Olivier Braissant

Characteristics and turnover of exopolymeric substances in a hypersaline microbial mat

The properties and microbial turnover of exopolymeric substances (EPS) were measured in a hypersaline nonlithifying microbial mat (Eleuthera, Bahamas) to investigate their potential role in calcium carbonate (CaCO(3)) precipitation. Depth profiles of EPS abundance and enzyme activities indicated that c. 80% of the EPS were turned over in the upper 15-20 mm. Oxic and anoxic mat homogenates amended with low-molecular-weight (LMW) organic carbon, sugar monomers, and different types of EPS revealed rapid consumption of all substrates. When comparing the consumption of EPS with that of other substrates, only marginally longer lag times and lower rates were observed. EPS (5-8%) were readily consumed during the conversion of labile to refractory EPS. This coincided with a decrease in glucosidase activity and a decrease in the number of acidic functional groups on the EPS. Approximately half of the calcium bound to the EPS remained after 10 dialyses steps. This tightly bound calcium was readily available to precipitate as CaCO(3). We present a conceptual model in which LMW organic carbon complexed with the tightly bound calcium is released upon enzyme activity. This increases alkalinity and creates binding sites for carbonate and allows CaCO(3) to precipitate. Therefore, this model explains interactions between EPS and CaCO(3) precipitation, and underscores the critical role of aerobic and anaerobic microorganisms in early diagenesis and lithification processes.

Is the contribution of bacteria to terrestrial carbon budget greatly underestimated

Abstract. Some commonly found species of soil bacteria use low molecular weight organic acids as their sole source of carbon and energy. This study shows that acids such as citrate and oxalate (produced in large amounts by fungi and plants) can rapidly be consumed by these bacteria. Two strains, Ralstonia eutropha and Xanthobacter autotrophicus, were cultured on acetate- and citrate-rich media. The resulting CO2 and/or HCO3– reacted with calcium ions to precipitate two polymorphs of calcium carbonate (CaCO3), calcite and vaterite, depending on the quantity of slime produced by the strains. This production of primary calcium carbonate crystals by oxalate- and citrate-degrading bacteria from soil organic carbon sources highlights the existence of an important and underestimated potential carbon sink.

Bacteria associated with spores of the arbuscular mycorrhizal fungi Glomus geosporum and Glomus constrictum.

ABSTRACT Spores of the arbuscular mycorrhizal fungi (AMF) Glomus geosporum and Glomus constrictum were harvested from single-spore-derived pot cultures with either Plantago lanceolata or Hieracium pilosella as host plants. PCR-denaturing gradient gel electrophoresis analysis revealed that the bacterial communities associated with the spores depended more on AMF than host plant identity. The composition of the bacterial populations linked to the spores could be predominantly influenced by a specific spore wall composition or AMF exudate rather than by specific root exudates. The majority of the bacterial sequences that were common to both G. geosporum and G. constrictum spores were affiliated with taxonomic groups known to degrade biopolymers (Cellvibrio, Chondromyces, Flexibacter, Lysobacter, and Pseudomonas). Scanning electron microscopy of G. geosporum spores revealed that these bacteria are possibly feeding on the outer hyaline spore layer. The process of maturation and eventual germination of AMF spores might then benefit from the activity of the surface microorganisms degrading the outer hyaline wall layer.

Inside the alkalinity engine: the role of electron donors in the organomineralization potential of sulfate-reducing bacteria.

Mineral precipitation in microbial mats may have been the key to their preservation as fossil stromatolites, potentially documenting evidence of the earliest life on Earth. Two factors that contribute to carbonate mineral precipitation are the saturation index (SI) and the presence of nucleation sites. Both of these can be influenced by micro-organisms, which can either alter SI through their metabolisms, or produce and consume organic substances such as extracellular polymeric substances (EPS) that can affect nucleation. It is the balance of individual metabolisms within the mat community that determines the pH and the dissolved inorganic carbon concentration, thereby potentially increasing the alkalinity and consequently the SI. Sulfate-reducing bacteria (SRB) are an important component of this alkalinity engine. The activity of SRB often peaks in layers where CaCO(3) precipitates, and mineral precipitation has been demonstrated in SRB cultures; however, the effect of their metabolism on the alkalinity engine and actual contribution to mineral precipitation is the subject of controversy. Here, we show through culture experiments, theoretical calculations, and geochemical modeling studies that the pH, alkalinity, and organomineralization potential will vary depending on the type of electron donor. Specifically, hydrogen and formate can increase the pH, but electron donors like lactate and ethanol, and to a lesser extent glycolate, decrease the pH. The implication of this for the lithification of mats is that the combination of processes supplying electron donors and the utilization of these compounds by SRB may be critical to promoting mineral precipitation.

