Fabrice Martin-Laurent

Bio: Fabrice Martin-Laurent is an academic researcher from Institut national de la recherche agronomique. The author has contributed to research in topics: Atrazine & Soil water. The author has an hindex of 43, co-authored 177 publications receiving 7458 citations. Previous affiliations of Fabrice Martin-Laurent include Centre national de la recherche scientifique & National Institute of Education.

DNA extraction from soils: old bias for new microbial diversity analysis methods.

Abstract: The impact of three different soil DNA extraction methods on bacterial diversity was evaluated using PCR-based 16S ribosomal DNA analysis. DNA extracted directly from three soils showing contrasting physicochemical properties was subjected to amplified ribosomal DNA restriction analysis and ribosomal intergenic spacer analysis (RISA). The obtained RISA patterns revealed clearly that both the phylotype abundance and the composition of the indigenous bacterial community are dependent on the DNA recovery method used. In addition, this effect was also shown in the context of an experimental study aiming to estimate the impact on soil biodiversity of the application of farmyard manure or sewage sludge onto a monoculture of maize for 15 years.

Role of a Single Aquaporin Isoform in Root Water Uptake

Abstract: Aquaporins are ubiquitous channel proteins that facilitate the transport of water across cell membranes. Aquaporins show a typically high isoform multiplicity in plants, with 35 homologs in Arabidopsis. The integrated function of plant aquaporins and the function of each individual isoform remain poorly understood. Matrix-assisted laser desorption/ionization time-of-flight analyses suggested that Plasma Membrane Intrinsic Protein2;2 (PIP2;2) is one of the abundantly expressed aquaporin isoforms in Arabidopsis root plasma membranes. Two independent Arabidopsis knockout mutants of PIP2;2 were isolated using a PCR-based strategy from a library of plant lines mutagenized by the insertion of Agrobacterium tumefaciens T-DNA. Expression in transgenic Arabidopsis of a PIP2;2 promoter–β-glucuronidase gene fusion indicated that PIP2;2 is expressed predominantly in roots, with a strong expression in the cortex, endodermis, and stele. The hydraulic conductivity of root cortex cells, as measured with a cell pressure probe, was reduced by 25 to 30% in the two allelic PIP2;2 mutants compared with the wild type. In addition, free exudation measurements revealed a 14% decrease, with respect to wild-type values, in the osmotic hydraulic conductivity of roots excised from the two PIP2;2 mutants. Together, our data provide evidence for the contribution of a single aquaporin gene to root water uptake and identify PIP2;2 as an aquaporin specialized in osmotic fluid transport. PIP2;2 has a close homolog, PIP2;3, showing 96.8% amino acid identity. The phenotype of PIP2;2 mutants demonstrates that, despite their high homology and isoform multiplicity, plant aquaporins have evolved with nonredundant functions.

Mapping field-scale spatial patterns of size and activity of the denitrifier community.

Abstract: There is ample evidence that microbial processes can exhibit large variations in activity on a field scale. However, very little is known about the spatial distribution of the microbial communities mediating these processes. Here we used geostatistical modelling to explore spatial patterns of size and activity of the denitrifying community, a functional guild involved in N-cycling, in a grassland field subjected to different cattle grazing regimes. We observed a non-random distribution pattern of the size of the denitrifier community estimated by quantification of the denitrification genes copy numbers with a macro-scale spatial dependence (6-16 m) and mapped the distribution of this functional guild in the field. The spatial patterns of soil properties, which were strongly affected by presence of cattle, imposed significant control on potential denitrification activity, potential N(2)O production and relative abundance of some denitrification genes but not on the size of the denitrifier community. Absolute abundance of most denitrification genes was not correlated with the distribution patterns of potential denitrification activity or potential N(2)O production. However, the relative abundance of bacteria possessing the nosZ gene encoding the N(2)O reductase in the total bacterial community was a strong predictor of the N(2)O/(N(2) + N(2)O) ratio, which provides evidence for a relationship between bacterial community composition based on the relative abundance of denitrifiers in the total bacterial community and ecosystem processes. More generally, the presented geostatistical approach allows integrated mapping of microbial communities, and hence can facilitate our understanding of relationships between the ecology of microbial communities and microbial processes along environmental gradients.

Plant drought stress: effects, mechanisms and management

Abstract: Scarcity of water is a severe environmental constraint to plant productivity. Drought-induced loss in crop yield probably exceeds losses from all other causes, since both the severity and duration of the stress are critical. Here, we have reviewed the effects of drought stress on the growth, phenology, water and nutrient relations, photosynthesis, assimilate partitioning, and respiration in plants. This article also describes the mechanism of drought resistance in plants on a morphological, physiological and molecular basis. Various management strategies have been proposed to cope with drought stress. Drought stress reduces leaf size, stem extension and root proliferation, disturbs plant water relations and reduces water-use efficiency. Plants display a variety of physiological and biochemical responses at cellular and whole-organism levels towards prevailing drought stress, thus making it a complex phenomenon. CO2 assimilation by leaves is reduced mainly by stomatal closure, membrane damage and disturbed activity of various enzymes, especially those of CO2 fixation and adenosine triphosphate synthesis. Enhanced metabolite flux through the photorespiratory pathway increases the oxidative load on the tissues as both processes generate reactive oxygen species. Injury caused by reactive oxygen species to biological macromolecules under drought stress is among the major deterrents to growth. Plants display a range of mechanisms to withstand drought stress. The major mechanisms include curtailed water loss by increased diffusive resistance, enhanced water uptake with prolific and deep root systems and its efficient use, and smaller and succulent leaves to reduce the transpirational loss. Among the nutrients, potassium ions help in osmotic adjustment; silicon increases root endodermal silicification and improves the cell water balance. Low-molecular-weight osmolytes, including glycinebetaine, proline and other amino acids, organic acids, and polyols, are crucial to sustain cellular functions under drought. Plant growth substances such as salicylic acid, auxins, gibberrellins, cytokinin and abscisic acid modulate the plant responses towards drought. Polyamines, citrulline and several enzymes act as antioxidants and reduce the adverse effects of water deficit. At molecular levels several drought-responsive genes and transcription factors have been identified, such as the dehydration-responsive element-binding gene, aquaporin, late embryogenesis abundant proteins and dehydrins. Plant drought tolerance can be managed by adopting strategies such as mass screening and breeding, marker-assisted selection and exogenous application of hormones and osmoprotectants to seed or growing plants, as well as engineering for drought resistance.

