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4. Diversity of the holopelagic Sargassum microbiome from the Great Atlantic Sargassum Belt to coastal stranding locations

Author

Theirlynck, T., Mendonça, I.R.W., Engelen, A.H., Bolhuis, H., Collado-Vides, L., van Tussenbroek, B.I., García-Sánchez, M., Zettler, E.R., Muyzer, G., Amaral-Zettler, L., Theirlynck, T., Mendonça, I.R.W., Engelen, A.H., Bolhuis, H., Collado-Vides, L., van Tussenbroek, B.I., García-Sánchez, M., Zettler, E.R., Muyzer, G., and Amaral-Zettler, L.

Abstract

The holopelagic brown macroalgae Sargassum natans and Sargassum fluitans form essential habitats for attached and mobile fauna which contributes to a unique biodiversity in the Atlantic Ocean.However, holopelagic Sargassum natans (genotype I & VIII) and Sargassum fluitans (genotype III) have begun forming large accumulations with subsequent strandings on the western coast of Africa, the Caribbean and northern Brazil, threatening local biodiversity of coastal ecosystems and triggering economic losses. Moreover, stranded masses of holopelagic Sargassum may introduce or facilitate growthof bacteria that are not normally abundant in coastal regions where Sargassum is washing ashore. Hitherto, it is not clear how the holopelagic Sargassum microbiome varies across its growing biogeographic range and what factors drive the microbial composition. We determined the microbiome associated with holopelagic Sargassum from the Great Atlantic Sargassum Belt to coastal stranding sites in Mexico and Florida. We characterized the Sargassum microbiome via amplicon sequencing of the 16S V4 region hypervariable region of the rRNA gene. The microbial community of holopelagic Sargassum was mainly composed of photo(hetero)trophs, organic matter degraders andpotentially pathogenic bacteria from thePseudomonadaceae, Rhodobacteraceae andVibrionaceae. Sargassum genotypes S. natans I, S. natans VIII and S. fluitans III contained similar microbial families, but relative abundances and diversity varied. LEfSEanalyses further indicated biomarker genera that were indicative of Sargassum S. natans I/VIII and S. fluitans III. The holopelagic Sargassum microbiome showed biogeographic patterning with high relative abundances of Vibrio spp., but additional work is required to determine whether that represents health risks i

Published
2023

27. Subcellular view of host-microbiome nutrient exchange in sponges: insights into the ecological success of an early metazoan-microbe symbiosis

Author

Hudspith, M, Rix, L, Achlatis, M, Bougoure, J, Guagliardo, P, Clode, PL, Webster, NS, Muyzer, G, Pernice, M, and de Goeij, JM

Subjects
0602 Ecology, 0605 Microbiology, 1108 Medical Microbiology
Abstract

BackgroundSponges are increasingly recognised as key ecosystem engineers in many aquatic habitats. They play an important role in nutrient cycling due to their unrivalled capacity for processing both dissolved and particulate organic matter (DOM and POM) and the exceptional metabolic repertoire of their diverse and abundant microbial communities. Functional studies determining the role of host and microbiome in organic nutrient uptake and exchange, however, are limited. Therefore, we coupled pulse-chase isotopic tracer techniques with nanoscale secondary ion mass spectrometry (NanoSIMS) to visualise the uptake and translocation of 13C- and 15N-labelled dissolved and particulate organic food at subcellular level in the high microbial abundance sponge Plakortis angulospiculatus and the low microbial abundance sponge Halisarca caerulea.ResultsThe two sponge species showed significant enrichment of DOM- and POM-derived 13C and 15N into their tissue over time. Microbial symbionts were actively involved in the assimilation of DOM, but host filtering cells (choanocytes) appeared to be the primary site of DOM and POM uptake in both sponge species overall, via pinocytosis and phagocytosis, respectively. Translocation of carbon and nitrogen from choanocytes to microbial symbionts occurred over time, irrespective of microbial abundance, reflecting recycling of host waste products by the microbiome.ConclusionsHere, we provide empirical evidence indicating that the prokaryotic communities of a high and a low microbial abundance sponge obtain nutritional benefits from their host-associated lifestyle. The metabolic interaction between the highly efficient filter-feeding host and its microbial symbionts likely provides a competitive advantage to the sponge holobiont in the oligotrophic environments in which they thrive, by retaining and recycling limiting nutrients. Sponges present a unique model to link nutritional symbiotic interactions to holobiont function, and, via cascading effects, ecosystem functioning, in one of the earliest metazoan-microbe symbioses. Video abstract.

