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Clanton R, Saucier D, Ford J, Akabani G. Microbial influences on hormesis, oncogenesis, and therapy: A review of the literature. ENVIRONMENTAL RESEARCH 2015; 142:239-256. [PMID: 26183884 DOI: 10.1016/j.envres.2015.06.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 06/11/2015] [Accepted: 06/23/2015] [Indexed: 06/04/2023]
Abstract
Utilization of environmental stimuli for growth is the main factor contributing to the evolution of prokaryotes and eukaryotes, independently and mutualistically. Epigenetics describes an organism's ability to vary expression of certain genes based on their environmental stimuli. The diverse degree of dose-dependent responses based on their variances in expressed genetic profiles makes it difficult to ascertain whether hormesis or oncogenesis has or is occurring. In the medical field this is shown where survival curves used in determining radiotherapeutic doses have substantial uncertainties, some as large as 50% (Barendsen, 1990). Many in-vitro radiobiological studies have been limited by not taking into consideration the innate presence of microbes in biological systems, which have either grown symbiotically or pathogenically. Present in-vitro studies neglect to take into consideration the varied responses that commensal and opportunistic pathogens will have when exposed to the same stimuli and how such responses could act as stimuli for their macro/microenvironment. As a result many theories such as radiation carcinogenesis explain microscopic events but fail to describe macroscopic events (Cohen, 1995). As such, this review shows how microorganisms have the ability to perturb risks of cancer and enhance hormesis after irradiation. It will also look at bacterial significance in the microenvironment of the tumor before and during treatment. In addition, bacterial systemic communication after irradiation and the host's immune responses to infection could explain many of the phenomena associated with bystander effects. Therefore, the present literature review considers the paradigms of hormesis and oncogenesis in order to find a rationale that ties them all together. This relationship was thus characterized to be the microbiome.
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Affiliation(s)
- Ryan Clanton
- Department of Nuclear Engineering, Texas A&M University, College Station, TX 77843, USA; Texas A&M Institute for Preclinical Studies, Texas A&M University, College Station, TX 77843, USA
| | - David Saucier
- Department of Nuclear Engineering, Texas A&M University, College Station, TX 77843, USA
| | - John Ford
- Department of Nuclear Engineering, Texas A&M University, College Station, TX 77843, USA
| | - Gamal Akabani
- Department of Nuclear Engineering, Texas A&M University, College Station, TX 77843, USA; Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA; Texas A&M Institute for Preclinical Studies, Texas A&M University, College Station, TX 77843, USA
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2
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Mullins DE. Physiology of environmental adaptations and resource acquisition in cockroaches. ANNUAL REVIEW OF ENTOMOLOGY 2015; 60:473-492. [PMID: 25564743 DOI: 10.1146/annurev-ento-011613-162036] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Cockroaches are a group of insects that evolved early in geological time. Because of their antiquity, they for the most part display generalized behavior and physiology and accordingly have frequently been used as model insects to examine physiological and biochemical mechanisms involved with water balance, nutrition, reproduction, genetics, and insecticide resistance. As a result, a considerable amount of information on these topics is available. However, there is much more to be learned by employing new protocols, microchemical analytical techniques, and molecular biology tools to explore many unanswered questions.
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Affiliation(s)
- Donald E Mullins
- Department of Entomology, Virginia Tech, Blacksburg, Virginia 24061;
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3
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Tomazetto G, Wibberg D, Schlüter A, Oliveira VM. New FeFe-hydrogenase genes identified in a metagenomic fosmid library from a municipal wastewater treatment plant as revealed by high-throughput sequencing. Res Microbiol 2014; 166:9-19. [PMID: 25446611 DOI: 10.1016/j.resmic.2014.11.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2014] [Revised: 10/08/2014] [Accepted: 11/04/2014] [Indexed: 12/18/2022]
Abstract
A fosmid metagenomic library was constructed with total community DNA obtained from a municipal wastewater treatment plant (MWWTP), with the aim of identifying new FeFe-hydrogenase genes encoding the enzymes most important for hydrogen metabolism. The dataset generated by pyrosequencing of a fosmid library was mined to identify environmental gene tags (EGTs) assigned to FeFe-hydrogenase. The majority of EGTs representing FeFe-hydrogenase genes were affiliated with the class Clostridia, suggesting that this group is the main hydrogen producer in the MWWTP analyzed. Based on assembled sequences, three FeFe-hydrogenase genes were predicted based on detection of the L2 motif (MPCxxKxxE) in the encoded gene product, confirming true FeFe-hydrogenase sequences. These sequences were used to design specific primers to detect fosmids encoding FeFe-hydrogenase genes predicted from the dataset. Three identified fosmids were completely sequenced. The cloned genomic fragments within these fosmids are closely related to members of the Spirochaetaceae, Bacteroidales and Firmicutes, and their FeFe-hydrogenase sequences are characterized by the structure type M3, which is common to clostridial enzymes. FeFe-hydrogenase sequences found in this study represent hitherto undetected sequences, indicating the high genetic diversity regarding these enzymes in MWWTP. Results suggest that MWWTP have to be considered as reservoirs for new FeFe-hydrogenase genes.