Soil bacterial and fungal communities across a pH gradient in an arable soil.

Abstract: Soils collected across a long-term liming experiment (pH 4.0-8.3), in which variation in factors other than pH have been minimized, were used to investigate the direct influence of pH on the abundance and composition of the two major soil microbial taxa, fungi and bacteria. We hypothesized that bacterial communities would be more strongly influenced by pH than fungal communities. To determine the relative abundance of bacteria and fungi, we used quantitative PCR (qPCR), and to analyze the composition and diversity of the bacterial and fungal communities, we used a bar-coded pyrosequencing technique. Both the relative abundance and diversity of bacteria were positively related to pH, the latter nearly doubling between pH 4 and 8. In contrast, the relative abundance of fungi was unaffected by pH and fungal diversity was only weakly related with pH. The composition of the bacterial communities was closely defined by soil pH; there was as much variability in bacterial community composition across the 180-m distance of this liming experiment as across soils collected from a wide range of biomes in North and South America, emphasizing the dominance of pH in structuring bacterial communities. The apparent direct influence of pH on bacterial community composition is probably due to the narrow pH ranges for optimal growth of bacteria. Fungal community composition was less strongly affected by pH, which is consistent with pure culture studies, demonstrating that fungi generally exhibit wider pH ranges for optimal growth.

Fast Tree: Computing Large Minimum-Evolution Trees with Profiles instead of a Distance Matrix

Abstract: Gene families are growing rapidly, but standard methods for inferring phylogenies do not scale to alignments with over 10,000 sequences. We present FastTree, a method for constructing large phylogenies and for estimating their reliability. Instead of storing a distance matrix, FastTree stores sequence profiles of internal nodes in the tree. FastTree uses these profiles to implement neighbor-joining and uses heuristics to quickly identify candidate joins. FastTree then uses nearest-neighbor interchanges to reduce the length of the tree. For an alignment with N sequences, L sites, and a different characters, a distance matrix requires O(N^2) space and O(N^2 L) time, but FastTree requires just O( NLa + N sqrt(N) ) memory and O( N sqrt(N) log(N) L a ) time. To estimate the tree's reliability, FastTree uses local bootstrapping, which gives another 100-fold speedup over a distance matrix. For example, FastTree computed a tree and support values for 158,022 distinct 16S ribosomal RNAs in 17 hours and 2.4 gigabytes of memory. Just computing pairwise Jukes-Cantor distances and storing them, without inferring a tree or bootstrapping, would require 17 hours and 50 gigabytes of memory. In simulations, FastTree was slightly more accurate than neighbor joining, BIONJ, or FastME; on genuine alignments, FastTree's topologies had higher likelihoods. FastTree is available at http://microbesonline.org/fasttree.

Microbial diversity and soil functions

Abstract: Summary Soil is a complex and dynamic biological system, and still in 2003 it is difficult to determine the composition of microbial communities in soil. We are also limited in the determination of microbially mediated reactions because present assays for determining the overall rate of entire metabolic processes (such as respiration) or specific enzyme activities (such as urease, protease and phosphomonoesterase activity) do not allow any identification of the microbial species directly involved in the measured processes. The central problem posed by the link between microbial diversity and soil function is to understand the relations between genetic diversity and community structure and between community structure and function. A better understanding of the relations between microbial diversity and soil functions requires not only the use of more accurate assays for taxonomically and functionally characterizing DNA and RNA extracted from soil, but also high-resolution techniques with which to detect inactive and active microbial cells in the soil matrix. Soil seems to be characterized by a redundancy of functions; for example, no relationship has been shown to exist between microbial diversity and decomposition of organic matter. Generally, a reduction in any group of species has little effect on overall processes in soil because other microorganisms can take on its function. The determination of the composition of microbial communities in soil is not necessary for a better quantification of nutrient transformations. The holistic approach, based on the division of the systems in pools and the measurement of fluxes linking these pools, is the most efficient. The determination of microbial C, N, P and S contents by fumigation techniques has allowed a better quantification of nutrient dynamics in soil. However, further advances require determining new pools, such as active microbial biomass, also with molecular techniques. Recently investigators have separated 13C- and 12C-DNA, both extracted from soil treated with a 13C source, by density-gradient centrifugation. This technique should allow us to calculate the active microbial C pool by multiplying the ratio between labelled and total DNA by the microbial biomass C content of soil. In addition, the taxonomic and functional characterization of 13C-DNA allows us to understand more precisely the changes in the composition of microbial communities affected by the C-substrate added to soil.