russian Academy of Science Irkutsk, Russia
| | - Tamara I Zemskaya
- Laboratory of Hydrocarbon Microbiology, Limnological Institute, Russian Academy of Science Irkutsk, Russia
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85
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Hamilton TL, Bovee RJ, Sattin SR, Mohr W, Gilhooly WP, Lyons TW, Pearson A, Macalady JL. Carbon and Sulfur Cycling below the Chemocline in a Meromictic Lake and the Identification of a Novel Taxonomic Lineage in the FCB Superphylum, Candidatus Aegiribacteria. Front Microbiol 2016; 7:598. [PMID: 27199928 PMCID: PMC4846661 DOI: 10.3389/fmicb.2016.00598] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 04/11/2016] [Indexed: 11/13/2022] Open
Abstract
Mahoney Lake in British Columbia is an extreme meromictic system with unusually high levels of sulfate and sulfide present in the water column. As is common in strongly stratified lakes, Mahoney Lake hosts a dense, sulfide-oxidizing phototrophic microbial community where light reaches the chemocline. Below this "plate," the euxinic hypolimnion is anoxic, eutrophic, saline, and rich in sulfide, polysulfides, elemental sulfur, and other sulfur intermediates. While much is known regarding microbial communities in sunlit portions of euxinic systems, the composition and genetic potential of organisms living at aphotic depths have rarely been studied. Metagenomic sequencing of samples from the hypolimnion and the underlying sediments of Mahoney Lake indicate that multiple taxa contribute to sulfate reduction below the chemocline and that the hypolimnion and sediments each support distinct populations of sulfate reducing bacteria (SRB) that differ from the SRB populations observed in the chemocline. After assembling and binning the metagenomic datasets, we recovered near-complete genomes of dominant populations including two Deltaproteobacteria. One of the deltaproteobacterial genomes encoded a 16S rRNA sequence that was most closely related to the sulfur-disproportionating genus Dissulfuribacter and the other encoded a 16S rRNA sequence that was most closely related to the fatty acid- and aromatic acid-degrading genus Syntrophus. We also recovered two near-complete genomes of Firmicutes species. Analysis of concatenated ribosomal protein trees suggests these genomes are most closely related to extremely alkaliphilic genera Alkaliphilus and Dethiobacter. Our metagenomic data indicate that these Firmicutes contribute to carbon cycling below the chemocline. Lastly, we recovered a nearly complete genome from the sediment metagenome which represents a new genus within the FCB (Fibrobacteres, Chlorobi, Bacteroidetes) superphylum. Consistent with the geochemical data, we found little or no evidence for organisms capable of sulfide oxidation in the aphotic zone below the chemocline. Instead, comparison of functional genes below the chemocline are consistent with recovery of multiple populations capable of reducing oxidized sulfur. Our data support previous observations that at least some of the sulfide necessary to support the dense population of phototrophs in the chemocline is supplied from sulfate reduction in the hypolimnion and sediments. These studies provide key insights regarding the taxonomic and functional diversity within a euxinic environment and highlight the complexity of biogeochemical carbon and sulfur cycling necessary to maintain euxinia.
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Affiliation(s)
- Trinity L Hamilton
- Department of Biological Sciences, University of Cincinnati Cincinnati, OH, USA
| | - Roderick J Bovee
- Department of Earth and Planetary Sciences, Harvard University Cambridge, MA, USA
| | - Sarah R Sattin
- Department of Earth and Planetary Sciences, Harvard University Cambridge, MA, USA
| | - Wiebke Mohr
- Department of Earth and Planetary Sciences, Harvard University Cambridge, MA, USA
| | - William P Gilhooly
- Department of Earth Sciences, Indiana University-Purdue University Indianapolis Indianapolis, IN, USA
| | - Timothy W Lyons
- Department of Earth Sciences, University of California Riverside, CA, USA
| | - Ann Pearson
- Department of Earth and Planetary Sciences, Harvard University Cambridge, MA, USA
| | - Jennifer L Macalady
- Penn State Astrobiology Research Center, Department of Geosciences, Pennsylvania State University University Park, TX, USA
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86
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Stamps BW, Lyles CN, Suflita JM, Masoner JR, Cozzarelli IM, Kolpin DW, Stevenson BS. Municipal Solid Waste Landfills Harbor Distinct Microbiomes. Front Microbiol 2016; 7:534. [PMID: 27148222 PMCID: PMC4837139 DOI: 10.3389/fmicb.2016.00534] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 03/31/2016] [Indexed: 11/16/2022] Open
Abstract
Landfills are the final repository for most of the discarded material from human society and its “built environments.” Microorganisms subsequently degrade this discarded material in the landfill, releasing gases (largely CH4 and CO2) and a complex mixture of soluble chemical compounds in leachate. Characterization of “landfill microbiomes” and their comparison across several landfills should allow the identification of environmental or operational properties that influence the composition of these microbiomes and potentially their biodegradation capabilities. To this end, the composition of landfill microbiomes was characterized as part of an ongoing USGS national survey studying the chemical composition of leachates from 19 non-hazardous landfills across 16 states in the continental U.S. The landfills varied in parameters such as size, waste composition, management strategy, geography, and climate zone. The diversity and composition of bacterial and archaeal populations in leachate samples were characterized by 16S rRNA gene sequence analysis, and compared against a variety of physical and chemical parameters in an attempt to identify their impact on selection. Members of the Epsilonproteobacteria, Gammaproteobacteria, Clostridia, and candidate division OP3 were the most abundant. The distribution of the observed phylogenetic diversity could best be explained by a combination of variables and was correlated most strongly with the concentrations of chloride and barium, rate of evapotranspiration, age of waste, and the number of detected household chemicals. This study illustrates how leachate microbiomes are distinct from those of other natural or built environments, and sheds light on the major selective forces responsible for this microbial diversity.
