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Van Dexter S, Oubre C, Boopathy R. Carbon ecology of termite gut and phenol degradation by a bacterium isolated from the gut of termite. J Ind Microbiol Biotechnol 2019; 46:1265-1271. [PMID: 31053982 DOI: 10.1007/s10295-019-02183-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 04/26/2019] [Indexed: 10/26/2022]
Abstract
Metagenomics and transcriptomics have had some success analyzing community and functional ecology of the termite gut, but carbon utilization ecology and the effect of diet on the gut community are not well understood. This study was done to determine the effect of three hardwood tree types, oak (Quercus spp.), red maple (Acer rubrum), and tupelo (Nyssa aquatica) on the termite species, Reticulitermes flavipes in the family Rhinotermitidae. Termite abdomen homogenates were incubated on agar plates containing three common carbon sources in the termite gut, namely, acetate, cellobiose, and phenol under aerobic and anaerobic conditions. Bacterial growth was higher on cellobiose than any other carbon source. Higher bacterial growth on cellobiose was observed from termite colonies feeding on oak than on phenol from the other two wood types. The difference between aerobic and anaerobic conditions was not significant. A bacterium, Acinetobacter tandoii isolated and identified from our previous study was subjected to high concentrations of phenol as the sole carbon source and this bacterium was able to degrade phenol concentration up to 600 mg/L.
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Affiliation(s)
- Seth Van Dexter
- Department of Biological Sciences, Nicholls State University, Thibodaux, LA, 70310, USA.,Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Christopher Oubre
- Department of Biological Sciences, Nicholls State University, Thibodaux, LA, 70310, USA
| | - Raj Boopathy
- Department of Biological Sciences, Nicholls State University, Thibodaux, LA, 70310, USA.
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52
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Martinez-Fernandez G, Denman SE, McSweeney CS. Sample Processing Methods Impacts on Rumen Microbiome. Front Microbiol 2019; 10:861. [PMID: 31114550 PMCID: PMC6502991 DOI: 10.3389/fmicb.2019.00861] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Accepted: 04/04/2019] [Indexed: 01/02/2023] Open
Abstract
The standardization of collection and processing methods for rumen samples is crucial to reduce the level of errors that may affect the analysis and interpretation of the data. The aim of this study was to compare two processing methods and their impacts on the microbial community composition analysis, from material that was either immediately frozen or samples that were stored as cell pellets after removing the supernatant prior to freezing. Eight rumen-fistulated Brahman steers received chloroform as an antimethanogenic compound for 21 days. Rumen fluid samples (60 mL per animal) were collected using a probe covered with two layers of cheesecloth at 3 h post feeding at day 0 prior-treatment (control period) and day 21 of treatment. One sub-set of samples were placed in dry ice and stored at −80°C (Method 1) for subsequent DNA extraction, while a second subset of samples was centrifuged, the supernatant removed and the microbial pellet and rumen contents placed in dry ice and stored at −80°C (Method 2) prior to DNA extractions. Phylogenetic based methods (Illumina Miseq) targeting the 16S rRNA gene were used to characterize the bacterial and archaeal communities from both collection methods for the control and treatment periods. The results from this study showed that the chloroform treatment was significantly different for all beta diversity measures regardless of the processing method used. Significant differences in the relative abundances of some bacteria and archaea, such as Elusimicrobia, Fibrobacteres, Lentisphaerae, Spirochaetes, and Verrucomicrobia and Methanomassiliicoccaceae, were observed at higher levels in the Method 2. These microbial populations are known to have fragile cell wall structures and are susceptible to cell lysis. Regardless of the processing method used, both identified the key microbial groups and can be used to compare the relative shifts in the rumen microbiome between treatments. However, immediately freezing samples might alter the abundance of material from species that are more readily lysed and will not be suitable for studies that aim to assign absolute abundance values to these species within the rumen.
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Affiliation(s)
- Gonzalo Martinez-Fernandez
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Agriculture and Food, St Lucia, QLD, Australia
| | - Stuart E Denman
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Agriculture and Food, St Lucia, QLD, Australia
| | - Christopher S McSweeney
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Agriculture and Food, St Lucia, QLD, Australia
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53
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Vuillemin A, Ariztegui D, Horn F, Kallmeyer J, Orsi WD. Microbial community composition along a 50 000-year lacustrine sediment sequence. FEMS Microbiol Ecol 2019; 94:4880442. [PMID: 29471361 PMCID: PMC5905624 DOI: 10.1093/femsec/fiy029] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 02/19/2018] [Indexed: 02/01/2023] Open
Abstract
For decades, microbial community composition in subseafloor sediments has been the focus of extensive studies. In deep lacustrine sediments, however, the taxonomic composition of microbial communities remains undercharacterized. Greater knowledge on microbial diversity in lacustrine sediments would improve our understanding of how environmental factors, and resulting selective pressures, shape subsurface biospheres in marine and freshwater sediments. Using high-throughput sequencing of 16S rRNA genes across high-resolution climate intervals covering the last 50 000 years in Laguna Potrok Aike, Argentina, we identified changes in microbial populations in response to both past environmental conditions and geochemical changes of the sediment during burial. Microbial communities in Holocene sediments were most diverse, reflecting a layering of taxa linked to electron acceptors availability. In deeper intervals, the data show that salinity, organic matter and the depositional conditions over the Last Glacial-interglacial cycle were all selective pressures in the deep lacustrine assemblage resulting in a genetically distinct biosphere from the surface dominated primarily by Bathyarchaeota and Atribacteria groups. However, similar to marine sediments, some dominant taxa in the shallow subsurface persisted into the subsurface as minor fraction of the community. The subsequent establishment of a deep subsurface community likely results from a combination of paleoenvironmental factors that have shaped the pool of available substrates, together with substrate depletion and/or reworking of organic matter with depth.
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Affiliation(s)
- Aurèle Vuillemin
- Department of Earth & Environmental Science, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333 Munich, Germany.,Section of Earth & Environmental Sciences, University of Geneva, rue des Maraichers 13, 1205 Geneva, Switzerland.,GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3: Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany
| | - Daniel Ariztegui
- Section of Earth & Environmental Sciences, University of Geneva, rue des Maraichers 13, 1205 Geneva, Switzerland
| | - Fabian Horn
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3: Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany
| | - Jens Kallmeyer
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3: Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany
| | - William D Orsi
- Department of Earth & Environmental Science, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333 Munich, Germany.,Geobio-Center, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333 Munich, Germany
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54
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Liu J, Zhao R, Zhang J, Zhang G, Yu K, Li X, Li B. Occurrence and Fate of Ultramicrobacteria in a Full-Scale Drinking Water Treatment Plant. Front Microbiol 2018; 9:2922. [PMID: 30568635 PMCID: PMC6290093 DOI: 10.3389/fmicb.2018.02922] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 11/14/2018] [Indexed: 12/23/2022] Open
Abstract
Ultramicrobacteria (UMB) are omnipresent and numerically dominate in freshwater, as microbes can present in drinking water systems, however, the UMB communities that occur and their removal behaviors remain poorly characterized in drinking water treatment plants (DWTPs). To gain insights into these issues, we profiled bacterial cell density, community structure and functions of UMB and their counterpart large bacteria (LB) using flow cytometry and filtration paired with 16S rRNA gene high-throughput sequencing in a full-scale DWTP. Contrary to the reduction of bacterial density and diversity, the proportion of UMB in the total bacteria community increased as the drinking water treatment process progressed, and biological activated carbon facilitated bacterial growth. Moreover, UMB were less diverse than LB, and their community structure and predicted functions were significantly different. In the DWTP, UMB indicator taxa were mainly affiliated with α/β/γ-Proteobacteria, Deinococcus-Thermus, Firmicutes, Acidobacteria, and Dependentiae. In particular, the exclusive clustering of UMB at the phylum level, e.g., Parcubacteria, Elusimicrobia, and Saccharibacteria, confirmed the fact that the ultra-small size of UMB is a naturally and evolutionarily conserved trait. Additionally, the streamlined genome could be connected to UMB, such as candidate phyla radiation (CPR) bacteria, following a symbiotic or parasitic lifestyle, which then leads to the observed high connectedness, i.e., non-random intra-taxa co-occurrence patterns within UMB. Functional prediction analysis revealed that environmental information processing and DNA replication and repair likely contribute to the higher resistance of UMB to drinking water treatment processes in comparison to LB. Overall, the study provides valuable insights into the occurrence and fate of UMB regarding community structure, phylogenetic characteristics and potential functions in a full-scale DWTP, and it is a useful reference for beneficial manipulation of the drinking water microbiome.