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Affiliation(s)
- Geizecler Tomazetto
- Division of Microbial Resources, Research Center for Chemistry, Biology and Agriculture (CPQBA), Campinas University - UNICAMP, CP 6171, CEP 13081-970 Campinas, SP, Brazil.
| | - Daniel Wibberg
- Institute for Genome Research and Systems Biology, CeBiTec, Bielefeld University, Bielefeld, Germany
| | - Andreas Schlüter
- Institute for Genome Research and Systems Biology, CeBiTec, Bielefeld University, Bielefeld, Germany
| | - Valéria M Oliveira
- Division of Microbial Resources, Research Center for Chemistry, Biology and Agriculture (CPQBA), Campinas University - UNICAMP, CP 6171, CEP 13081-970 Campinas, SP, Brazil.
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4
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Wrighton KC, Castelle CJ, Wilkins MJ, Hug LA, Sharon I, Thomas BC, Handley KM, Mullin SW, Nicora CD, Singh A, Lipton MS, Long PE, Williams KH, Banfield JF. Metabolic interdependencies between phylogenetically novel fermenters and respiratory organisms in an unconfined aquifer. ISME JOURNAL 2014; 8:1452-63. [PMID: 24621521 DOI: 10.1038/ismej.2013.249] [Citation(s) in RCA: 137] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Revised: 11/07/2013] [Accepted: 12/01/2013] [Indexed: 11/09/2022]
Abstract
Fermentation-based metabolism is an important ecosystem function often associated with environments rich in organic carbon, such as wetlands, sewage sludge and the mammalian gut. The diversity of microorganisms and pathways involved in carbon and hydrogen cycling in sediments and aquifers and the impacts of these processes on other biogeochemical cycles remain poorly understood. Here we used metagenomics and proteomics to characterize microbial communities sampled from an aquifer adjacent to the Colorado River at Rifle, CO, USA, and document interlinked microbial roles in geochemical cycling. The organic carbon content in the aquifer was elevated via acetate amendment of the groundwater occurring over 2 successive years. Samples were collected at three time points, with the objective of extensive genome recovery to enable metabolic reconstruction of the community. Fermentative community members include organisms from a new phylum, Melainabacteria, most closely related to Cyanobacteria, phylogenetically novel members of the Chloroflexi and Bacteroidales, as well as candidate phyla genomes (OD1, BD1-5, SR1, WWE3, ACD58, TM6, PER and OP11). These organisms have the capacity to produce hydrogen, acetate, formate, ethanol, butyrate and lactate, activities supported by proteomic data. The diversity and expression of hydrogenases suggests the importance of hydrogen metabolism in the subsurface. Our proteogenomic data further indicate the consumption of fermentation intermediates by Proteobacteria can be coupled to nitrate, sulfate and iron reduction. Thus, fermentation carried out by previously unknown members of sediment microbial communities may be an important driver of nitrogen, hydrogen, sulfur, carbon and iron cycling.