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Affiliation(s)
- Blake W Stamps
- Department of Microbiology and Plant Biology, University of Oklahoma Norman, OK
| | - Christopher N Lyles
- Department of Microbiology and Plant Biology, University of Oklahoma Norman, OK
| | - Joseph M Suflita
- Department of Microbiology and Plant Biology, University of Oklahoma Norman, OK
| | | | | | | | - Bradley S Stevenson
- Department of Microbiology and Plant Biology, University of Oklahoma Norman, OK
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87
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Colman DR, Jay ZJ, Inskeep WP, Jennings RD, Maas KR, Rusch DB, Takacs-Vesbach CD. Novel, Deep-Branching Heterotrophic Bacterial Populations Recovered from Thermal Spring Metagenomes. Front Microbiol 2016; 7:304. [PMID: 27014227 PMCID: PMC4791363 DOI: 10.3389/fmicb.2016.00304] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2015] [Accepted: 02/24/2016] [Indexed: 11/24/2022] Open
Abstract
Thermal spring ecosystems are a valuable resource for the discovery of novel hyperthermophilic Bacteria and Archaea, and harbor deeply-branching lineages that provide insight regarding the nature of early microbial life. We characterized bacterial populations in two circumneutral (pH ~8) Yellowstone National Park thermal (T ~80°C) spring filamentous “streamer” communities using random metagenomic DNA sequence to investigate the metabolic potential of these novel populations. Four de novo assemblies representing three abundant, deeply-branching bacterial phylotypes were recovered. Analysis of conserved phylogenetic marker genes indicated that two of the phylotypes represent separate groups of an uncharacterized phylum (for which we propose the candidate phylum name “Pyropristinus”). The third new phylotype falls within the proposed Calescamantes phylum. Metabolic reconstructions of the “Pyropristinus” and Calescamantes populations showed that these organisms appear to be chemoorganoheterotrophs and have the genomic potential for aerobic respiration and oxidative phosphorylation via archaeal-like V-type, and bacterial F-type ATPases, respectively. A survey of similar phylotypes (>97% nt identity) within 16S rRNA gene datasets suggest that the newly described organisms are restricted to terrestrial thermal springs ranging from 70 to 90°C and pH values of ~7–9. The characterization of these lineages is important for understanding the diversity of deeply-branching bacterial phyla, and their functional role in high-temperature circumneutral “streamer” communities.