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Affiliation(s)
- Jie Liu
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen, China
| | - Renxin Zhao
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen, China
| | - Jiayu Zhang
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen, China
| | - Guijuan Zhang
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen, China
| | - Ke Yu
- School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, China
| | - Xiaoyan Li
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen, China
| | - Bing Li
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen, China
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55
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Gu M, Yin Q, Wang Z, He K, Wu G. Color and nitrogen removal from synthetic dye wastewater in an integrated mesophilic hydrolysis/acidification and multiple anoxic/aerobic process. CHEMOSPHERE 2018; 212:881-889. [PMID: 30195168 DOI: 10.1016/j.chemosphere.2018.08.162] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 06/30/2018] [Accepted: 08/31/2018] [Indexed: 06/08/2023]
Abstract
Dye wastewater is one kind of refractory pollutant and it is commonly treated by the integrated anaerobic and aerobic process. A new integrated hydrolysis/acidification and multiple anoxic/aerobic (AO) process was proposed for the removal of color and nitrogen from azo dye wastewater. System performance, the degradation pathway of azo dye and nitrogen metabolic pathway were investigated with quadrupole-time-of-flight and metagenomic analyses. The proposed process removed color and nitrogen efficiently, with the removal percentages of 89.4% and 54.0%, respectively. A colorful intermediate C16H11N3O7S2 during the degradation of azo dye was detected. Controlling a low dissolved oxygen concentration in the multiple AO process could enhance nitrogen removal. The detected bacteria possessing azoreductase for the azo dye degradation included Desulfovibrio aminophilus, Thermoanaerobacter, Lactococcus raffinolactis, Ruminiclostridium and Rhodopirellula. The nitrifying genes of amo and hao were mainly detected in Nitrosomonas, while the denitrifying genes were detected in Thauera, Candidatus Accumulibacter and Rhodothermus marinus.
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Affiliation(s)
- Mengqi Gu
- Guangdong Province Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, China
| | - Qidong Yin
- Guangdong Province Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, China
| | - Zhongzhong Wang
- Guangdong Province Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, China
| | - Kai He
- Research Centre for Environmental Quality Management, Kyoto University, 1-2 Yumihama, Otsu, Shiga, 520-0811, Japan
| | - Guangxue Wu
- Guangdong Province Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, China.
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56
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Nishihara A, Thiel V, Matsuura K, McGlynn SE, Haruta S. Phylogenetic Diversity of Nitrogenase Reductase Genes and Possible Nitrogen-Fixing Bacteria in Thermophilic Chemosynthetic Microbial Communities in Nakabusa Hot Springs. Microbes Environ 2018; 33:357-365. [PMID: 30404970 PMCID: PMC6307998 DOI: 10.1264/jsme2.me18030] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Chemosynthetic microbial communities develop and form dense cell aggregates in slightly alkaline sulfidic hot springs in the temperature range of 70–86°C at Nakabusa, Japan. Nitrogenase activity has recently been detected in the microbial communities collected. To identify possible members capable of nitrogen fixation, we examined the diversities of 16S rRNA and nitrogenase reductase (NifH) gene sequences in four types of chemosynthetic communities with visually different colors and thicknesses. The results of a 16S rRNA gene analysis indicated that all four microbial communities had similar bacterial constituents; the phylum Aquificae was the dominant member, followed in abundance by Thermodesulfobacteria, Firmicutes, and Thermotogae. Most of the NifH sequences were related to sequences reported in hydrothermal vents and terrestrial hot springs. The results of a phylogenetic analysis of NifH sequences revealed diversity in this gene among the communities collected, distributed within 7 phylogenetic groups. NifH sequences affiliated with Aquificae (Hydrogenobacter/Thermocrinis) and Firmicutes (Caldicellulosiruptor) were abundant. At least two different energy metabolic pathways appeared to be related to nitrogen fixation in the communities analyzed; aerobic sulfur/hydrogen-oxidizing bacteria in Aquificae and fermentative bacteria in Firmicutes. The metabolic characteristics of these two dominant phyla differed from those previously inferred from nitrogenase activity assays on chemosynthetic communities, which were associated with hydrogen-dependent autotrophic sulfate reduction. These assays may correspond to the observed NifH sequences that are distantly related to the known species of Thermodesulfovibrio sp. (Nitrospirae) detected in the present study. The activities of nitrogen-fixing organisms in communities may depend on redox states as well as the availability of electron donors, acceptors, and carbon sources.
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Affiliation(s)
- Arisa Nishihara
- Department of Biological Sciences, Tokyo Metropolitan University
| | - Vera Thiel
- Department of Biological Sciences, Tokyo Metropolitan University
| | - Katsumi Matsuura
- Department of Biological Sciences, Tokyo Metropolitan University
| | - Shawn E McGlynn
- Department of Biological Sciences, Tokyo Metropolitan University.,Earth-Life Science Institute, Tokyo Institute of Technology.,Biofunctional Catalyst Research Team, RIKEN Center for Sustainable Resource Science.,Blue Marble Space Institute of Science
| | - Shin Haruta
- Department of Biological Sciences, Tokyo Metropolitan University
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57
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58
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Zhou N, Sun YT, Chen DW, Du W, Yang H, Liu SJ. Harnessing microfluidic streak plate technique to investigate the gut microbiome of Reticulitermes chinensis. Microbiologyopen 2018; 8:e00654. [PMID: 29897677 PMCID: PMC6436436 DOI: 10.1002/mbo3.654] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Revised: 04/04/2018] [Accepted: 04/23/2018] [Indexed: 02/01/2023] Open
Abstract
The termite gut microbiome is a model system to investigate microbial interactions and their associations with host. For decades, extensive research with molecular tools and conventional cultivation method has been carried out to define the microbial diversity in termite gut. Yet, many bacterial groups of the termite gut microbiome have not been successfully cultivated in laboratory. In this study, we adapted the recently developed microfluidic streak plate (MSP) technique for cultivation of termite gut microbial communities at both aerobic and anaerobic conditions. We found that 99 operational taxonomic units (OTUs) were cultivable by MSP approach and 18 OTUs were documented first time for termite gut microbiota. Further analysis of the bacterial diversities derived by culture‐dependent MSP approach and culture‐independent 16S rRNA gene typing revealed that both methods have bias in recovery of gut microbiota. In total 396 strains were isolated with MSP technique, and potential new taxa at species and/or genus levels were obtained that were phylogenetically related to Burkholderia, Micrococcus, and Dysgonomonas. Results from this study indicate that MSP technique is applicable for cultivating previously unknown and new microbial groups of termite gut microbiota.
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Affiliation(s)
- Nan Zhou
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yu-Tong Sun
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Science, at Hebei University, Baoding, China
| | - Dong-Wei Chen
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Wenbin Du
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Hong Yang
- School of Life Sciences at Central, China Normal University, Wuhan, China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,College of Life Science, at Hebei University, Baoding, China
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59
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Huang YY, Martínez-del Campo A, Balskus EP. Anaerobic 4-hydroxyproline utilization: Discovery of a new glycyl radical enzyme in the human gut microbiome uncovers a widespread microbial metabolic activity. Gut Microbes 2018; 9:437-451. [PMID: 29405826 PMCID: PMC6219649 DOI: 10.1080/19490976.2018.1435244] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The discovery of enzymes responsible for previously unappreciated microbial metabolic pathways furthers our understanding of host-microbe and microbe-microbe interactions. We recently identified and characterized a new gut microbial glycyl radical enzyme (GRE) responsible for anaerobic metabolism of trans-4-hydroxy-l-proline (Hyp). Hyp dehydratase (HypD) catalyzes the removal of water from Hyp to generate Δ1-pyrroline-5-carboxylate (P5C). This enzyme is encoded in the genomes of a diverse set of gut anaerobes and is prevalent and abundant in healthy human stool metagenomes. Here, we discuss the roles HypD may play in different microbial metabolic pathways as well as the potential implications of this activity for colonization resistance and pathogenesis within the human gut. Finally, we present evidence of anaerobic Hyp metabolism in sediments through enrichment culturing of Hyp-degrading bacteria, highlighting the wide distribution of this pathway in anoxic environments beyond the human gut.
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Affiliation(s)
- Yolanda Y. Huang
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | | | - Emily P. Balskus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA,CONTACT Emily P. Balskus Commense Inc., 100 Edwin H. Land Blvd, Cambridge, MA 02142
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60
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Zhang L, Zhang J, Loh KC. Activated carbon enhanced anaerobic digestion of food waste - Laboratory-scale and Pilot-scale operation. WASTE MANAGEMENT (NEW YORK, N.Y.) 2018; 75:270-279. [PMID: 29456123 DOI: 10.1016/j.wasman.2018.02.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 01/08/2018] [Accepted: 02/11/2018] [Indexed: 06/08/2023]
Abstract
Effects of activated carbon (AC) supplementation on anaerobic digestion (AD) of food waste were elucidated in lab- and pilot-scales. Lab-scale AD was performed in 1 L and 8 L digesters, while pilot-scale AD was conducted in a 1000 L digester. Based on the optimal dose of 15 g AC per working volume derived from the 1 L digester, for the same AC dosage in the 8 L digester, an improved operation stability coupled with a higher methane yield was achieved even when digesters without AC supplementation failed after 59 days due to accumulation of substantial organic intermediates. At the same time, color removal from the liquid phase of the digestate was dramatically enhanced and the particle size of the digestate solids was increased by 53% through AC supplementation after running for 59 days. Pyrosequencing of 16S rRNA gene showed the abundance of predominant phyla Firmicutes, Elusimicrobia and Proteobacteria selectively enhanced by 1.7-fold, 2.9-fold and 2.1-fold, respectively. Pilot-scale digester without AC gave an average methane yield of 0.466 L⋅(gVS)-1⋅d-1 at a composition of 53-61% v/v methane. With AC augmentation, an increase of 41% in methane yield was achieved in the 1000 L digester under optimal organic loading rate (1.6 g VSFW·L-1·d-1).
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Affiliation(s)
- Le Zhang
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, S117576, Singapore
| | - Jingxin Zhang
- NUS Environmental Research Institute, National University of Singapore, 1 Create Way, Create Tower #15-02, S138602, Singapore
| | - Kai-Chee Loh
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, S117576, Singapore.
