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 (102-106years), 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 sin

Role of Fungi in the Biomineralization of Calcite

In the field of microbial biomineralization, much of the scientific attention is focused on processes carried out by prokaryotes, in particular bacteria, even though fungi are also known to be involved in biogeochemical cycles in numerous ways. They are traditionally recognized as key players in organic matter recycling, as nutrient suppliers via mineral weathering, as well as large producers of organic acids such as oxalic acid for instance, an activity leading to the genesis of various metal complexes such as metal-oxalate. Their implications in the transformation of various mineral and metallic compounds has been widely acknowledged during the last decade, however, currently, their contribution to the genesis of a common biomineral, calcite, needs to be more thoroughly documented. Calcite is observed in many ecosystems and plays an essential role in the biogeochemical cycles of both carbon (C) and calcium (Ca). It may be physicochemical or biogenic in origin and numerous organisms have been recognized to control or induce its biomineralization. While fungi have often been suspected of being involved in this process in terrestrial environments, only scarce information supports this hypothesis in natural settings. As a result, calcite biomineralization by microbes is still largely attributed to bacteria at present. However, in some terrestrial environments there are particular calcitic habits that have been described as being fungal in origin. In addition to this, several studies dealing with axenic cultures of fungi have demonstrated the ability of fungi to produce calcite. Examples of fungal biomineralization range from induced to organomineralization processes. More examples of calcite biomineralization related to direct fungal activity, or at least to their presence, have been described within the last decade. However, the peculiar mechanisms leading to calcite biomineralization by fungi remain incompletely understood and more research is necessary, posing new exciting questions linked to microbial biomineralization processes

Identification of active oxalotrophic bacteria by Bromodeoxyuridine DNA labeling in a microcosm soil experiments

The oxalate-carbonate pathway (OCP) leads to a potential carbon sink in terrestrial environments. This process is linked to the activity of oxalotrophic bacteria. Although isolation and molecular characterizations are used to study oxalotrophic bacteria, these approaches do not give information on the active oxalotrophs present in soil undergoing the OCP. The aim of this study was to assess the diversity of active oxalotrophic bacteria in soil microcosms using the Bromodeoxyuridine (BrdU) DNA labeling technique. Soil was collected near an oxalogenic tree (Milicia excelsa). Different concentrations of calcium oxalate (0.5%, 1%, and 4% w/w) were added to the soil microcosms and compared with an untreated control. After 12 days of incubation, a maximal pH of 7.7 was measured for microcosms with oxalate (initial pH 6.4). At this time point, a DGGE profile of the frc gene was performed from BrdU-labeled soil DNA and unlabeled soil DNA. Actinobacteria (Streptomyces- and Kribbella-like sequences), Gammaproteobacteria and Betaproteobacteria were found as the main active oxalotrophic bacterial groups. This study highlights the relevance of Actinobacteria as members of the active bacterial community and the identification of novel uncultured oxalotrophic groups (i.e. Kribbella) active in soil

Isolation of oxalotrophic bacteria able to disperse on fungal mycelium

A technique based on an inverted Petri dish system was developed for the growth and isolation of soil oxalotrophic bacteria able to disperse on fungal mycelia. The method is related to the ‘fungal highways' dispersion theory in which mycelial fungal networks allow active movement of bacteria in soil. Quantification of this phenomenon showed that bacterial dispersal occurs preferentially in upper soil horizons. Eight bacteria and one fungal strain were isolated by this method. The oxalotrophic activity of the isolated bacteria was confirmed through calcium oxalate dissolution in solid selective medium. After separation of the bacteria-fungus couple, partial sequencing of the 16S and the ITS1 and ITS2 sequences of the ribosomal RNA genes were used for the identification of bacteria and the associated fungus. The isolated oxalotrophic bacteria included strains related to Stenotrophomonas, Achromobacter, Lysobacter, Pseudomonas, Agrobacterium, Cohnella, and Variovorax. The recovered fungus corresponded to Trichoderma sp. A test carried out to verify bacterial transport in an unsaturated medium showed that all the isolated bacteria were able to migrate on Trichoderma hyphae or glass fibers to re-colonize an oxalate-rich medium. The results highlight the importance of fungus-driven bacterial dispersal to understand the functional role of oxalotrophic bacteria and fungi in soil

Moving carbon between spheres, the potential oxalate-carbonate pathway of Brosimum alicastrum Sw.; Moraceae.

Aims The Oxalate-Carbonate Pathway (OCP) is a biogeochemical process that transfers atmospheric CO2 into the geologic reservoir as CaCO3; however, until now all investigations on this process have focused on species with limited food benefits. This study evaluates a potential OCP associated with Brosimum alicastrum, a Neotropical species with agroforestry potential (ca. 70–200 kg-nuts yr−1), in the calcareous soils of Haiti and Mexico. Methods / results Enzymatic analysis demonstrated significant concentrations of calcium oxalate (5.97 % D.W.) were associated with B. alicastrum tissue in all sample sites. The presence of oxalotrophism was also confirmed with microbiological analyses in both countries. High concentrations of total calcium (>7 g kg−1) and lithogenic carbonate obscured the localised alkalinisation and identification of secondary carbonate associated with the OCP at most sample sites, except Ma Rouge, Haiti. Soils adjacent to subjects in Ma Rouge demonstrated an increase in pH (0.63) and CaCO3 concentration (5.9 %) that, when coupled with root-like secondary carbonate deposits in Mexico, implies that the OCP does also occur in calcareous soils. Conclusions Therefore this study confirms that the OCP also occurs in calcareous soils, adjacent to B. alicastrum, and could play a fundamental and un-accounted role in the global calcium-carbon coupled cycle