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Andredenis G Wright - One of the best experts on this subject based on the ideXlab platform.
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Dominance of Methanosarcinales Phylotypes and Depth-Wise Distribution of Methanogenic Community in Fresh Water Sediments of Sitka Stream from Czech Republic
Current Microbiology, 2014Co-Authors: Prem Prashant Chaudhary, Andredenis G Wright, Lenka Brablcová, Iva Buriánková, Adam Bednařík, Martin RulíkAbstract:The variation in the diversity of Methanogens in sediment depths from Sitka stream was studied by constructing a 16S rRNA gene library using methanogen-specific primers and a denaturing gradient gel electrophoresis (DGGE)-based approach. A total of nine different phylotypes from the 16S rRNA library were obtained, and all of them were clustered within the order Methanosarcinales . These nine phylotypes likely represent nine new species and at least 5–6 new genera. Similarly, DGGE analysis revealed an increase in the diversity of Methanogens with an increase in sediment depth. These results suggest that Methanosarcinales phylotypes might be the dominant Methanogens in the sediment from Sitka stream, and the diversity of Methanogens increases as the depth increases. Results of the present study will help in making effective strategies to monitor the dominant methanogen phylotypes and methane emissions in the environment.
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lean breed landrace pigs harbor fecal Methanogens at higher diversity and density than obese breed erhualian pigs
Archaea, 2012Co-Authors: Andredenis G Wright, Yong Su, Lingli Zhang, Hauke SmidtAbstract:The diversity of fecal Methanogens of Erhualian (obese type) and Landrace (lean type) pigs was examined using separate 16S rRNA gene libraries for each breed. A total of 763 clones were analyzed; 381 from the Erhualian library and 382 from the Landrace library were identified belonging to the genus Methanobrevibacter. Others were identified belonging to the genus Methanosphaera. The two libraries showed significant differences in diversity (P < 0.05) and composition (P < 0.0001). Only two operational taxonomic units (OTUs) were found in both libraries, whereas six OTUs were found only in the Erhualian library and 23 OTUs were found only in the Landrace library. Real-time PCR showed that the abundance of fecal Methanogens in Landrace pigs was significantly higher than that in Erhualian pigs (P < 0.05). Results showed that the Landrace pig (lean) harbored a greater diversity and higher numbers of methanogen mcrA gene copies than the Erhualian pig (obese). These differences may be related to the fatness or leanness in these two pig breeds. The results provide new leads for further investigations on the fat storage of pigs or even humans.
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Impact of High-Concentrate Feeding and Low Ruminal pH on Methanogens and Protozoa in the Rumen of Dairy Cows
Microbial Ecology, 2011Co-Authors: Sarah E Hook, Korinne S Northwood, Andredenis G Wright, Michael A. Steele, Brian W. McbrideAbstract:Non-lactating dairy cattle were transitioned to a high-concentrate diet to investigate the effect of ruminal pH suppression, commonly found in dairy cattle, on the density, diversity, and community structure of rumen Methanogens, as well as the density of rumen protozoa. Four ruminally cannulated cows were fed a hay diet and transitioned to a 65% grain and 35% hay diet. The cattle were maintained on an high-concentrate diet for 3 weeks before the transition back to an hay diet, which was fed for an additional 3 weeks. Rumen fluid and solids and fecal samples were obtained prior to feeding during weeks 0 (hay), 1, and 3 (high-concentrate), and 4 and 6 (hay). Subacute ruminal acidosis was induced during week 1. During week 3 of the experiment, there was a significant increase in the number of protozoa present in the rumen fluid ( P = 0.049) and rumen solids ( P = 0.004), and a significant reduction in protozoa in the rumen fluid in week 6 ( P = 0.003). No significant effect of diet on density of rumen Methanogens was found in any samples, as determined by real-time PCR. Clone libraries were constructed for weeks 0, 3, and 6, and the methanogen diversity of week 3 was found to differ from week 6. Week 3 was also found to have a significantly altered methanogen community structure, compared to the other weeks. Twenty-two unique 16S rRNA phylotypes were identified, three of which were found only during high-concentrate feeding, three were found during both phases of hay feeding, and seven were found in all three clone libraries. The genus Methanobrevibacter comprised 99% of the clones present. The rumen fluid at weeks 0, 3, and 6 of all the animals was found to contain a type A protozoal population. Ultimately, high-concentrate feeding did not significantly affect the density of rumen Methanogens, but did alter methanogen diversity and community structure, as well as protozoal density within the rumen of nonlactating dairy cattle. Therefore, it may be necessary to monitor the rumen methanogen and protozoal communities of dairy cattle susceptible to depressed pH when methane abatement strategies are being investigated.