Published
2020

28. A genomic catalog of Earth’s microbiomes

Author

Nayfach, S., Roux, S., Seshadri, R., Udwary, D., Varghese, N., Schulz, F., Wu, D., Paez-Espino, D., Chen, I., Huntemann, M., Palaniappan, K., Ladau, J., Mukherjee, S., Reddy, T., Nielsen, T., Kirton, E., Faria, J., Edirisinghe, J., Henry, C., Jungbluth, S., Chivian, D., Dehal, P., Wood-Charlson, E., Arkin, A., Tringe, S., Visel, A., Abreu, H., Acinas, S., Allen, E., Allen, M., Alteio, L., Andersen, G., Anesio, A., Attwood, G., Avila-Magaña, V., Badis, Y., Bailey, J., Baker, B., Baldrian, P., Barton, H., Beck, D., Becraft, E., Beller, H., Beman, J., Bernier-Latmani, R., Berry, T., Bertagnolli, A., Bertilsson, S., Bhatnagar, J., Bird, J., Blanchard, J., Blumer-Schuette, S., Bohannan, B., Borton, M., Brady, A., Brawley, S., Brodie, J., Brown, S., Brum, J., Brune, A., Bryant, D., Buchan, A., Buckley, D., Buongiorno, J., Cadillo-Quiroz, H., Caffrey, S., Campbell, A., Campbell, B., Carr, S., Carroll, J., Cary, S., Cates, A., Cattolico, R., Cavicchioli, R., Chistoserdova, L., Coleman, M., Constant, P., Conway, J., Mac Cormack, W., Crowe, S., Crump, B., Currie, C., Daly, R., DeAngelis, K., Denef, V., Denman, S., Desta, A., Dionisi, H., Dodsworth, J., Dombrowski, N., Donohue, T., Dopson, M., Driscoll, T., Dunfield, P., Dupont, C., Dynarski, K., Edgcomb, V., Edwards, E., Elshahed, M., Figueroa, I., Flood, B., Fortney, N., Fortunato, C., Francis, C., Gachon, C., Garcia, S., Gazitua, M., Gentry, T., Gerwick, L., Gharechahi, J., Girguis, P., Gladden, J., Gradoville, M., Grasby, S., Gravuer, K., Grettenberger, C., Gruninger, R., Guo, J., Habteselassie, M., Hallam, S., Hatzenpichler, R., Hausmann, B., Hazen, T., Hedlund, B., Henny, C., Herfort, L., Hernandez, M., Hershey, O., Hess, M., Hollister, E., Hug, L., Hunt, D., Jansson, J., Jarett, J., Kadnikov, V., Kelly, C., Kelly, R., Kelly, W., Kerfeld, C., Kimbrel, J., Klassen, J., Konstantinidis, K., Lee, L., Li, W., Loder, A., Loy, A., Lozada, M., MacGregor, B., Magnabosco, C., Maria da Silva, A., McKay, R., McMahon, K., McSweeney, C., Medina, M., Meredith, L., Mizzi, J., Mock, T., Momper, L., Moran, M., Morgan-Lang, C., Moser, D., Muyzer, G., Myrold, D., Nash, M., Nesbø, C., Neumann, A., Neumann, R., Noguera, D., Northen, T., Norton, J., Nowinski, B., Nüsslein, K., O’Malley, M., Oliveira, R., Maia de Oliveira, V., Onstott, T., Osvatic, J., Ouyang, Y., Pachiadaki, M., Parnell, J., Partida-Martinez, L., Peay, K., Pelletier, D., Peng, X., Pester, M., Pett-Ridge, J., Peura, S., Pjevac, P., Plominsky, A., Poehlein, A., Pope, P., Ravin, N., Redmond, M., Reiss, R., Rich, V., Rinke, C., Rodrigues, J., Rodriguez-Reillo, W., Rossmassler, K., Sackett, J., Salekdeh, G., Saleska, S., Scarborough, M., Schachtman, D., Schadt, C., Schrenk, M., Sczyrba, A., Sengupta, A., Setubal, J., Shade, A., Sharp, C., Sherman, D., Shubenkova, O., Sierra-Garcia, I., Simister, R., Simon, H., Sjöling, S., Slonczewski, J., Correa de Souza, R., Spear, J., Stegen, J., Stepanauskas, R., Stewart, F., Suen, G., Sullivan, M., Sumner, D., Swan, B., Swingley, W., Tarn, J., Taylor, G., Teeling, H., Tekere, M., Teske, A., Thomas, T., Thrash, C., Tiedje, J., Ting, C., Tully, B., Tyson, G., Ulloa, O., Valentine, D., Van Goethem, M., VanderGheynst, J., Verbeke, T., Vollmers, J., Vuillemin, A., Waldo, N., Walsh, D., Weimer, B., Whitman, T., van der Wielen, P., Wilkins, M., Williams, T., Woodcroft, B., Woolet, J., Wrighton, K., Ye, J., Young, E., Youssef, N., Yu, F., Zemskaya, T., Ziels, R., Woyke, T., Mouncey, N., Ivanova, N., Kyrpides, N., Eloe-Fadrosh, E., Consortium, I., and Agencia Estatal de Investigación (España)