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Affiliation(s)
- Daniel R Colman
- Department of Biology, University of New Mexico Albuquerque, NM, USA
| | - Zackary J Jay
- Thermal Biology Institute and Department of Land Resources and Environmental Sciences, Montana State University Bozeman, MT, USA
| | - William P Inskeep
- Thermal Biology Institute and Department of Land Resources and Environmental Sciences, Montana State University Bozeman, MT, USA
| | - Ryan deM Jennings
- Thermal Biology Institute and Department of Land Resources and Environmental Sciences, Montana State University Bozeman, MT, USA
| | - Kendra R Maas
- Department of Biology, University of New Mexico Albuquerque, NM, USA
| | - Douglas B Rusch
- Center for Genomics and Bioinformatics, Indiana University Bloomington, IN, USA
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88
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Baker BJ, Saw JH, Lind AE, Lazar CS, Hinrichs KU, Teske AP, Ettema TJG. Genomic inference of the metabolism of cosmopolitan subsurface Archaea, Hadesarchaea. Nat Microbiol 2016; 1:16002. [PMID: 27572167 DOI: 10.1038/nmicrobiol.2016.2] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 01/08/2016] [Indexed: 11/09/2022]
Abstract
The subsurface biosphere is largely unexplored and contains a broad diversity of uncultured microbes(1). Despite being one of the few prokaryotic lineages that is cosmopolitan in both the terrestrial and marine subsurface(2-4), the physiological and ecological roles of SAGMEG (South-African Gold Mine Miscellaneous Euryarchaeal Group) Archaea are unknown. Here, we report the metabolic capabilities of this enigmatic group as inferred from genomic reconstructions. Four high-quality (63-90% complete) genomes were obtained from White Oak River estuary and Yellowstone National Park hot spring sediment metagenomes. Phylogenomic analyses place SAGMEG Archaea as a deeply rooting sister clade of the Thermococci, leading us to propose the name Hadesarchaea for this new Archaeal class. With an estimated genome size of around 1.5 Mbp, the genomes of Hadesarchaea are distinctly streamlined, yet metabolically versatile. They share several physiological mechanisms with strict anaerobic Euryarchaeota. Several metabolic characteristics make them successful in the subsurface, including genes involved in CO and H2 oxidation (or H2 production), with potential coupling to nitrite reduction to ammonia (DNRA). This first glimpse into the metabolic capabilities of these cosmopolitan Archaea suggests they are mediating key geochemical processes and are specialized for survival in the subsurface biosphere.
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Affiliation(s)
- Brett J Baker
- Department of Marine Science, University of Texas Austin, Marine Science Institute, Port Aransas, Texas 78373, USA
| | - Jimmy H Saw
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123 Uppsala, Sweden
| | - Anders E Lind
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123 Uppsala, Sweden
| | - Cassandre Sara Lazar
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Kai-Uwe Hinrichs
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Andreas P Teske
- Department of Marine Sciences, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Thijs J G Ettema
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123 Uppsala, Sweden
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89
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Mende DR, Aylward FO, Eppley JM, Nielsen TN, DeLong EF. Improved Environmental Genomes via Integration of Metagenomic and Single-Cell Assemblies. Front Microbiol 2016; 7:143. [PMID: 26904016 PMCID: PMC4749706 DOI: 10.3389/fmicb.2016.00143] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 01/25/2016] [Indexed: 11/13/2022] Open
Abstract
Assembling complete or near complete genomes from complex microbial communities remains a significant challenge in metagenomic studies. Recent developments in single cell amplified genomes (SAGs) have enabled the sequencing of individual draft genomes representative of uncultivated microbial populations. SAGs suffer from incomplete and uneven coverage due to artifacts that arise from multiple displacement amplification techniques. Conversely, metagenomic sequence data does not suffer from the same biases as SAGs, and significant improvements have been realized in the recovery of draft genomes from metagenomes. Nevertheless, the inherent genomic complexity of many microbial communities often obfuscates facile generation of population genome assemblies from metagenomic data. Here we describe a new method for metagenomic-guided SAG assembly that leverages the advantages of both methods and significantly improves the completeness of initial SAGs assemblies. We demonstrate that SAG assemblies of two cosmopolitan marine lineages-Marine Group 1 Thaumarchaeota and SAR324 clade bacterioplankton-were substantially improved using this approach. Moreover, the improved assemblies strengthened biological inferences. For example, the improved SAR324 clade genome assembly revealed the presence of many genes in phenylalanine catabolism and flagellar assembly that were absent in the original SAG.
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Affiliation(s)
- Daniel R Mende
- Daniel K. Inouye Center for Microbial Oceanography Research and Education, University of Hawai'i at Manoa, Honolulu HI, USA
| | - Frank O Aylward
- Daniel K. Inouye Center for Microbial Oceanography Research and Education, University of Hawai'i at Manoa, Honolulu HI, USA
| | - John M Eppley
- Daniel K. Inouye Center for Microbial Oceanography Research and Education, University of Hawai'i at Manoa, Honolulu HI, USA
| | - Torben N Nielsen
- Daniel K. Inouye Center for Microbial Oceanography Research and Education, University of Hawai'i at Manoa, Honolulu HI, USA
| | - Edward F DeLong
- Daniel K. Inouye Center for Microbial Oceanography Research and Education, University of Hawai'i at Manoa, Honolulu HI, USA
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90
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Biteen JS, Blainey PC, Cardon ZG, Chun M, Church GM, Dorrestein PC, Fraser SE, Gilbert JA, Jansson JK, Knight R, Miller JF, Ozcan A, Prather KA, Quake SR, Ruby EG, Silver PA, Taha S, van den Engh G, Weiss PS, Wong GCL, Wright AT, Young TD. Tools for the Microbiome: Nano and Beyond. ACS NANO 2016; 10:6-37. [PMID: 26695070 DOI: 10.1021/acsnano.5b07826] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The microbiome presents great opportunities for understanding and improving the world around us and elucidating the interactions that compose it. The microbiome also poses tremendous challenges for mapping and manipulating the entangled networks of interactions among myriad diverse organisms. Here, we describe the opportunities, technical needs, and potential approaches to address these challenges, based on recent and upcoming advances in measurement and control at the nanoscale and beyond. These technical needs will provide the basis for advancing the largely descriptive studies of the microbiome to the theoretical and mechanistic understandings that will underpin the discipline of microbiome engineering. We anticipate that the new tools and methods developed will also be more broadly useful in environmental monitoring, medicine, forensics, and other areas.