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61
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Angel R, Nepel M, Panhölzl C, Schmidt H, Herbold CW, Eichorst SA, Woebken D. Evaluation of Primers Targeting the Diazotroph Functional Gene and Development of NifMAP - A Bioinformatics Pipeline for Analyzing nifH Amplicon Data. Front Microbiol 2018; 9:703. [PMID: 29760683 PMCID: PMC5936773 DOI: 10.3389/fmicb.2018.00703] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Accepted: 03/27/2018] [Indexed: 11/13/2022] Open
Abstract
Diazotrophic microorganisms introduce biologically available nitrogen (N) to the global N cycle through the activity of the nitrogenase enzyme. The genetically conserved dinitrogenase reductase (nifH) gene is phylogenetically distributed across four clusters (I-IV) and is widely used as a marker gene for N2 fixation, permitting investigators to study the genetic diversity of diazotrophs in nature and target potential participants in N2 fixation. To date there have been limited, standardized pipelines for analyzing the nifH functional gene, which is in stark contrast to the 16S rRNA gene. Here we present a bioinformatics pipeline for processing nifH amplicon datasets - NifMAP ("NifH MiSeq Illumina Amplicon Analysis Pipeline"), which as a novel aspect uses Hidden-Markov Models to filter out homologous genes to nifH. By using this pipeline, we evaluated the broadly inclusive primer pairs (Ueda19F-R6, IGK3-DVV, and F2-R6) that target the nifH gene. To evaluate any systematic biases, the nifH gene was amplified with the aforementioned primer pairs in a diverse collection of environmental samples (soils, rhizosphere and roots samples, biological soil crusts and estuarine samples), in addition to a nifH mock community consisting of six phylogenetically diverse members. We noted that all primer pairs co-amplified nifH homologs to varying degrees; up to 90% of the amplicons were nifH homologs with IGK3-DVV in some samples (rhizosphere and roots from tall oat-grass). In regards to specificity, we observed some degree of bias across the primer pairs. For example, primer pair F2-R6 discriminated against cyanobacteria (amongst others), yet captured many sequences from subclusters IIIE and IIIL-N. These aforementioned subclusters were largely missing by the primer pair IGK3-DVV, which also tended to discriminate against Alphaproteobacteria, but amplified sequences within clusters IIIC (affiliated with Clostridia) and clusters IVB and IVC. Primer pair Ueda19F-R6 exhibited the least bias and successfully captured diazotrophs in cluster I and subclusters IIIE, IIIL, IIIM, and IIIN, but tended to discriminate against Firmicutes and subcluster IIIC. Taken together, our newly established bioinformatics pipeline, NifMAP, along with our systematic evaluations of nifH primer pairs permit more robust, high-throughput investigations of diazotrophs in diverse environments.
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Affiliation(s)
- Roey Angel
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network ‘Chemistry meets Microbiology’, University of Vienna, Vienna, Austria
| | | | | | | | | | | | - Dagmar Woebken
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network ‘Chemistry meets Microbiology’, University of Vienna, Vienna, Austria
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62
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Oren A, Garrity GM. List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2018; 68:693-694. [PMID: 29493486 DOI: 10.1099/ijsem.0.002570] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - George M Garrity
- Department of Microbiology and Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
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63
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Tegtmeier D, Belitz A, Radek R, Heimerl T, Brune A. Ereboglobus luteus gen. nov. sp. nov. from cockroach guts, and new insights into the oxygen relationship of the genera Opitutus and Didymococcus ( Verrucomicrobia : Opitutaceae ). Syst Appl Microbiol 2018; 41:101-112. [DOI: 10.1016/j.syapm.2017.10.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 10/19/2017] [Accepted: 10/28/2017] [Indexed: 11/25/2022]
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64
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Gaby JC, Rishishwar L, Valderrama-Aguirre LC, Green SJ, Valderrama-Aguirre A, Jordan IK, Kostka JE. Diazotroph Community Characterization via a High-Throughput nifH Amplicon Sequencing and Analysis Pipeline. Appl Environ Microbiol 2018; 84:e01512-17. [PMID: 29180374 PMCID: PMC5795091 DOI: 10.1128/aem.01512-17] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 11/21/2017] [Indexed: 11/20/2022] Open
Abstract
The dinitrogenase reductase gene (nifH) is the most widely established molecular marker for the study of nitrogen-fixing prokaryotes in nature. A large number of PCR primer sets have been developed for nifH amplification, and the effective deployment of these approaches should be guided by a rapid, easy-to-use analysis protocol. Bioinformatic analysis of marker gene sequences also requires considerable expertise. In this study, we advance the state of the art for nifH analysis by evaluating nifH primer set performance, developing an improved amplicon sequencing workflow, and implementing a user-friendly bioinformatics pipeline. The developed amplicon sequencing workflow is a three-stage PCR-based approach that uses established technologies for incorporating sample-specific barcode sequences and sequencing adapters. Based on our primer evaluation, we recommend the Ando primer set be used with a modified annealing temperature of 58°C, as this approach captured the largest diversity of nifH templates, including paralog cluster IV/V sequences. To improve nifH sequence analysis, we developed a computational pipeline which infers taxonomy and optionally filters out paralog sequences. In addition, we employed an empirical model to derive optimal operational taxonomic unit (OTU) cutoffs for the nifH gene at the species, genus, and family levels. A comprehensive workflow script named TaxADivA (TAXonomy Assignment and DIVersity Assessment) is provided to ease processing and analysis of nifH amplicons. Our approach is then validated through characterization of diazotroph communities across environmental gradients in beach sands impacted by the Deepwater Horizon oil spill in the Gulf of Mexico, in a peat moss-dominated wetland, and in various plant compartments of a sugarcane field.IMPORTANCE Nitrogen availability often limits ecosystem productivity, and nitrogen fixation, exclusive to prokaryotes, comprises a major source of nitrogen input that sustains food webs. The nifH gene, which codes for the iron protein of the nitrogenase enzyme, is the most widely established molecular marker for the study of nitrogen-fixing microorganisms (diazotrophs) in nature. In this study, a flexible sequencing/analysis pipeline, named TaxADivA, was developed for nifH amplicons produced by Illumina paired-end sequencing, and it enables an inference of taxonomy, performs clustering, and produces output in formats that may be used by programs that facilitate data exploration and analysis. Diazotroph diversity and community composition are linked to ecosystem functioning, and our results advance the phylogenetic characterization of diazotroph communities by providing empirically derived nifH similarity cutoffs for species, genus, and family levels. The utility of our pipeline is validated for diazotroph communities in a variety of ecosystems, including contaminated beach sands, peatland ecosystems, living plant tissues, and rhizosphere soil.
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Affiliation(s)
- John Christian Gaby
- School of Biology, The Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Lavanya Rishishwar
- School of Biology, The Georgia Institute of Technology, Atlanta, Georgia, USA
- Applied Bioinformatics Laboratory, Atlanta, Georgia, USA
- PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia
| | - Lina C Valderrama-Aguirre
- Laboratory of Microorganismal Production (Bioinoculums), Department of Field Research in Sugarcane, Incauca S.A.S, Cali, Valle del Cauca, Colombia
- School of Natural Resources and Environmental Engineering, PhD Program in Sanitary and Environmental Engineering, Universidad del Valle, Cali, Valle del Cauca, Colombia
| | - Stefan J Green
- DNA Services Facility, Research Resources Center, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Augusto Valderrama-Aguirre
- PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia
- Biomedical Research Institute, Universidad Libre, Cali, Valle del Cauca, Colombia
- Regenerar, Center of Excellence for Regenerative and Personalized Medicine, Valle del Cauca, Colombia
| | - I King Jordan
- School of Biology, The Georgia Institute of Technology, Atlanta, Georgia, USA
- Applied Bioinformatics Laboratory, Atlanta, Georgia, USA
- PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia
| | - Joel E Kostka
- School of Biology, The Georgia Institute of Technology, Atlanta, Georgia, USA
- PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia
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Tang Y, Li M, Xu D, Huang J, Sun J. Application potential of aerobic denitrifiers coupled with a biostimulant for nitrogen removal from urban river sediment. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:5980-5993. [PMID: 29236243 DOI: 10.1007/s11356-017-0903-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Accepted: 12/01/2017] [Indexed: 06/07/2023]
Abstract
Aerobic denitrifiers coupled with a denitrification agent were applied in the sediment of an urban river for the bioremediation of nitrogen pollution. The results revealed that 14.7% of the total nitrogen in the sediment was removed after 115 days of treatment and the nitrate nitrogen concentration removal rate was enhanced in the overlying water. Compared with the control, the total transferable nitrogen in the sediment increased from 0.097 to 0.166 mg/g, indicating that more nitrogen is likely to be involved in the biogeochemical cycling of nitrogen. Increased urease activity indicated the possible further potential of nitrogen biodegradation, while the decreased protease pointed to the low concentration of protein remaining in the sediment. Sequencing revealed that the bacterial community diversity in the sediment increased significantly after 43 days of treatment and that the effect persisted. Compared with other microcosms, the dominant phyla in the sediment after 43 days were Firmicutes, Elusimicrobia, Spirochaetae and Fibrobacteres; whereas, after 115 of treatment, the dominant bacteria were Nitrospirae, Deferribacteres and Chloroflexi. The dominant bacteria in the sediment are mainly associated with nitrogen cycling and thus contributed considerably to nitrogen removal in the sediment. Overall, the direction of species succession was similar to natural succession; namely, there were no undesirable ecological risks involved. This study highlights the possible benefits and feasibility of using bioaugmentation technology coupled with biostimulation to remediate nitrogen-polluted sediments.
