A critical role of heterotrophic bacteria in early diagenesis of carbonates through exopolymer degradation and calcium release

Abstract. Extracellular polymeric substances (EPSs) are an important organic carbon reservoir in many pelagic and benthic environments. The production of EPS is intimately associated with the growth of phyto- and picoplankton. EPS plays a critical role in carbonate precipitation through the binding of cations and by acting as a nucleation site for minerals. Large-scale episodes of fine-grained calcium carbonate precipitation in the water column (whiting events) have been linked to cyanobacterial blooms, including of Synechococcus spp. The mechanisms that trigger these precipitation events are still debated. We pose that the cyanobacterial EPS, produced during exponential and stationary growth phases, plays a critical role in the formation of whitings. The aim of this study was to investigate the production of EPS during a 2-month cyanobacterial growth, mimicking a bloom. The production and characteristics of EPS were examined in different growth stages of Synechococcus spp. using various techniques such as Fourier transform infrared (FT-IR) spectroscopy as well as colorimetric and sodium dodecyl sulfate–polyacrylamide gel electrophoresis (SDS–PAGE) assays. We further evaluated the potential role of EPS in carbonate precipitation through in vitro-forced precipitation experiments. EPS produced during the early and late stationary phase contained a larger amount of negatively charged groups than present in EPS produced during the exponential phase. Consequently, a higher Ca2+-binding affinity of the stationary-phase EPS led to the formation of a larger amount of smaller carbonate minerals (< 50 µm) compared to crystals formed in exponential-phase EPS, which were less abundant and larger (> 50 µm). These findings were used to establish a conceptual model for picoplankton-bloom-mediated CaCO3 precipitation that can explain the role of EPS in whitings.

Exopolymeric substances (EPS) can determine plant-microorganism interactions and have great potential as bioactive compounds. The different amounts of EPS obtained from cultures of three endophytic Fusarium culmorum strains with different aggressiveness—growth promoting (PGPF), deleterious (DRMO), and pathogenic towards cereal plants—depended on growth conditions. The EPS concentrations (under optimized culture conditions) were the lowest (0.2 g/L) in the PGPF, about three times higher in the DRMO, and five times higher in the pathogen culture. The EPS of these strains differed in the content of proteins, phenolic components, total sugars, glycosidic linkages, and sugar composition (glucose, mannose, galactose, and smaller quantities of arabinose, galactosamine, and glucosamine). The pathogen EPS exhibited the highest total sugar and mannose concentration. FTIR analysis confirmed the β configuration of the sugars. The EPS differed in the number and weight of polysaccharidic subfractions. The EPS of PGPF and DRMO had two subfractions and the pathogen EPS exhibited a subfraction with the lowest weight (5 kDa). The three EPS preparations (ethanol-precipitated EP, crude C, and proteolysed P) had antioxidant activity (particularly high for the EP-EPS soluble in high concentrations). The EP-EPS of the PGPF strain had the highest antioxidant activity, most likely associated with the highest content of phenolic compounds in this EPS.

ABSTRACTSulfate‐reducing bacteria (SRB) have been recognized as key players in the precipitation of calcium carbonate in lithifying microbial communities. These bacteria increase the alkalinity by reducing sulfate ions, and consuming organic acids. SRB also produce copious amounts of exopolymeric substances (EPS). All of these processes influence the morphology and mineralogy of the carbonate minerals. Interactions of EPS with metals, calcium in particular, are believed to be the main processes through which the extracellular matrix controls the precipitation of the carbonate minerals. SRB exopolymers were purified from lithifying mat and type cultures, and their potential role in CaCO3 precipitation was determined from acid‐base titrations and calcium‐binding experiments. Major EPS characteristics were established using infrared spectroscopy and gas chromatography to characterize the chemical functional groups and the sugar monomers composition. Our results demonstrate that all of the three SRB strains tested were able to produce large amounts of EPS. This EPS exhibited three main buffering capacities, which correspond to carboxylic acids (pKa = 3.0), sulfur‐containing groups (thiols, sulfonic and sulfinic acids – pKa = 7.0–7.1) and amino groups (pKa = 8.4–9.2). The calcium‐binding capacity of these exopolymers in solution at pH 9.0 ranged from 0.12gCa gEPS−1–0.15 gCa gEPS−1. These results suggest that SRB could play a critical role in the formation of CaCO3 in lithifying microbial mats. The unusually high sulfur content, which has not been reported for EPS before, indicates a possible strong interaction with iron. In addition to changing the saturation index through metabolic activity, our results imply that SRB affect the rock record through EPS production and its effect on the CaCO3 precipitation. Furthermore, EPS produced by SRB may account for the incorporation of metals (e.g. Sr, Fe, Mg) associated with carbonate minerals in the rock record.

