80 results on '"Maignien, L."'
Search Results
2. Cold-water coral mounds on the Pen Duick Escarpment, Gulf of Cadiz: The MiCROSYSTEMS project approach
- Author
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Van Rooij, D., Blamart, D., De Mol, L., Mienis, F., Pirlet, H., Wehrmann, L.M., Barbieri, R., Maignien, L., Templer, S.P., de Haas, H., Hebbeln, D., Frank, N., Larmagnat, S., Stadnitskaia, A., Stivaletta, N., van Weering, T., Zhang, Y., Hamoumi, N., Cnudde, V., Duyck, P., and Henriet, J.-P.
- Published
- 2011
- Full Text
- View/download PDF
3. Diversity and Biogeography of Bathyal and Abyssal Seafloor Bacteria and Archaea Along a Mediterranean—Atlantic Gradient
- Author
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Trouche, B., Brandt, M.I., Belser, C., Orejas, Covadonga, Pesant, S., Poulain, J., Wincker, P., Auguet, J.C., Arnaud-Haond, S., Maignien, L., Trouche, B., Brandt, M.I., Belser, C., Orejas, Covadonga, Pesant, S., Poulain, J., Wincker, P., Auguet, J.C., Arnaud-Haond, S., and Maignien, L.
- Abstract
Seafloor sediments cover the majority of planet Earth and microorganisms inhabiting these environments play a central role in marine biogeochemical cycles. Yet, description of the biogeography and distribution of sedimentary microbial life is still too sparse to evaluate the relative contribution of processes driving this distribution, such as the levels of drift, connectivity, and specialization. To address this question, we analyzed 210 archaeal and bacterial metabarcoding libraries from a standardized and horizon-resolved collection of sediment samples from 18 stations along a longitudinal gradient from the eastern Mediterranean to the western Atlantic. Overall, we found that biogeographic patterns depended on the scale considered: while at local scale the selective influence of contemporary environmental conditions appeared strongest, the heritage of historic processes through dispersal limitation and drift became more apparent at regional scale, and ended up superseding contemporary influences at inter-regional scale. When looking at environmental factors, the structure of microbial communities was correlated primarily with water depth, with a clear transition between 800 and 1,200 meters below sea level. Oceanic basin, water temperature, and sediment depth were other important explanatory parameters of community structure. Finally, we propose increasing dispersal limitation and ecological drift with sediment depth as a probable factor for the enhanced divergence of deeper horizons communities.
- Published
- 2021
4. Anaerobic oxidation of methane in a cold-water coral carbonate mound from the Gulf of Cadiz
- Author
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Maignien, L., Depreiter, D., Foubert, A., Reveillaud, J., De Mol, L., Boeckx, P., Blamart, D., Henriet, J.-P., and Boon, N.
- Published
- 2011
- Full Text
- View/download PDF
5. An Assessment of Environmental Metabarcoding Protocols Aiming at Favoring Contemporary Biodiversity in Inventories of Deep-Sea Communities
- Author
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Brandt M, Trouche B, Henry N, Liautard-Haag C, Maignien L, de Vargas C, Wincker P, Poulain J, Zeppilli D, and Arnaud-Haond S
- Abstract
The abyssal seafloor covers more than 50% of planet Earth and is a large reservoir of still mostly undescribed biodiversity. It is increasingly targeted by resource-extraction industries and yet is drastically understudied. In such remote and hard-to-access ecosystems, environmental DNA (eDNA) metabarcoding is a useful and efficient tool for studying biodiversity and implementing environmental impact assessments. Yet, eDNA analysis outcomes may be biased toward describing past rather than present communities as sediments contain both contemporary and ancient DNA. Using commercially available kits, we investigated the impacts of five molecular processing methods on eDNA metabarcoding biodiversity inventories targeting prokaryotes (16S), unicellular eukaryotes (18S-V4), and metazoans (18S-V1, COI). As the size distribution of ancient DNA is skewed toward small fragments, we evaluated the effect of removing short DNA fragments via size selection and ethanol reconcentration using eDNA extracted from 10 g of sediment at five deep-sea sites. We also compare communities revealed by eDNA and environmental RNA (eRNA) co-extracted from 2 g of sediment at the same sites. Results show that removing short DNA fragments does not affect alpha and beta diversity estimates in any of the biological compartments investigated. Results also confirm doubts regarding the possibility to better describe live communities using eRNA. With ribosomal loci, eRNA, while resolving similar spatial patterns than co-extracted eDNA, resulted in significantly higher richness estimates, supporting hypotheses of increased persistence of ribosomal RNA (rRNA) in the environment and unmeasured bias due to overabundance of rRNA and RNA release. With the mitochondrial locus, eRNA detected lower metazoan richness and resolved fewer spatial patterns than co-extracted eDNA, reflecting high messenger RNA lability. Results also highlight the importance of using large amounts of sediment (10 g) for accurately surveying eukaryotic diversity. We conclude that eDNA should be favored over eRNAfor logistically realistic, repeatable, and reliable surveys and confirm that large sediment samples (10 g) deliver more complete and accurate assessments of benthic eukaryotic biodiversity and that increasing the number of biological rather than technical replicates is important to infer robust ecological patterns.
- Published
- 2020
6. Integrated research on the Pen Duick cold-water coral mounds: the MiCROSYSTEMS approach
- Author
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Van Rooij D., De Mol L., Blamart D., Mienis F., Wehrmann L. M., Maignien L., Templer S. P., de Haas H., Henriet J. P., BARBIERI, ROBERTO, Van Rooij D., De Mol L., Blamart D., Mienis F., Wehrmann L.M., Barbieri R., Maignien L., Templer S.P., de Haas H., and Henriet J.-P.
- Subjects
Coral mound ,Methane seep - Published
- 2010
7. The imprint of methane seepage on the geochemical record and early diagenetic processes in cold-water coral mounds on Pen Duick Escarpment, Gulf of Cadiz
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Wehrmann, L.M., Templer, S.P., Brunner, B., Bernasconi, S.M., Maignien, L., and Ferdelman, T.G.
- Subjects
fungi - Abstract
The diagenetic history and biogeochemical processes in three cold-water coral mounds located in close proximity to each other on Pen Duick Escarpment in the Gulf of Cadiz were examined. The influence of ascending methane-rich fluids from underlying sediment strata delineated two mound groups: Alpha and Beta Mound showed evidence for the presence of a sulfate-methane transition zone (SMTZ) at shallow depth, whereas Gamma Mound appeared to lack a shallow SMTZ. In the methane influenced Alpha and Beta Mound, upward diffusion of hydrogen sulfide from the shallow SMTZ caused extensive pyritization of reactive iron phases as indicated by values for the degree-of-pyritization > 0.7. This secondary pyritization overprinted the sulfur isotope composition of sulfides formed during organoclastic sulfate reduction. The almost complete consumption of reactive iron phases by upward diffusing sulfide limited dissimilatory iron reduction to the top layer in these mounds while organic matter in the pyritized zones below was primarily degraded by organoclastic sulfate reduction. Hydrogen sulfide produced during sulfate reduction coupled to the anaerobic oxidation of methane (ADM) diffused upward and induced aragonite dissolution as evidenced in strongly corroded corals in Alpha Mound. This mound has been affected by strong fluctuations in the depth of the SMTZ, as observed by distinct layers with abundant diagenetic high-Mg calcite with a 13C-depleted carbon isotope composition. In the non-methane influenced Gamma Mound low sulfate reduction rates, elevated concentrations of dissolved iron, and solid-phase iron speciation indicated that organic matter mineralization was driven by dissimilatory iron reduction and organoclastic sulfate reduction coupled to oxidative sulfur cycling. The latter process led to 34S-depletion in pyrite of up to 70% relative to pore-water sulfate.
- Published
- 2011
8. PHB-degrading bacteria isolated from the gastrointestinal tract of aquatic animals as protective actors against luminescent vibriosis
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Liu, Y., De Schryver, P., Van Delsen, B., Maignien, L., Boon, N., Sorgeloos, P., Verstraete, W., Bossier, P., and Defoirdt, T.