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Affiliation(s)
- Kelly C Wrighton
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | - Cindy J Castelle
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, USA
| | - Michael J Wilkins
- 1] Department of Microbiology, The Ohio State University, Columbus, OH, USA [2] School of Earth Sciences, The Ohio State University, Columbus, OH, USA
| | - Laura A Hug
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, USA
| | - Itai Sharon
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, USA
| | - Brian C Thomas
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, USA
| | - Kim M Handley
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Sean W Mullin
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, USA
| | - Carrie D Nicora
- Pacific Northwest National Laboratory, Department of Energy, Biological Sciences Department, Richland, WA, USA
| | - Andrea Singh
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, USA
| | - Mary S Lipton
- Pacific Northwest National Laboratory, Department of Energy, Biological Sciences Department, Richland, WA, USA
| | - Philip E Long
- Lawrence Berkeley National Laboratory, Department of Energy, Berkeley, CA, USA
| | - Kenneth H Williams
- Lawrence Berkeley National Laboratory, Department of Energy, Berkeley, CA, USA
| | - Jillian F Banfield
- 1] Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, USA [2] Pacific Northwest National Laboratory, Department of Energy, Biological Sciences Department, Richland, WA, USA
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The cockroach origin of the termite gut microbiota: patterns in bacterial community structure reflect major evolutionary events. Appl Environ Microbiol 2014; 80:2261-9. [PMID: 24487532 DOI: 10.1128/aem.04206-13] [Citation(s) in RCA: 166] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Termites digest wood and other lignocellulosic substrates with the help of their intestinal microbiota. While the functions of the symbionts in the digestive process are slowly emerging, the origin of the bacteria colonizing the hindgut bioreactor is entirely unknown. Recently, our group discovered numerous representatives of bacterial lineages specific to termite guts in a closely related omnivorous cockroach, but it remains unclear whether they derive from the microbiota of a common ancestor or were independently selected by the gut environment. Here, we studied the bacterial gut microbiota in 34 species of termites and cockroaches using pyrotag analysis of the 16S rRNA genes. Although the community structures differed greatly between the major host groups, with dramatic changes in the relative abundances of particular bacterial taxa, we found that the majority of sequence reads belonged to bacterial lineages that were shared among most host species. When mapped onto the host tree, the changes in community structure coincided with major events in termite evolution, such as acquisition and loss of cellulolytic protists and the ensuing dietary diversification. UniFrac analysis of the core microbiota of termites and cockroaches and construction of phylogenetic tree of individual genus level lineages revealed a general host signal, whereas the branching order often did not match the detailed phylogeny of the host. It remains unclear whether the lineages in question have been associated with the ancestral cockroach since the early Cretaceous (cospeciation) or are diet-specific lineages that were independently acquired from the environment (host selection).
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Vršanský P, van de Kamp T, Azar D, Prokin A, Vidlička L, Vagovič P. Cockroaches probably cleaned up after dinosaurs. PLoS One 2013; 8:e80560. [PMID: 24324610 PMCID: PMC3851186 DOI: 10.1371/journal.pone.0080560] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 10/04/2013] [Indexed: 11/18/2022] Open
Abstract
Dinosaurs undoubtedly produced huge quantities of excrements. But who cleaned up after them? Dung beetles and flies with rapid development were rare during most of the Mesozoic. Candidates for these duties are extinct cockroaches (Blattulidae), whose temporal range is associated with herbivorous dinosaurs. An opportunity to test this hypothesis arises from coprolites to some extent extruded from an immature cockroach preserved in the amber of Lebanon, studied using synchrotron X-ray microtomography. 1.06% of their volume is filled by particles of wood with smooth edges, in which size distribution directly supports their external pre-digestion. Because fungal pre-processing can be excluded based on the presence of large particles (combined with small total amount of wood) and absence of damages on wood, the likely source of wood are herbivore feces. Smaller particles were broken down biochemically in the cockroach hind gut, which indicates that the recent lignin-decomposing termite and cockroach endosymbionts might have been transferred to the cockroach gut upon feeding on dinosaur feces.