MEPS Marine Ecology Progress Series Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsTheme Sections MEPS 342:55-67 (2007) - doi:10.3354/meps342055 Enrichment of nutrients, exopolymeric substances and microorganisms in newly formed sea ice on the Mackenzie shelf Andrea Riedel1,*, Christine Michel2, Michel Gosselin1, Bernard LeBlanc2 1Institut des sciences de la mer (ISMER), Université du Québec à Rimouski, 310 allée des Ursulines, Rimouski, Québec G5L 3A1, Canada 2Fisheries and Oceans Canada, Freshwater Institute, 501 University Crescent, Winnipeg, Manitoba R3T 2N6, Canada *Email: riedela@dfo-mpo.gc.ca ABSTRACT: Newly formed sea ice was sampled at 32 stations on the Mackenzie shelf, between 30 September and 19 November 2003. At each station, sea ice and surface waters were analysed to assess the concentration and enrichment of nutrients, exopolymeric substances (EPS, measured with Alcian blue), chlorophyll a (chl a), autotrophic and heterotrophic protists, and heterotrophic bacteria. Dark incubations were also conducted to estimate net heterotrophic NH4 regeneration rates in sea ice <5 cm thick. Large (≥5 µm) autotrophs were selectively enriched during sea-ice formation, having the highest average enrichment index (IS = 62), although heterotrophic protists (IS = 19), EPS (IS = 17), bacteria (IS = 6) and dissolved inorganic nitrogen (IS = 3 to 5) were also significantly enriched in the sea ice. Significant relationships were observed between sea-ice EPS and total chl a concentrations (r = 0.59, p < 0.001) and between sea-ice EPS and ≥5 µm autotroph enrichment indices (r = 0.48, p < 0.01), suggesting that EPS were actively produced by algae entrapped in the sea ice. These relationships also suggest that the presence of EPS may enhance the selective enrichment of large autotrophs. Heterotrophic regeneration contributed to the observed enrichment of NH4 in the sea ice, with an average regeneration rate of 0.48 µM d–1, contributing 67% of the sea-ice NH4 concentrations. In the newly formed ice, NH4 regeneration was coupled to NO3 and Si(OH)4 consumption and was significantly related to EPS concentrations (r = 0.87, p < 0.05). Our data suggest that EPS enhance NH4 regeneration by acting as a carbon source for sea-ice heterotrophs or a substrate for sea-ice bacteria. KEY WORDS: Newly formed sea ice · Arctic · Exopolymeric substances · EPS · Enrichment · Ammonium · Regeneration · Protists · Bacteria Full text in pdf format PreviousNextExport citation RSS - Facebook - Tweet - linkedIn Cited by Published in MEPS Vol. 342. Online publication date: July 24, 2007 Print ISSN: 0171-8630; Online ISSN: 1616-1599 Copyright © 2007 Inter-Research.

Carbonate mud is crucial in the global carbon cycle and serves as a key sedimentary archive for paleoclimate reconstruction. Understanding the mechanisms behind its formation is crucial for explaining long-term carbon storage, including atmospheric carbon dioxide transfer to the hydrosphere and variations in mud production over geological timescales. Various mechanisms explain carbonate mud formation in both lake and marine sediments. Using bio-physicochemical methods on deep sediments of Lake Ilay, Jura, France, we propose a model of micrite formation. Our study shows that micrite mineralization occurs in sediments due to the degradation of ooze rich in exopolymeric substances throughout the sediment core’s depth. This mineralization continues as long as exopolymeric substances are present, persisting for at least 2000 years. Cryo-Scanning electron microscope imaging reveals calcite nucleation at degraded exopolymeric substance nodes, advancing with substance degradation and calcium release. These findings provide insights into fossil carbonate mud origins and formation processes.

The role of culture conditions on the production of exopolymeric substances (EPS) by Synechococcus strain PCC7942 was investigated. Carbonate mineral precipitation in these EPS was assessed in forced precipitation experiments. Cultures were grown in HEPES-buffered medium and non-buffered medium. The pH of buffered medium remained constant at 7.5, but in non-buffered medium it increased to 9.5 within a day and leveled off at 10.5. The cell yield at harvest was twice as high in non-buffered medium than in buffered medium. High molecular weight (&gt;10 kDa) and low molecular weight (3–10 kDa) fractions of EPS were obtained from both cultures. The cell-specific EPS production in buffered medium was twice as high as in non-buffered medium. EPS from non-buffered cultures contained more negatively charged macromolecules and more proteins than EPS from buffered cultures. The higher protein content at elevated pH may be due to the induction of carbon-concentrating mechanisms, necessary to perform photosynthetic carbon fixation in these conditions. Forced precipitation showed smaller calcite carbonate crystals in EPS from non-buffered medium and larger minerals in polymers from buffered medium. Vaterite formed only at low EPS concentrations. Experimental results are used to conceptually model the impact of pH on the potential of cyanobacterial blooms to produce minerals. We hypothesize that in freshwater systems, small crystal production may benefit the picoplankton by minimizing the mineral ballast, and thus prolonging the residence time in the photic zone, which might result in slow sinking rates.