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Affiliation(s)
- Yinqi Tang
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300350, People's Republic of China
- State Key Laboratory of Hydraulic Engineering Simulation and Safety, Tianjin University, Tianjin, 300350, People's Republic of China
| | - Meng Li
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300350, People's Republic of China
- State Key Laboratory of Hydraulic Engineering Simulation and Safety, Tianjin University, Tianjin, 300350, People's Republic of China
| | - Danning Xu
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300350, People's Republic of China
- State Key Laboratory of Hydraulic Engineering Simulation and Safety, Tianjin University, Tianjin, 300350, People's Republic of China
| | - Jianjun Huang
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300350, People's Republic of China
| | - Jingmei Sun
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300350, People's Republic of China.
- State Key Laboratory of Hydraulic Engineering Simulation and Safety, Tianjin University, Tianjin, 300350, People's Republic of China.
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Rissanen AJ, Karvinen A, Nykänen H, Peura S, Tiirola M, Mäki A, Kankaala P. Effects of alternative electron acceptors on the activity and community structure of methane-producing and consuming microbes in the sediments of two shallow boreal lakes. FEMS Microbiol Ecol 2017. [PMID: 28637304 DOI: 10.1093/femsec/fix078] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The role of anaerobic CH4 oxidation in controlling lake sediment CH4 emissions remains unclear. Therefore, we tested how relevant EAs (SO42-, NO3-, Fe3+, Mn4+, O2) affect CH4 production and oxidation in the sediments of two shallow boreal lakes. The changes induced to microbial communities by the addition of Fe3+ and Mn4+ were studied using next-generation sequencing targeting the 16S rRNA and methyl-coenzyme M reductase (mcrA) genes and mcrA transcripts. Putative anaerobic CH4-oxidizing archaea (ANME-2D) and bacteria (NC 10) were scarce (up to 3.4% and 0.5% of archaeal and bacterial 16S rRNA genes, respectively), likely due to the low environmental stability associated with shallow depths. Consequently, the potential anaerobic CH4 oxidation (0-2.1 nmol g-1dry weight (DW)d-1) was not enhanced by the addition of EAs, nor important in consuming the produced CH4 (0.6-82.5 nmol g-1DWd-1). Instead, the increased EA availability suppressed CH4 production via the outcompetition of methanogens by anaerobically respiring bacteria and via the increased protection of organic matter from microbial degradation induced by Fe3+ and Mn4+. Future studies could particularly assess whether anaerobic CH4 oxidation has any ecological relevance in reducing CH4 emissions from the numerous CH4-emitting shallow lakes in boreal and tundra landscapes.
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Affiliation(s)
- Antti J Rissanen
- Laboratory of Chemistry and Bioengineering, Tampere University of Technology, FI-33101 Tampere, Finland
- Department of Biological and Environmental Science, University of Jyväskylä, FI-40014 Jyväskylä, Finland
| | - Anu Karvinen
- Department of Environmental and Biological Sciences, University of Eastern Finland, FI-80101 Joensuu, Finland
| | - Hannu Nykänen
- Department of Biological and Environmental Science, University of Jyväskylä, FI-40014 Jyväskylä, Finland
- Department of Environmental and Biological Sciences, University of Eastern Finland, FI-70211 Kuopio, Finland
| | - Sari Peura
- Department of Biological and Environmental Science, University of Jyväskylä, FI-40014 Jyväskylä, Finland
- Science for Life Laboratories, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, SE-750 07 Uppsala, Sweden
| | - Marja Tiirola
- Department of Biological and Environmental Science, University of Jyväskylä, FI-40014 Jyväskylä, Finland
| | - Anita Mäki
- Department of Biological and Environmental Science, University of Jyväskylä, FI-40014 Jyväskylä, Finland
| | - Paula Kankaala
- Department of Environmental and Biological Sciences, University of Eastern Finland, FI-80101 Joensuu, Finland
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Mikaelyan A, Thompson CL, Meuser K, Zheng H, Rani P, Plarre R, Brune A. High-resolution phylogenetic analysis of Endomicrobia reveals multiple acquisitions of endosymbiotic lineages by termite gut flagellates. ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:477-483. [PMID: 28677262 DOI: 10.1111/1758-2229.12565] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 06/09/2017] [Accepted: 06/21/2017] [Indexed: 05/25/2023]
Abstract
Bacteria of the class Endomicrobia form a deep-branching clade in the Elusimicrobia phylum. They are found almost exclusively in the intestinal tract of animals and are particularly abundant in many termites, where they reside as intracellular symbionts in the cellulolytic gut flagellates. Although small populations of putatively free-living lineages have been detected in faunated and flagellate-free hosts, the evolutionary origin of the endosymbionts is obscured by the limited amount of phylogenetic information provided by the 16S rRNA gene fragment amplified with Endomicrobia-specific primers. Here, we present a robust phylogenetic framework based on the near-full-length 16S-23S rRNA gene region of a diverse set of Endomicrobia from termites and cockroaches, which also allowed us to classify the shorter reads from previous studies. Our data revealed that endosymbionts arose independently at least four times from different free-living lineages, which were already present in ancestral cockroaches but became associated with their respective hosts long after the digestive symbiosis between termites and flagellates had been established. Pyrotag sequencing revealed that the proportion of putatively free-living lineages increased, when all flagellates and their symbionts were removed from the gut of lower termites by starvation, starch feeding or hyperbaric oxygen, but results varied between different methods.
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Affiliation(s)
- Aram Mikaelyan
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, Marburg 35043, Germany
| | - Claire L Thompson
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, Marburg 35043, Germany
| | - Katja Meuser
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, Marburg 35043, Germany
| | - Hao Zheng
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, Marburg 35043, Germany
| | - Pinki Rani
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, Marburg 35043, Germany
| | - Rudy Plarre
- Federal Institute for Materials Research and Testing, Unter den Eichen 87, Berlin 12205, Germany
| | - Andreas Brune
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, Marburg 35043, Germany
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Brune A. Ectosymbiotic Endomicrobia - a transition stage towards intracellular symbionts? ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:474-476. [PMID: 28892291 DOI: 10.1111/1758-2229.12587] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 08/26/2017] [Indexed: 06/07/2023]
Affiliation(s)
- Andreas Brune
- Insect Gut Microbiology and Symbiosis Group, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
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Genome Analysis of Endomicrobium proavitum Suggests Loss and Gain of Relevant Functions during the Evolution of Intracellular Symbionts. Appl Environ Microbiol 2017. [PMID: 28646115 DOI: 10.1128/aem.00656-17] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacterial endosymbionts of eukaryotes show progressive genome erosion, but detailed investigations of the evolutionary processes involved in the transition to an intracellular lifestyle are generally hampered by the lack of extant free-living lineages. Here, we characterize the genome of the recently isolated, free-living Endomicrobium proavitum, the second member of the Elusimicrobia phylum brought into pure culture, and compare it to the closely related "Candidatus Endomicrobium trichonymphae" strain Rs-D17, a previously described but uncultured endosymbiont of termite gut flagellates. A reconstruction of the metabolic pathways of Endomicrobium proavitum matched the fermentation products formed in pure culture and underscored its restriction to glucose as the substrate. However, several pathways present in the free-living strain, e.g., for the uptake and activation of glucose and its subsequent fermentation, ammonium assimilation, and outer membrane biogenesis, were absent or disrupted in the endosymbiont, probably lost during the massive genome rearrangements that occurred during symbiogenesis. While the majority of the genes in strain Rs-D17 have orthologs in Endomicrobium proavitum, the endosymbiont also possesses a number of functions that are absent from the free-living strain and may represent adaptations to the intracellular lifestyle. Phylogenetic analysis revealed that the genes encoding glucose 6-phosphate and amino acid transporters, acetaldehyde/alcohol dehydrogenase, and the pathways of glucuronic acid catabolism and thiamine pyrophosphate biosynthesis were either acquired by horizontal gene transfer or may represent ancestral traits that were lost in the free-living strain. The polyphyletic origin of Endomicrobia in different flagellate hosts makes them excellent models for future studies of convergent and parallel evolution during symbiogenesis.IMPORTANCE The isolation of a free-living relative of intracellular symbionts provides the rare opportunity to identify the evolutionary processes that occur in the course of symbiogenesis. Our study documents that the genome of "Candidatus Endomicrobium trichonymphae," which represents a clade of endosymbionts that have coevolved with termite gut flagellates for more than 40 million years, is not simply a subset of the genes present in Endomicrobium proavitum, a member of the ancestral, free-living lineage. Rather, comparative genomics revealed that the endosymbionts possess several relevant functions that were either prerequisites for colonization of the intracellular habitat or might have served to compensate for genes losses that occurred during genome erosion. Some gene sets found only in the endosymbiont were apparently acquired by horizontal transfer from other gut bacteria, which suggests that the intracellular bacteria of flagellates are not entirely cut off from gene flow.
