Patrice Cannavo

Bacterial and fungal communities vary with the type of organic substrate: implications for biocontrol of soilless crops

Biocontrol strategies using organic substrates such as wood fibers and biocontrol agents such as Trichoderma are currently developed to control soil pathogens such as Fusarium oxysporum. Nonetheless, such biocontrol methods give discording results, notably because microbial communities of organic substrates actually are not taken into account. Therefore, there is a lack of information concerning the variability of microbial composition related to the organic substrate type. Here we studied peat, wood and coir fibers, that are substrates known for their different biocontrol efficiency against Fusarium wilt of cucumber. We analyzed in microcosms the microbial composition of wood fibers, coir fibers and peat, incubated up to 60 days, by using an amplicon-sequencing approach based on 16S rRNA gene for bacteria and the internal transcribed spacer (ITS) for fungi. Diversity was assessed by sequencing the 16S rRNA for bacteria and ITS2 region for fungi. Results showed that bacterial richness was threefold higher for coir fiber and peat than for wood fiber. Fungal richness was three times higher for wood and coir fibers compared to peat. Bacterial and fungal patterns showed a dominance of α- and γ- Proteobacteria and Sordariomycetes for coir fiber; β- and γ-Proteobacteria and Eurotiomycetes for wood fibers; Flavobacteria, Leotiomycetes and Sordariomycetes for peat. In conclusion, results show that substrates have different microbial composition. Finally, for a proper use of a biocontrol strategy is important to take into account the type of substrate.

Estimation of soil organic carbon stocks of two cities, New York City and Paris

In cities, the strong heterogeneity of soils, added to the lack of standardized assessment methods, serves as a barrier to the estimation of their soil organic carbon content (SOC), soil organic carbon stocks (SOCS; kgC m-2) and soil organic carbon citywide totals (SOCCT; kgC). Are urban soils, even the subsoils and sealed soils, contributing to the global stock of C? To address this question, the SOCS and SOCCT of two cities, New York City (NYC) and Paris, were compared. In NYC, soil samples were collected with a pedological standardized method to 1 m depth. The bulk density (Db) was measured; SOC and SOCS were calculated for 0-30 cm and 30-100 cm depths in open (unsealed) soils and sealed soils. In Paris, the samples were collected for 0-30 cm depth in open soils and sealed soils by different sampling methods. If SOC was measured, Db had to be estimated using pedotransfer functions (PTFs) refitted from the literature on NYC data; hence, SOCS was estimated. Globally, SOCS for open soils were not significantly different between both cities (11.3 ± 11.5 kgC m-2 in NYC; 9.9 ± 3.9 kgC m-2 in Paris). Nevertheless, SOCS was lower in sealed soils (2.9 ± 2.6 kgC m-2 in NYC and 3.4 ± 1.2 kgC m-2 in Paris). The SOCCT was similar between both cities for 0-30 cm (3.8 TgC in NYC and 3.5 TgC in Paris) and was also significant for the 30-100 cm layer in NYC (5.8 TgC). A comparison with estimated SOCCT in agricultural and forest soils demonstrated that the citys open soils represent important pools of organic carbon (respectively 110.4% and 44.5% more C in NYC and Paris than in agricultural soils, for 0-30 cm depth). That was mainly observable for the 1 m depth (146.6% more C in NYC than in agricultural soils). The methodology to assess urban SOCS was also discussed.