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Affiliation(s)
- Julie S Biteen
- Department of Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Paul C Blainey
- Department of Biological Engineering, Massachusetts Institute of Technology , and Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02138, United States
| | - Zoe G Cardon
- The Ecosystems Center, Marine Biological Laboratory , Woods Hole, Massachusetts 02543-1015, United States
| | - Miyoung Chun
- The Kavli Foundation , Oxnard, California 93030, United States
| | - George M Church
- Wyss Institute for Biologically Inspired Engineering and Biophysics Program, Harvard University , Boston, Massachusetts 02115, United States
| | | | - Scott E Fraser
- Translational Imaging Center, University of Southern California , Molecular and Computational Biology, Los Angeles, California 90089, United States
| | - Jack A Gilbert
- Institute for Genomic and Systems Biology, Argonne National Laboratory , Argonne, Illinois 60439, United States
- Department of Ecology and Evolution and Department of Surgery, University of Chicago , Chicago, Illinois 60637, United States
| | - Janet K Jansson
- Earth and Biological Sciences Division, Pacific Northwest National Laboratory , Richland, Washington 99352, United States
| | | | | | | | | | | | - Edward G Ruby
- Kewalo Marine Laboratory, University of Hawaii-Manoa , Honolulu, Hawaii 96813, United States
| | - Pamela A Silver
- Wyss Institute for Biologically Inspired Engineering and Biophysics Program, Harvard University , Boston, Massachusetts 02115, United States
| | - Sharif Taha
- The Kavli Foundation , Oxnard, California 93030, United States
| | - Ger van den Engh
- Center for Marine Cytometry , Concrete, Washington 98237, United States
- Instituto Milenio de Oceanografía, Universidad de Concepción , Concepción, Chile
| | | | | | - Aaron T Wright
- Earth and Biological Sciences Division, Pacific Northwest National Laboratory , Richland, Washington 99352, United States
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91
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Gawad C, Koh W, Quake SR. Single-cell genome sequencing: current state of the science. Nat Rev Genet 2016; 17:175-88. [PMID: 26806412 DOI: 10.1038/nrg.2015.16] [Citation(s) in RCA: 846] [Impact Index Per Article: 105.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The field of single-cell genomics is advancing rapidly and is generating many new insights into complex biological systems, ranging from the diversity of microbial ecosystems to the genomics of human cancer. In this Review, we provide an overview of the current state of the field of single-cell genome sequencing. First, we focus on the technical challenges of making measurements that start from a single molecule of DNA, and then explore how some of these recent methodological advancements have enabled the discovery of unexpected new biology. Areas highlighted include the application of single-cell genomics to interrogate microbial dark matter and to evaluate the pathogenic roles of genetic mosaicism in multicellular organisms, with a focus on cancer. We then attempt to predict advances we expect to see in the next few years.