- Subjects
technology, industry, and agriculture ,lipids (amino acids, peptides, and proteins) ,macromolecular substances - Abstract
The use of poly-beta-hydroxybutyrate (PHB) was shown to be successful in increasing the resistance of brine shrimp against pathogenic infections. In this study, we isolated for the first time PHB-degrading bacteria from a gastrointestinal environment. Pure strains of PHB-degrading bacteria were isolated from Siberian sturgeon, European sea bass and giant river prawn. The capability of selected isolates to degrade PHB was confirmed in at least two of three setups: (1) growth in minimal medium containing PHB as the sole carbon (C) source, (2) production of clearing zones on minimal agar containing PHB as the sole C source and (3) degradation of PHB (as determined by HPLC analysis) in 10% Luria-Bertani medium containing PHB. Challenge tests showed that the PHB-degrading activity of the selected isolates increased the survival of brine shrimp larvae challenged to a pathogenic Vibrio campbellii strain by a factor 2-3. Finally, one of the PHB-degrading isolates from sturgeon showed a double biocontrol effect because it was also able to inactivate acylhomoserine lactones, a type of quorum-sensing molecule that regulates the virulence of different pathogenic bacteria. Thus, the combined supplementation of a PHB-degrading bacterium and PHB as a synbioticum provides perspectives for improving the gastrointestinal health of aquatic animals.
- Published
- 2010
9. Integrated research on the Pen Duick cold-water coral mounds: the MiCROSYSTEMS approach
- Author
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Van Rooij, D., De Mol, L., Blamart, D., Mienis, F., Wehrmann, L.M., Barbieri, R., Maignien, L., Templer, S.P., de Haas, H., Henriet, J.-P., and The MiCROSYSTEMS Science Team
- Abstract
The ESF EuroDIVERSITY MiCROSYSTEMS project aimed to turn the cold-water coral (CWC) mounds on the Pen Duick Escarpment (PDE) in the Gulf of Cadiz into a natural laboratory, exploring this highly complex biotope and to characterize its biodiversity. A common point of discussion with all other CWC mound provinces, surpassing its broad range of regional and morphological variability, concerns the driving forces regarding the initiation of these complex deep-water systems. Both oceanographic and geological processes have been proposed to play a significant role in the mound nucleation, growth and decline. During IODP Expedition 307, the importance of biogeochemical processes was already elucidated. Here, we present the preliminary results of the MD169 campaign as an integrated case study of three PDE CWC mounds: Alpha, Beta and Gamma mounds.Although cold-water corals are a common feature on the adjacent cliffs, mud volcanoes and seafloor, no actual living reef has been observed during the many ROV surveys. This multidisciplinary study aims to present a comprehensive and holistic view on the local dynamic geological and oceanographic environment. Coring data suggests (past or present) methane seepage near the Pen Duick Escarpment. Several sources and pathways are proposed, among which a stratigraphic migration through uplifted Miocene series underneath PDE. Its dominant morphology has influenced the local hydrodynamics within the course of the Pliocene, as documented by the emplacement of a sediment drift. Predominantly during post-Middle Pleistocene glacial episodes, favourable conditions were present for mound growth. An additional advantage for CWC mound nucleation near the top of PDE is offered through seepage-related carbonate crusts which might offer elevated colonization positions. Present-day seabed observations also suggested a possible important role of open coral rubble frameworks in the mound building process. These graveyards not only act as sediment trap but also as micro-habitat for a wide range of organisms. The presence of a fluctuating Sulphate-Methane Transition Zone is responsible for diagenesis, affecting both geochemical as physical characteristics, transforming the buried reef into a solid mound. Nevertheless, these seepage fluxes seem to be locally variable. As such, the origin and evolution of the PDE CWC mounds is, probably more than any other NE Atlantic cold-water coral mound province, located on the crossroads of environmental (hydrodynamic) and geological (seepage) pathways.
- Published
- 2010
10. Stratified community responses to methane and sulfate supplies in mud volcano deposits: insights from an in vitro experiment
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Zhang, Y., Maignien, L., Stadnitskaia, A., Boeckx, P., Xiao, X., Boon, N., Zhang, Y., Maignien, L., Stadnitskaia, A., Boeckx, P., Xiao, X., and Boon, N.
- Abstract
Numerous studies on marine prokaryotic communities have postulated that a process of anaerobic oxidation of methane (AOM) coupled with sulfate reduction (SR) is the main methane sink in the world's oceans. AOM has also been reported in the deep biosphere. But the responses of the primary microbial players in eliciting changes in geochemical environments, specifically in methane and sulfate supplies, have yet to be fully elucidated. Marine mud volcanoes (MVs) expel a complex fluid mixture of which methane is the primary component, forming an environment in which AOM is a common phenomenon. In this context, we attempted to identify how the prokaryotic community would respond to changes in methane and sulfate intensities, which often occur in MV environments in the form of eruptions, diffusions or seepage. We applied an integrated approach, including (i) biochemical surveys of pore water originated from MV, (ii) in vitro incubation of mud breccia, and (iii) prokaryotic community structure analysis. Two distinct AOM regions were clearly detected. One is related to the sulfate methane transition zone (SMTZ) at depth of 30-55 cm below the sea floor (bsf); the second is at 165-205 cm bsf with ten times higher rates of AOM and SR. This finding contrasts with the sulfide concentrations in pore waters and supports the suggestion that potential AOM activity below the SMTZ might be an important methane sink that is largely ignored or underestimated in oceanic methane budget calculations. Moreover, the incubation conditions below the SMTZ favor the growth of methanotrophic archaeal group ANME-2 compared to ANME-1, and promote the rapid growth and high diversity of bacterial communities. These incubation conditions also promote the increase of richness in bacterial communities. Our results provide direct evidence of the mechanisms by which deep AOM processes can affect carbon cycling in the deep biosphere and global methane biochemistry.
- Published
- 2014
11. Environmental constrains on microbial methane oxidation activity and community structure in Gulf of Cadiz mud volcanoes
- Author
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Maignien, L., Nico Boon, and Rv Jc, James Cook Shipboard
- Published
- 2009
12. Simulation of the deep-sea biosphere by a continuous high-pressure bioreactor
- Author
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Zhang, Y., Maignien, L., Verstraete, W., Henriet, J.-P., and Boon, N.
- Abstract
In ocean system Anaerobic Oxidation of Methane (AOM) followed by carbonate precipitation has a significant effect on the climate regulation, since this process avoids large methane emissions to the atmosphere and fixes carbon dioxide into carbonate structures. However the main difficulty to study AOM is that the consortia involved have extremely long doubling time (2-7 months) at ambient or low pressures. To simulate the in situ condition better and obtain a faster growth, we designed and constructed a unique continuous high-pressure bioreactor. The reactor can reach pressure up to 100 bars, representing a depth of 1000m below sea level; it can be operated in continuous or non-continuous style, simulating the different types of methane resource. By the help of this high pressure bioreactor system, we are also able to study the effect of environmental factors on AOM activity and on microbial community. Captain Arutyunov Mud Volcano (Gulf of Cadiz) sediment has been used as biomass resource and different molecular techniques (DGGE, cloning library, FISH) have been applied to examine the microbial community structure. By increasing methane partial pressure, an immediate increase of AOM activity has been observed before significant enrichment of biomass. A continuous methane flux is necessary to obtain optimal AOMactivity. Bacterial community is more sensitive to the change of pressure compared with archaeal community.
- Published
- 2009
13. Authigenic carbonates from cold-water carbonate mounds in the Gulf of Cadiz: Microbial diversity and imprint on carbonate minerals
- Author
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Templer, S.P., Maignien, L., Bernasconi, S. M., Vasconcelos, C., and McKenzie, J.A.
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fungi - Abstract
The Pen Duick Escarpment off Morocco consists of recent carbonate mounds in water depths of 500-600 m, flanked by giant mud volcanoes. These mounds are covered by mainly lifeless cold-water corals and have been associated with extensive fields of seep-related carbonates in off-reef regions. Three piston cores (from 350 to 640 cm long), coming from different sites on these juvenile mounds, were sampled and analyzed for mineralogy, stable isotopic composition of carbonates, geochemistry, and microbial communities. Most of the sediment comprises pelagic calcite (coccoliths), detrital quartz and authigenic dolomite, often observed encasing coccoliths. The decalcification of the sediment resulted in a dolomite dominated matrix that showed stable carbon istotope values of as low as -30 permil in contrast to the bulk sample values of -7 to -15 permil, which implies the involvement of microbes in the production of bicarbonate ions. Initial results from 16S rRNA gene clone libraries support the theory, that anaerobic oxidation of methane is one of the most important biogeochemical process leading to carbonate precipitation. Preliminary results of stable carbon isotopes of bulk samples from different carbonate mounds from the same area, indicates that the sulphate-methane transition zone moves in depth through time. We will show and discuss multidisciplinary data obtained after several cruises aimed to elucidate the impact of microorganisms on the construction of these carbonate mounds. The special emphasis in this research will be on the correlation between microbial ecosystems and their metabolic influence on mineral formation and diagenesis.