Diatoms as important phytoplankton components interact with and are colonized by heterotrophic bacteria. This colonization has been studied extensively in the past but a distinction between the bacterial colonization directly on diatom cells or on the aggregated organic material, exopolymeric substances (EPS), was little addressed. Here we show that the diatom Thalassiosira rotula and EPS were differently colonized by strains of Roseobacteraceae and Flavobacteriaceae in two and tree partner treatments and an enriched natural bacterial community as inoculum. In two partner treatments, the algae and EPS were generally less colonized than in the three partner treatments. Two strains benefitted greatly from the presence of another partner as the proportions of their subpopulations colonizing the diatom cell and the EPS were much enhanced relative to their two partner treatments. Highest proportions of bacteria colonizing the diatom and EPS occurred in the treatment inoculated with the enriched natural bacterial community. Dissolved organic carbon, amino acids and carbohydrates produced by T. rotula were differently used by the bacteria in the two and three partner treatments and most efficiently by the enriched natural bacterial community. Our approach is a valid model system to study physico-chemical bacteria-diatom interactions with increasing complexity.

Enhanced protein and carbohydrate hydrolyses in plume-associated deepwaters initially sampled during the early stages of the Deepwater Horizon oil spill

The relationship between environmental conditions and the development, mineralization and preservation of modern tufa microbialites was investigated in a 1.1 km long freshwater stream in Villiers-le-Bâcle, a tributary of Mérantaise river. Detailed mapping of the tufa microbialite distribution combined with sedimentological, petrographical and mineralogical analyses were coupled with chemical measurements. Six organosedimentary structures were identified; their distribution appears heterogeneous along the stream and responds to physicochemical conditions of water and specific biological components (e.g., microorganism, exopolymeric substance). Two of the organosedimentary structures show evidence of mineralization and only one is lithified. Based on field observations and in-situ deployment of mineralization markers (bricks), three zones with increasing mineralization intensities are defined, ranging from no mineralization to thick mineralized crusts forming riverine tufa. Both biotic and abiotic processes were proposed for the tufa microbialite formation. We explained changes in mineralization intensities by the specific physicochemical conditions (e.g., calcite saturation index (SIcalc) and partial pressure of CO2 (pCO2) and a closed proximity of the cyanobacterial biofilm and carbonates precipitates. The physical and chemical composition of substrate impact development of microbial communities, mineralization potential of tufa microbialite. Even though the physicochemical and biological conditions were optimal for mineral precipitation, the potential of lithification depended on the presence of a suitable (physical and chemical) substrate.

Winter–spring dynamics in sea-ice carbon cycling in the coastal Arctic Ocean

AME Aquatic Microbial Ecology Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsSpecials AME 50:25-38 (2007) - DOI: https://doi.org/10.3354/ame01155 Grazing of large-sized bacteria by sea-ice heterotrophic protists on the Mackenzie Shelf during the winter–spring transition Andrea Riedel1,2,*, Christine Michel2, Michel Gosselin1 1Institut des sciences de la mer (ISMER), Université du Québec à Rimouski, 310 allée des Ursulines, Rimouski, Québec G5L 3A1, Canada 2Fisheries and Oceans Canada, Freshwater Institute, 501 University Crescent, Winnipeg, Manitoba R3T 2N6, Canada *Email: andrea.niemi@dfo-mpo.gc.ca ABSTRACT: Heterotrophic bacterial dynamics were assessed in the sea ice and surface waters on the Mackenzie Shelf (Beaufort Sea), from 5 March to 3 May 2004. On 11 occasions, heterotrophic protist bacterivory was assessed from the disappearance of fluorescently labeled bacteria (FLB) in sea-ice samples collected from areas of high and low snow cover. Concurrently, sea-ice and surface water samples were analyzed for dissolved organic carbon (DOC), exopolymeric substances (EPS) and chlorophyll a concentrations, and protist and bacterial abundances. Total bacterial abundances were significantly higher in the sea ice than in surface waters. However, DOC concentrations and abundances of large (≥0.7 µm) bacteria were not significantly higher in the sea ice as compared to surface waters. This suggests that DOC was being released from the sea ice, potentially supporting the growth of large-sized bacteria at the ice–water interface. Heterotrophic protist (HP) bacterivory averaged 57% d–1 of large-sized bacterial abundances in the sea ice with ingestion rates averaging 768 and 441 bacteria HP–1 d–1, under high and low snow cover, respectively. High concentrations of EPS during the sea-ice algal bloom may have interfered with the grazing activities of heterotrophic protists as indicated by the significant negative correlations between ingestion rates and EPS-carbon concentrations under high (τ = –0.57, p < 0.05) and low (τ = –0.56, p < 0.05) snow cover. Bacterivory satisfied heterotrophic protist carbon requirements prior to, but not during, the sea-ice algal bloom, under high and low snow cover. EPS may have been an additional carbon source for the heterotrophs, especially during the sea-ice algal bloom period. This study provides evidence of an active heterotrophic microbial food web in first-year sea ice, prior to and during the sea-ice algal bloom. This study also highlights the significance of DOC and EPS as integral components of the microbial food web within the sea ice and surface waters of Arctic shelves. KEY WORDS: Bacteria · FLB · Grazing · DOC · EPS · Sea ice · Arctic Full text in pdf format PreviousNextCite this article as: Riedel A, Michel C, Gosselin M (2007) Grazing of large-sized bacteria by sea-ice heterotrophic protists on the Mackenzie Shelf during the winter–spring transition. Aquat Microb Ecol 50:25-38. https://doi.org/10.3354/ame01155 Export citation RSS - Facebook - Tweet - linkedIn Cited by Published in AME Vol. 50, No. 1. Online publication date: December 12, 2007 Print ISSN: 0948-3055; Online ISSN: 1616-1564 Copyright © 2007 Inter-Research.