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Affiliation(s)
- Charles Gawad
- Departments of Oncology and Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Winston Koh
- Departments of Bioengineering and Applied Physics, Stanford University, Stanford, California 94304, USA.,Howard Hughes Medical Institute, Stanford University, California 94304, USA
| | - Stephen R Quake
- Departments of Bioengineering and Applied Physics, Stanford University, Stanford, California 94304, USA.,Howard Hughes Medical Institute, Stanford University, California 94304, USA
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92
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Genome-Resolved Metagenomic Analysis Reveals Roles for Candidate Phyla and Other Microbial Community Members in Biogeochemical Transformations in Oil Reservoirs. mBio 2016; 7:e01669-15. [PMID: 26787827 PMCID: PMC4725000 DOI: 10.1128/mbio.01669-15] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Oil reservoirs are major sites of methane production and carbon turnover, processes with significant impacts on energy resources and global biogeochemical cycles. We applied a cultivation-independent genomic approach to define microbial community membership and predict roles for specific organisms in biogeochemical transformations in Alaska North Slope oil fields. Produced water samples were collected from six locations between 1,128 m (24 to 27°C) and 2,743 m (80 to 83°C) below the surface. Microbial community complexity decreased with increasing temperature, and the potential to degrade hydrocarbon compounds was most prevalent in the lower-temperature reservoirs. Sulfate availability, rather than sulfate reduction potential, seems to be the limiting factor for sulfide production in some of the reservoirs under investigation. Most microorganisms in the intermediate- and higher-temperature samples were related to previously studied methanogenic and nonmethanogenic archaea and thermophilic bacteria, but one candidate phylum bacterium, a member of the Acetothermia (OP1), was present in Kuparuk sample K3. The greatest numbers of candidate phyla were recovered from the mesothermic reservoir samples SB1 and SB2. We reconstructed a nearly complete genome for an organism from the candidate phylum Parcubacteria (OD1) that was abundant in sample SB1. Consistent with prior findings for members of this lineage, the OD1 genome is small, and metabolic predictions support an obligately anaerobic, fermentation-based lifestyle. At moderate abundance in samples SB1 and SB2 were members of bacteria from other candidate phyla, including Microgenomates (OP11), Atribacteria (OP9), candidate phyla TA06 and WS6, and Marinimicrobia (SAR406). The results presented here elucidate potential roles of organisms in oil reservoir biological processes. The activities of microorganisms in oil reservoirs impact petroleum resource quality and the global carbon cycle. We show that bacteria belonging to candidate phyla are present in some oil reservoirs and provide the first insights into their potential roles in biogeochemical processes based on several nearly complete genomes.
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93
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Mwirichia R, Alam I, Rashid M, Vinu M, Ba-Alawi W, Anthony Kamau A, Kamanda Ngugi D, Göker M, Klenk HP, Bajic V, Stingl U. Metabolic traits of an uncultured archaeal lineage--MSBL1--from brine pools of the Red Sea. Sci Rep 2016; 6:19181. [PMID: 26758088 PMCID: PMC4725937 DOI: 10.1038/srep19181] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 12/04/2015] [Indexed: 11/24/2022] Open
Abstract
The candidate Division MSBL1 (Mediterranean Sea Brine Lakes 1) comprises a monophyletic group of uncultured archaea found in different hypersaline environments. Previous studies propose methanogenesis as the main metabolism. Here, we describe a metabolic reconstruction of MSBL1 based on 32 single-cell amplified genomes from Brine Pools of the Red Sea (Atlantis II, Discovery, Nereus, Erba and Kebrit). Phylogeny based on rRNA genes as well as conserved single copy genes delineates the group as a putative novel lineage of archaea. Our analysis shows that MSBL1 may ferment glucose via the Embden-Meyerhof-Parnas pathway. However, in the absence of organic carbon, carbon dioxide may be fixed via the ribulose bisphosphate carboxylase, Wood-Ljungdahl pathway or reductive TCA cycle. Therefore, based on the occurrence of genes for glycolysis, absence of the core genes found in genomes of all sequenced methanogens and the phylogenetic position, we hypothesize that the MSBL1 are not methanogens, but probably sugar-fermenting organisms capable of autotrophic growth. Such a mixotrophic lifestyle would confer survival advantage (or possibly provide a unique narrow niche) when glucose and other fermentable sugars are not available.