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Methanogens methane producers of the rumen and mitigation strategies
Archaea, 2010Co-Authors: Sarah E Hook, Andredenis G Wright, B W McbrideAbstract:Methanogens are the only known microorganisms capable of methane production, making them of interest when investigating methane abatement strategies. A number of experiments have been conducted to study the methanogen population in the rumen of cattle and sheep, as well as the relationship that Methanogens have with other microorganisms. The rumen methanogen species differ depending on diet and geographical location of the host, as does methanogenesis, which can be reduced by modifying dietary composition, or by supplementation of monensin, lipids, organic acids, or plant compounds within the diet. Other methane abatement strategies that have been investigated are defaunation and vaccines. These mitigation methods target the methanogen population of the rumen directly or indirectly, resulting in varying degrees of efficacy. This paper describes the Methanogens identified in the rumens of cattle and sheep, as well as a number of methane mitigation strategies that have been effective in vivo.
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community composition and density of Methanogens in the foregut of the tammar wallaby macropus eugenii
Applied and Environmental Microbiology, 2009Co-Authors: Paul N. Evans, Chris Mcsweeney, Lyn A Hinds, Mark Morrison, Andredenis G WrightAbstract:The composition of the methanogenic archaeal community in the foregut contents of Tammar wallabies (Macropus eugenii) was studied using 16S rRNA and methyl coenzyme reductase subunit A (mcrA) gene clone libraries. Methanogens belonging to the Methanobacteriales and a well-supported cluster of uncultivated archaeon sequences previously observed in the ovine and bovine rumens were found. Methanogen densities ranged from 7.0 × 105 and 3.9 × 106 cells per gram of wet weight.
Jing Zhang - One of the best experts on this subject based on the ideXlab platform.
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microbial reduction of fe iii in smectite minerals by thermophilic methanogen methanothermobacter thermautotrophicus
Geochimica et Cosmochimica Acta, 2013Co-Authors: Jing Zhang, Hailiang Dong, Abinash AgrawalAbstract:Abstract Clay minerals and thermophilic Methanogens can co-exist in hot anoxic environments, including the continental subsurface, geysers, terrestrial hot springs, and deep-sea hydrothermal vent systems. However, it is unclear whether thermophilic Methanogens are able to reduce structural Fe(III) in clay minerals. In this study, the ability of a thermophilic methanogen Methanothermobacter thermautotrophicus to reduce structural Fe(III) in iron-rich and iron-poor smectites, (nontronite NAu-2 and Wyoming montmorillonite SWy-2) and the relationship between iron reduction and methanogenesis were investigated. M. thermautotrophicus reduced Fe(III) in nontronite NAu-2 and montmorillonite SWy-2 with H2/CO2 as substrate. The extent of bioreduction was 27% for nontronite and 13–15% for montmorillonite. Anthraquinone-2,6-disulfonate (AQDS) did not enhance the extent of bioreduction, but accelerated the rate. When methanogenesis was inhibited via addition of 2-bromoethane sulfonate (BES), the extent of bioreduction decreased to 16% for NAu-2 and 9% for SWy-2. These data suggest that Fe(III) bioreduction and methanogenesis were mutually beneficial. The likely mechanism was that Fe(III) bioreduction lowered the reduction potential of the system so that methanogenesis became favorable, and methanogenesis in turn stimulated the growth of the methanogen, which enhanced Fe(III) bioreduction. NAu-2 was partly dissolved and high charge smectite and biogenic silica formed as a result of bioreduction.