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Molybdenum-Based Diazotrophy in a Sphagnum Peatland in Northern Minnesota. Appl Environ Microbiol 2017; 83:AEM.01174-17. [PMID: 28667112 DOI: 10.1128/aem.01174-17] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 06/28/2017] [Indexed: 11/20/2022] Open
Abstract
Microbial N2 fixation (diazotrophy) represents an important nitrogen source to oligotrophic peatland ecosystems, which are important sinks for atmospheric CO2 and are susceptible to the changing climate. The objectives of this study were (i) to determine the active microbial group and type of nitrogenase mediating diazotrophy in an ombrotrophic Sphagnum-dominated peat bog (the S1 peat bog, Marcell Experimental Forest, Minnesota, USA); and (ii) to determine the effect of environmental parameters (light, O2, CO2, and CH4) on potential rates of diazotrophy measured by acetylene (C2H2) reduction and 15N2 incorporation. A molecular analysis of metabolically active microbial communities suggested that diazotrophy in surface peat was primarily mediated by Alphaproteobacteria (Bradyrhizobiaceae and Beijerinckiaceae). Despite higher concentrations of dissolved vanadium ([V] 11 nM) than molybdenum ([Mo] 3 nM) in surface peat, a combination of metagenomic, amplicon sequencing, and activity measurements indicated that Mo-containing nitrogenases dominate over the V-containing form. Acetylene reduction was only detected in surface peat exposed to light, with the highest rates observed in peat collected from hollows with the highest water contents. Incorporation of 15N2 was suppressed 90% by O2 and 55% by C2H2 and was unaffected by CH4 and CO2 amendments. These results suggest that peatland diazotrophy is mediated by a combination of C2H2-sensitive and C2H2-insensitive microbes that are more active at low concentrations of O2 and show similar activity at high and low concentrations of CH4 IMPORTANCE Previous studies indicate that diazotrophy provides an important nitrogen source and is linked to methanotrophy in Sphagnum-dominated peatlands. However, the environmental controls and enzymatic pathways of peatland diazotrophy, as well as the metabolically active microbial populations that catalyze this process, remain in question. Our findings indicate that oxygen levels and photosynthetic activity override low nutrient availability in limiting diazotrophy and that members of the Alphaproteobacteria (Rhizobiales) catalyze this process at the bog surface using the molybdenum-based form of the nitrogenase enzyme.
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71
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Petri RM, Pourazad P, Khiaosa-ard R, Klevenhusen F, Metzler-Zebeli BU, Zebeli Q. Temporal dynamics of in-situ fiber-adherent bacterial community under ruminal acidotic conditions determined by 16S rRNA gene profiling. PLoS One 2017; 12:e0182271. [PMID: 28763489 PMCID: PMC5538656 DOI: 10.1371/journal.pone.0182271] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 07/14/2017] [Indexed: 12/20/2022] Open
Abstract
Subacute rumen acidotic (SARA) conditions are a consequence of high grain feeding. Recent work has shown that the pattern of grain feeding can significantly impact the rumen epimural microbiota. In a continuation of these works, the objective of this study was to determine the role of grain feeding patterns on the colonization and associated changes in predicted functional properties of the fiber-adherent microbial community over a 48 h period. Eight rumen-cannulated Holstein cows were randomly assigned to interrupted or continuous 60%-grain challenge model (n = 4 per model) to induce SARA conditions. Cows in the continuous model were challenged for 4 weeks, whereas cows of interrupted model had a 1-wk break in between challenges. To determine dynamics of rumen fiber-adherent microbial community we incubated the same hay from the diet samples for 24 and 48 h in situ during the baseline (no grain fed), week 1 and 4 of the continuous grain feeding model as well as during the week 1 following the break in the interrupted model. Microbial DNA was extracted and 16SrRNA amplicon (V3-V5 region) sequencing was done with the Illumina MiSeq platform. A significant decrease (P < 0.001) in fiber-adherent rumen bacterial species richness and diversity was observed at the end of a 4 week continuous SARA challenge in comparison to the baseline. A total of 159 operational taxonominc units (OTUs) were identified from the microbial population representing > 0.1% relative abundance in the rumen, 18 of which were significantly impacted by the feeding challenge model. Correlation analysis of the significant OTUs to rumen pH as an indicator of SARA showed genus Succiniclasticum had a positive correlation to SARA conditions regardless of treatment. Predictive analysis of functional microbial properties suggested that the glyoxylate/dicarboxylate pathway was increased in response to SARA conditions, decreased between 24h to 48h of incubation, negatively correlated with propanoate metabolism and positively correlated to members of the Veillonellaceae family including Succiniclasticum spp. This may indicate an adaptive response in bacterial metabolism under SARA conditions. This research clearly indicates that changes to the colonizing fiber-adherent rumen microbial population and their predicted functional genes occur in both the short (48 h) and long term (4 wk) under both continuous and interrupted SARA challenge models.
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Affiliation(s)
- Renee M. Petri
- Institute of Animal Nutrition and Functional Plant Compounds, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Poulad Pourazad
- Institute of Animal Nutrition and Functional Plant Compounds, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Ratchaneewan Khiaosa-ard
- Institute of Animal Nutrition and Functional Plant Compounds, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Fenja Klevenhusen
- Institute of Animal Nutrition and Functional Plant Compounds, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Barbara U. Metzler-Zebeli
- Clinic for Swine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Qendrim Zebeli
- Institute of Animal Nutrition and Functional Plant Compounds, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Vienna, Austria
- * E-mail:
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Izawa K, Kuwahara H, Sugaya K, Lo N, Ohkuma M, Hongoh Y. Discovery of ectosymbiotic Endomicrobium lineages associated with protists in the gut of stolotermitid termites. ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:411-418. [PMID: 28556617 DOI: 10.1111/1758-2229.12549] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 05/19/2017] [Accepted: 05/18/2017] [Indexed: 06/07/2023]
Abstract
The genus Endomicrobium is a dominant bacterial group in the gut of lower termites, and most phylotypes are intracellular symbionts of gut protists. Here we report the discovery of Endomicrobium ectosymbionts of termite gut protists. We found that bristle-like Endomicrobium cells attached to the surface of spirotrichosomid protist cells inhabiting the termite Stolotermes victoriensis. Transmission electron microscopy revealed that a putative Endomicrobium cell likely attached to the protist surface via a protrusion from the tip of the bacterium. A phylotype, sharing 98.9% 16S rRNA sequence identity with the Endomicrobium ectosymbionts of the spirotrichosomid protists, was also found on the cell surface of the protist Trichonympha magna in the gut of the termite Porotermes adamsoni. We propose the novel species 'Candidatus Endomicrobium superficiale' for these bacteria. T. magna simultaneously harboured another Endomicrobium ectosymbiont that shared 93.5-94.2% 16S rRNA sequence identities with 'Ca. Endomicrobium superficiale'. Furthermore, Spirotrichonympha-like protists in P. adamsoni guts were associated with an Endomicrobium phylotype that possibly attached to the host flagella. A phylogenetic analysis suggested that these ectosymbiotic lineages have evolved multiple times from free-living Endomicrobium lineages and are relatively distant from the endosymbionts. Our results provide novel insights into the ecology and evolution of the Endomicrobium.
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Affiliation(s)
- Kazuki Izawa
- Department of Biological Sciences, Tokyo Institute of Technology, Tokyo, 152-8550, Japan
| | - Hirokazu Kuwahara
- Department of Biological Sciences, Tokyo Institute of Technology, Tokyo, 152-8550, Japan
| | - Kaito Sugaya
- Department of Biological Sciences, Tokyo Institute of Technology, Tokyo, 152-8550, Japan
| | - Nathan Lo
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Moriya Ohkuma
- RIKEN BioResource Center, Japan Collection of Microorganisms, Tsukuba, 305-0074, Japan
| | - Yuichi Hongoh
- Department of Biological Sciences, Tokyo Institute of Technology, Tokyo, 152-8550, Japan
- RIKEN BioResource Center, Japan Collection of Microorganisms, Tsukuba, 305-0074, Japan
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Jin W, Xue C, Liu J, Yin Y, Zhu W, Mao S. Effects of Disodium Fumarate on In Vitro Rumen Fermentation, The Production of Lipopolysaccharide and Biogenic Amines, and The Rumen Bacterial Community. Curr Microbiol 2017; 74:1337-1342. [PMID: 28761980 DOI: 10.1007/s00284-017-1322-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 07/25/2017] [Indexed: 01/01/2023]
Abstract
The effect of disodium fumarate (DF) on the ruminal fermentation profiles, the accumulation of lipopolysaccharide (LPS) and bioamines, and the composition of the ruminal bacterial community was investigated by in vitro rumen fermentation. The addition of DF increased the total gas production; the concentrations of propionate, valerate, total volatile fatty acids, and ammonia-nitrogen; and the rumen pH after a 24 h fermentation. By contrast, DF addition decreased the ratio of acetate to propionate and the concentrations of lactate, lipopolysaccharide, methylamine, tryptamine, putrescine, histamine, and tyramine (P < 0.05). Principal coordinates analysis and molecular variance analysis showed that DF altered the ruminal bacterial community (P < 0.05). At the phylum level, DF decreased the proportion of Proteobacteria, and increased the proportions of Spirochaetae and Elusimicrobia (P < 0.05). At the genus level, DF decreased the percentage of Ruminobacter, while increasing the percentage of Succinivibrio and Treponema (P < 0.05). Overall, the results indicate that DF modified rumen fermentation and mitigated the production of several toxic compounds. Thus, DF has great potential for preventing subacute rumen acidosis in dairy cows and for improving the health of ruminants.