Subjects
Resource, Life sciences, biology, Biomedical Engineering, FILOGENIA, Bioengineering, Genomics, Biology, Microbiology, Applied Microbiology and Biotechnology, Genome, purl.org/becyt/ford/1 [https], 03 medical and health sciences, ddc:570, EARTH MICROBIOME PROJECT, Microbiome, purl.org/becyt/ford/1.6 [https], 030304 developmental biology, 2. Zero hunger, 0303 health sciences, 030306 microbiology, Phylum, 15. Life on land, biology.organism_classification, Computational biology and bioinformatics, Phylogenetic diversity, Evolutionary biology, Earth Microbiome Project, Molecular Medicine, Evolutionary ecology, MAGS, GENOMICS, Biotechnology, Archaea, MICROBIAL DIVERSITY
Abstract

13 pages, 5 figures, supplementary information https://doi.org/10.1038/s41587-020-0718-6.-- Data availability: All available metagenomic data, bins and annotations are available through the IMG/M portal (https://img.jgi.doe.gov/). Bulk download for the 52,515 MAGs is available at https://genome.jgi.doe.gov/GEMs and https://portal.nersc.gov/GEM. Genome-scale metabolic models for the nonredundant, high-quality GEMs are summarized at https://doi.org/10.25982/53247.64/1670777 and available in KBase (https://narrative.kbase.us/#org/jgimags). IMG/M identifiers of all metagenomes binned, including detailed information for each metagenome, are available in Supplementary Table 1.-- The pipeline used to generate the metagenome bins is available at https://bitbucket.org/berkeleylab/metabat/src/master/, Publisher Correction: A genomic catalog of Earth’s microbiomes; Nature Biotechnology 39: 520 (2021); https://doi.org/10.1038/s41587-020-00769-4, The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled insights into the ecology and evolution of environmental and host-associated microbiomes. Here we applied this approach to >10,000 metagenomes collected from diverse habitats covering all of Earth’s continents and oceans, including metagenomes from human and animal hosts, engineered environments, and natural and agricultural soils, to capture extant microbial, metabolic and functional potential. This comprehensive catalog includes 52,515 metagenome-assembled genomes representing 12,556 novel candidate species-level operational taxonomic units spanning 135 phyla. The catalog expands the known phylogenetic diversity of bacteria and archaea by 44% and is broadly available for streamlined comparative analyses, interactive exploration, metabolic modeling and bulk download. We demonstrate the utility of this collection for understanding secondary-metabolite biosynthetic potential and for resolving thousands of new host linkages to uncultivated viruses. This resource underscores the value of genome-centric approaches for revealing genomic properties of uncultivated microorganisms that affect ecosystem processes, This work was conducted by the US DOE Joint Genome Institute, a DOE Office of Science User Facility (contract no. DE-AC02–05CH11231), and used resources of the National Energy Research Scientific Computing Center, which is supported by the Office of Science of the US DOE (contract no. DE-AC02–05CH11231). This work was also supported as part of the Genomic Sciences Program DOE Systems Biology KBase (award nos. DE-AC02-05CH11231, DE-AC02-06CH11357, DE-AC05-00OR22725, and DE-AC02-98CH10886).-- With the funding support of the ‘Severo Ochoa Centre of Excelle

Published
2020

29. Molecular and physiological adaptations to low temperature in Thioalkalivibrio strains isolated from soda lakes with different temperature regimes

Author

Ahn, A.-C., Jongepier, E., Schuurmans, J.M., Rijpstra, W.I.C., Sinninghe Damsté, J.S, Galinski, E.A., Roman, P., Sorokin, D.Y., Muyzer, G., Ahn, A.-C., Jongepier, E., Schuurmans, J.M., Rijpstra, W.I.C., Sinninghe Damsté, J.S, Galinski, E.A., Roman, P., Sorokin, D.Y., and Muyzer, G.

