Use of the frc gene as a molecular marker to characterize oxalate-oxidizing bacterial abundance and diversity structure in soil

Abstract

International audienceOxalate catabolism, which can have both medical and environmental implications, is performed by phylogenetically diverse bacteria. The formyl-CoA-transferase gene was chosen as a molecular marker of the oxalotrophic function. Degenerated primers were deduced from an alignment of frc gene sequences available in databases. The specificity of primers was tested on a variety of frc-containing and frc-lacking bacteria. The frc-primers were then used to develop PCR-DGGE and real-time SybrGreen PCR assays in soils containing various amounts of oxalate. Some PCR products from pure cultures and from soil samples were cloned and sequenced. Data were used to generate a phylogenetic tree showing that environmental PCR products belonged to the target physiological group. The extent of diversity visualised on DGGE pattern was higher for soil samples containing carbonate resulting from oxalate catabolism. Moreover, the amount of frc gene copies in the investigated soils was detected in the range of 1.64×107 to 1.75×108/g of dry soil under oxalogenic tree (representing 0.5 to 1.2% of total 16S rRNA gene copies), whereas the number of frc gene copies in the reference soil was 6.4×106 (or 0.2% of 16S rRNA gene copies). This indicates that oxalotrophic bacteria are numerous and widespread in soils and that a relationship exists between the presence of the oxalogenic trees Milicia excelsa and Afzelia africana and the relative abundance of oxalotrophic guilds in the total bacterial communities. This is obviously related to the accomplishment of the oxalate–carbonate pathway, which explains the alkalinization and calcium carbonate accumulation occurring below these trees in an otherwise acidic soil. The molecular tools developed in this study will allow in-depth understanding of the functional implication of these bacteria on carbonate accumulation as a way of atmospheric CO2 sequestration

Chitin Amendment Increases Soil Suppressiveness toward Plant Pathogens and Modulates the Actinobacterial and Oxalobacteraceal Communities in an Experimental Agricultural Field

“…Moreover, molecular and genetic studies have revealed the presence of chitinolytic genes among important members of the Oxalobacteraceae (23,(51)(52)(53)60). Thus, the genus Streptomyces, along with Oxalicibacterium (in the presence of fungi), might play key roles in disease-suppressive soils as being part of the amendment-reactive microbiota (5,19,20,54). A further lead, obtained from chiAbased Roche 454 deep pyrosequencing analysis of the June-10 chitin-amended field and soil from a microcosm experiment (17,21), recently indicated an increase in the abundance of Oxalobacteraceae-like sequences.…”

Oxalotrophy, a widespread trait of plant-associated Burkholderia species, is involved in successful root colonization of lupin and maize by Burkholderia phytofirmans

“…Carboxylates such as citrate and malate are a major source of carbon for rhizosphere bacteria, and malate has even been postulated to act as a signal to recruit beneficial microorganisms (Rudrappa et al, 2008). In contrast, using oxalate as carbon source, a phenotype referred to as “oxalotrophy,” is a rare trait of bacteria, although it occurs across a wide range of phylogenetically distant groups (Sahin, 2003; Khammar et al, 2009). In addition to citrate and malate, which are common components of root exudates, oxalate has also been shown to be a major root exudate of soil-grown plants (Dessureault-Rompre et al, 2007).…”

Oxalyl-Coenzyme A Reduction to Glyoxylate Is the Preferred Route of Oxalate Assimilation in Methylobacterium extorquens AM1

“…Although oxalate is a rather "poor" substrate, a number of oxalotrophic bacteria have been isolated from various ecological niches, including terrestrial (10) and aquatic (64) habitats and the gastrointestinal tract, under both aerobic and anaerobic conditions. Phylogenetically, oxalotrophic bacteria belong to distinct groups (33,(55)(56)(57).…”