Damaris Desgarennes

Bio: Damaris Desgarennes is an academic researcher from Instituto Politécnico Nacional. The author has contributed to research in topics: Phyllosphere & Globodera rostochiensis. The author has an hindex of 9, co-authored 23 publications receiving 541 citations. Previous affiliations of Damaris Desgarennes include Universidad Autónoma del Estado de México & CINVESTAV.

Plant Compartment and Biogeography Affect Microbiome Composition in Cultivated and Native Agave Species

Abstract: Desert plants are hypothesized to survive the environmental stress inherent to these regions in part thanks to symbioses with microorganisms, and yet these microbial species, the communities they form, and the forces that influence them are poorly understood. Here we report the first comprehensive investigation of the microbial communities associated with species of Agave, which are native to semiarid and arid regions of Central and North America and are emerging as biofuel feedstocks. We examined prokaryotic and fungal communities in the rhizosphere, phyllosphere, leaf and root endosphere, as well as proximal and distal soil samples from cultivated and native agaves, through Illumina amplicon sequencing. Phylogenetic profiling revealed that the composition of prokaryotic communities was primarily determined by the plant compartment, whereas the composition of fungal communities was mainly influenced by the biogeography of the host species. Cultivated A. tequilana exhibited lower levels of prokaryotic diversity compared with native agaves, although no differences in microbial diversity were found in the endosphere. Agaves shared core prokaryotic and fungal taxa known to promote plant growth and confer tolerance to abiotic stress, which suggests common principles underpinning Agave-microbe interactions.

Functional Signatures of the Epiphytic Prokaryotic Microbiome of Agaves and Cacti

Abstract: Microbial symbionts account for survival, development, fitness and evolution of eukaryotic hosts. These microorganisms together with their host form a biological unit known as holobiont. Recent studies have revealed that the holobiont of agaves and cacti comprises a diverse and structured microbiome, which might be important for its adaptation to drylands. Here, we investigated the functional signatures of the prokaryotic communities of the soil and the episphere, that includes the rhizosphere and phyllosphere, associated with the cultivated Agave tequilana and the native and sympatric Agave salmiana, Opuntia robusta and Myrtillocactus geometrizans by mining shotgun metagenomic data. Consistent with previous phylogenetic profiling, we found that Proteobacteria, Actinobacteria and Firmicutes were the main represented phyla in the episphere of agaves and cacti, and that clustering of metagenomes correlated with the plant compartment. In native plants, genes related to aerobic anoxygenic phototrophy and photosynthesis were enriched in the phyllosphere and soil, while genes coding for biofilm formation and quorum sensing were enriched in both epiphytic communities. In the episphere of cultivated A. tequilana fewer genes were identified, but they belonged to similar pathways than those found in native plants. A. tequilana showed a depletion in several genes belonging to carbon metabolism, secondary metabolite biosynthesis and xenobiotic degradation suggesting that its lower microbial diversity might be linked to functional losses. However, this species also showed an enrichment in biofilm and quorum sensing in the epiphytic compartments, and evidence for nitrogen fixation in the rhizosphere. Aerobic anoxygenic phototrophic markers were represented by Rhizobiales (Methylobacterium) and Rhodospirillales (Belnapia) in the phyllosphere, while photosystem genes were widespread in Bacillales and Cyanobacteria. Nitrogen fixation and biofilm formation genes were mostly related to Proteobacteria. These analyses support the idea of niche differentiation in the rhizosphere and phyllosphere of agaves and cacti and shed light on the potential mechanisms by which epiphytic microbial communities survive and colonize plants of arid and semiarid ecosystems. This study establishes a guideline for testing the relevance of the identified functional traits on the microbial community and the plant fitness.

Diversity and Composition of the Gut Microbiota in the Developmental Stages of the Dung Beetle Copris incertus Say (Coleoptera, Scarabaeidae).

Abstract: Dung beetles are holometabolous insects that feed on herbivorous mammal dung and provide services to the ecosystem including nutrient cycling and soil fertilization. It has been suggested that organisms developing on incomplete diets such as dungs require the association with microorganisms for the synthesis and utilization of nutrients. We describe the diversity and composition of the gut-microbiota during the life cycle of the dung beetle Copris incertus using 16S rRNA gene sequencing. We found that C. incertus gut contained a broad diversity of bacterial groups (1,699 OTUs and 302 genera). The taxonomic composition varied during the beetle life cycle, with the predominance of some bacterial genera in a specific developmental stage (Mothers: Enterobacter and Serratia; Eggs: Nocardioides and Hydrogenophaga; Larval and pupal stages: Dysgonomonas and Parabacteroides; offspring: Ochrobactrum). The beta diversity evidenced similarities among developmental stages, clustering (i) the adult stages (mother, male and female offsprings), (ii) intermediate developmental (larvae and pupa), and (iii) initial stage (egg). Microbiota differences could be attributed to dietary specialization or/and morpho-physiological factors involved in the transition from a developmental stage to the next. The predicted functional profile (PICRUSt2 analysis) for the development bacterial core of the level 3 categories, indicated grouping by developmental stage. Only 36 categories were significant in the SIMPER analysis, including the metabolic categories of amino acids and antibiotic synthesis, which were enriched in the larval and pupal stages; both categories are involved in the metamorphosis process. At the gene level, we found significant differences only in the KOs encoding functions related to nitrogen fixation, uric acid metabolism, and plant cell wall degradation for all developmental stages. Nitrogen fixation and plant cell wall degradation were enriched in the intermediate stages and uric acid metabolism was enriched in mothers. The data reported here suggested the influence of the maternal microbiota in the composition and diversity of the gut microbiota of the offspring.