Abstract

The genus Thioalkalivibrio comprises sulfur-oxidizing bacteria thriving in soda lakes at high pH and salinity. Depending on the geographical location and the season, these lakes can strongly vary in temperature. To obtain a comprehensive understanding of the molecular and physiological adaptations to low temperature, we compared the responses of two Thioalkalivibrio strains to low (10°C) and high (30°C) temperatures. For this, the strains were grown under controlled conditions in chemostats and analyzed for their gene expression (RNA sequencing [RNA-Seq]), membrane lipid composition, and glycine betaine content. The strain Thioalkalivibrio versutus AL2T originated from a soda lake in southeast Siberia that is exposed to strong seasonaltemperature differences, including freezing winters, whereas Thioalkalivibrio nitratis ALJ2 was isolated from an East African Rift Valley soda lake with a constant warm temperature the year round. The strain AL2T grew faster than ALJ2 at 10°C, likely due to its 3-fold-higher concentration of the osmolyte glycine betaine. Moreover, significant changes in the membrane lipid composition were observed for both strains, leading to an increase in their unsaturated fatty acid content via the Fab pathway to avoid membrane stiffness. Genes for the transcriptional and translational machinery, as well as for counteracting cold-induced hampering of nucleotides and proteins, were upregulated. Oxidative stress was reduced by induction of vitamin B12 biosynthesis genes, and growth at 10°C provoked downregulation of genes involved in the second half of the sulfur oxidation pathway. Genes for intracellular signal transduction were differentially expressed, and interestingly, AL2T upregulated flagellin expression, whereas ALJ2 downregulated it.

Published
2021

30. Resilience of microbial communities after hydrogen peroxide treatment of a eutrophic lake to suppress harmful cyanobacterial blooms

Author

Piel, T., Sandrini, G., Muyzer, G., Brussaard, C.P.D., Slot, P.C., van Herk, M.J., Huisman, J., Visser, P.M., Piel, T., Sandrini, G., Muyzer, G., Brussaard, C.P.D., Slot, P.C., van Herk, M.J., Huisman, J., and Visser, P.M.

Abstract

Applying low concentrations of hydrogen peroxide (H2O 2) to lakes is an emerging method to mitigate harmfulcyanobacterial blooms. While cyanobacteria are very sensitive to H2O2, little is known about the impacts of these H 2O2 treatments on other members of the microbial community. In this study, we investigated changes in microbial community composition during two lake treatments with low H2O2 concentrations (target: 2.5 mg L−1) and in two series ofcontrolled lake incubations. The results show that the H2O2 treatments effectively suppressed the dominant cyanobacteria Aphanizomenon klebahnii, Dolichospermum sp. and, to a lesser extent, Planktothrix agardhii. Microbial community analysis revealed that several Proteobacteria (e.g., Alteromonadales, Pseudomonadales, Rhodobacterales) profited from the treatments, whereas some bacterial taxa declined (e.g., Verrucomicrobia). In particular, the taxa known to be resistant to oxidative stress (e.g., Rheinheimera) strongly increased in relative abundance during the first 24 h after H 2O2 addition, but subsequently declined again. Alpha and beta diversity showed a temporary decline but recovered within a few days, demonstrating resilience of the microbial community. The predicted functionality of the microbial community revealed a temporary increase of anti-ROS defenses and glycoside hydrolases but otherwise remained stable throughout the treatments. We conclude that the use of low concentrations of H2O2 to suppress cyanobacterial blooms provides a short-term pulse disturbance but is not detrimental to lake microbial communities and their ecosystem functioning.

Published
2021

31. Subcellular view of host-microbiome nutrient exchange in sponges: insights into the ecological success of an early metazoan-microbe symbiosis.

Author

Hudspith, M, Rix, L, Achlatis, M, Bougoure, J, Guagliardo, P, Clode, PL, Webster, NS, Muyzer, G, Pernice, M, de Goeij, JM, Hudspith, M, Rix, L, Achlatis, M, Bougoure, J, Guagliardo, P, Clode, PL, Webster, NS, Muyzer, G, Pernice, M, and de Goeij, JM

Abstract

Background

Sponges are increasingly recognised as key ecosystem engineers in many aquatic habitats. They play an important role in nutrient cycling due to their unrivalled capacity for processing both dissolved and particulate organic matter (DOM and POM) and the exceptional metabolic repertoire of their diverse and abundant microbial communities. Functional studies determining the role of host and microbiome in organic nutrient uptake and exchange, however, are limited. Therefore, we coupled pulse-chase isotopic tracer techniques with nanoscale secondary ion mass spectrometry (NanoSIMS) to visualise the uptake and translocation of 13C- and 15N-labelled dissolved and particulate organic food at subcellular level in the high microbial abundance sponge Plakortis angulospiculatus and the low microbial abundance sponge Halisarca caerulea.

Results

The two sponge species showed significant enrichment of DOM- and POM-derived 13C and 15N into their tissue over time. Microbial symbionts were actively involved in the assimilation of DOM, but host filtering cells (choanocytes) appeared to be the primary site of DOM and POM uptake in both sponge species overall, via pinocytosis and phagocytosis, respectively. Translocation of carbon and nitrogen from choanocytes to microbial symbionts occurred over time, irrespective of microbial abundance, reflecting recycling of host waste products by the microbiome.