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Affiliation(s)
- Peter Vršanský
- Geological Institute, Slovak Academy of Sciences, Bratislava, Slovakia
- Arthropoda Laboratory, Paleontological Institute, Russian Academy of Sciences, Moscow, Russia
- * E-mail:
| | - Thomas van de Kamp
- ANKA/Institute for Photon Science and Synchrotron Radiation (IPS), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
| | - Dany Azar
- Faculty of Science II, Natural Sciences Department, Lebanese University, Fanar, Fanar-Matn, Lebanon
| | - Alexander Prokin
- I.D. Papanin Institute for biology of inland waters Russian Academy of Sciences, Borok, Russia
- Voronezh State University, Voronezh, Russia
| | - L'ubomír Vidlička
- Institute of Zoology, Slovak Academy of Sciences, Bratislava, Slovakia
- Department of Biology, Faculty of Education, Comenius University, Bratislava, Slovakia
| | - Patrik Vagovič
- ANKA/Institute for Photon Science and Synchrotron Radiation (IPS), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Japan
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7
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Zheng H, Bodington D, Zhang C, Miyanaga K, Tanji Y, Hongoh Y, Xing XH. Comprehensive phylogenetic diversity of [FeFe]-hydrogenase genes in termite gut microbiota. Microbes Environ 2013; 28:491-4. [PMID: 24240187 PMCID: PMC4070709 DOI: 10.1264/jsme2.me13082] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Phylogenetic diversity of [FeFe]-hydrogenase (HydA) in termite guts was assessed by pyrosequencing PCR amplicons obtained using newly designed primers. Of 8,066 reads, 776 hydA phylotypes, defined with 97% nucleotide sequence identity, were recovered from the gut homogenates of three termite species, Hodotermopsis sjoestedti, Reticulitermes speratus, and Nasutitermes takasagoensis. The phylotype coverage was 92–98%, and the majority shared only low identity with database sequences. It was estimated that 194–745 hydA phylotypes existed in the gut of each termite species. Our results demonstrate that hydA gene diversity in the termite gut microbiota is much higher than previously estimated.
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Affiliation(s)
- Hao Zheng
- Department of Chemical Engineering, Tsinghua University
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He S, Ivanova N, Kirton E, Allgaier M, Bergin C, Scheffrahn RH, Kyrpides NC, Warnecke F, Tringe SG, Hugenholtz P. Comparative metagenomic and metatranscriptomic analysis of hindgut paunch microbiota in wood- and dung-feeding higher termites. PLoS One 2013; 8:e61126. [PMID: 23593407 PMCID: PMC3625147 DOI: 10.1371/journal.pone.0061126] [Citation(s) in RCA: 110] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2012] [Accepted: 03/07/2013] [Indexed: 11/19/2022] Open
Abstract
Termites effectively feed on many types of lignocellulose assisted by their gut microbial symbionts. To better understand the microbial decomposition of biomass with varied chemical profiles, it is important to determine whether termites harbor different microbial symbionts with specialized functionalities geared toward different feeding regimens. In this study, we compared the microbiota in the hindgut paunch of Amitermes wheeleri collected from cow dung and Nasutitermes corniger feeding on sound wood by 16S rRNA pyrotag, comparative metagenomic and metatranscriptomic analyses. We found that Firmicutes and Spirochaetes were the most abundant phyla in A. wheeleri, in contrast to N. corniger where Spirochaetes and Fibrobacteres dominated. Despite this community divergence, a convergence was observed for functions essential to termite biology including hydrolytic enzymes, homoacetogenesis and cell motility and chemotaxis. Overrepresented functions in A. wheeleri relative to N. corniger microbiota included hemicellulose breakdown and fixed-nitrogen utilization. By contrast, glycoside hydrolases attacking celluloses and nitrogen fixation genes were overrepresented in N. corniger microbiota. These observations are consistent with dietary differences in carbohydrate composition and nutrient contents, but may also reflect the phylogenetic difference between the hosts.
