Agricultural practices shape microbial communities and change fresh and soil organic matter mineralization in a tropical soil : S11.07-P -1

Priming effect (PE) is defined as a stimulation of the mineralization of soil organic matter (SOM) due to fresh organic matter (FOM) supply. This process leads simultaneously to a loss of carbon to the atmosphere and to a remobilization of nutrients. PE should thus be considered in the management of residues or amendments in agricultural soils, especially where soil fertility is essentially based on organic supply. In Madagascar, the Direct-seeding Mulch based cropping (DMC) systems appeared to be an opportunity for the development of a sustainable upland rice culture. In DMC systems soil is not tilled and protected from physical erosion by dead or alive cover plants and/or mulches of crop residues. DMC systems are also known to increase soil organic matter stocks in the first centimetres below the mulch layer. As the quality of FOM is a determinant of the priming effect process, we were interested to evaluate whether the quality of mulches could shape the belowground microbial community and impact its capacity to mineralize SOM. In 2010, we sampled soil samples from a field experimentation set up in 2003 in the centre of Madagascar. The 10 first centimetres under three crop mulches (two grasses and one legume) and two different fertilizations (organic and organic + mineral), were sampled during the rice growing season. Soils were incubated in the presence of 13C-enriched wheat straw residue to measure their FOM and SOM mineralization capacity. Bacteria involved in both fluxes were identified by the coupling between DNA-SIP and pyrosequencing techniques. (Texte intégral

Impact of N availability on heterotrophic microbial dynamic during decomposition of miscanthus x giganteus leaves in a soil. : S11.04-P -7

Carbon and N cycles are intimately associated during the residue decomposition process in soils. The overall N availability (residue + soil N) controls the rate of residue decomposition under N limiting conditions. Therefore studies have demonstrated low N availability reduced C mineralization rate on short term by reducing opportunist microbial biomass growth. However the effect of N availability on C mineralization and microbial biomass growth and composition on longer term, are still poorly understood. In the context of biofuel perennial plant production with Miscanthus, in which N amendments are limited, we investigated the effects of N availability on C and N dynamics, microbial dynamics and enzymatic functions on the short and long terms. Miscanthus leaves were incubated in an agricultural soil for > 500 days at two levels of soil N availability by adding inorganic N or not. C and N mineralization, microbial biomass C, ergosterol, xylanase and laccase activities and 18S-rRNA and 16S-rRNA were determined at several dates during the experiment. Results showed that a high N availability increased the rate of residue C mineralized in the short term (< 1 year) together with an increase in microbial C, fungal ergosterol, and enzymatic activities related to C degradation (xylanase). However, the high N availability suppressed laccase activity while it has no significant effect on 18S- and 16S r-RNA microbial communities. On longer term (> 1 year), high N availability slightly decreased C mineralization compared to low N treatment demonstrating the antagonist effect of N on residue decomposition. (Texte intégral

Modification of a commercial dna extraction kit to simultaneously recover rna, safely and rapidly, and to assess molecular biomass of the total and the active part of microbial communities, from soils with diverse mineralogy and carbon content : S11.04-P -15

We have modified a commercial DNA extraction kit for soil to simultaneously co-extract RNA. In this new procedure RNA and DNA are separated by two selective purifications in cascade without the need of DNAase or RNAse digestion. Consequently DNA and RNA are respectively purified from the whole co-extraction solution. Nucleic acids extraction is based on the action of SDS coupled with an efficient bead-beating step, but it does not require any solvent. Avoiding the use of solvents, which are damaging for human health and environmental quality, was one of our most important motivations to develop this protocol. In a second time, we have optimized this protocol to improve the DNA and RNA yield, but kipping those yields below the saturation limit of the kit to assess and quantify the variations of molecular biomass of the total (DNA) and the active (RNA) part of microbial communities in natural samples. We have also introduced a first step of homogenization of soil sample in liquid nitrogen to improve the reliability of the fungal 18S gene sequence quantification. Finally, we have shown that this protocol can be applied to a wide diversity of soils whatever their mineralogy and metal content (2 Ferralsols, 1 Vertisol, 2 Andosols from Madagascar), texture or biomass content (1 poor sandy soil from Congo and one carbon rich temperate soil sample submitted or not to a 1 month cold stress). * E Tournier, L. Amenc and AL. Pablo contributed equally to this study. (Texte intégral

Microbial communities associated to rubber tree plantations along a chronosequence in North East Thailand. [P2.162]