Conclusions

Here, we provide empirical evidence indicating that the prokaryotic communities of a high and a low microbial abundance sponge obtain nutritional benefits from their host-associated lifestyle. The metabolic interaction between the highly efficient filter-feeding host and its microbial symbionts likely provides a competitive advantage to the sponge holobiont in the oligotrophic environments in which they thrive, by retaining and recycling limiting nutrients. Sponges present a unique model to link nutriti

Published
2021

32. Anaerobic growth of the haloalkaliphilic denitrifying sulfur-oxidizing bacterium Thialkalivibrio thiocyanodenitrificans sp. nov. with thiocyanate

Author

Sorokin, Dimitry Yu., Tourova, Tat'yana P., Antipov, Alexey N., Muyzer, G., and Kuenen, J. Gijs

Subjects
Thiocyanates -- Research, Sulfur bacteria -- Research, Biological sciences
Abstract

Two strains of obligate chemolithoautotrophic sulfur-oxidizing bacteria were isolated from soda-lake sediments by enrichment culture with thiocyanate and nitrate at pH 9.9. The isolates were capable of growth with thiocyanate or thiosulfate as electron donor, either aerobically or anaerobically, and with nitrate or nitrite as electron acceptor. Cyanate was identified as an intermediate of thiocyanate oxidation, while sulfate, ammonia and dinitrogen gas were the final products. The anaerobic growth on thiocyanate plus nitrate was much slower ([[micro].sub.max] = 0.006 [h.sup.-1]) than on thiosulfate plus nitrate ([[micro].sub.max] = 0.02 [h.sup.-1]), while growth yields were similar (4.8 and 5.1 g protein [mol.sup.-1], respectively). On the basis of their phenotypic and genetic properties, strains ARhD [1.sup.T] and ARhD 2 are described as a novel species of the genus Thialkalivibrio, with the highest similarity to Thialkalivibrio denitrificans. The name Thialkalivibrio thiocyanodenitrificans sp. nov. is proposed for this novel species.

Published
2004

35. Diveristy of thiosulfate-oxidizing bacteria from marine sediments and hydrothermal vents

Author

Teske, A., Brinkhoff, T., Muyzer, G., Moser, D.P., Rethmeier, J., and Jannasch, H.W.

Subjects
Marine bacteria -- Research, Hydrothermal vent ecology -- Research, Biological sciences
Abstract

Thiosulfate-oxidizing bacteria from deep-sea sediments off the coast of New England are related to Antarctic marine Psychroflexus species, cold-water marine strains of the Cytophaga-Flavobacterium-Bacteroides phylum, and to the genera Pseudoalteromonas and Halomonas-Deleya.

Published
2000

38. Stromatolites as biosignatures of atmospheric oxygenation: Carbonate biomineralization and UV-C resilience in a Geitlerinema sp. - dominated culture

Author

Popall, R.M., Bolhuis, H., Muyzer, G., Sánchez-Román, M., Popall, R.M., Bolhuis, H., Muyzer, G., and Sánchez-Román, M.

Abstract

Modern stromatolites are key to the record of past microbial activity preserved in fossil carbonate deposits. Mono-phototrophic cultures dominated by the cyanobacterium Geitlerinema sp. were obtained from a laboratory-maintained, low magnesium-calcite stromatolite originating from Lagoa Vermelha, Brazil. This lagoonal system has been described as a Precambrian analog, illustrating a period of photosynthetically induced atmospheric oxygenation, which created a global sanctuary from shortwave solar radiation and enabled the evolution of modern life on Earth. The enrichment cultures precipitate carbonates in minimal media, suggesting that cyanobacterial photosynthesis and extracellular polymeric substance production may be crucial in the mineralization of the studied stromatolite. We further show that Geitlerinema sp. can build and maintain filamentous mats under long-term UV-C exposure. Our results suggest that present day stromatolites dominated by cyanobacteria may be interpreted as biosignatures of atmospheric oxygenation and have implications for the search for putative biological traces on Mars.

Published
2020

39. Denaturing gradient gel electrophoresis profiles of 16S rRNA-defined populations inhabiting a hot spring microbial mat community

Author

Ferris, M.J., Muyzer, G., and Ward, D.M.

Subjects
Gel electrophoresis -- Usage, Cyanobacteria -- Observations, Biological sciences
Abstract

Denaturing gradient gel electrophoresis (DGGE) of 16S rRNA gene segments is an efficient method for determining the distribution of different microbes in the hot Octopus springs of the Yellowstone National Park. The DGGE method rapidly tests the amplified sequences. The sequencing of DGGE bands allows the simultaneous detection of many microbial mat populations. The results compare well with the oligonucleotide probe analysis. The cyanobacteria, which are phenotypically similar, adapt to different temperatures in the hot springs.