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Affiliation(s)
- Wei Jin
- Jiangsu Province Key Laboratory of Gastrointestinal Nutrition and Animal Health, Laboratory of Gastrointestinal Microbiology, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Chunxu Xue
- Jiangsu Province Key Laboratory of Gastrointestinal Nutrition and Animal Health, Laboratory of Gastrointestinal Microbiology, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Junhua Liu
- Jiangsu Province Key Laboratory of Gastrointestinal Nutrition and Animal Health, Laboratory of Gastrointestinal Microbiology, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yuyang Yin
- Jiangsu Province Key Laboratory of Gastrointestinal Nutrition and Animal Health, Laboratory of Gastrointestinal Microbiology, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Weiyun Zhu
- Jiangsu Province Key Laboratory of Gastrointestinal Nutrition and Animal Health, Laboratory of Gastrointestinal Microbiology, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shengyong Mao
- Jiangsu Province Key Laboratory of Gastrointestinal Nutrition and Animal Health, Laboratory of Gastrointestinal Microbiology, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.
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Zheng H, Powell JE, Steele MI, Dietrich C, Moran NA. Honeybee gut microbiota promotes host weight gain via bacterial metabolism and hormonal signaling. Proc Natl Acad Sci U S A 2017; 114:4775-4780. [PMID: 28420790 PMCID: PMC5422775 DOI: 10.1073/pnas.1701819114] [Citation(s) in RCA: 339] [Impact Index Per Article: 48.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Social bees harbor a simple and specialized microbiota that is spatially organized into different gut compartments. Recent results on the potential involvement of bee gut communities in pathogen protection and nutritional function have drawn attention to the impact of the microbiota on bee health. However, the contributions of gut microbiota to host physiology have yet to be investigated. Here we show that the gut microbiota promotes weight gain of both whole body and the gut in individual honey bees. This effect is likely mediated by changes in host vitellogenin, insulin signaling, and gustatory response. We found that microbial metabolism markedly reduces gut pH and redox potential through the production of short-chain fatty acids and that the bacteria adjacent to the gut wall form an oxygen gradient within the intestine. The short-chain fatty acid profile contributed by dominant gut species was confirmed in vitro. Furthermore, metabolomic analyses revealed that the gut community has striking impacts on the metabolic profiles of the gut compartments and the hemolymph, suggesting that gut bacteria degrade plant polymers from pollen and that the resulting metabolites contribute to host nutrition. Our results demonstrate how microbial metabolism affects bee growth, hormonal signaling, behavior, and gut physicochemical conditions. These findings indicate that the bee gut microbiota has basic roles similar to those found in some other animals and thus provides a model in studies of host-microbe interactions.
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Affiliation(s)
- Hao Zheng
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712;
| | - J Elijah Powell
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712
| | - Margaret I Steele
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712
| | - Carsten Dietrich
- Strategy and Innovation Technology Center, Siemens Healthcare GmbH, 91052 Erlangen, Germany
| | - Nancy A Moran
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712;
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75
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Campanaro S, Treu L, Cattani M, Kougias PG, Vendramin V, Schiavon S, Tagliapietra F, Giacomini A, Corich V. In vitro fermentation of key dietary compounds with rumen fluid: A genome-centric perspective. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 584-585:683-691. [PMID: 28131445 DOI: 10.1016/j.scitotenv.2017.01.096] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Revised: 01/11/2017] [Accepted: 01/15/2017] [Indexed: 06/06/2023]
Abstract
The anaerobic decomposition of organic substrates leads to the generation of gases, such as methane, which can either be a valuable energy carrier in industrial applications or can be considered as a main greenhouse gas when it is naturally emitted. In this study we investigated in vitro the effect of dietary compounds, such as starch and proteins, on the microbial community present in the rumen fluid. High throughput shotgun sequencing, followed by metagenomic assembly and binning allowed the extraction of 18 genome bins. A composite bioinformatic analysis led to the prediction of metabolic pathways involved in the degradation of dietary compounds and in the biosynthesis of crucial products like propionate, methane and ammonia. The identification of genomes belonging to poorly characterized phyla such as Thermoplasmata and Elusimicrobia shed light on their putative role. The high abundance of methylotrophic archaea in the inoculum suggests a relevant role in methane production.
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Affiliation(s)
- Stefano Campanaro
- Department of Biology, University of Padova, Via U. Bassi 58/b, Padova 35121, Italy.
| | - Laura Treu
- Department of Agronomy, Food, Natural Resources, Animals and the Environment (DAFNAE), University of Padova, Viale dell'Università 16, Legnaro, PD 35020, Italy; Department of Environmental Engineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Mirko Cattani
- Department of Comparative Biomedicine and Food Science (BCA), University of Padova, Viale dell'Università 16, Legnaro, PD 35020, Italy
| | - Panagiotis G Kougias
- Department of Environmental Engineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Veronica Vendramin
- Department of Agronomy, Food, Natural Resources, Animals and the Environment (DAFNAE), University of Padova, Viale dell'Università 16, Legnaro, PD 35020, Italy
| | - Stefano Schiavon
- Department of Agronomy, Food, Natural Resources, Animals and the Environment (DAFNAE), University of Padova, Viale dell'Università 16, Legnaro, PD 35020, Italy
| | - Franco Tagliapietra
- Department of Agronomy, Food, Natural Resources, Animals and the Environment (DAFNAE), University of Padova, Viale dell'Università 16, Legnaro, PD 35020, Italy
| | - Alessio Giacomini
- Department of Agronomy, Food, Natural Resources, Animals and the Environment (DAFNAE), University of Padova, Viale dell'Università 16, Legnaro, PD 35020, Italy
| | - Viviana Corich
- Department of Agronomy, Food, Natural Resources, Animals and the Environment (DAFNAE), University of Padova, Viale dell'Università 16, Legnaro, PD 35020, Italy
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76
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Sapountzis P, de Verges J, Rousk K, Cilliers M, Vorster BJ, Poulsen M. Potential for Nitrogen Fixation in the Fungus-Growing Termite Symbiosis. Front Microbiol 2016; 7:1993. [PMID: 28018322 PMCID: PMC5156715 DOI: 10.3389/fmicb.2016.01993] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 11/28/2016] [Indexed: 11/13/2022] Open
Abstract
Termites host a gut microbiota of diverse and essential symbionts that enable specialization on dead plant material; an abundant, but nutritionally imbalanced food source. To supplement the severe shortage of dietary nitrogen (N), some termite species make use of diazotrophic bacteria to fix atmospheric nitrogen (N2). Fungus-growing termites (subfamily Macrotermitinae) host a fungal exosymbiont (genus Termitomyces) that provides digestive services and the main food source for the termites. This has been thought to obviate the need for N2-fixation by bacterial symbionts. Here, we challenge this notion by performing acetylene reduction assays of live colony material to show that N2 fixation is present in two major genera (Macrotermes and Odontotermes) of fungus-growing termites. We compare and discuss fixation rates in relation to those obtained from other termites, and suggest avenues of research that may lead to a better understanding of N2 fixation in fungus-growing and other termites.
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Affiliation(s)
- Panagiotis Sapountzis
- Centre for Social Evolution, Section for Ecology and Evolution, Department of Biology, University of CopenhagenCopenhagen, Denmark
| | - Jane de Verges
- Centre for Social Evolution, Section for Ecology and Evolution, Department of Biology, University of CopenhagenCopenhagen, Denmark
| | - Kathrin Rousk
- Section for Terrestrial Ecology, Department of Biology, University of CopenhagenCopenhagen, Denmark
| | - Magdeleen Cilliers
- Department of Plant Production and Soil Science, Forestry and Agricultural Biotechnology Institute, University of PretoriaPretoria, South Africa
| | - Barend J. Vorster
- Department of Plant Production and Soil Science, Forestry and Agricultural Biotechnology Institute, University of PretoriaPretoria, South Africa
| | - Michael Poulsen
- Centre for Social Evolution, Section for Ecology and Evolution, Department of Biology, University of CopenhagenCopenhagen, Denmark
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77
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Kuwahara H, Yuki M, Izawa K, Ohkuma M, Hongoh Y. Genome of 'Ca. Desulfovibrio trichonymphae', an H 2-oxidizing bacterium in a tripartite symbiotic system within a protist cell in the termite gut. ISME JOURNAL 2016; 11:766-776. [PMID: 27801909 PMCID: PMC5322295 DOI: 10.1038/ismej.2016.143] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 08/19/2016] [Accepted: 09/02/2016] [Indexed: 11/23/2022]
Abstract
The cellulolytic protist Trichonympha agilis in the termite gut permanently hosts two symbiotic bacteria, ‘Candidatus Endomicrobium trichonymphae' and ‘Candidatus Desulfovibrio trichonymphae'. The former is an intracellular symbiont, and the latter is almost intracellular but still connected to the outside via a small pore. The complete genome of ‘Ca. Endomicrobium trichonymphae' has previously been reported, and we here present the complete genome of ‘Ca. Desulfovibrio trichonymphae'. The genome is small (1 410 056 bp), has many pseudogenes, and retains biosynthetic pathways for various amino acids and cofactors, which are partially complementary to those of ‘Ca. Endomicrobium trichonymphae'. An amino acid permease gene has apparently been transferred between the ancestors of these two symbionts; a lateral gene transfer has affected their metabolic capacity. Notably, ‘Ca. Desulfovibrio trichonymphae' retains the complex system to oxidize hydrogen by sulfate and/or fumarate, while genes for utilizing other substrates common in desulfovibrios are pseudogenized or missing. Thus, ‘Ca. Desulfovibrio trichonymphae' is specialized to consume hydrogen that may otherwise inhibit fermentation processes in both T. agilis and ‘Ca. Endomicrobium trichonymphae'. The small pore may be necessary to take up sulfate. This study depicts a genome-based model of a multipartite symbiotic system within a cellulolytic protist cell in the termite gut.