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Affiliation(s)
- Romano Mwirichia
- Red Sea Research Center, King Abdullah University of Science and
Technology (KAUST), Thuwal, Saudi Arabia
| | - Intikhab Alam
- Computational Bioscience Research Center, King Abdullah
University of Science and Technology (KAUST), Thuwal,
Saudi Arabia
| | - Mamoon Rashid
- Red Sea Research Center, King Abdullah University of Science and
Technology (KAUST), Thuwal, Saudi Arabia
| | - Manikandan Vinu
- Red Sea Research Center, King Abdullah University of Science and
Technology (KAUST), Thuwal, Saudi Arabia
| | - Wail Ba-Alawi
- Computational Bioscience Research Center, King Abdullah
University of Science and Technology (KAUST), Thuwal,
Saudi Arabia
| | - Allan Anthony Kamau
- Computational Bioscience Research Center, King Abdullah
University of Science and Technology (KAUST), Thuwal,
Saudi Arabia
| | - David Kamanda Ngugi
- Red Sea Research Center, King Abdullah University of Science and
Technology (KAUST), Thuwal, Saudi Arabia
| | - Markus Göker
- German Collection for Microorganisms and Cell Cultures GmbH
(DSMZ), Inhoffenstraße 7b, 38124
Braunschweig, Germany
| | - Hans-Peter Klenk
- School of Biology, Newcastle University, Newcastle
upon Tyne, United Kingdom
| | - Vladimir Bajic
- Computational Bioscience Research Center, King Abdullah
University of Science and Technology (KAUST), Thuwal,
Saudi Arabia
| | - Ulrich Stingl
- Red Sea Research Center, King Abdullah University of Science and
Technology (KAUST), Thuwal, Saudi Arabia
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94
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Wong HL, Ahmed-Cox A, Burns BP. Molecular Ecology of Hypersaline Microbial Mats: Current Insights and New Directions. Microorganisms 2016; 4:microorganisms4010006. [PMID: 27681900 PMCID: PMC5029511 DOI: 10.3390/microorganisms4010006] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 12/08/2015] [Accepted: 12/15/2015] [Indexed: 11/17/2022] Open
Abstract
Microbial mats are unique geobiological ecosystems that form as a result of complex communities of microorganisms interacting with each other and their physical environment. Both the microorganisms present and the network of metabolic interactions govern ecosystem function therein. These systems are often found in a range of extreme environments, and those found in elevated salinity have been particularly well studied. The purpose of this review is to briefly describe the molecular ecology of select model hypersaline mat systems (Guerrero Negro, Shark Bay, S’Avall, and Kiritimati Atoll), and any potentially modulating effects caused by salinity to community structure. In addition, we discuss several emerging issues in the field (linking function to newly discovered phyla and microbial dark matter), which illustrate the changing paradigm that is seen as technology has rapidly advanced in the study of these extreme and evolutionally significant ecosystems.
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Affiliation(s)
- Hon Lun Wong
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney 2052, Australia.
- Australian Centre for Astrobiology, University of New South Wales, Sydney 2052, Australia.
| | - Aria Ahmed-Cox
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney 2052, Australia.
| | - Brendan Paul Burns
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney 2052, Australia.
- Australian Centre for Astrobiology, University of New South Wales, Sydney 2052, Australia.
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95
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Ghasimi DSM, Tao Y, de Kreuk M, Abbas B, Zandvoort MH, van Lier JB. Digester performance and microbial community changes in thermophilic and mesophilic sequencing batch reactors fed with the fine sieved fraction of municipal sewage. WATER RESEARCH 2015; 87:483-493. [PMID: 25976021 DOI: 10.1016/j.watres.2015.04.027] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 04/20/2015] [Accepted: 04/21/2015] [Indexed: 06/04/2023]
Abstract
This study investigates the start-up and operation of bench-scale mesophilic (35 °C) and thermophilic (55 °C) anaerobic sequencing batch reactor (SBR) digesters treating the fine sieved fraction (FSF) from raw municipal sewage. FSF was sequestered from raw municipal wastewater, in the Netherlands, using a rotating belt filter equipped with a 350 micron mesh. For the given wastewater, the major component of FSF was toilet paper, which is estimated to be 10-14 kg per year per average person in the western European countries. A seven months adaptation time was allowed for the thermophilic and mesophilic digesters in order to adapt to FSF as the sole substrate with varying dry solids content of 10-25%. Different SBR cycle durations (14, 9 and 2 days) were applied for both temperature conditions to study methane production rates, volatile fatty acids (VFAs) dynamics, lag phases, as well as changes in microbial communities. The prevailing sludge in the two digesters consisted of very different bacterial and archaeal communities, with OP9 lineage and Methanothermobacter being pre-dominant in the thermophilic digester and Bacteroides and Methanosaeta dominating the mesophilic one. Eventually, decreasing the SBR cycle period, thus increasing the FSF load, resulted in improved digester performances, particularly with regard to the thermophilic digester, i.e. shortened lag phases following the batch feedings, and reduced VFA peaks. Over time, the thermophilic digester outperformed the mesophilic one with 15% increased volatile solids (VS) destruction, irrespective to lower species diversity found at high temperature.