Published
1996

40. Exploring biodiversity and arsenic metabolism of microbiota inhabiting arsenic-rich groundwaters in Northern Italy

Author

Cavalca, L, Zecchin, S, Zaccheo, P, Abbas, B, Rotiroti, M, Bonomi, T, Muyzer, G, Abbas, BA, Cavalca, L, Zecchin, S, Zaccheo, P, Abbas, B, Rotiroti, M, Bonomi, T, Muyzer, G, and Abbas, BA

Abstract

Arsenic contamination of groundwater aquifers is an issue of global concern. Among the affected sites, in several Italian groundwater aquifers arsenic levels above the WHO limits for drinking water are present, with consequent issues of public concern. In this study, for the first time, the role of microbial communities in metalloid cycling in groundwater samples from Northern Italy lying on Pleistocene sediments deriving from Alps mountains has been investigated combining environmental genomics and cultivation approaches. 16S rRNA gene libraries revealed a high number of yet uncultured species, which in some of the study sites accounted for more of the 50% of the total community. Sequences related to arsenic-resistant bacteria (arsenate-reducing and arsenite-oxidizing) were abundant in most of the sites, while arsenate-respiring bacteria were negligible. In some of the sites, sulfur-oxidizing bacteria of the genus Sulfuricurvum accounted for more than 50% of the microbial community, whereas iron-cycling bacteria were less represented. In some aquifers, arsenotrophy, growth coupled to autotrophic arsenite oxidation, was suggested by detection of arsenite monooxygenase (aioA) and 1,5-ribulose bisphosphate carboxylase (RuBisCO) cbbL genes of microorganisms belonging to Rhizobiales and Burkholderiales. Enrichment cultures established from sampled groundwaters in laboratory conditions with 1.5 mmol L-1 of arsenite as sole electron donor were able to oxidize up to 100% of arsenite, suggesting that this metabolism is active in groundwaters. The presence of heterotrophic arsenic resistant bacteria was confirmed by enrichment cultures in most of the sites. The overall results provided a first overview of the microorganisms inhabiting arsenic-contaminated aquifers in Northern Italy and suggested the importance of sulfur-cycling bacteria in the biogeochemistry of arsenic in these ecosystems. The presence of active arsenite-oxidizing bacteria indicates that biological oxidatio

Published
2019

41. Unraveling seaweeds bacteriomes: From field site to computer screen

Author

Aires, T., Muyzer, G., Serrão, E.A., Engelen, A.H., Charrier, B., Wichard, T., Reddy, C.R.K., and Freshwater and Marine Ecology (IBED, FNWI)

Abstract

The study of seaweeds with their associated microbiomes (the holobiome) has been growing and emerging as a necessary tool to study evolution, adaptation, development, and global function of the seaweed hosts, and possible applications of this knowledge to modulate their morphogenesis, growth, health, and defense. Here, we describe the materials and methods, from field sampling to data analysis, to unravel the structure, diversity, and the predicted function (as a starting point to further functional studies) of bacterial communities associated to seaweeds.

Published
2018

42. Syntrophic acetate oxidation at haloalkaline conditions

Author

Timmers, Peer H. A., Vavourakis, C., Muyzer, G., Sorokin, D., Stams, Alfons Johannes Maria, Plugge, Caroline M., and Universidade do Minho

Subjects
education, reproductive and urinary physiology, health care economics and organizations, humanities
Abstract

Microbiology Centennial Symposium 2017 - Exploring Microbes for the Quality of Life (Book of Abstracts), Syntrophic acetate oxidation (SAO) is a process where syntrophic acetate-oxidizing bacteria (SAOB) convert acetate to form CO2 and reducing equivalents. These reducing equivalents are utilized by a syntrophic partner which in most cases is a hydrogenotrophic methanogen or sulfate-reducing bacterium. Until now, SAO has been found to be dominant over aceticlastic methanogenesis under extreme conditions such as high ammonia or high fatty acid concentrations and high temperatures. Here, we investigated the pathway of acetate utilization and the mechanism of SAO in haloalkaline soda lakes that have extremely high soda concentrations and pH. Enrichment cultures of SAOB together with a methanogenic (M-SAO) or sulfate-reducing (S-SAO) syntrophic partner showed that hydrogen is an important interspecies electron carrier. Metagenome analysis of the M-SAO enrichment culture showed that Candidatus Syntrophonatronum acetioxidans is the dominant SAOB, and its genome contained all genes necessary for operating the Wood Ljungdahl pathway in reverse. The genome contained an F1F0 ATP synthase that uses a proton motive force (pmf), but it also contained an energy conserving hydrogenase (Ehb) that pumps out Na+ instead of H+ while consuming intracellular H+ to form H2. This simultaneously generates a pmf while pumping out Na+, which is probably an adaptation to the high Na+ concentrations in soda lakes. Highthroughput 16S rRNA gene sequencing results of five different soda lake sediments showed that Candidatus Syntrophonatronum acetioxidans related sequences were up to 1.3% of all reads and the overarching Syntrophomonadaceae family was highly abundant (up to 24.5% of total reads). Known aceticlastic methanogenic genera were mostly absent. These results show that SAO, and syntrophy in general, is an important process in soda lakes which is probably a result of the extreme haloalkaline conditions., info:eu-repo/semantics/publishedVersion