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Affiliation(s)
- Hirokazu Kuwahara
- Department of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Masahiro Yuki
- Biomass Research Platform Team, RIKEN Biomass Engineering Program Cooperation Division, RIKEN Center for Sustainable Resource Science, Tsukuba, Japan
| | - Kazuki Izawa
- Department of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Moriya Ohkuma
- Biomass Research Platform Team, RIKEN Biomass Engineering Program Cooperation Division, RIKEN Center for Sustainable Resource Science, Tsukuba, Japan.,Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Japan
| | - Yuichi Hongoh
- Department of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan.,Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Japan
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78
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Izawa K, Kuwahara H, Kihara K, Yuki M, Lo N, Itoh T, Ohkuma M, Hongoh Y. Comparison of Intracellular "Ca. Endomicrobium Trichonymphae" Genomovars Illuminates the Requirement and Decay of Defense Systems against Foreign DNA. Genome Biol Evol 2016; 8:3099-3107. [PMID: 27635050 PMCID: PMC5174739 DOI: 10.1093/gbe/evw227] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
“Candidatus Endomicrobium trichonymphae” (Bacteria; Elusimicrobia) is an obligate intracellular symbiont of the cellulolytic protist genus Trichonympha in the termite gut. A previous genome analysis of “Ca. Endomicrobium trichonymphae” phylotype Rs-D17 (genomovar Ri2008), obtained from a Trichonympha agilis cell in the gut of the termite Reticulitermes speratus, revealed that its genome is small (1.1 Mb) and contains many pseudogenes; it is in the course of reductive genome evolution. Here we report the complete genome sequence of another Rs-D17 genomovar, Ti2015, obtained from a different T. agilis cell present in an R. speratus gut. These two genomovars share most intact protein-coding genes and pseudogenes, showing 98.6% chromosome sequence similarity. However, characteristic differences were found in their defense systems, which comprised restriction-modification and CRISPR/Cas systems. The repertoire of intact restriction-modification systems differed between the genomovars, and two of the three CRISPR/Cas loci in genomovar Ri2008 are pseudogenized or missing in genomovar Ti2015. These results suggest relaxed selection pressure for maintaining these defense systems. Nevertheless, the remaining CRISPR/Cas system in each genomovar appears to be active; none of the “spacer” sequences (112 in Ri2008 and 128 in Ti2015) were shared whereas the “repeat” sequences were identical. Furthermore, we obtained draft genomes of three additional endosymbiotic Endomicrobium phylotypes from different host protist species, and discovered multiple, intact CRISPR/Cas systems in each genome. Collectively, unlike bacteriome endosymbionts in insects, the Endomicrobium endosymbionts of termite-gut protists appear to require defense against foreign DNA, although the required level of defense has likely been reduced during their intracellular lives.
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Affiliation(s)
- Kazuki Izawa
- Department of Biological Sciences, Tokyo Institute of Technology, Tokyo, Japan
| | - Hirokazu Kuwahara
- Department of Biological Sciences, Tokyo Institute of Technology, Tokyo, Japan
| | - Kumiko Kihara
- Department of Biological Sciences, Tokyo Institute of Technology, Tokyo, Japan Department of Biological and Chemical Systems Engineering, National Institute of Technology Kumamoto College, Yatsushiro, Japan
| | - Masahiro Yuki
- Biomass Research Platform Team, RIKEN Biomass Engineering Program Cooperation Division, RIKEN Center for Sustainable Resource Science, Tsukuba, Japan
| | - Nathan Lo
- School of Biological Sciences, University of Sydney, Sydney, NSW, Australia
| | - Takehiko Itoh
- Department of Biological Information, Tokyo Institute of Technology, Tokyo, Japan
| | - Moriya Ohkuma
- Biomass Research Platform Team, RIKEN Biomass Engineering Program Cooperation Division, RIKEN Center for Sustainable Resource Science, Tsukuba, Japan Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Japan
| | - Yuichi Hongoh
- Department of Biological Sciences, Tokyo Institute of Technology, Tokyo, Japan Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Japan
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79
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Strassert JFH, Mikaelyan A, Woyke T, Brune A. Genome analysis of 'Candidatus Ancillula trichonymphae', first representative of a deep-branching clade of Bifidobacteriales, strengthens evidence for convergent evolution in flagellate endosymbionts. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:865-873. [PMID: 27518440 DOI: 10.1111/1758-2229.12451] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The flagellate protists in the hindgut of lower termites play an essential role in the digestion of lignocellulose. Most flagellate species are associated with host-specific symbionts from various bacterial lineages, which typically lack cultured representatives. In this study, we analyzed the genome of 'Candidatus Ancillula trichonymphae', an endosymbiont of Trichonympha flagellates from dry-wood termites, which represents a novel, family-level lineage of uncultured Actinobacteria encountered so far only in termite guts. The draft genome of 'Ca. A. trichonymphae' (ca. 1.48 Mbp; 95% complete) revealed a purely fermentative metabolism that is probably fueled by xylose, N-acetyl-glucosamine and glycerol 3-phosphate acquired from the flagellate host. The absence of fructose bisphosphate aldolase and the presence of a complete gene set encoding the phosphoketolase pathway underscore the sister position of the new lineage to Bifidobacteriaceae. The preservation of the pathways for the assimilation of ammonia and the synthesis of 18 amino acids and several cofactors and vitamins suggests that 'Ca. A. trichonymphae' - like other endosymbionts of termite gut flagellates - provides essential amino acids and vitamins to its host. Our findings corroborate the emerging concept that numerous lineages of unrelated flagellate endosymbionts have convergently evolved to fill similar ecological niches.
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Affiliation(s)
- Jürgen F H Strassert
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Aram Mikaelyan
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Tanja Woyke
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Andreas Brune
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
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80
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Igai K, Itakura M, Nishijima S, Tsurumaru H, Suda W, Tsutaya T, Tomitsuka E, Tadokoro K, Baba J, Odani S, Natsuhara K, Morita A, Yoneda M, Greenhill AR, Horwood PF, Inoue JI, Ohkuma M, Hongoh Y, Yamamoto T, Siba PM, Hattori M, Minamisawa K, Umezaki M. Nitrogen fixation and nifH diversity in human gut microbiota. Sci Rep 2016; 6:31942. [PMID: 27554344 PMCID: PMC4995403 DOI: 10.1038/srep31942] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 07/27/2016] [Indexed: 12/04/2022] Open
Abstract
It has been hypothesized that nitrogen fixation occurs in the human gut. However, whether the gut microbiota truly has this potential remains unclear. We investigated the nitrogen-fixing activity and diversity of the nitrogenase reductase (NifH) genes in the faecal microbiota of humans, focusing on Papua New Guinean and Japanese individuals with low to high habitual nitrogen intake. A 15N2 incorporation assay showed significant enrichment of 15N in all faecal samples, irrespective of the host nitrogen intake, which was also supported by an acetylene reduction assay. The fixed nitrogen corresponded to 0.01% of the standard nitrogen requirement for humans, although our data implied that the contribution in the gut in vivo might be higher than this value. The nifH genes recovered in cloning and metagenomic analyses were classified in two clusters: one comprising sequences almost identical to Klebsiella sequences and the other related to sequences of Clostridiales members. These results are consistent with an analysis of databases of faecal metagenomes from other human populations. Collectively, the human gut microbiota has a potential for nitrogen fixation, which may be attributable to Klebsiella and Clostridiales strains, although no evidence was found that the nitrogen-fixing activity substantially contributes to the host nitrogen balance.