- Published
- 2008
14. Biogeochemistry of carbonate mounds from the Pen Duick escarpment in the Gulf of Cadiz
- Author
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Maignien, L., Depreiter, D., Foubert, A., Boon, N., Verstraete, W., and Henriet, J.-P.
- Abstract
In the Gulf of Cadiz, carbonate mounds build by cold-water corals were recently discovered on the Renard Ridge, a zone of active fluid flow and mud volcanism. Their sizes vary from 25 to more than 60 m high, at a depth of 520 m and they are aligned along the ridge axis. These mounds, located in the close vicinity of fluid flow markers such as carbonate crusts and mud volcanoes, provided a novel opportunity to study a possible fluid flow control on the mound processes and distribution. Previous geochemical studies on the southernmost mound of the ridge indeed showed that this mound was located on focused fluid flow compared to surrounding sediments, and we observed typical profiles of methane migration and anoxic oxidation (AOM) at 3,8 m below the sea floor within the mound. Such AOM occurrence imprinted a characteristic d13C signature (down to –21,9 %¸ Vs. PDB) and significantly contributes to the overall carbonate budget of the mound.During the recent R/V Maria S. Merian cruise (April-June 2006), we sampled by mean of a gravity corer six new structures likely to be cold-water carbonate mounds, along the Pen Duick escarpment and the Renard Ridge. Our aim was to determine if the geochemical profiles observed in the first mound could be generalized to all the mounds in this area.Each core yielded a full sequence of cold-water corals down to about 5 meters below the sea floor. Hence, the numerous knoll-like structures revealed by high-resolution bathymetry along the ridge are indeed carbonate mounds build by cold-water corals and the entire Ridge has been massively colonized by corals. No live reef-forming coral could be recovered from the cores, nor observed by towed video instruments. Then, fluid migration seems to be a common feature all along the ridge. However, important discrepancies were observed: methane concentrations are higher and sulfate gradients steeper on both side of the ridge, whereas the central part of the ridge seems less active in term of fluid migration. In this case, the sulfate to methane transition zone could not be reached using conventional gravity corer. In order to obtain the full biogeochemical picture of these mounds, the use of a long piston corer, or drilling devices, will be required.The reasons of the formation of massive reefs in this area are still unknown and are probably linked to locally enhanced hydrologic conditions. However, it is possible that cold-water coral could have benefited from the hard substrate and the topographic elevations provided by fluid related structures such as carbonate crusts, chimneys and clasts, as observed in several other locations in the Gulf of Cadiz.
- Published
- 2007
15. Atlantic carbonate mounds: challenges for ocean drilling, from Porcupine to the Morocco Margin
- Author
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Henriet, J.-P., Foubert, A., Maignien, L., and Proposals 573-Light and 673-Pre2 Teams and Expedition 307 Shipboard Party
- Subjects
ANE, Porcupine Abyssal Plain ,Carbonate rocks ,Drilling ,ASE, Morocco - Published
- 2006
16. Biogeochemical evidence for anoxic oxidation of methane occurrences in the juvenile carbonate mounds from the Gulf of Cadiz
- Author
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Maignien, L., Foubert, A., Depreiter, D., Boon, N., Blamart, D., Verstraete, W., and Henriet, J.-P.
- Abstract
Carbonate mounds are conspicuous features of the European margins. Only fossil examples of these mounds were known when modern giant carbonate mounds were discovered in the S.-W. Irish margin. A decade of thorough studies in this area provided remarkable insight on mound processes and distribution. However, the question of the genesis and stabilization over geological times of these carbonate mounds remain wide open.Our work hypothesis is that moderate fluxes of low molecular hydrocarbons are oxidized and produces carbonates that may serve as cement for the mound stabilization. The recent discovery and mapping (R/V Belgica 2003, 2005) of the Pen Duick escarpment on the Moroccan margin (Gulf of Cadiz) by swath bathymetry shed light on new carbonate mounds associated with fluid migration markers such as pockmarks, carbonate crusts and mud volcanoes. Pore water biogeochemical profiles show that the sulphate to methane transition zone occurs at 3.5 meters below the sea floor within the mound, whereas the depth of no sulphate is much deeper in the surrounding sediments. At the same depth, carbonates are released with d13C values as low as -21 permil indicating a methane and possibly other light hydrocarbons origin. Hence anoxic oxidation of hydrocarbons, and subsequent carbonate production, may play a key role in the mound formation and/or stabilization. Interestingly, Lophelia coral rubbles were present all along the sediment column suggesting that this mound is a potential habitat for cold coral and associated communities.
- Published
- 2006
17. The mud volcano province on the Atlantic Moroccan margin: Towards a natural laboratory for joint European-Maghreb research
- Author
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Henriet, J.P., Hamoumi, N., Ivanov, M., Pinheiro, L., Suzyumov, A., Swennen, R., Blinova, V., Bouimetarhan, I., De Boever, E., Depreiter, D., Foubert, A., Kozlova, E., Maignien, L., Poort, J., Van Rensbergen, P., and Van Rooij, D.
- Published
- 2006
18. Biogeochemistry of carbonate mounds from the Pen Duick escarpement, Gulf of Cadiz
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Maignien, L., Wouters, N., and Henriet, J.P.
- Subjects
Carbonate rocks ,ANE, Cadiz Gulf ,Biogeochemistry - Published
- 2006
19. Pen Duick escarpment on the Moroccan margin: a new mound lab?
- Author
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Foubert, A., Maignien, L., Beck, T., Depreiter, D., Blamart, D., and Henriet, J.-P.
- Published
- 2005
20. Biodiversity of cold seep ecosystems along the European margins
- Author
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Vanreusel, A., Andersen, A.C., Boetius, A., Connelly, D., Cunha, M.R., Decker, C., Hilario, A., Kormas, K.A., Maignien, L., Olu, K., Pachiadaki, M., Ritt, B., Rodrigues, C., Sarrazin, J., Tyler, P., Van Gaever, S., Vanneste, H., Vanreusel, A., Andersen, A.C., Boetius, A., Connelly, D., Cunha, M.R., Decker, C., Hilario, A., Kormas, K.A., Maignien, L., Olu, K., Pachiadaki, M., Ritt, B., Rodrigues, C., Sarrazin, J., Tyler, P., Van Gaever, S., and Vanneste, H.
- Published
- 2009
21. Accumulation of trans C18:1 fatty acids in the rumen after dietary algal supplementation is associated with canges in the Butyrivibrio communitytrans
- Author
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Boeckaert, C., Vlaeminck, B., Fievez, V., Maignien, L., Dijkstra, J., Boon, N., Boeckaert, C., Vlaeminck, B., Fievez, V., Maignien, L., Dijkstra, J., and Boon, N.