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microbial reduction of fe iii in illite smectite minerals by methanogen methanosarcina mazei
Chemical Geology, 2012Co-Authors: Hailiang Dong, Jing Zhang, Timothy B Fischer, Shang Wang, Liuqin HuangAbstract:Abstract Clay minerals are ubiquitous in soils, sediments and sedimentary rocks, and could coexist with Methanogens in anoxic environments, but whether or not Methanogens can reduce structural Fe(III) in clay minerals other than smectite is not known. The objective of this study was to understand the capability of a mesophilic methanogen, Methanosarcina mazei in reducing structural Fe(III) in illite–smectite clay minerals and its potential role in inducing mineralogical changes. Bioreduction experiments were performed in batch systems, where four different clay minerals (nontronite NAu-2, mixed-layer illite–smectite RAr-1 and ISCz-1, and illite IMt-1) were exposed to M. mazei in growth medium with and without anthraquinone-2,6-disulfonate (AQDS) as electron shuttle. The extent and rate of bioreduction were quantified via wet chemistry and mineralogical transformed by X-ray diffraction and scanning and transmission electron microscopy. Our results demonstrated that M. mazei was able to reduce structural Fe(III) in clay minerals with Fe(III) in smectite being the most reducible and illite the least. AQDS enhanced the reduction rate and extent. The bioavailability of structural Fe(III) to M. mazei was correlated to the smectite proportion in each clay mineral . Methanogenesis was inhibited by Fe(III) bioreduction, possibly due to diversion of electrons from the methanogenesis pathway to structural Fe(III) in clay minerals. Bioreduction of Fe(III) in clay minerals induced formation of biogenic mixed-layer illite–smectite, silica, and vivianite. These data collectively showed that mesophilic methanogen is capable of reducing structural Fe(III) in illite–smectite minerals and of inducing a number of mineralogical changes.
K.n. Joblin - One of the best experts on this subject based on the ideXlab platform.
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Establishment and Development of Ruminal Hydrogenotrophs in Methanogen-Free Lambs
Applied and Environmental Microbiology, 2007Co-Authors: Gérard Fonty, K.n. Joblin, Michel Chavarot, Remy Roux, Graham E. Naylor, Fabien MichallonAbstract:The aim of this work was to determine whether reductive acetogenesis can provide an alternative to methanogenesis in the rumen. Gnotobiotic lambs were inoculated with a functional rumen microbiota lacking Methanogens and reared to maturity on a fibrous diet. Lambs with a methanogen-free rumen grew well, and the feed intake and ruminal volatile fatty acid concentrations for lambs lacking ruminal Methanogens were lower but not markedly dissimilar from those for conventional lambs reared on the same diet. A high population density (107 to 108 cells g−1) of ruminal acetogens slowly developed in methanogen-free lambs. Sulfate- and fumarate-reducing bacteria were present, but their population densities were highly variable. In methanogen-free lambs, the hydrogen capture from fermentation was low (28 to 46%) in comparison with that in lambs containing ruminal Methanogens (>90%). Reductive acetogenesis was not a significant part of ruminal fermentation in conventional lambs but contributed 21 to 25% to the fermentation in methanogen-free meroxenic animals. Ruminal H2 utilization was lower in lambs lacking ruminal Methanogens, but when a methanogen-free lamb was inoculated with a methanogen, the ruminal H2 utilization was similar to that in conventional lambs. H2 utilization in lambs containing a normal ruminal microflora was age dependent and increased with the animal age. The animal age effect was less marked in lambs lacking ruminal Methanogens. Addition of fumarate to rumen contents from methanogen-free lambs increased H2 utilization. These findings provide the first evidence from animal studies that reductive acetogens can sustain a functional rumen and replace Methanogens as a sink for H2 in the rumen.