Fungi in Biogeochemical Cycles: The oxalate–carbonate pathway in soil carbon storage: the role of fungi and oxalotrophic bacteria

Introduction Although fungi are generally disregarded in the biogeochemical literature, they undoubtedly constitute crucial biogeochemical factors in many elemental cycles. This fact, combined with their abundance in the soil warrants greater detailed study into their geoecological impact. The network formed by fungal filaments can represent 10 000 km of thread-like mycelia in 1m of fertile soil. Their mass is evaluated at 3500 kg ha 1 at a depth of 20 cm in an average continental soil, i.e. taking into account all the different terrestrial environments on the Earth (Gobat et al., 2004). In comparison, bacteria and algae would represent 1500 and 10–1000kgha 1 respectively, in the same virtual average soil. Fungi are not only biologically important as saprophytes in the recycling of organic matter, but also play a geological role by excreting notable amounts of organic acids, among which oxalic acid is particularly important (Gadd, 1999), contributing to continental weathering as well as to mineral neogenesis (Verrecchia & Dumont, 1996; Verrecchia, 2000; Burford et al., 2003 a, b). The first fossil fungi have been identified in rocks dated from the Ordovician, i.e. 460 to 455Ma ago (Redecker et al., 2000). However, molecular clock estimates for the evolution of fungi have suggested a Late Precambrian (600Ma) colonization on land (Berbee & Taylor 2000). Recent molecular studies, based on protein sequence analysis, indicate that fungi were present on continents 1 billion years ago and possibly affected (together with plants) the evolution of Earth’s atmosphere and climate since 700Ma (Heckman et al., 2001). Therefore, if fungi have been present on the Earth’s surface for such a long time, producing large amounts of oxalic acid able to precipitate as metal oxalates, why is there no evidence of oxalate accumulation in paleosols?

Biomineralization in plants as a long-term carbon sink

Carbon sequestration in the global carbon cycle is almost always attributed to organic carbon storage alone, while soil mineral carbon is generally neglected. However, due to the longer residence time of mineral carbon in soils (102–106xa0years), if stored in large quantities it represents a potentially more efficient sink. The aim of this study is to estimate the mineral carbon accumulation due to the tropical iroko tree (Milicia excelsa) in Ivory Coast. The iroko tree has the ability to accumulate mineral carbon as calcium carbonate (CaCO3) in ferralitic soils, where CaCO3 is not expected to precipitate. An estimate of this accumulation was made by titrating carbonate from two characteristic soil profiles in the iroko environment and by identifying calcium (Ca) sources. The system is considered as a net carbon sink because carbonate accumulation involves only atmospheric CO2 and Ca from Ca-carbonate-free sources. Around one ton of mineral carbon was found in and around an 80-year-old iroko stump, proving the existence of a mineral carbon sink related to the iroko ecosystem. Conservation of iroko trees and the many other biomineralizing plant species is crucial to the maintenance of this mineral carbon sink.

Biogeochemistry of Carbon Cycling in Hypersaline Mats: Linking the Present to the Past through Biosignatures

Prokaryotes are capable of using a wide variety of reduction–oxidation (redox) reactions to fulfill their biochemical energy needs (Nealson and Stahl, 1997; Visscher and Stolz, 2005). This metabolic flexibility enables microbes to thrive under a wide variety of planetary environmental conditions. The geochemical conditions of a given environment will determine which metabolic redox reactions may take place; for example, the presence of oxygen allows for aerobic respiration, and the absence of organic carbon favors metabolism supported by inorganic electron donors (H2, S2−, NH3, etc.). The redox reactions that supply energy alter the geochemical environment in which the microbes live, creating conditions that may enable other metabolic reactions to take place. This environmental change can be short-term or long-term or cyclic or permanent. Some of these environmental changes can be preserved as biogenic signatures in the atmosphere and in the permanent rock record of planets. Many such signatures of life exist, ranging from biomolecules and bio-mediated mineral deposits, to biogenic gases.