- Abstract
Optimization of the fatty acid composition of ruminant milk and meat is desirable. Dietary supplementation of algae was previously shown to inhibit rumen biohydrogenation, resulting in an altered milk fatty acid profile. Bacteria involved in biohydrogenation belong to the Butyrivibrio group. This study was aimed at relating accumulation of biohydrogenation intermediates with shifts in Butyrivibrio spp. in the rumen of dairy cows. Therefore, an experiment was performed with three rumen-fistulated dairy cows receiving a concentrate containing algae (9.35 g/kg total dry matter [DM] intake) for 20 days. Supplementation of the diet with algae inhibited biohydrogenation of C18:2 omega 6 (n-6) and C18:3 n-3, resulting in increased concentrations of biohydrogenation intermediates, whereas C18:0 decreased. Addition of algae increased ruminal C18:1 trans fatty acid concentrations, mainly due to 6- and 20-fold increases in C18:1 trans 11 (t11) and C18:1 t10. The number of ciliates (5.37 log copies/g rumen digesta) and the composition of the ciliate community were unaffected by dietary algae. In contrast, supplementation of the diet with algae changed the composition of the bacterial community. Primers for the Butyrivibrio group, including the genera Butyrivibrio and Pseudobutyrivibrio, were specifically designed. Denaturing gradient gel electrophoresis showed community changes upon addition of algae without affecting the total amount of Butyrivibrio bacteria (7.06 log copies/g rumen DM). Clone libraries showed that algae affected noncultivated species, which cluster taxonomically between the genera Butyrivibrio and Pseudobutyrivibrio and might play a role in biohydrogenation. In addition, 20% of the clones from a randomly selected rumen sample were related to the C18:0-producing branch, although the associated C18:0 concentration decreased through supplementation of the diet with algae
- Published
- 2008
22. Atlantic carbonate mound drilling: challenges ahead, from Porcupine to the Morocco margin
- Author
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Henriet, Jean-Pierre, Foubert, Anneleen, Maignien, L., Proposal '573'-Light Team, Proposal '673-Pre' Team, Expedition 307 Shipboard Party incl. Bjerager, Morten, Henriet, Jean-Pierre, Foubert, Anneleen, Maignien, L., Proposal '573'-Light Team, Proposal '673-Pre' Team, and Expedition 307 Shipboard Party incl. Bjerager, Morten
- Abstract
deep water coral mounds, IODP
- Published
- 2005
23. Anaerobic oxidation of methane in a cold-water coral carbonate mound from the Gulf of Cadiz
- Author
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Maignien, L., primary, Depreiter, D., additional, Foubert, A., additional, Reveillaud, J., additional, De Mol, L., additional, Boeckx, P., additional, Blamart, D., additional, Henriet, J.-P., additional, and Boon, N., additional
- Published
- 2010
- Full Text
- View/download PDF
24. Role of the protozoan Isotricha prostoma, liquid-, and solid-associated bacteria in rumen biohydrogenation of linoleic acid
- Author
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Boeckaert, C., primary, Morgavi, D.P., additional, Jouany, J.-P., additional, Maignien, L., additional, Boon, N., additional, and Fievez, V., additional
- Published
- 2009
- Full Text
- View/download PDF
25. Metagenome-assembled genomes of deep-sea sediments: changes in microbial functional potential lag behind redox transitions.
- Author
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Schauberger C, Thamdrup B, Lemonnier C, Trouche B, Poulain J, Wincker P, Arnaud-Haond S, Glud RN, and Maignien L
- Abstract
Hadal sediments are hotspots of microbial activity in the deep sea and exhibit strong biogeochemical gradients. But although these gradients are widely assumed to exert selective forces on hadal microbial communities, the actual relationship between biogeochemistry, functional traits, and microbial community structure remains poorly understood. We tested whether the biogeochemical conditions in hadal sediments select for microbes based on their genomic capacity for respiration and carbohydrate utilization via a metagenomic analysis of over 153 samples from the Atacama Trench region (max. depth = 8085 m). The obtained 1357 non-redundant microbial genomes were affiliated with about one-third of all known microbial phyla, with more than half belonging to unknown genera. This indicated that the capability to withstand extreme hydrostatic pressure is a phylogenetically widespread trait and that hadal sediments are inhabited by diverse microbial lineages. Although community composition changed gradually over sediment depth, these changes were not driven by selection for respiratory or carbohydrate degradation capability in the oxic and nitrogenous zones, except in the case of anammox bacteria and nitrifying archaea. However, selection based on respiration and carbohydrate degradation capacity did structure the communities of the ferruginous zone, where aerobic and nitrogen respiring microbes declined exponentially (half-life = 125-419 years) and were replaced by subsurface communities. These results highlight a delayed response of microbial community composition to selective pressure imposed by redox zonation and indicated that gradual changes in microbial composition are shaped by the high-resilience and slow growth of microbes in the seafloor., Competing Interests: The authors declare no competing or conflicting interests., (© The Author(s) 2024. Published by Oxford University Press on behalf of the International Society for Microbial Ecology.)
- Published
- 2024
- Full Text
- View/download PDF
26. Impacts of sample handling and storage conditions on archiving physiologically active soil microbial communities.
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Brock MT, Morrison HG, Maignien L, and Weinig C
- Subjects
- Oklahoma, Soil chemistry, RNA, Ribosomal, 16S genetics, Montana, DNA, Bacterial genetics, Biodiversity, Soil Microbiology, Microbiota genetics, Bacteria genetics, Bacteria classification, Bacteria isolation & purification, Specimen Handling methods
- Abstract
Soil microbial communities are fundamental to ecosystem processes and plant growth, yet community composition is seasonally and successionally dynamic, which interferes with long-term iterative experimentation of plant-microbe interactions. We explore how soil sample handling (e.g. filtering) and sample storage conditions impact the ability to revive the original, physiologically active, soil microbial community. We obtained soil from agricultural fields in Montana and Oklahoma, USA and samples were sieved to 2 mm or filtered to 45 µm. Sieved and filtered soil samples were archived at -20°C or -80°C for 50 days and revived for 2 or 7 days. We extracted DNA and the more transient RNA pools from control and treatment samples and characterized microbial communities using 16S amplicon sequencing. Filtration and storage treatments significantly altered soil microbial communities, impacting both species richness and community composition. Storing sieved soil at -20°C did not alter species richness and resulted in the least disruption to the microbial community composition in comparison to nonarchived controls as characterized by RNA pools from soils of both sites. Filtration significantly altered composition but not species richness. Archiving sieved soil at -20°C could allow for long-term and repeated experimentation on preserved physiologically active microbial communities., (© The Author(s) 2024. Published by Oxford University Press on behalf of FEMS.)
- Published
- 2024
- Full Text
- View/download PDF
27. Distribution and genomic variation of ammonia-oxidizing archaea in abyssal and hadal surface sediments.
- Author
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Trouche B, Schauberger C, Bouderka F, Auguet JC, Belser C, Poulain J, Thamdrup B, Wincker P, Arnaud-Haond S, Glud RN, and Maignien L
- Abstract
Ammonia-oxidizing archaea of the phylum Thaumarchaeota play a central role in the biogeochemical cycling of nitrogen in benthic sediments, at the interface between pelagic and subsurface ecosystems. However, our understanding of their niche separation and of the processes controlling their population structure in hadal and abyssal surface sediments is still limited. Here, we reconstructed 47 AOA metagenome-assembled genomes (MAGs) from surface sediments of the Atacama and Kermadec trench systems. They formed deep-sea-specific groups within the family Nitrosopumilaceae and were assigned to six amoA gene-based clades. MAGs from different clades had distinct distribution patterns along oxygen-ammonium counter gradients in surface sediments. At the species level, MAGs thus seemed to form different ecotypes and follow deterministic niche-based distributions. In contrast, intraspecific population structure, defined by patterns of Single Nucleotide Variants (SNV), seemed to reflect more complex contributions of both deterministic and stochastic processes. Firstly, the bathymetric range had a strong effect on population structure, with distinct populations in abyssal plains and hadal trenches. Then, hadal populations were clearly separated by trench system, suggesting a strong isolation-by-topography effect, whereas abyssal populations were rather controlled by sediment depth or geographic distances, depending on the clade considered. Interestingly, genetic variability between samples was lowest in sediment layers where the mean MAG coverage was highest, highlighting the importance of selective pressure linked with each AOA clade's ecological niche. Overall, our results show that deep-sea AOA genome distributions seem to follow both deterministic and stochastic processes, depending on the genomic variability scale considered., (© 2023. The Author(s).)
- Published
- 2023
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28. Rhizosphere microbial community composition shifts diurnally and in response to natural variation in host clock phenotype.