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Affiliation(s)
- Dara S M Ghasimi
- Sanitary Engineering Section, Department of Water Management, Faculty of Civil Engineering and Geosciences, Delft University of Technology, Stevinweg 1, 2628 CN, Delft, The Netherlands.
| | - Yu Tao
- Sanitary Engineering Section, Department of Water Management, Faculty of Civil Engineering and Geosciences, Delft University of Technology, Stevinweg 1, 2628 CN, Delft, The Netherlands; State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, No. 73 Huanghe Road, Harbin, 150090, China
| | - Merle de Kreuk
- Sanitary Engineering Section, Department of Water Management, Faculty of Civil Engineering and Geosciences, Delft University of Technology, Stevinweg 1, 2628 CN, Delft, The Netherlands
| | - Ben Abbas
- Environmental Biotechnology Section, Department of Biotechnology, Faculty of Applied Science, Delft University of Technology, Julianalaan 67, 2628 BC, Delft, The Netherlands
| | - Marcel H Zandvoort
- Waternet, Korte Ouderkerkerdijk 7, P.O. Box 94370, 1090 GJ, Amsterdam, The Netherlands
| | - Jules B van Lier
- Sanitary Engineering Section, Department of Water Management, Faculty of Civil Engineering and Geosciences, Delft University of Technology, Stevinweg 1, 2628 CN, Delft, The Netherlands
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96
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Nunoura T, Takaki Y, Shimamura S, Kakuta J, Kazama H, Hirai M, Masui N, Tomaru H, Morono Y, Imachi H, Inagaki F, Takai K. Variance and potential niche separation of microbial communities in subseafloor sediments off Shimokita Peninsula, Japan. Environ Microbiol 2015; 18:1889-906. [PMID: 26486095 DOI: 10.1111/1462-2920.13096] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 08/21/2015] [Accepted: 10/05/2015] [Indexed: 01/23/2023]
Abstract
Subseafloor pelagic sediments with high concentrations of organic matter form habitats for diverse microorganisms. Here, we determined depth profiles of genes for SSU rRNA, mcrA, dsrA and amoA from just beneath the seafloor to 363.3 m below the seafloor (mbsf) using core samples obtained from the forearc basin off the Shimokita Peninsula. The molecular profiles were combined with data on lithostratigraphy, depositional age, sedimentation rate and pore-water chemistry. The SSU rRNA gene tag structure and diversity changed at around the sulfate-methane transition zone (SMTZ), whereas the profiles varied further with depth below the SMTZ, probably in connection with the variation in pore-water chemistry. The depth profiles of diversity and abundance of dsrA, a key gene for sulfate reduction, suggested the possible niche separations of sulfate-reducing populations, even below the SMTZ. The diversity and abundance patterns of mcrA, a key gene for methanogenesis/anaerobic methanotrophy, suggested a stratified distribution and separation of anaerobic methanotrophy and hydrogenotrophic or methylotrophic methanogensis below the SMTZ. This study provides novel insights into the relationships between the composition and function of microbial communities and the chemical environment in the nutrient-rich continental margin subseafloor sediments, which may result in niche separation and variability in subseafloor microbial populations.
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Affiliation(s)
- Takuro Nunoura
- Marine Functional Biology Group, Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Yoshihiro Takaki
- Marine Functional Biology Group, Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan.,Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Shigeru Shimamura
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Jungo Kakuta
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Hiromi Kazama
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Miho Hirai
- Marine Functional Biology Group, Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Noriaki Masui
- Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Nankoku, Kochi, Japan
| | - Hitoshi Tomaru
- Department of Earth Sciences, Chiba University, Chiba, Inageku, Japan
| | - Yuki Morono
- Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Nankoku, Kochi, Japan
| | - Hiroyuki Imachi
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Fumio Inagaki
- Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Nankoku, Kochi, Japan
| | - Ken Takai
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
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97
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Single-Cell-Genomics-Facilitated Read Binning of Candidate Phylum EM19 Genomes from Geothermal Spring Metagenomes. Appl Environ Microbiol 2015; 82:992-1003. [PMID: 26637598 DOI: 10.1128/aem.03140-15] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 11/12/2015] [Indexed: 12/17/2022] Open
Abstract
The vast majority of microbial life remains uncatalogued due to the inability to cultivate these organisms in the laboratory. This "microbial dark matter" represents a substantial portion of the tree of life and of the populations that contribute to chemical cycling in many ecosystems. In this work, we leveraged an existing single-cell genomic data set representing the candidate bacterial phylum "Calescamantes" (EM19) to calibrate machine learning algorithms and define metagenomic bins directly from pyrosequencing reads derived from Great Boiling Spring in the U.S. Great Basin. Compared to other assembly-based methods, taxonomic binning with a read-based machine learning approach yielded final assemblies with the highest predicted genome completeness of any method tested. Read-first binning subsequently was used to extract Calescamantes bins from all metagenomes with abundant Calescamantes populations, including metagenomes from Octopus Spring and Bison Pool in Yellowstone National Park and Gongxiaoshe Spring in Yunnan Province, China. Metabolic reconstruction suggests that Calescamantes are heterotrophic, facultative anaerobes, which can utilize oxidized nitrogen sources as terminal electron acceptors for respiration in the absence of oxygen and use proteins as their primary carbon source. Despite their phylogenetic divergence, the geographically separate Calescamantes populations were highly similar in their predicted metabolic capabilities and core gene content, respiring O2, or oxidized nitrogen species for energy conservation in distant but chemically similar hot springs.