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Analysis of Methanogen Diversity in the Rumen Using Temporal Temperature Gradient Gel Electrophoresis: Identification of Uncultured Methanogens
Microbial Ecology, 2007Co-Authors: Matthew J. Nicholson, Paul N. Evans, K.n. JoblinAbstract:A temporal temperature gradient gel electrophoresis (TTGE) method was developed to determine the diversity of methanogen populations in the rumen. Tests with amplicons from genomic DNA from 12 cultured Methanogens showed single bands for all strains, with only two showing apparently comigrating bands. Fingerprints of methanogen populations were analyzed from DNA extracted from rumen contents from two cattle and four sheep grazing pasture. For one sheep, dilution cultures selective for Methanogens were grown and the culturable Methanogens in each successive dilution examined by TTGE. A total of 66 methanogen sequences were retrieved from bands in fingerprints and analyzed to reveal the presence of Methanogens belonging to the Methanobacteriales, the Methanosarcinales, and to an uncultured archaeal lineage. Twenty-four sequences were most similar to Methanobrevibacter ruminantium, five to Methanobrevibacter smithii, four to Methanosphaera stadtmanae, and for three, the nearest match was Methanimicrococcus blatticola. The remaining 30 sequences did not cluster with sequences from cultured archaea, but when combined with published novel sequences from clone libraries formed a monophyletic lineage within the Euryarchaeota, which contained two previously unrecognized clusters. The TTGE bands from this lineage showed that the uncultured Methanogens had significant population densities in each of the six rumen samples examined. In cultures of dilutions from one rumen sample, TTGE examination revealed these Methanogens at a level of at least 105 g−1. Band intensities from low-dilution cultures indicated that these Methanogens were present at similar densities to Methanobrevibacter ruminantium-like Methanogens, the sole culturable Methanogens in high dilutions (106–10−10 g−1). It is suggested that the uncultured Methanogens together with Methanobrevibacter spp. may be the predominant Methanogens in the rumen. The TTGE method presented in this article provides a new opportunity for characterizing methanogen populations in the rumen microbial ecosystem.
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16s rdna directed pcr primers and detection of Methanogens in the bovine rumen
Letters in Applied Microbiology, 2006Co-Authors: Lucy C Skillman, Paul N. Evans, Carsten Strompl, K.n. JoblinAbstract:Aims: To assess the diversity of ruminal Methanogens in a grazing cow, and develop PCR primers targeting the predominant Methanogens. Methods and Results: DNA was extracted from rumen contents collected from a cow grazing pasture. Archaeal 16S rRNA genes were amplified by PCR using two pairs of archaea-specific primers, and clone libraries prepared. Selected clones were sequenced. Phylogenetic analysis revealed that for one primer pair, most sequences clustered with Methanobrevibacter spp. whereas with the other primer pair most clustered with Methanosphaera stadtmanae. One sequence belonged to the Crenarcheota. PCR primers were designed to detect Msp. stadtmanae and differentiate between Mbb. ruminantium and Mbb. smithii and successfully tested. Conclusions: The ruminal Methanogens included Mbb. ruminantium, Mbb. smithii, Mbb. thaueri and Methanogens similar to Msp.stadtmanae. The study showed that apparent methanogen diversity can be affected by selectivity from the archaea-specific primers used to create clone libraries. Significance and Impact of the Study: This study revealed a greater diversity of ruminal Methanogens in grazing cows than previously recognized. It also shows the need for care in interpreting methanogen diversity using PCR-based analyses. The new PCR primers will enable more information to be obtained on Msp. stadtmanae and Methanobrevibacter spp. in the rumen.