- Author
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Hubbard CJ, Harrison JG, McMinn R, Bennett Ponsford JC, Maignien L, Ewers B, and Weinig C
- Subjects
- Rhizosphere, Soil Microbiology, Phenotype, Plants, Microbiota genetics, Brassicaceae
- Abstract
Plant-associated microbial assemblages are known to shift at time scales aligned with plant phenology, as influenced by the changes in plant-derived nutrient concentrations and abiotic conditions observed over a growing season. But these same factors can change dramatically in a sub-24-hour period, and it is poorly understood how such diel cycling may influence plant-associated microbiomes. Plants respond to the change from day to night via mechanisms collectively referred to as the internal "clock," and clock phenotypes are associated with shifts in rhizosphere exudates and other changes that we hypothesize could affect rhizosphere microbes. The mustard Boechera stricta has wild populations that contain multiple clock phenotypes of either a 21- or a 24-hour cycle. We grew plants of both phenotypes (two genotypes per phenotype) in incubators that simulated natural diel cycling or that maintained constant light and temperature. Under both cycling and constant conditions, the extracted DNA concentration and the composition of rhizosphere microbial assemblages differed between time points, with daytime DNA concentrations often triple what were observed at night and microbial community composition differing by, for instance, up to 17%. While we found that plants of different genotypes were associated with variation in rhizosphere assemblages, we did not see an effect on soil conditioned by a particular host plant circadian phenotype on subsequent generations of plants. Our results suggest that rhizosphere microbiomes are dynamic at sub-24-hour periods, and those dynamics are shaped by diel cycling in host plant phenotype. IMPORTANCE We find that the rhizosphere microbiome shifts in composition and extractable DNA concentration in sub-24-hour periods as influenced by the plant host's internal clock. These results suggest that host plant clock phenotypes could be an important determinant of variation in rhizosphere microbiomes., Competing Interests: The authors declare no conflict of interest.
- Published
- 2023
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29. Whole-Genome Duplication and Host Genotype Affect Rhizosphere Microbial Communities.
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Ponsford JCB, Hubbard CJ, Harrison JG, Maignien L, Buerkle CA, and Weinig C
- Subjects
- Humans, Rhizosphere, Gene Duplication, Soil Microbiology, RNA, Ribosomal, 16S genetics, Tetraploidy, Bayes Theorem, Genotype, Bacteria, Arabidopsis genetics, Microbiota
- Abstract
The composition of microbial communities found in association with plants is influenced by host phenotype and genotype. However, the ways in which specific genetic architectures of host plants shape microbiomes are unknown. Genome duplication events are common in the evolutionary history of plants and influence many important plant traits, and thus, they may affect associated microbial communities. Using experimentally induced whole-genome duplication (WGD), we tested the effect of WGD on rhizosphere bacterial communities in Arabidopsis thaliana. We performed 16S rRNA amplicon sequencing to characterize differences between microbiomes associated with specific host genetic backgrounds (Columbia versus Landsberg) and ploidy levels (diploid versus tetraploid). We modeled relative abundances of bacterial taxa using a hierarchical Bayesian approach. We found that host genetic background and ploidy level affected rhizosphere community composition. We then tested to what extent microbiomes derived from a specific genetic background or ploidy level affected plant performance by inoculating sterile seedlings with microbial communities harvested from a prior generation. We found a negative effect of the tetraploid Columbia microbiome on growth of all four plant genetic backgrounds. These findings suggest an interplay between host genetic background and ploidy level and bacterial community assembly with potential ramifications for host fitness. Given the prevalence of ploidy-level variation in both wild and managed plant populations, the effects on microbiomes of this aspect of host genetic architecture could be a widespread driver of differences in plant microbiomes. IMPORTANCE Plants influence the composition of their associated microbial communities, yet the underlying host-associated genetic determinants are typically unknown. Genome duplication events are common in the evolutionary history of plants and affect many plant traits. Using Arabidopsis thaliana, we characterized how whole-genome duplication affected the composition of rhizosphere bacterial communities and how bacterial communities associated with two host plant genetic backgrounds and ploidy levels affected subsequent plant growth. We observed an interaction between ploidy level and genetic background that affected both bacterial community composition and function. This research reveals how genome duplication, a widespread genetic feature of both wild and crop plant species, influences bacterial assemblages and affects plant growth.
- Published
- 2022
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30. The mosquito microbiome includes habitat-specific but rare symbionts.
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Schrieke H, Maignien L, Constancias F, Trigodet F, Chakloute S, Rakotoarivony I, Marie A, L'Ambert G, Makoundou P, Pages N, Murat Eren A, Weill M, Sicard M, and Reveillaud J
- Abstract
Microbial communities are known to influence mosquito lifestyles by modifying essential metabolic and behavioral processes that affect reproduction, development, immunity, digestion, egg survival, and the ability to transmit pathogens. Many studies have used 16S rRNA gene amplicons to characterize mosquito microbiota and investigate factors that influence host-microbiota dynamics. However, a relatively low taxonomic resolution due to clustering methods based on arbitrary threshold and the overall dominance of Wolbachia or Asaia symbionts obscured the investigation of rare members of mosquito microbiota in previous studies. Here, we used high resolution Shannon entropy-based oligotyping approach to analyze the microbiota of Culex pipiens , Culex quinquefasciatus and Aedes individuals from continental Southern France and overseas Guadeloupe as well as from laboratories with or without antibiotics treatment. Our experimental design that resulted in a series of mosquito samples with a gradient of Wolbachia density and relative abundance along with high-resolution analyses of amplicon sequences enabled the recovery of a robust signal from typically less accessible bacterial taxa. Our data confirm species-specific mosquito-bacteria associations with geography as a primary factor that influences bacterial community structure. But interestingly, they also reveal co-occurring symbiotic bacterial variants within single individuals for both Elizabethkingia and Erwinia genera, distinct and specific Asaia and Chryseobacterium in continental and overseas territories, and a putative rare Wolbachia variant. Overall, our study reveals the presence of previously overlooked microdiversity and multiple closely related symbiotic strains within mosquito individuals with a remarkable habitat-specificity., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2021 The Author(s).)
- Published
- 2021
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31. Microbial community structure in hadal sediments: high similarity along trench axes and strong changes along redox gradients.
- Author
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Schauberger C, Glud RN, Hausmann B, Trouche B, Maignien L, Poulain J, Wincker P, Arnaud-Haond S, Wenzhöfer F, and Thamdrup B
- Subjects
- Archaea genetics, Oxidation-Reduction, RNA, Ribosomal, 16S genetics, Bacteria genetics, Microbiota
- Abstract
Hadal trench sediments are hotspots of biogeochemical activity in the deep sea, but the biogeochemical and ecological factors that shape benthic hadal microbial communities remain unknown. Here, we sampled ten hadal sites from two trench regions with a vertical resolution of down to 1 cm. We sequenced 16S rRNA gene amplicons using universal and archaea-specific primer sets and compared the results to biogeochemical parameters. Despite bathymetric and depositional heterogeneity we found a high similarity of microbial communities within each of the two trench axes, while composition at the phylum level varied strongly with sediment depth in conjunction with the redox stratification into oxic, nitrogenous, and ferruginous zones. As a result, communities of a given sediment horizon were more similar to each other across a distance of hundreds of kilometers within each trench, than to those of adjacent horizons from the same sites separated only by centimeters. Total organic carbon content statistically only explained a small part of the variation within and between trenches, and did not explain the community differences observed between the hadal and adjacent shallower sites. Anaerobic taxa increased in abundance at the top of the ferruginous zone, seeded by organisms deposited at the sediment surface and surviving burial through the upper redox zones. While an influence of other potential factors such as geographic isolation, hydrostatic pressure, and non-steady state depositional regimes could not be discerned, redox stratification and diagenesis appear to be the main selective forces that structure community composition in hadal sediments., (© 2021. The Author(s).)
- Published
- 2021
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32. Anammox bacteria drive fixed nitrogen loss in hadal trench sediments.