Rubber tree (Hevea brasiliensis) is a crop of major socio-economic importance in Southern Asia as it represents a substantial source of income for small land holders. In Thailand (1/3 of world latex production) rubber tree plantations are currently greatly expanding in adverse eco-climatic zones, especially in Isan provinces, where soils have sandy texture, low fertility and are prone to erosion and leaching of applied fertilizers. A major potential for increased production in these conditions relies on the important roles of rhizosphere microbial communities in supporting soil fertility and plant nutrition. A chronosequence of 3, 6 and 16 year-old plantations was identified and cassava fields were used as no-rubber controls for comparison. Soils from each treatment were characterized for texture and chemistry. Using 454 sequencing, total bacterial and fungal communities as well as arbuscular mycorrhizal fungi (AMF) community were analyzed. Because they are known to contribute to plant P and N nutrition by increasing mineral nutrient availability or by enhancing plant nutrient uptake, root-interacting P-solubilizing bacteria (PSB) and free living N fixing bacteria were assessed after culturing on selective media. Nematodes populations were characterized as there are good soil fertility indicators. Functional traits were also analyzed by both qPCR and Ecoplates (Biolog) methods. Results showed significant differences between rubber and cassava associated communities but didn't reveal a strong impact of the age of the plantations on the different communities. For instance, the AMF community in cassava roots was twice as rich as in rubber tree samples but was not affected by the age of rubber trees. The improved understanding of the diversity of root-associated microbes will contribute to the development of alternative sustainable practices to improve and sustain soil fertility. (Résumé d'auteur

Nematofauna as indicator of soil N availability in mixed plantations? A case study from tropical forest of Eucalyptus and Acacia in Congo. [P2.179]

Nitrogen is a limiting factor for the growth of Eucalyptus plantations, particularly in subtropical areas characterized by very low soil fertility (e.g.degraded pastures). The association with N2- fixing species such as Acacia mangium is an alternative for ecological intensification of these ecosystems. Enhancement of Eucalyptus trees growth may happen by direct transfer of N fixed by Acacia trees or indirectly through litter decomposition. Field assessments in Congo showed that the productivity of Eucalyptus trees in mixed plantations was significantly increased compared with Eucalyptus alone. Higher N contents in soil of mixed plantations explained such positive impact. In a microcosm experiment, we measured N mineralization in soil sampled from pure stands of Acacia, pure stands of Eucalyptus and from the mixed plantations. The results showed an accumulation of nitrate in the rhizosphere of Acacia. We found that the introduction of Acacia trees changed significantly the structure of the community of nematodes by increasing the proportion of bacterial-feeding nematodes. Similar results were obtained in mixed-plantations in Brazil and in France, suggesting that nematofauna could be a key indicator of N availability in soil. Microbial communities involved in nitrification were also studied by targeting AOA and AOB genes using the quantitative PCR method. An increase of the number of copies of AOA gene was observed in the rhizosphere of Acacia while AOB gene was difficult to detect. This suggests that Archae communities may play an important role in N cycling in soil of Eucalyptus plantations. Our results demonstrate that the introduction of Acacia in mixed plantations systems influences the N cycle in the soil and associated biological activities. (Résumé d'auteur

Shifts in the bacterial community composition along deep soil profiles in monospecific and mixed stands of Eucalyptus grandis and Acacia mangium

Our knowledge of the rhizosphere bacterial communities in deep soils and the role of Eucalyptus and Acacia on the structure of these communities remains very limited. In this study, we targeted the bacterial community along a depth profile (0 to 800 cm) and compared community structure in monospecific or mixed plantations of Acacia mangium and Eucalyptus grandis. We applied quantitative PCR (qPCR) and sequence the V6 region of the 16S rRNA gene to characterize composition of bacterial communities. We identified a decrease in bacterial abundance with soil depth, and differences in community patterns between monospecific and mixed cultivations. Sequence analysis indicated a prevalent effect of soil depth on bacterial communities in the mixed plant cultivation system, and a remarkable differentiation of bacterial communities in areas solely cultivated with Eucalyptus. The groups most influenced by soil depth were Proteobacteria and Acidobacteria (more frequent in samples between 0 and 300 cm). The predominant bacterial groups differentially displayed in the monospecific stands of Eucalyptus were Firmicutes and Proteobacteria. Our results suggest that the addition of an N2-fixing tree in a monospecific cultivation system modulates bacterial community composition even at a great depth. We conclude that co-cultivation systems may represent a key strategy to improve soil resources and to establish more sustainable cultivation of Eucalyptus in Brazil. (Résumé d'auteur

Impacts of organic residue management in eucalyptus forest on microbial communities : S11.04-P -8

Harvest residue management during inter-rotation period greatly influences the availability of nutrients in the soils and the sustainability of future rotations in fast growing plantations established on highly weathered tropical forest. Impact of forest management treatment on productivity was shown, particularly in plantations where organic matter (OM) content is extremely low like in Congo. Consequences of OM management on microbial communities were rarely taken in account. However, changes in microbial biodiversity can impact decomposition processes indicating that understanding the significance of biodiversity is essential to assess the consequences of forestry practices for carbon and nutrient cycles. Experiment was conducted in Eucalyptus plantations in Congo. Three treatments were studied (all aboveground organic residues removed from the plot; only stemwood harvested which correspond to Congolese commercial plantation; or double supply of residues). DNA and RNA were co-extracted from leaf-litter and upper soil layers (0-10 cm). Density and structure of bacterial and fungal communities were assessed by the quantitative PCR (qPCR) and fingerprinting technique (DGGE), respectively based on 16S and 18S rRNA. We also investigated functional microbial communities potentially involved in C cycling: the phylum of the Actinobacteria, known for their saprophytic activities; the BphDox bacterial community involved in the degradation of aromatic compounds and Laccase fungal community implicated in the degradation of phenolic compounds. Altogether, these data allowed to progress in the establishment of links between nutrients flux measured in field and microbial analyses which is a challenge to a better understanding of the functioning of forest ecosystems. (Texte intégral)

Did belowground N transfer in mixed plantations of Acacia mangium and Eucalyptus meet the Stress Gradient Hypothesis?