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Affiliation(s)
- Katsura Igai
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan.,Department of Human Ecology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Department of International Health, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Manabu Itakura
- Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, Miyagi, Japan
| | - Suguru Nishijima
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Hirohito Tsurumaru
- Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, Miyagi, Japan
| | - Wataru Suda
- Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Takumi Tsutaya
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Eriko Tomitsuka
- Department of Human Ecology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kiyoshi Tadokoro
- Department of Human Ecology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Jun Baba
- Department of Sociological Studies, Faculty of Human Sciences, Wako University, Tokyo, Japan
| | - Shingo Odani
- Faculty of Letters, Chiba University, Chiba, Japan
| | | | - Ayako Morita
- Department of Human Ecology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Minoru Yoneda
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Andrew R Greenhill
- Papua New Guinea Institute of Medical Research, Eastern Highlands Province, Papua New Guinea.,School of Applied and Biomedical Sciences, Federation University Australia, Victoria, Australia
| | - Paul F Horwood
- Papua New Guinea Institute of Medical Research, Eastern Highlands Province, Papua New Guinea
| | - Jun-Ichi Inoue
- Japan Collection of Microorganisms, RIKEN BioResource Center, Ibaraki, Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource Center, Ibaraki, Japan
| | - Yuichi Hongoh
- Department of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Taro Yamamoto
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan.,Department of International Health, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Peter M Siba
- Papua New Guinea Institute of Medical Research, Eastern Highlands Province, Papua New Guinea
| | - Masahira Hattori
- Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Kiwamu Minamisawa
- Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, Miyagi, Japan
| | - Masahiro Umezaki
- Department of Human Ecology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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81
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Genome Evolution and Nitrogen Fixation in Bacterial Ectosymbionts of a Protist Inhabiting Wood-Feeding Cockroaches. Appl Environ Microbiol 2016; 82:4682-4695. [PMID: 27235430 DOI: 10.1128/aem.00611-16] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 05/18/2016] [Indexed: 12/30/2022] Open
Abstract
UNLABELLED By combining genomics and isotope imaging analysis using high-resolution secondary ion mass spectrometry (NanoSIMS), we examined the function and evolution of Bacteroidales ectosymbionts of the protist Barbulanympha from the hindguts of the wood-eating cockroach Cryptocercus punctulatus In particular, we investigated the structure of ectosymbiont genomes, which, in contrast to those of endosymbionts, has been little studied to date, and tested the hypothesis that these ectosymbionts fix nitrogen. Unlike with most obligate endosymbionts, genome reduction has not played a major role in the evolution of the Barbulanympha ectosymbionts. Instead, interaction with the external environment has remained important for this symbiont as genes for synthesis of transporters, outer membrane proteins, lipopolysaccharides, and lipoproteins have been retained. The ectosymbiont genome carried two complete operons for nitrogen fixation, a urea transporter, and a urease, indicating the availability of nitrogen as a driving force behind the symbiosis. NanoSIMS analysis of C. punctulatus hindgut symbionts exposed in vivo to (15)N2 supports the hypothesis that Barbulanympha ectosymbionts are capable of nitrogen fixation. This genomic and in vivo functional investigation of protist ectosymbionts highlights the diversity of evolutionary forces and trajectories that shape symbiotic interactions. IMPORTANCE The ecological and evolutionary importance of symbioses is increasingly clear, but the overall diversity of symbiotic interactions remains poorly explored. In this study, we investigated the evolution and nitrogen fixation capabilities of ectosymbionts attached to the protist Barbulanympha from the hindgut of the wood-eating cockroach Cryptocercus punctulatus In addressing genome evolution of protist ectosymbionts, our data suggest that the ecological pressures influencing the evolution of extracellular symbionts clearly differ from intracellular symbionts and organelles. Using NanoSIMS analysis, we also obtained direct imaging evidence of a specific hindgut microbe playing a role in nitrogen fixation. These results demonstrate the power of combining NanoSIMS and genomics tools for investigating the biology of uncultivable microbes. This investigation paves the way for a more precise understanding of microbial interactions in the hindguts of wood-eating insects and further exploration of the diversity and ecological significance of symbiosis between microbes.
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82
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Tegtmeier D, Riese C, Geissinger O, Radek R, Brune A. Breznakia blatticola gen. nov. sp. nov. and Breznakia pachnodae sp. nov., two fermenting bacteria isolated from insect guts, and emended description of the family Erysipelotrichaceae. Syst Appl Microbiol 2016; 39:319-29. [PMID: 27270136 DOI: 10.1016/j.syapm.2016.05.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 05/13/2016] [Accepted: 05/17/2016] [Indexed: 11/30/2022]
Abstract
Two novel, obligately anaerobic Firmicutes from the family Erysipelotrichaceae were isolated from the intestinal tracts of a cockroach (strain ErySL, Shelfordella lateralis) and a scarab beetle larva (strain Pei061, Pachnoda ephippiata). Phylogenetic analysis indicated that the strains belong to a monophyletic group of hitherto uncultured bacteria from insect guts that are only distantly related to any described species (<90% 16S rRNA gene sequence similarity). Ultrastructural analysis revealed a Gram-positive cell envelope and, in the case of strain ErySL, a wide electron-lucent space between the cytoplasmic membrane and cell wall. In older cultures, cells formed pleomorphic rods with a thicker peptidoglycan layer. Both strains were obligately anaerobic and fermented glucose to formate, ethanol, and acetate as major products, but strain Pei061 tolerated up to 1% oxygen in the headspace. The same type of metabolism was observed with Erysipelothrix inopinata, except that the latter grew, albeit poorly, even under air. However, previous claims of a microaerophilic or facultatively anaerobic metabolism in the genus Erysipelothrix could not be substantiated. Based on phenotypic and phylogenetic evidence, we propose to classify the isolates as members of a new genus, Breznakia blatticola gen. nov. sp. nov. and Breznakia pachnodae sp. nov., with strain ErySL(T) (=DSM 28867(T)=JCM 30190(T)) and strain Pei061(T) (=DSM 16784(T)=JCM 30191(T)) as type strains, and provide an emended description of the family Erysipelotrichaceae.
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Affiliation(s)
- Dorothee Tegtmeier
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043 Marburg, Germany
| | - Cornelius Riese
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043 Marburg, Germany
| | - Oliver Geissinger
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043 Marburg, Germany
| | - Renate Radek
- Institute of Biology/Zoology, Free University of Berlin, Königin-Luise-Strasse 1-3, 14195 Berlin, Germany
| | - Andreas Brune
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043 Marburg, Germany.
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83
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Peterson BF, Scharf ME. Lower Termite Associations with Microbes: Synergy, Protection, and Interplay. Front Microbiol 2016; 7:422. [PMID: 27092110 PMCID: PMC4824777 DOI: 10.3389/fmicb.2016.00422] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 03/16/2016] [Indexed: 11/15/2022] Open
Abstract
Lower-termites are one of the best studied symbiotic systems in insects. Their ability to feed on a nitrogen-poor, wood-based diet with help from symbiotic microbes has been under investigation for almost a century. A unique microbial consortium living in the guts of lower termites is essential for wood-feeding. Host and symbiont cellulolytic enzymes synergize each other in the termite gut to increase digestive efficiency. Because of their critical role in digestion, gut microbiota are driving forces in all aspects of termite biology. Social living also comes with risks for termites. The combination of group living and a microbe-rich habitat makes termites potentially vulnerable to pathogenic infections. However, the use of entomopathogens for termite control has been largely unsuccessful. One mechanism for this failure may be symbiotic collaboration; i.e., one of the very reasons termites have thrived in the first place. Symbiont contributions are thought to neutralize fungal spores as they pass through the termite gut. Also, when the symbiont community is disrupted pathogen susceptibility increases. These recent discoveries have shed light on novel interactions for symbiotic microbes both within the termite host and with pathogenic invaders. Lower termite biology is therefore tightly linked to symbiotic associations and their resulting physiological collaborations.
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Affiliation(s)
| | - Michael E Scharf
- Department of Entomology, Purdue University, West Lafayette IN, USA
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84
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Ohkuma M. The outset of another nitrogenase. Environ Microbiol 2016; 18:4. [DOI: 10.1111/1462-2920.13001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Moriya Ohkuma
- Japan Collection of Microorganisms; RIKEN BioResource Center; 3-1-1 Koyadai Tsukuba Ibaraki 305-0074 Japan
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85
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Zheng H, Dietrich C, Hongoh Y, Brune A. Restriction-Modification Systems as Mobile Genetic Elements in the Evolution of an Intracellular Symbiont. Mol Biol Evol 2015; 33:721-5. [PMID: 26568615 PMCID: PMC4760077 DOI: 10.1093/molbev/msv264] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Long-term vertical transmission of intracellular bacteria causes massive genomic erosion and results in extremely small genomes, particularly in ancient symbionts. Genome reduction is typically preceded by the accumulation of pseudogenes and proliferation of mobile genetic elements, which are responsible for chromosome rearrangements during the initial stage of endosymbiosis. We compared the genomes of an endosymbiont of termite gut flagellates, “Candidatus Endomicrobium trichonymphae,” and its free-living relative Endomicrobium proavitum and discovered many remnants of restriction-modification (R-M) systems that are consistently associated with genome rearrangements in the endosymbiont genome. The rearrangements include apparent insertions, transpositions, and the duplication of a genomic region; there was no evidence of transposon structures or other mobile elements. Our study reveals a so far unrecognized mechanism for genome rearrangements in intracellular symbionts and sheds new light on the general role of R-M systems in genome evolution.
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Affiliation(s)
- Hao Zheng
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Carsten Dietrich
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Yuichi Hongoh
- Department of Biological Sciences, Tokyo Institute of Technology, Tokyo, Japan
| | - Andreas Brune
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
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Complete Genome Sequence of Endomicrobium proavitum, a Free-Living Relative of the Intracellular Symbionts of Termite Gut Flagellates (Phylum Elusimicrobia). GENOME ANNOUNCEMENTS 2015; 3:3/4/e00679-15. [PMID: 26184928 PMCID: PMC4505116 DOI: 10.1128/genomea.00679-15] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
We sequenced the complete genome of Endomicrobium proavitum strain Rsa215, the first isolate of the class Endomicrobia (phylum Elusimicrobia). It is the closest free-living relative of the endosymbionts of termite gut flagellates and thereby provides an excellent model for studying the evolutionary processes during the establishment of an intracellular symbiosis.
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