Carbonate microbialites provide a window to understand microbe–mineral interactions in modern environments and in the geological record. Unraveling microbial versus physicochemical controls and biogeochemical signatures is not always straightforward. Environmental and laboratory studies have shown that microbial activity can play a central role in calcium carbonate precipitation. Most studies have focused on the effects of Bacteria and Archaea activity on carbonate precipitation processes (e.g., cyanobacteria, sulfate-reducing bacteria, sulfide-oxidizing bacteria and iron-reducing bacteria). The influence of eukaryotic activity, such as diatoms and other microalgae, on carbonate precipitation and microbialite formation has been the focus of less attention. This study explores carbonate mineralization in active diatom-rich microbial mats developed in a high-altitude groundwater-fed hypersaline lake in the Puna region of Catamarca, Argentina. Previous work has focused on the texture, mineralogy, and stable-isotope chemistry of the subfossil oncoidal and laminar microbialites. Here, using 16S rDNA Bacteria diversity analysis, confocal scanning laser microscopy, scanning electron microscopy, and transmitted-light microscopy, we explore the Bacteria and diatom diversity in the microbial mats and the related carbonates textures and make comparisons with similar textures in the associated oncoidal microbialites. Diatom-rich subspherical aggregates, which have not been previously described in the literature, show a diverse microbial community with abundant exopolymeric substances (EPSs) where carbonate precipitation takes place. These aggregates are a main component of the Laguna Negra microbial mats and show anhedral micritic calcite in the EPS matrix as the main mineral component. Similar calcite micrite textures are also preserved as one lamina type in the associated oncoids. On the other hand, where EPS are absent, carbonate precipitation, related to pennate diatom blooms, is represented by euhedral aragonite needles suggesting different mechanisms and controls. Changes in the microbial communities are recorded in the oncoids as different lamina types, providing a link between the currently active mats and the subfossil oncoidal structures. This is a first survey of these previously unexplored diatom-rich microbial mats developed under extreme environmental conditions in the Laguna Negra. Understanding the effect that the interaction between diatoms and prokaryotic communities has on carbonate precipitation may provide some insight on the evolution of microbialite textures and fabrics, and on the change from prokaryote-dominated systems to mixed eukaryotic–prokaryotic systems.

Microbial mats are synergistic microbial consortia through which major elements, including sulfur, are cycled due to microbial and geological processes. Depth profiles of pH, O2, sulfide, exopolymeric substances (EPS), and the rate of sulfate reduction were determined in an Oscillatoria sp. and Microcoleus-dominated marine microbial mat at the Great Sippewissett salt marsh, Massachusetts. In addition, measurements in spirochete enrichments and Spirochaetae litoralis cultures showed sulfide consumption during which polysulfides, thiosulfate, and presumably sulfate formed. These data suggest that spirochetes can play a role in the cycling of sulfur in these mats. The obligate to facultative anaerobic spirochetes may consume sulfide to remove oxygen. Furthermore, spirochetes may enhance preservation of microbial mats within the rock record by degrading EPS and producing low molecular weight organic compounds (LMWOC). Both sulfide oxidation (i.e., oxygen removal) and EPS degradation (i.e., production of LMW organic compounds) stimulate the activity of sulfate-reducing bacteria (SRB), which are responsible for the precipitation of calcium carbonate in most lithifying mats

Microbial nucleation of calcium carbonate in the Precambrian

Physico-chemical and biological controls in a travertine system in the high Andes of northwestern Argentina