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98
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Contemporary molecular tools in microbial ecology and their application to advancing biotechnology. Biotechnol Adv 2015; 33:1755-73. [DOI: 10.1016/j.biotechadv.2015.09.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Revised: 09/19/2015] [Accepted: 09/20/2015] [Indexed: 12/30/2022]
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99
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Sträuber H, Lucas R, Kleinsteuber S. Metabolic and microbial community dynamics during the anaerobic digestion of maize silage in a two-phase process. Appl Microbiol Biotechnol 2015; 100:479-91. [PMID: 26411455 DOI: 10.1007/s00253-015-6996-0] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 08/30/2015] [Accepted: 09/08/2015] [Indexed: 01/22/2023]
Abstract
Two-phasic anaerobic digestion processes (hydrolysis/acidogenesis separated from acetogenesis/methanogenesis) can be used for biogas production on demand or a combined chemicals/bioenergy production. For an effective process control, detailed knowledge about the microbial catalysts and their correlation to process conditions is crucial. In this study, maize silage was digested in a two-phase process and interrelationships between process parameters and microbial communities were revealed. In the first-phase reactor, alternating metabolic periods were observed which emerged independently from the feeding frequency. During the L-period, up to 11.8 g L(-1) lactic acid was produced which significantly correlated to lactic acid bacteria of the genus Lactobacillus as the most abundant community members. During the alternating G-period, the production of volatile fatty acids (up to 5.3, 4.0 and 3.1 g L(-1) for propionic, n-butyric and n-caproic acid, respectively) dominated accompanied by a high gas production containing up to 28 % hydrogen. The relative abundance of various Clostridiales increased during this metabolic period. In the second-phase reactor, the metabolic fluctuations of the first phase were smoothed out resulting in a stable biogas production as well as stable bacterial and methanogenic communities. However, the biogas composition followed the metabolic dynamics of the first phase: the hydrogen content increased during the L-period whereas highest CH4/CO2 ratios (up to 2.8) were reached during the G-period. Aceticlastic Methanosaeta as well as hydrogenotrophic Methanoculleus and Methanobacteriaceae were identified as dominant methanogens. Consequently, a directed control of the first-phase stabilizing desired metabolic states can lead to an enhanced productivity regarding chemicals and bioenergy.
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Affiliation(s)
- Heike Sträuber
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research (UFZ), Permoserstr. 15, 04318, Leipzig, Germany.
| | - Rico Lucas
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research (UFZ), Permoserstr. 15, 04318, Leipzig, Germany
| | - Sabine Kleinsteuber
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research (UFZ), Permoserstr. 15, 04318, Leipzig, Germany
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100
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Monodisperse Picoliter Droplets for Low-Bias and Contamination-Free Reactions in Single-Cell Whole Genome Amplification. PLoS One 2015; 10:e0138733. [PMID: 26389587 PMCID: PMC4577099 DOI: 10.1371/journal.pone.0138733] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 09/02/2015] [Indexed: 12/30/2022] Open
Abstract
Whole genome amplification (WGA) is essential for obtaining genome sequences from single bacterial cells because the quantity of template DNA contained in a single cell is very low. Multiple displacement amplification (MDA), using Phi29 DNA polymerase and random primers, is the most widely used method for single-cell WGA. However, single-cell MDA usually results in uneven genome coverage because of amplification bias, background amplification of contaminating DNA, and formation of chimeras by linking of non-contiguous chromosomal regions. Here, we present a novel MDA method, termed droplet MDA, that minimizes amplification bias and amplification of contaminants by using picoliter-sized droplets for compartmentalized WGA reactions. Extracted DNA fragments from a lysed cell in MDA mixture are divided into 105 droplets (67 pL) within minutes via flow through simple microfluidic channels. Compartmentalized genome fragments can be individually amplified in these droplets without the risk of encounter with reagent-borne or environmental contaminants. Following quality assessment of WGA products from single Escherichia coli cells, we showed that droplet MDA minimized unexpected amplification and improved the percentage of genome recovery from 59% to 89%. Our results demonstrate that microfluidic-generated droplets show potential as an efficient tool for effective amplification of low-input DNA for single-cell genomics and greatly reduce the cost and labor investment required for determination of nearly complete genome sequences of uncultured bacteria from environmental samples.
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