Phytophthora Root Rot Modifies the Composition of the Avocado Rhizosphere Microbiome and Increases the Abundance of Opportunistic Fungal Pathogens.

Abstract: The structure and function of rhizosphere microbial communities are affected by the plant health status. In this study, we investigated the effect of root rot on the avocado rhizosphere microbiome, using 16S rDNA and ITS sequencing. Furthermore, we isolated potential fungal pathogens associated with root rot symptoms and assessed their pathogenic activity on avocado. We found that root rot did not affect species richness, diversity or community structure, but induced changes in the relative abundance of several microbial taxa. Root rot increased the proportion of Pseudomonadales and Burkholderiales in the rhizosphere but reduced that of Actinobacteria, Bacillus spp. and Rhizobiales. An increase in putative opportunistic fungal pathogens was also detected in the roots of symptomatic trees; the potential pathogenicity of Mortierella sp., Fusarium spp., Lasiodiplodia sp. and Scytalidium sp., is reported for the first time for the State of Veracruz, Mexico. Root rot also potentially modified the predicted functions carried out by rhizobacteria, reducing the proportion of categories linked with the lipid and amino-acid metabolisms whilst promoting those associated with quorum sensing, virulence, and antibiotic resistance. Altogether, our results could help identifying microbial taxa associated to the disease causal agents and direct the selection of plant growth-promoting bacteria for the development of biocontrol microbial consortia.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

Abstract: The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

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.

Plant–microbiome interactions: from community assembly to plant health

Abstract: Healthy plants host diverse but taxonomically structured communities of microorganisms, the plant microbiota, that colonize every accessible plant tissue. Plant-associated microbiomes confer fitness advantages to the plant host, including growth promotion, nutrient uptake, stress tolerance and resistance to pathogens. In this Review, we explore how plant microbiome research has unravelled the complex network of genetic, biochemical, physical and metabolic interactions among the plant, the associated microbial communities and the environment. We also discuss how those interactions shape the assembly of plant-associated microbiomes and modulate their beneficial traits, such as nutrient acquisition and plant health, in addition to highlighting knowledge gaps and future directions. In this Review, Trivedi and colleagues explore the interactions between plants, their associated microbial communities and the environment, and also discuss how those interactions shape the assembly of plant-associated microbiomes and modulate their beneficial traits.

Plant Growth-Promoting Rhizobacteria: Context, Mechanisms of Action, and Roadmap to Commercialization of Biostimulants for Sustainable Agriculture.

Abstract: Microbes of the phytomicrobiome are associated with every plant tissue and, in combination with the plant form the holobiont. Plants regulate the composition and activity of their associated bacterial community carefully. These microbes provide a wide range of services and benefits to the plant; in return, the plant provides the microbial community with reduced carbon and other metabolites. Soils are generally a moist environment, rich in reduced carbon which supports extensive soil microbial communities. The rhizomicrobiome is of great importance to agriculture owing to the rich diversity of root exudates and plant cell debris that attract diverse and unique patterns of microbial colonization. Microbes of the rhizomicrobiome play key roles in nutrient acquisition and assimilation, improved soil texture, secreting, and modulating extracellular molecules such as hormones, secondary metabolites, antibiotics, and various signal compounds, all leading to enhancement of plant growth. The microbes and compounds they secrete constitute valuable biostimulants and play pivotal roles in modulating plant stress responses. Research has demonstrated that inoculating plants with plant-growth promoting rhizobacteria (PGPR) or treating plants with microbe-to-plant signal compounds can be an effective strategy to stimulate crop growth. Furthermore, these strategies can improve crop tolerance for the abiotic stresses (e.g., drought, heat, and salinity) likely to become more frequent as climate change conditions continue to develop. This discovery has resulted in multifunctional PGPR-based formulations for commercial agriculture, to minimize the use of synthetic fertilizers and agrochemicals. This review is an update about the role of PGPR in agriculture, from their collection to commercialization as low-cost commercial agricultural inputs. First, we introduce the concept and role of the phytomicrobiome and the agricultural context underlying food security in the 21st century. Next, mechanisms of plant growth promotion by PGPR are discussed, including signal exchange between plant roots and PGPR and how these relationships modulate plant abiotic stress responses via induced systemic resistance. On the application side, strategies are discussed to improve rhizosphere colonization by PGPR inoculants. The final sections of the paper describe the applications of PGPR in 21st century agriculture and the roadmap to commercialization of a PGPR-based technology.