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Thamdrup B, Schauberger C, Larsen M, Trouche B, Maignien L, Arnaud-Haond S, Wenzhöfer F, and Glud RN
- Subjects
- Anaerobic Ammonia Oxidation physiology, Denitrification physiology, Microbiota physiology, Nitrates metabolism, Nitrification physiology, Nitrogen Cycle physiology, Oceans and Seas, Geologic Sediments microbiology, Nitrogen metabolism, Nitrogen Fixation physiology, Nitrogen-Fixing Bacteria metabolism
- Abstract
Benthic N
2 production by microbial denitrification and anammox is the largest sink for fixed nitrogen in the oceans. Most N2 production occurs on the continental shelves, where a high flux of reactive organic matter fuels the depletion of nitrate close to the sediment surface. By contrast, N2 production rates in abyssal sediments are low due to low inputs of reactive organics, and nitrogen transformations are dominated by aerobic nitrification and the release of nitrate to the bottom water. Here, we demonstrate that this trend is reversed in the deepest parts of the oceans, the hadal trenches, where focusing of reactive organic matter enhances benthic microbial activity. Thus, at ∼8-km depth in the Atacama Trench, underlying productive surface waters, nitrate is depleted within a few centimeters of the sediment surface, N2 production rates reach those reported from some continental margin sites, and fixed nitrogen loss is mainly conveyed by anammox bacteria. These bacteria are closely related to those known from shallow oxygen minimum zone waters, and comparison of activities measured in the laboratory and in situ suggest they are piezotolerant. Even the Kermadec Trench, underlying oligotrophic surface waters, exhibits substantial fixed N removal. Our results underline the role of hadal sediments as hot spots of deep-sea biological activity, revealing a fully functional benthic nitrogen cycle at high hydrostatic pressure and pointing to hadal sediments as a previously unexplored niche for anaerobic microbial ecology and diagenesis., Competing Interests: The authors declare no competing interest.- Published
- 2021
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33. Diversity and Biogeography of Bathyal and Abyssal Seafloor Bacteria and Archaea Along a Mediterranean-Atlantic Gradient.
- Author
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Trouche B, Brandt MI, Belser C, Orejas C, Pesant S, Poulain J, Wincker P, Auguet JC, Arnaud-Haond S, and Maignien L
- Abstract
Seafloor sediments cover the majority of planet Earth and microorganisms inhabiting these environments play a central role in marine biogeochemical cycles. Yet, description of the biogeography and distribution of sedimentary microbial life is still too sparse to evaluate the relative contribution of processes driving this distribution, such as the levels of drift, connectivity, and specialization. To address this question, we analyzed 210 archaeal and bacterial metabarcoding libraries from a standardized and horizon-resolved collection of sediment samples from 18 stations along a longitudinal gradient from the eastern Mediterranean to the western Atlantic. Overall, we found that biogeographic patterns depended on the scale considered: while at local scale the selective influence of contemporary environmental conditions appeared strongest, the heritage of historic processes through dispersal limitation and drift became more apparent at regional scale, and ended up superseding contemporary influences at inter-regional scale. When looking at environmental factors, the structure of microbial communities was correlated primarily with water depth, with a clear transition between 800 and 1,200 meters below sea level. Oceanic basin, water temperature, and sediment depth were other important explanatory parameters of community structure. Finally, we propose increasing dispersal limitation and ecological drift with sediment depth as a probable factor for the enhanced divergence of deeper horizons communities., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Trouche, Brandt, Belser, Orejas, Pesant, Poulain, Wincker, Auguet, Arnaud-Haond and Maignien.)
- Published
- 2021
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34. Time outweighs the effect of host developmental stage on microbial community composition.
- Author
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Dibner RR, Weaver AM, Brock MT, Custer GF, Morrison HG, Maignien L, and Weinig C
- Subjects
- Plant Roots, Rhizosphere, Soil, Microbiota, Soil Microbiology
- Abstract
Thousands of microbial taxa in the soil form symbioses with host plants, and due to their contribution to plant performance, these microbes are often considered an extension of the host genome. Given microbial effects on host performance, it is important to understand factors that govern microbial community assembly. Host developmental stage could affect rhizosphere microbial diversity while, alternatively, microbial assemblages could change simply as a consequence of time and the opportunity for microbial succession. Previous studies suggest that rhizosphere microbial assemblages shift across plant developmental stages, but time since germination is confounded with developmental stage. We asked how elapsed time and potential microbial succession relative to host development affected microbial diversity in the rhizosphere using monogenic flowering-time mutants of Arabidopsis thaliana. Under our experimental design, different developmental stages were present among host genotypes after the same amount of time following germination, e.g. at 76 days following germination some host genotypes were flowering while others were fruiting or senescing. We found that elapsed time was a strong predictor of microbial diversity whereas there were few differences among developmental stages. Our results support the idea that time and, likely, microbial succession more strongly affect microbial community assembly than host developmental stage., (© The Author(s) 2021. Published by Oxford University Press on behalf of FEMS. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)
- Published
- 2021
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35. Thermococcus camini sp. nov., a hyperthermophilic and piezophilic archaeon isolated from a deep-sea hydrothermal vent at the Mid-Atlantic Ridge.
- Author
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Courtine D, Vince E, Maignien L, Philippon X, Gayet N, Shao Z, and Alain K
- Subjects
- Atlantic Ocean, Bacterial Typing Techniques, Base Composition, DNA, Archaeal genetics, DNA, Bacterial genetics, Fatty Acids chemistry, Nucleic Acid Hybridization, RNA, Ribosomal, 16S genetics, Sequence Analysis, DNA, Sulfur, Thermococcus isolation & purification, Hydrothermal Vents microbiology, Phylogeny, Seawater microbiology, Thermococcus classification
- Abstract
A coccoid-shaped, strictly anaerobic, hyperthermophilic and piezophilic organoheterotrophic archaeon, strain Iri35c
T , was isolated from a hydrothermal chimney rock sample collected at a depth of 2300 m at the Mid-Atlantic Ridge (Rainbow vent field). Cells of strain Iri35cT grew at NaCl concentrations ranging from 1-5 % (w/v) (optimum 2.0 %), from pH 5.0 to 9.0 (optimum 7.0-7.5), at temperatures between 50 and 90 °C (optimum 75-80 °C) and at pressures from 0.1 to at least 50 MPa (optimum: 10-30 MPa). The novel isolate grew on complex organic substrates, such as yeast extract, tryptone, peptone or beef extract, preferentially in the presence of elemental sulphur or l-cystine; however, these molecules were not necessary for growth. Its genomic DNA G+C content was 54.63 mol%. The genome has been annotated and the metabolic predictions are in accordance with the metabolic characteristics of the strain and of Thermococcales in general. Phylogenetic analyses based on 16S rRNA gene sequences and concatenated ribosomal protein sequences showed that strain Iri35cT belongs to the genus Thermococcus, and is closer to the species T. celericrescens and T. siculi . Average nucleotide identity scores and in silico DNA-DNA hybridization values between the genome of strain Iri35cT and the genomes of the type species of the genus Thermococcus were below the species delineation threshold. Therefore, and considering the phenotypic data presented, strain Iri35cT is suggested to represent a novel species, for which the name Thermococcus camini sp. nov. is proposed, with the type strain Iri35cT (=UBOCC M-2026T =DSM 111003T ).- Published
- 2021
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36. Thermococcus henrietii sp. nov., a novel extreme thermophilic and piezophilic sulfur-reducing archaeon isolated from a deep-sea hydrothermal chimney.
- Author
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Alain K, Vince E, Courtine D, Maignien L, Zeng X, Shao Z, and Jebbar M
- Subjects
- Base Composition, DNA, Archaeal genetics, Hot Temperature, Nucleic Acid Hybridization, Pacific Ocean, RNA, Ribosomal, 16S genetics, Sequence Analysis, DNA, Sulfur metabolism, Thermococcus isolation & purification, Hydrothermal Vents microbiology, Phylogeny, Seawater microbiology, Thermococcus classification
- Abstract
A novel extreme thermophilic and piezophilic chemoorganoheterotrophic archaeon, strain EXT12c
T , was isolated from a hydrothermal chimney sample collected at a depth of 2496 m at the East Pacific Rise 9° N. Cells were strictly anaerobic, motile cocci. The strain grew at NaCl concentrations ranging from 1 to 5 % (w/v; optimum, 2.0%), from pH 6.0 to 7.5 (optimum, pH 6.5-7.0), at temperatures between 60 and 95 °C (optimum, 80-85 °C), and at pressures from 0.1 to at least 50 MPa (optimum, 30 MPa). Strain EXT12cT grew chemoorganoheterotrophically on complex proteinaceous substrates. Its growth was highly stimulated by the presence of elemental sulphur or l-cystine, which were reduced to hydrogen sulfide. The DNA G+C content was 54.58 mol%. Phylogenetic analyses based on 16S rRNA gene sequences and concatenated ribosomal protein sequences showed that strain EXT12cT falls into the genus Thermococcus and is most closely related to Thermococcus nautili strain 30-1T . Overall genome relatedness index analyses (average nucleotide identity scores and in silico DNA-DNA hybridizations) showed a sufficient genomic distance between the new genome and the ones of the Thermococcus type strains for the delineation of a new species. On the basis of genotypic and phenotypic data, strain EXT12cT is considered to represent a novel species, for which the name Thermococcus henrietii sp. nov. is proposed, with the type strain EXT12cT (=UBOCC M-2417T =DSM 111004T ).- Published
- 2021
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37. Soil Microsite Outweighs Cultivar Genotype Contribution to Brassica Rhizobacterial Community Structure.