Published
2017

43. Draft genome sequence of Dethiobacter alkaliphilus strain AHT1T, a gram-positive sulfidogenic polyextremophile

Author

Melton, ED, Sorokin, DY, Overmars, L, Lapidus, AL, Pillay, M, Ivanova, N, del Rio, TG, Kyrpides, NC, Woyke, T, and Muyzer, G

Abstract

© 2017 The Author(s). Dethiobacter alkaliphilus strain AHT1Tis an anaerobic, sulfidogenic, moderately salt-tolerant alkaliphilic chemolithotroph isolated from hypersaline soda lake sediments in northeastern Mongolia. It is a Gram-positive bacterium with low GC content, within the phylum Firmicutes. Here we report its draft genome sequence, which consists of 34 contigs with a total sequence length of 3.12 Mbp. D. alkaliphilus strain AHT1Twas sequenced by the Joint Genome Institute (JGI) as part of the Community Science Program due to its relevance to bioremediation and biotechnological applications.

Published
2017
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45. Comparison of a new Thiomicrospira strain from the Mid-Atlantic ridge with known hydrothermal vent isolates

Author

Wirsen, C.O., Brinkhoff, T., Kuever, J., Muyzer, G., Molyneaux, S., and Jannasch, H.W.

Subjects
Sulfides -- Research, DNA -- Research, Bacteria -- Research, Biological sciences
Abstract

A study was conducted to analyze the isolation of a novel autotrophic Thiomicrospira strain from the surface of a polymetal sulfide deposit determined at a Mid-Atlantic hydrothermal vent site. The survival of pregrown cells of the strain were examined against different concentrations of Fe2+ at near-neutral pH under anoxic environments. Experimental results indicated a cosmopolitan distribution of the species.

Published
1998

46. Metabolism and occurrence of methanogenic and sulfate-reducing syntrophic acetate oxidizing communities in haloalkaline environments

Author

Timmers, P.H.A., Vavourakis, C.D., Kleerebezem, R., Sinninghe Damsté, J.S, Muyzer, G., Stams, A.J.M., Sorokin, D.Y., Plugge, C.M., Timmers, P.H.A., Vavourakis, C.D., Kleerebezem, R., Sinninghe Damsté, J.S, Muyzer, G., Stams, A.J.M., Sorokin, D.Y., and Plugge, C.M.

Abstract

Anaerobic syntrophic acetate oxidation (SAO) is a thermodynamically unfavorable process involving a syntrophic acetate oxidizing bacterium (SAOB) that forms interspecies electron carriers (IECs). These IECs are consumed by syntrophic partners, typically hydrogenotrophic methanogenic archaea or sulfate reducing bacteria. In this work, the metabolism and occurrence of SAOB at extremely haloalkaline conditions were investigated, using highly enriched methanogenic (M-SAO) and sulfate-reducing (S-SAO) cultures from south-western Siberian hypersaline soda lakes. Activity tests with the M-SAO and S-SAO cultures and thermodynamic calculations indicated that H2 and formate are important IECs in both SAO cultures. Metagenomic analysis of the M-SAO cultures showed that the dominant SAOB was ‘Candidatus Syntrophonatronum acetioxidans,’ and a near-complete draft genome of this SAOB was reconstructed. ‘Ca. S. acetioxidans’ has all genes necessary for operating the Wood–Ljungdahl pathway, which is likely employed for acetate oxidation. It also encodes several genes essential to thrive at haloalkaline conditions; including a Na+-dependent ATP synthase and marker genes for ‘salt-out‘ strategies for osmotic homeostasis at high soda conditions. Membrane lipid analysis of the M-SAO culture showed the presence of unusual bacterial diether membrane lipids which are presumably beneficial at extreme haloalkaline conditions. To determine the importance of SAO in haloalkaline environments, previously obtained 16S rRNA gene sequencing data and metagenomic data of five different hypersaline soda lake sediment samples were investigated, including the soda lakes where the enrichment cultures originated from. The draft genome of ‘Ca. S. acetioxidans’ showed highest identity with two metagenome-assembled genomes (MAGs) of putative SAOBs that belonged to the highly abundant and diverse Syntrophomonadaceae family present in the soda lake sediments. The 16S rRNA ge

Published
2018

47. Complete genome sequence of Thioalkalivibrio paradoxus type strain ARh 1T, an obligately chemolithoautotrophic haloalkaliphilic sulfur-oxidizing bacterium isolated from a Kenyan soda lake