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16s ribosomal dna directed pcr primers for ruminal Methanogens and identification of Methanogens colonising young lambs
Anaerobe, 2004Co-Authors: Lucy C Skillman, Graham E. Naylor, Paul N. Evans, Brieuc Morvan, Graeme Jarvis, K.n. JoblinAbstract:The population densities and identities of Methanogens colonising new-born lambs in a grazing flock were determined from rumen samples collected at regular intervals after birth. Methanogen colonisation was found at the first sampling (1-3 days after birth) and population densities reached around 10(4) Methanogens per gram at 1 week of age. Population densities increased in an exponential manner to a maximum of 10(8)-10(9) per gram at 3 weeks of age. To identify Methanogens, PCR primers specific for each of the Archaea; a grouping of the orders Methanomicrobiales, Methanosarcinales and Methanococcales; the order Methanobacteriales; the order Methanococcales; the order Methanosarcinales; the genus Methanobacterium; and the genus Methanobrevibacter were designed. Primer-pair specificities were confirmed in tests with target and non-target micro-organisms. PCR analysis of DNA extracts revealed that all the detectable ruminal Methanogens belonged to the order Methanobacteriales, with no Methanogens belonging to the Methanomicrobiales, the Methanosarcinales, or the Methanococcales being detected. In 3 lambs, the initial colonising Methanogens were Methanobrevibacter spp. and in 2 lambs were a mixture of Methanobrevibacter and Methanobacterium spp. In the latter case, the initial colonising Methanobacterium spp. subsequently disappeared and were not detectable 12-19 days after birth. Seven weeks after birth, lambs contained only Methanobrevibacter spp. This study, the first to provide information on the identities of Methanogens colonising pre-ruminants, suggests that the predominant Methanogens found in the mature rumen establish very soon after birth and well before a functioning rumen develops.
Kenji Kato - One of the best experts on this subject based on the ideXlab platform.
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Microbial methane production in deep aquifer associated with the accretionary prism in Southwest Japan
The ISME Journal, 2010Co-Authors: Hiroyuki Kimura, Hiroaki Nashimoto, Mikio Shimizu, Shohei Hattori, Keita Yamada, Naohiro Yoshida, Keisuke Koba, Kenji KatoAbstract:To identify the methanogenic pathways present in a deep aquifer associated with an accretionary prism in Southwest Japan, a series of geochemical and microbiological studies of natural gas and groundwater derived from a deep aquifer were performed. Stable carbon isotopic analysis of methane in the natural gas and dissolved inorganic carbon (mainly bicarbonate) in groundwater suggested that the methane was derived from both thermogenic and biogenic processes. Archaeal 16S rRNA gene analysis revealed the dominance of H_2-using Methanogens in the groundwater. Furthermore, the high potential of methane production by H_2-using Methanogens was shown in enrichments using groundwater amended with H_2 and CO_2. Bacterial 16S rRNA gene analysis showed that fermentative bacteria inhabited the deep aquifer. Anaerobic incubations using groundwater amended with organic substrates and bromoethanesulfonate (a methanogen inhibitor) suggested a high potential of H_2 and CO_2 generation by fermentative bacteria. To confirm whether or not methane is produced by a syntrophic consortium of H_2-producing fermentative bacteria and H_2-using Methanogens, anaerobic incubations using the groundwater amended with organic substrates were performed. Consequently, H_2 accumulation and rapid methane production were observed in these enrichments incubated at 55 and 65 °C. Thus, our results suggested that past and ongoing syntrophic biodegradation of organic compounds by H_2-producing fermentative bacteria and H_2-using Methanogens, as well as a thermogenic reaction, contributes to the significant methane reserves in the deep aquifer associated with the accretionary prism in Southwest Japan.
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Microbial methane production in deep aquifer associated with the accretionary prism in Southwest Japan
ISME Journal, 2010Co-Authors: Hiroyuki Kimura, Hiroaki Nashimoto, Mikio Shimizu, Shohei Hattori, Keita Yamada, Naohiro Yoshida, Keisuke Koba, Kenji KatoAbstract:To identify the methanogenic pathways present in a deep aquifer associated with an accretionary prism in Southwest Japan, a series of geochemical and microbiological studies of natural gas and groundwater derived from a deep aquifer were performed. Stable carbon isotopic analysis of methane in the natural gas and dissolved inorganic carbon (mainly bicarbonate) in groundwater suggested that the methane was derived from both thermogenic and biogenic processes. Archaeal 16S rRNA gene analysis revealed the dominance of H(2)-using Methanogens in the groundwater. Furthermore, the high potential of methane production by H(2)-using Methanogens was shown in enrichments using groundwater amended with H(2) and CO(2). Bacterial 16S rRNA gene analysis showed that fermentative bacteria inhabited the deep aquifer. Anaerobic incubations using groundwater amended with organic substrates and bromoethanesulfonate (a methanogen inhibitor) suggested a high potential of H(2) and CO(2) generation by fermentative bacteria. To confirm whether or not methane is produced by a syntrophic consortium of H(2)-producing fermentative bacteria and H(2)-using Methanogens, anaerobic incubations using the groundwater amended with organic substrates were performed. Consequently, H(2) accumulation and rapid methane production were observed in these enrichments incubated at 55 and 65 degrees C. Thus, our results suggested that past and ongoing syntrophic biodegradation of organic compounds by H(2)-producing fermentative bacteria and H(2)-using Methanogens, as well as a thermogenic reaction, contributes to the significant methane reserves in the deep aquifer associated with the accretionary prism in Southwest Japan.