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Affiliation(s)
- Shaomei He
- Energy Biosciences Institute, University of California, Berkeley, California, United States of America
- US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, California, United States of America
| | - Natalia Ivanova
- Energy Biosciences Institute, University of California, Berkeley, California, United States of America
- US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, California, United States of America
| | - Edward Kirton
- US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, California, United States of America
| | - Martin Allgaier
- US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, California, United States of America
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Berlin Center for Genomics in Biodiversity Research, Berlin, Germany
| | - Claudia Bergin
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Rudolf H. Scheffrahn
- Fort Lauderdale Research and Education Center, University of Florida, Davie, Florida, United States of America
| | - Nikos C. Kyrpides
- Energy Biosciences Institute, University of California, Berkeley, California, United States of America
- US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, California, United States of America
| | - Falk Warnecke
- Energy Biosciences Institute, University of California, Berkeley, California, United States of America
- US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, California, United States of America
| | - Susannah G. Tringe
- US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, California, United States of America
| | - Philip Hugenholtz
- Energy Biosciences Institute, University of California, Berkeley, California, United States of America
- US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, California, United States of America
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences & Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland, Australia
- * E-mail:
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Köhler T, Dietrich C, Scheffrahn RH, Brune A. High-resolution analysis of gut environment and bacterial microbiota reveals functional compartmentation of the gut in wood-feeding higher termites (Nasutitermes spp.). Appl Environ Microbiol 2012; 78:4691-701. [PMID: 22544239 PMCID: PMC3370480 DOI: 10.1128/aem.00683-12] [Citation(s) in RCA: 152] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Accepted: 04/13/2012] [Indexed: 11/20/2022] Open
Abstract
Higher termites are characterized by a purely prokaryotic gut microbiota and an increased compartmentation of their intestinal tract. In soil-feeding species, each gut compartment has different physicochemical conditions and is colonized by a specific microbial community. Although considerable information has accumulated also for wood-feeding species of the genus Nasutitermes, including cellulase activities and metagenomic data, a comprehensive study linking physicochemical gut conditions with the structure of the microbial communities in the different gut compartments is lacking. In this study, we measured high-resolution profiles of H(2), O(2), pH, and redox potential in the gut of Nasutitermes corniger termites, determined the fermentation products accumulating in the individual gut compartments, and analyzed the bacterial communities in detail by pyrotag sequencing of the V3-V4 region of the 16S rRNA genes. The dilated hindgut paunch (P3 compartment) was the only anoxic gut region, showed the highest density of bacteria, and accumulated H(2) to high partial pressures (up to 12 kPa). Molecular hydrogen is apparently produced by a dense community of Spirochaetes and Fibrobacteres, which also dominate the gut of other Nasutitermes species. All other compartments, such as the alkaline P1 compartment (average pH, 10.0), showed high redox potentials and comprised small but distinct populations characteristic for each gut region. In the crop and the posterior hindgut compartments, the community was even more diverse than in the paunch. Similarities in the communities of the posterior hindgut and crop suggested that proctodeal trophallaxis or coprophagy also occurs in higher termites. The large sampling depths of pyrotag sequencing in combination with the determination of important physicochemical parameters allow cautious conclusions concerning the functions of particular bacterial lineages in the respective gut sections to be drawn.
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Affiliation(s)
- Tim Köhler
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Carsten Dietrich
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Rudolf H. Scheffrahn
- Fort Lauderdale Research and Education Center, University of Florida, Davie, Florida, USA
| | - Andreas Brune
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
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Patterns of [FeFe] hydrogenase diversity in the gut microbial communities of lignocellulose-feeding higher termites. Appl Environ Microbiol 2012; 78:5368-74. [PMID: 22636002 DOI: 10.1128/aem.08008-11] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Hydrogen is the central free intermediate in the degradation of wood by termite gut microbes and can reach concentrations exceeding those measured for any other biological system. Degenerate primers targeting the largest family of [FeFe] hydrogenases observed in a termite gut metagenome have been used to explore the evolution and representation of these enzymes in termites. Sequences were cloned from the guts of the higher termites Amitermes sp. strain Cost010, Amitermes sp. strain JT2, Gnathamitermes sp. strain JT5, Microcerotermes sp. strain Cost008, Nasutitermes sp. strain Cost003, and Rhyncotermes sp. strain Cost004. Each gut sample harbored a more rich and evenly distributed population of hydrogenase sequences than observed previously in the guts of lower termites and Cryptocercus punctulatus. This accentuates the physiological importance of hydrogen for higher termite gut ecosystems and may reflect an increased metabolic burden, or metabolic opportunity, created by a lack of gut protozoa. The sequences were phylogenetically distinct from previously sequenced [FeFe] hydrogenases. Phylogenetic and UniFrac comparisons revealed congruence between host phylogeny and hydrogenase sequence library clustering patterns. This may reflect the combined influences of the stable intimate relationship of gut microbes with their host and environmental alterations in the gut that have occurred over the course of termite evolution. These results accentuate the physiological importance of hydrogen to termite gut ecosystems.
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