MICROBIOLOGICAL ACTIVITIES IN MOONMILK MONITORED USING ISOTHERMAL MICROCALORIMETRY (CAVE OF VERS CHEZ LE BRANDT, NEUCHATEL, SWITZERLAND)

Studies of the influence of microbial communities on calcium carbonate deposits mostly rely on classical or molecular microbiology, isotopic analyses, and microscopy. Using these techniques, it is difficult to infer microbial activities in such deposits. In this context, we used isothermal microcalorimetry, a sensitive and non- destructive tool, to measure microbial activities associated with moonmilk ex-situ. Upon the addition of diluted LB medium and other carbon sources to fresh moonmilk samples, we estimated the number of colony forming units per gram of moonmilk to be 4.8 3 10 5 6 0.2 3 10 5 . This number was close to the classical plate counts, but one cannot assume that all active cells producing metabolic heat were culturable. Using a similar approach, we estimated the overall growth rate and generation time of the microbial community associated with the moonmilk upon addition of various carbon sources. The range of apparent growth rates of the chemoheterotrophic microbial community observed was between 0.025 and 0.067 h 21 and generation times were between 10 and 27 hours. The highest growth rates were observed for citrate and diluted LB medium, while the highest carbon-source consumption rates were observed for low molecular weight organic acids (oxalate and acetate) and glycerol. Considering the rapid degradation of organic acids, glucose, and other carbon sources observed in the moonmilk, it is obvious that upon addition of nutrients during snow melting or rainfall these communities can have high overall activities comparable to those observed in some soils. Such communities can influence the physico-chemical conditions and participate directly or indirectly to the formation of moonmilk.

The Role of Fungal Biofilm and Networks in the Terrestrial Calcium Carbonate Cycle

In terrestrial environments, fungi constitute one of the most important microbial agents, but also due to their ability to decay organic matter but also because of their role in various biogeochemical cycles (Gadd, 1999; Verrecchia, 2000). Fungal involvement in carbonate rock destruction, dissolution and precipitation has been suspected for over 150 years (Braconnot, 1825) but convincing hypotheses to explain the processes of carbonate dissolution and precipitation were not proposed before the W’s. Nevertheless, their role in the calcium carbonate cycle remains largely underestimated. The aim of this chapter is to emphasize the great potential of fungi in CaCO3 redistribution and sequestration at the surface of continents.

Comparison of Tunable Diode Laser Absorption Spectroscopy and Isothermal Micro-calorimetry for Non-invasive Detection of Microbial Growth in Media Fills

Two methods were investigated for non-invasive microbial growth-detection in intact glass vials as possible techniques for automated inspection of media-filled units. Tunable diode laser absorption spectroscopy (TDLAS) was used to determine microbially induced changes in O2 and CO2 concentrations within the vial headspaces. Isothermal microcalorimetry (IMC) allowed the detection of metabolic heat production. Bacillus subtilis and Streptococcus salivarius were chosen as test organisms. Parameters as robustness, sensitivity, comparability and time to detection (TtD) were evaluated to assess method adequacy. Both methods robustly detected growth of the tested microorganisms within less than 76u2009hours using an initial inoculum of <10CFU. TDLA turned out to be less sensitive than TDLA and IMC, as some false negative results were observed. Compared to the visual media-fill examination of spiked samples, the investigated techniques were slightly slower regarding TtD. Although IMC showed shorter TtD than TDLAS the latter is proposed for automating the media-fill inspection, as larger throughput can be achieved. For routine use either TDLA or a combination of TDLA and TDLA should be considered. IMC may be helpful for replacing the sterility assessment of commercial drug products before release.