Yoichi Kamagata - One of the best experts on this subject based on the ideXlab platform.
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comparative proteomic analysis of methanothermobacter themautotrophicus δh in pure culture and in co culture with a butyrate oxidizing bacterium
PLOS ONE, 2011Co-Authors: Naoya Shinzato, Miho Enoki, Hiroaki Sato, Kohei Nakamura, Yoichi KamagataAbstract:To understand the physiological basis of methanogenic archaea living on interspecies H2 transfer, the protein expression of a hydrogenotrophic methanogen, Methanothermobacter thermautotrophicus strain DH, was investigated in both pure culture and syntrophic coculture with an anaerobic butyrate oxidizer Syntrophothermus lipocalidus strain TGB-C1 as an H2 supplier. Comparative proteomic analysis showed that global protein expression of methanogen cells in the model coculture was substantially different from that of pure cultured cells. In brief, in syntrophic coculture, although methanogenesis-driven energy generation appeared to be maintained by shifting the pathway to the alternative methyl coenzyme M reductase isozyme I and cofactor F420-dependent process, the machinery proteins involved in carbon fixation, amino acid synthesis, and RNA/DNA metabolisms tended to be down-regulated, indicating restrained cell growth rather than vigorous proliferation. In addition, our proteome analysis revealed that a subunits of proteasome were differentially acetylated between the two culture conditions. Since the relevant modification has been suspected to regulate proteolytic activity of the proteasome, the global protein turnover rate could be controlled under syntrophic growth conditions. To our knowledge, the present study is the first report on N-acetylation of proteasome subunits in methanogenic archaea. These results clearly indicated that physiological adaptation of hydrogenotrophic Methanogens to syntrophic growth is more complicated than that of hitherto proposed.
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isolation of key Methanogens for global methane emission from rice paddy fields a novel isolate affiliated with the clone cluster rice cluster i
Applied and Environmental Microbiology, 2007Co-Authors: Sanae Sakai, Hiroyuki Imachi, Yuji Sekiguchi, Akiyoshi Ohashi, Hideki Harada, Yoichi KamagataAbstract:Despite the fact that rice paddy fields (RPFs) are contributing 10 to 25% of global methane emissions, the organisms responsible for methane production in RPFs have remained uncultivated and thus uncharacterized. Here we report the isolation of a methanogen (strain SANAE) belonging to an abundant and ubiquitous group of Methanogens called rice cluster I (RC-I) previously identified as an ecologically important microbial component via culture-independent analyses. To enrich the RC-I Methanogens from rice paddy samples, we attempted to mimic the in situ conditions of RC-I on the basis of the idea that Methanogens in such ecosystems should thrive by receiving low concentrations of substrate (H2) continuously provided by heterotrophic H2-producing bacteria. For this purpose, we developed a coculture method using an indirect substrate (propionate) in defined medium and a propionate-oxidizing, H2-producing syntroph, Syntrophobacter fumaroxidans, as the H2 supplier. By doing so, we significantly enriched the RC-I Methanogens and eventually obtained a methanogen within the RC-I group in pure culture. This is the first report on the isolation of a methanogen within RC-I.