- Author
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Klasek SA, Brock MT, Morrison HG, Weinig C, and Maignien L
- Abstract
Microorganisms residing on root surfaces play a central role in plant development and performance and may promote growth in agricultural settings. Studies have started to uncover the environmental parameters and host interactions governing their assembly. However, soil microbial communities are extremely diverse and heterogeneous, showing strong variations over short spatial scales. Here, we quantify the relative effect of meter-scale variation in soil bacterial community composition among adjacent field microsites, to better understand how microbial communities vary by host plant genotype as well as soil microsite heterogeneity. We used bacterial 16S rDNA amplicon sequencing to compare rhizosphere communities from four Brassica rapa cultivars grown in three contiguous field plots (blocks) and evaluated the relative contribution of resident soil communities and host genotypes in determining rhizosphere community structure. We characterize concomitant meter-scale variation in bacterial community structure among soils and rhizospheres and show that this block-scale variability surpasses the influence of host genotype in shaping rhizosphere communities. We identified biomarker amplicon sequence variants (ASVs) associated with bulk soil and rhizosphere habitats, each block, and three of four cultivars. Numbers and percent abundances of block-specific biomarkers in rhizosphere communities far surpassed those from bulk soils. These results highlight the importance of fine-scale variation in the pool of colonizing microorganisms during rhizosphere assembly and demonstrate that microsite variation may constitute a confounding effect while testing biotic and abiotic factors governing rhizosphere community structure., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Klasek, Brock, Morrison, Weinig and Maignien.)
- Published
- 2021
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38. Community-led, integrated, reproducible multi-omics with anvi'o.
- Author
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Eren AM, Kiefl E, Shaiber A, Veseli I, Miller SE, Schechter MS, Fink I, Pan JN, Yousef M, Fogarty EC, Trigodet F, Watson AR, Esen ÖC, Moore RM, Clayssen Q, Lee MD, Kivenson V, Graham ED, Merrill BD, Karkman A, Blankenberg D, Eppley JM, Sjödin A, Scott JJ, Vázquez-Campos X, McKay LJ, McDaniel EA, Stevens SLR, Anderson RE, Fuessel J, Fernandez-Guerra A, Maignien L, Delmont TO, and Willis AD
- Subjects
- Big Data, Genomics methods, Humans, Microbiology, Computational Biology methods, Data Analysis, Software
- Published
- 2021
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39. Isopropanol production from carbon dioxide in Cupriavidus necator in a pressurized bioreactor.
- Author
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Garrigues L, Maignien L, Lombard E, Singh J, and Guillouet SE
- Subjects
- 2-Propanol chemistry, Carbon Dioxide chemistry, Cupriavidus necator metabolism, 2-Propanol metabolism, Bioreactors, Carbon Dioxide metabolism, Cupriavidus necator chemistry
- Abstract
A bioreactor was designed to provide high gas mass transfer to reach cell and product titres in the g L
-1 level from CO2 for realistic, laboratory scale, engineered autotrophic strain evaluation. The design was based on independent CO2 , H2 and air inputs and the ability to operate at high pressures. The bioreactor configuration and cultivation strategy enabled growth of Cupriavidus necator strains for long periods, to reach over 3 g L-1 dry cell weight. No negative impact of the high pressure was observed on viability of the strains up to more than 4 bar overpressure. The cultivation was then carried out using an engineered isopropanol producing strain; in this case, 3.5 g L-1 isopropanol was obtained from CO2 as the sole carbon source. This is the first reported demonstration of a successful production from engineered bacteria of product in the g L-1 range on CO2 , raising the prospect of future development of CO2 -based bioprocesses., (Crown Copyright © 2019. Published by Elsevier B.V. All rights reserved.)- Published
- 2020
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40. The effect of rhizosphere microbes outweighs host plant genetics in reducing insect herbivory.
- Author
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Hubbard CJ, Li B, McMinn R, Brock MT, Maignien L, Ewers BE, Kliebenstein D, and Weinig C
- Subjects
- Animals, Aphids, Brassicaceae chemistry, Brassicaceae genetics, Coleoptera, Metabolome, RNA, Ribosomal, 16S genetics, Secondary Metabolism, Brassicaceae microbiology, Glucosinolates chemistry, Herbivory, Rhizosphere, Soil Microbiology
- Abstract
Rhizosphere microbes affect plant performance, including plant resistance against insect herbivores; yet, a direct comparison of the relative influence of rhizosphere microbes versus plant genetics on herbivory levels and on metabolites related to defence is lacking. In the crucifer Boechera stricta, we tested the effects of rhizosphere microbes and plant population on herbivore resistance, the primary metabolome, and select secondary metabolites. Plant populations differed significantly in the concentrations of six glucosinolates (GLS), secondary metabolites known to provide herbivore resistance in the Brassicaceae. The population with lower GLS levels experienced ~60% higher levels of aphid (Myzus persicae) attack; no association was observed between GLS and damage by a second herbivore, flea beetles (Phyllotreta cruciferae). Rhizosphere microbiome (disrupted vs. intact native microbiome) had no effect on plant GLS concentrations. However, aphid number and flea beetle damage were respectively about three- and seven-fold higher among plants grown in the disrupted versus intact native microbiome treatment. These differences may be attributable to shifts in primary metabolic pathways previously implicated in host defence against herbivores, including increases in pentose and glucoronate interconversion among plants grown with an intact microbiome. Furthermore, native microbiomes with distinct community composition (as estimated from 16s rRNA amplicon sequencing) differed two-fold in their effect on host plant susceptibility to aphids. The findings suggest that rhizosphere microbes, including distinct native microbiomes, can play a greater role than population in defence against insect herbivores, and act through metabolic mechanisms independent of population., (© 2018 John Wiley & Sons Ltd.)
- Published
- 2019
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41. Electroactive Bacteria Associated With Stainless Steel Ennoblement in Seawater.
- Author
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Trigodet F, Larché N, Morrison HG, Jebbar M, Thierry D, and Maignien L
- Abstract
Microorganisms can increase the open-circuit potential of stainless steel immersed in seawater of several hundred millivolts in a phenomenon called ennoblement. It raises the chance of corrosion as the open-circuit potential may go over the pitting corrosion potential. Despite the large impact of the ennoblement, no unifying mechanisms have been described as responsible for the phenomenon. Here we show that the strict electrotroph bacterium " Candidatus Tenderia electrophaga" is detected as an ennoblement biomarker and is only present at temperatures at which we observe ennoblement. This bacterium was previously enriched in biocathode systems. Our results suggest that " Candidatus Tenderia electrophaga," and its previously described extracellular electron transfer metabolism coupled to oxygen reduction activity, could play a central role in modulating stainless steel open-circuit potential and consequently mediating ennoblement.
- Published
- 2019
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42. Microplastic bacterial communities in the Bay of Brest: Influence of polymer type and size.