Belowground interactions in mixed forest plantations remain poorly understood as that of short-tenn nitrogen (N) transfer from N-fixing trees to non-N-fixing trees (Non-NFT) depending on nutrient availability. We investigated in this facilitation process met the Stress Gradient Hypothesis. which predicts that under stressful environmental conditions competition decreases and facilitation increases. A 15N pulse-labelling study was conducted in a five-year-old mixture of 50% Eucalyptus grandis x E. urophylla and 50% Acacia mangium with the hypothesis of higher transfer from acacia when no fertilization was applied. A complete randomized block design was set up with three replicates of fertilized and non-fertilized mixture. In each treatment of each block, a labeled solution of potassium nitrate (98 atom% 15N-N03) was injected into the stem of an Acacia tree with the same basal area as the average of the stand. The x (15N) was monitored over two months in each labeled acacia and four neighboring eucalypts. For both species, young leaves and tine roots were sampled at 7.14 and 30 days after injection. After 60 days. the x (15N) was determined in the wood, bark, branches, total foliage and fine roots of the 6 labeled acacias and 12 eucalypts trees The preliminary results showed that complete absorption of the labeled solution occurred between 28 and 60 days after labeling depending on Acacia trees and treatments. The dynamics in the proportion of Eucalyptus N derived from transfer will give insights into how this process may promote N nutrition of non-NFTs growing in unfertile tropical soils

N2 fixing trees (Acacia mangium) introduce in eucalypt plantations modify rapidly the pools of organic P and low-molecular-weight organic acids (LMWOAs) in tropical soils contrasted for their C/P stoichiometry

In this study, soil organic P (Po) and low-molecular-weight organic acids (LMWOAs) were quantified under different land uses in order to investigate the effect of N2 fixing tree introduction on phosphorus cycle. Soils were collected from plantations of pure acacia (Ac), pure eucalyptus (Euc) or both species (50/50) and original savannahs (S) that were located in Brazil (low P, high N and high C soil) and in Congo (high P. low N and low C soil). Po and LMWOAs were identified in sodium hydroxide soil extracts with ion chromatography (IC). Phosphate monoesters as AMP and glucose-6-phosphate (G6P) were the main Po forms in both sites. Phytate, ATP and fructose-bisphosphate (FrucbisP) were also present as well as the mineral form of pyrophosphate (PrP). Malate, oxalate and malonate were the major components of LMWOA fraction in the two soils. Citrate was also present at low concentrations. lnterresingly, phytate concentrations were always decreased under acacia plantations. This could result from a better mineralisation or lower inputs into these soils. In mixed stands, the effect of acacia introduction on Po and LMWOAs composition is more pronounced in high P than in low P soil, due to a much better N, fixation. Our results highlight that the introduction of a legume tree is able to strongly modify the composition of Po and LMWOAs in soil even after a first short-time rotation, especially when the rate of N2 fixation is high

Diversity of arbuscular mycorrhizal fungi and P-solubilising bacteria in rubber tree rhizospheres in Thailand

Rubber tree (Hevea brasiliensis) is a crop of major importance for smallholders in Southern Asia because it produces latex, a substantial source of income for farmers. Rubber tree can grow on very poor soils (sandy soils, low fertility, subject to erosion and leaching of applied fertilizers), which are unsuitable for other commonly cultivated cash crops. It covers 2.7 million ha across Thailand, but its establishment in areas with very poor soils, especially in Northeast Thailand, represents a major potential for increased production. The important roles of rhizosphere microbial communities in supporting soil fertility and plant nutrition has been widely recognized. In particular, root -interacting P-solubilizing bacteria (PSB) and arbuscular mycorrhizal fungi (AMF) contribute to plant P nutrition by increasing mineral nutrient availability and by enhancing plant nutrient uptake. The diversity of AMF in roots and of PSB in rhizosphere soil was assessed along a chronosequence of rubber tree plantations (3, 6 and 16 year-old) and compared to cassava fields. AMF diversity was assessed by 454 sequencing of SSU 18S rDNA. PSB strains were characterized after culturing on selective media. AMF communities in cassava roots were twice as rich as in rubber tree samples. AMF diversity was not affected by the age of rubber trees, but was related to the soil P content. The improved understanding of the diversity of root-or rhizosphere-associated microbes will contribute to the development of alternative sustainable practices to improve and sustain soil fertility. (Texte intégral