Author

Berben, T, Sorokin, DY, Ivanova, N, Pati, A, Kyrpides, N, Goodwin, LA, Woyke, T, and Muyzer, G

Abstract

© 2015 Berben et al. Thioalkalivibrio paradoxus strain ARh 1Tis a chemolithoautotrophic, non-motile, Gram-negative bacterium belonging to the Gammaproteobacteria that was isolated from samples of haloalkaline soda lakes. It derives energy from the oxidation of reduced sulfur compounds and is notable for its ability to grow on thiocyanate as its sole source of electrons, sulfur and nitrogen. The full genome consists of 3,756,729 bp and comprises 3,500 protein-coding and 57 RNA-coding genes. This organism was sequenced as part of the community science program at the DOE Joint Genome Institute.

Published
2015
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48. Partial genome sequence of the haloalkaliphilic soda lake bacterium Thioalkalivibrio thiocyanoxidans ARh 2T

Author

Berben, T, Sorokin, DY, Ivanova, N, Pati, A, Kyrpides, N, Goodwin, LA, Woyke, T, and Muyzer, G

Abstract

© 2015 Berben et al. Thioalkalivibrio thiocyanoxidans strain ARh 2Tis a sulfur-oxidizing bacterium isolated from haloalkaline soda lakes. It is a motile, Gram-negative member of the Gammaproteobacteria. Remarkable properties include the ability to grow on thiocyanate as the sole energy, sulfur and nitrogen source, and the capability of growth at salinities of up to 4.3 M total Na+. This draft genome sequence consists of 61 scaffolds comprising 2,765,337 bp, and contains 2616 protein-coding and 61 RNA-coding genes. This organism was sequenced as part of the Community Science Program of the DOE Joint Genome Institute.

Published
2015
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49. Etude des interactions Microorganismes-métaux dans des sédiments marins et estuariens

Author

Quillet, L., Besaury, Ludovic, Ouddane, B., Buquet, S., Mesnage, V., De La Iglesia, R., Marty, F., Muyzer, G., Ghiglione, J. F., Laboratoire de Microbiologie Signaux et Microenvironnement (LMSM), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU), Morphodynamique Continentale et Côtière (M2C), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Avancé de Spectroscopie pour les Intéractions la Réactivité et l'Environnement - UMR 8516 (LASIRE), Institut de Chimie du CNRS (INC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Centrale Lille Institut (CLIL), Centro de Investigación Oceanográfica en el Pacífico Sur Oriental (COPAS), Universidad de Concepción [Chile], Department of Biotechnology, Delft University of Technology, Delft University of Technology (TU Delft), Laboratoire d'océanographie biologique de Banyuls (LOBB), Observatoire océanologique de Banyuls (OOB), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut de Chimie du CNRS (INC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), and Universidad de Concepción - University of Concepcion [Chile]

Subjects
[CHIM.ANAL]Chemical Sciences/Analytical chemistry, [SDU.STU.GC]Sciences of the Universe [physics]/Earth Sciences/Geochemistry, [SDU.ENVI]Sciences of the Universe [physics]/Continental interfaces, environment
Published
2015

50. Divergent members of the bacterial division Verrucomicrobiales in a temperate freshwater lake

Author

Zwart, G., Huismans, R., Agterveld, Mp, Yves Van de Peer, Rijk, P., Eenhoorn, H., Muyzer, G., Hannen, Ej, Gons, Hj, Laanbroek, Hj, Microbial Wetland Ecology (MWE), and Centre for Limnology (NIOO / CL)

Subjects
Freshwater pelagic zone, Verrucomicrobium, Bacterial diversity, Ecology, Denaturing gradient gel electrophoresis, Prosthecobacter, 16S rRNA, Biologie, Applied Microbiology and Biotechnology, Microbiology, Phylogeny
Abstract

Bacterial diversity in the water column of a freshwater lake in the Netherlands was investigated by analysis of 16S rRNA gene sequences recovered through PCR amplification from total community DNA. Among 23 unique cloned sequences, two appeared to belong to the recently described bacterial division Verrucomicrobiales. One of the two sequences was most similar to a group of environmental clones that form a distinct lineage within the division. The other sequence was divergent (less than 85% similarity) from all 16S rRNA gene sequences, both from cultivated species and from environmental clones, known in this division to date. Analysis by denaturing gradient gel electrophoresis (DGGE) and sequencing of DNA recovered through excision from the DGGE gel showed that the two sequence types were present in the lake throughout the year. [KEYWORDS: bacterial diversity; freshwater pelagic zone; denaturing gradient gel electrophoresis; phylogeny; 16S rRNA;Verrucomicrobium; Prosthecobacter 16s ribosomal-rna; polymerase chain-reaction; gene amplification; pcr; sequences; community; diversity; alignment; tool]

Published
1998
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