- Author
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Frère L, Maignien L, Chalopin M, Huvet A, Rinnert E, Morrison H, Kerninon S, Cassone AL, Lambert C, Reveillaud J, and Paul-Pont I
- Subjects
- Bays chemistry, Ecosystem, Polyethylene analysis, Polymers analysis, Polypropylenes analysis, Polystyrenes analysis, Seawater chemistry, Seawater microbiology, Water Microbiology, Bacteria, Environmental Monitoring, Plastics analysis, Water Pollutants, Chemical analysis
- Abstract
Microplastics (<5 mm) exhibit intrinsic features such as density, hydrophobic surface, or high surface/volume ratio, that are known to promote microbial colonization and biofilm formation in marine ecosystems. Yet, a relatively low number of studies have investigated the nature of microplastic associated bacterial communities in coastal ecosystems and the potential factors influencing their composition and structure. Here, we characterized microplastics collected in the Bay of Brest by manual sorting followed by Raman spectroscopy and studied their associated bacterial assemblages using 16S amplicon high-throughput sequencing. Our methodology allowed discriminating polymer type (polyethylene, polypropylene and polystyrene) within small size ranges (0.3-1 vs. 1-2 vs. 2-5 mm) of microplastics collected. Data showed high species richness and diversity on microplastics compared to surrounding seawater samples encompassing both free living and particle attached bacteria. Even though a high proportion of operational taxonomic units (OTU; 94 ± 4%) was shared among all plastic polymers, polystyrene fragments exhibited distinct bacterial assemblages as compared to polyethylene and polypropylene samples. No effect of microplastic size was revealed regardless of polymer type, site and date of collection. The Vibrio genus was commonly detected in the microplastic fraction and specific PCR were performed to determine the presence of potentially pathogenic Vibrio strains (namely V. aestuarianus and the V. splendidus polyphyletic group). V. splendidus related species harboring putative oyster pathogens were detected on most microplastic pools (77%) emphasizing the need of further research to understand the role of microplastics on pathogen population transport and ultimate disease emergence., (Copyright © 2018 Elsevier Ltd. All rights reserved.)
- Published
- 2018
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43. The plant circadian clock influences rhizosphere community structure and function.
- Author
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Hubbard CJ, Brock MT, van Diepen LT, Maignien L, Ewers BE, and Weinig C
- Subjects
- Arabidopsis Proteins metabolism, Ecosystem, Genome, Plant, Genotype, Plant Development, RNA, Ribosomal, 16S genetics, Sequence Analysis, DNA, Soil chemistry, Transcription Factors metabolism, Arabidopsis genetics, Arabidopsis microbiology, Circadian Clocks, Plant Roots microbiology, Rhizosphere, Soil Microbiology
- Abstract
Plants alter chemical and physical properties of soil, and thereby influence rhizosphere microbial community structure. The structure of microbial communities may in turn affect plant performance. Yet, outside of simple systems with pairwise interacting partners, the plant genetic pathways that influence microbial community structure remain largely unknown, as are the performance feedbacks of microbial communities selected by the host plant genotype. We investigated the role of the plant circadian clock in shaping rhizosphere community structure and function. We performed 16S ribosomal RNA gene sequencing to characterize rhizosphere bacterial communities of Arabidopsis thaliana between day and night time points, and tested for differences in community structure between wild-type (Ws) vs clock mutant (toc1-21, ztl-30) genotypes. We then characterized microbial community function, by growing wild-type plants in soils with an overstory history of Ws, toc1-21 or ztl-30 and measuring plant performance. We observed that rhizosphere community structure varied between day and night time points, and clock misfunction significantly altered rhizosphere communities. Finally, wild-type plants germinated earlier and were larger when inoculated with soils having an overstory history of wild-type in comparison with clock mutant genotypes. Our findings suggest the circadian clock of the plant host influences rhizosphere community structure and function.
- Published
- 2018
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44. Complete Genome Sequence of Hyperthermophilic Archaeon Thermococcus sp. EXT12c, Isolated from the East Pacific Rise 9°N.
- Author
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Courtine D, Alain K, Georges M, Bienvenu N, Morrison HG, Eren AM, and Maignien L
- Abstract
We report the genome sequence of Thermococcus sp. EXT12c isolated from a deep-sea hydrothermal vent at the East Pacific Rise 9°N. Microbes in the genus Thermococcus are able to grow anaerobically at high temperature, around neutral pH, and some of them under high hydrostatic pressure., (Copyright © 2017 Courtine et al.)
- Published
- 2017
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45. Draft Genome Sequence of Phaeobacter leonis Type Strain 306, an Alphaproteobacterium Isolated from Mediterranean Sea Sediments.
- Author
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Gaboyer F, Maignien L, Jebbar M, and Alain K
- Abstract
Phaeobacter leonis strain 306
T is an alphaproteobacterium isolated from Mediterranean Sea sediments. It belongs to the genus Phaeobacter , which was recently proposed and is still poorly characterized. In an effort to better understand the fundamental aspects of the microbiology of this genus, we present here the 4.82-Mb draft genome sequence of Phaeobacter leonis strain 306T ., (Copyright © 2017 Gaboyer et al.)- Published
- 2017
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46. Draft Genome of Halomonas lionensis RHS90 T , a Stress-Tolerant Gammaproteobacterium Isolated from Mediterranean Sea Sediments.
- Author
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Gaboyer F, Maignien L, Jebbar M, and Alain K
- Abstract
Members of the genus Halomonas are physiologically versatile and harbor ecological adaptations enabling the colonization of contrasted environments. We present here the draft genome of Halomonas lionensis RHS90
T , isolated from Mediterranean Sea sediments. Numerous genes related to stress tolerance, DNA repair, or external signal-sensing systems were predicted, which could represent selective advantages of this marine bacterium., (Copyright © 2017 Gaboyer et al.)- Published
- 2017
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47. Thermococcus piezophilus sp. nov., a novel hyperthermophilic and piezophilic archaeon with a broad pressure range for growth, isolated from a deepest hydrothermal vent at the Mid-Cayman Rise.
- Author
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Dalmasso C, Oger P, Selva G, Courtine D, L'Haridon S, Garlaschelli A, Roussel E, Miyazaki J, Reveillaud J, Jebbar M, Takai K, Maignien L, and Alain K
- Subjects
- Base Composition genetics, Base Sequence, DNA, Archaeal genetics, Genome, Bacterial genetics, Hot Temperature, Phylogeny, RNA, Ribosomal, 16S genetics, Seawater microbiology, Sequence Analysis, DNA, Thermococcus genetics, Thermococcus isolation & purification, West Indies, Hydrothermal Vents microbiology, Sulfur Compounds metabolism, Thermococcus growth & development, Thermococcus metabolism, Thermotolerance physiology
- Abstract
A novel strictly anaerobic, hyperthermophilic archaeon, designated strain CDGS
T , was isolated from a deep-sea hydrothermal vent in the Cayman Trough at 4964m water depth. The novel isolate is obligate anaerobe and grows chemoorganoheterotrophically with stimulation of growth by sulphur containing compounds. Its growth is optimal at 75°C, pH 6.0 and under a pressure of 50MPa. It possesses the broadest hydrostatic pressure range for growth that has ever been described for a microorganism. Its genomic DNA G+C content is 51.11mol%. The novel isolate belongs to the genus Thermococcus. Phylogenetic analyses indicated that it is most closely related to Thermococcus barossii DSM17882T based on its 16S rRNA gene sequence, and to 'Thermococcus onnurineus' NA1 based on its whole genome sequence. The average nucleotide identity scores with these strains are 77.66% for T. barossii and 84.84% for 'T. onnurineus', respectively. Based on the draft whole genome sequence and phenotypic characteristics, strain CDGST is suggested to be separated into a novel species within the genus Thermococcus, with proposed name Thermococcus piezophilus (type strain CDGST =ATCC TSD-33T =UBOCC 3296T )., (Copyright © 2016 Elsevier GmbH. All rights reserved.)- Published
- 2016
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48. Erratum for Dalmasso et al., Complete Genome Sequence of the Hyperthermophilic and Piezophilic Archaeon Thermococcus piezophilus CDGST, Able To Grow under Extreme Hydrostatic Pressures.
- Author
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Dalmasso C, Oger P, Courtine D, Georges M, Takai K, Maignien L, and Alain K
- Published
- 2016
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49. Editorial: New Insights into Microbial Ecology through Subtle Nucleotide Variation.
- Author
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Eren AM, Sogin ML, and Maignien L
- Published
- 2016
- Full Text
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50. Complete Genome Sequence of the Hyperthermophilic and Piezophilic Archeon Thermococcus piezophilus CDGST, Able To Grow under Extreme Hydrostatic Pressures.
- Author
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Dalmasso C, Oger P, Courtine D, Georges M, Takai K, Maignien L, and Alain K
- Abstract
We report the genome sequence of Thermococcus superprofundus strain CDGS(T), a new piezophilic and hyperthermophilic member of the order Thermococcales isolated from the world's deepest hydrothermal vents, at the Mid-Cayman Rise. The genome is consistent with a heterotrophic, anaerobic, and piezophilic lifestyle., (Copyright © 2016 Dalmasso et al.)
- Published
- 2016
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