Alison Berry
University of California, Davis, Plant Sciences, Faculty Member
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We report the genome sequence of Frankia sp. strain ArI3, recovered as a single contig from one run of the Oxford Nanopore Technologies (ONT) MinION instrument. The genome has a G+C content of 72%, is 7,541,222 bp long, and contains 5,427... more
We report the genome sequence of Frankia sp. strain ArI3, recovered as a single contig from one run of the Oxford Nanopore Technologies (ONT) MinION instrument. The genome has a G+C content of 72%, is 7,541,222 bp long, and contains 5,427 predicted protein-coding genes.
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The root nodule symbiosis of plants with nitrogen-fixing bacteria affects global nitrogen cycles and food production but is restricted to a subset of genera within a single clade of flowering plants. To explore the genetic basis for this... more
The root nodule symbiosis of plants with nitrogen-fixing bacteria affects global nitrogen cycles and food production but is restricted to a subset of genera within a single clade of flowering plants. To explore the genetic basis for this scattered occurrence, we sequenced the genomes of 10 plant species covering the diversity of nodule morphotypes, bacterial symbionts, and infection strategies. In a genome-wide comparative analysis of a total of 37 plant species, we discovered signatures of multiple independent loss-of-function events in the indispensable symbiotic regulator in 10 of 13 genomes of nonnodulating species within this clade. The discovery that multiple independent losses shaped the present-day distribution of nitrogen-fixing root nodule symbiosis in plants reveals a phylogenetically wider distribution in evolutionary history and a so-far-underestimated selection pressure against this symbiosis.
Research Interests: Genomics, Molecular Evolution, Science, Symbiosis, Biology, and 13 moreMedicine, Multidisciplinary, Phylogenomics, Phylogeny, Plant Genome Project, Nitrogen Fixation, Legumes, Nitrogen, Molecular Phylogenetics and Evolution, Genome, Ciencias Biológicas, Fabaceae, and Enseñanza - Aprendizaje Ciencias Naturales Y Exactas
Actinorhizal plants are a group of taxonomically diverse angiosperms with remarkable economic and ecological significance. Most actinorhizal plants are able to thrive under extreme adverse environmental conditions as well as to fix... more
Actinorhizal plants are a group of taxonomically diverse angiosperms with remarkable economic and ecological significance. Most actinorhizal plants are able to thrive under extreme adverse environmental conditions as well as to fix atmospheric nitrogen due to their capacity to establish root nodule symbioses with Frankia bacteria. This special issue of Functional Plant Biology is dedicated to actinorhizal plant research, covering part of the work presented at the 16th International Meeting onFrankia and Actinorhizal Plants, held on 5–8 September 2010, in Oporto, Portugal. The papers (4 reviews and 10 original articles) give an overall picture of the status of actinorhizal plant research and the imposed challenges, covering several aspects of the symbiosis, ecology and molecular tools.
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Despite advances in sequencing, lack of standardization makes comparisons across studies challenging and hampers insights into the structure and function of microbial communities across multiple habitats on a planetary scale. Here we... more
Despite advances in sequencing, lack of standardization makes comparisons across studies challenging and hampers insights into the structure and function of microbial communities across multiple habitats on a planetary scale. Here we present a multi-omics analysis of a diverse set of 880 microbial community samples collected for the Earth Microbiome Project. We include amplicon (16S, 18S, ITS) and shotgun metagenomic sequence data, and untargeted metabolomics data (liquid chromatography-tandem mass spectrometry and gas chromatography mass spectrometry). We used standardized protocols and analytical methods to characterize microbial communities, focusing on relationships and co-occurrences of microbially related metabolites and microbial taxa across environments, thus allowing us to explore diversity at extraordinary scale. In addition to a reference database for metagenomic and metabolomic data, we provide a framework for incorporating additional studies, enabling the expansion of e...
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The California Tree Failure Report Program database was established in 1987 to collect data on tree branch, trunk, and root breakage or uprooting. The database for the CTFRP is compiled from failure evaluation reports filled out by... more
The California Tree Failure Report Program database was established in 1987 to collect data on tree branch, trunk, and root breakage or uprooting. The database for the CTFRP is compiled from failure evaluation reports filled out by statewide cooperating arborists, tree assessors, and other horticultural professionals. Compilation of 186 reports for Monterey pine (Pinus radiata) has permitted development of a "failure profile" -a characterization of failure location, structural defects, decay, climatic conditions, and other factors associated with structural failure of Monterey pine. Monterey pine was found to be particularly failure prone compared to other tree species in Golden Gate Park, San Francisco, CA. Close to 60% of Monterey pine failures reported in the CTFRP database were limb failures, rather than trunk or root failures, and most of these were considered to be heavy lateral limbs - a structural defect. The majority of limb breakage occurred away from, rather tha...
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Data from the California Tree Failure Report Program (CTFRP) were analyzed to develop a profile of the structural failure characteristics for coast live oak (Quercus agrifolia). The most common pattern of structural failure for coast live... more
Data from the California Tree Failure Report Program (CTFRP) were analyzed to develop a profile of the structural failure characteristics for coast live oak (Quercus agrifolia). The most common pattern of structural failure for coast live oak reported in the CTFRP is a root or low trunk failure of a naturally occurring tree growing in a residential site. Decay, site grade changes, and low wind speeds are significantly more frequently associated with coast live oak failures than with other hardwoods, conifers, or eucalyptus. Decay of roots and lower trunk was a major contributing factor to failure of coast live oak (83%). Saturated soil conditions associated with root failure were also more frequent for coast live oak than for other species groups. Careful attention to controlling excess soil moisture, avoiding or correcting grade change and compaction, and monitoring decay are essential to maintain the health of coast live oak.
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Spring 2015 tree vigor and increase susceptibility to pests and diseases (Tubby & Webber 20 0). Restricted and limited water will lead to tradeoffs between conserving water and meeting the demands of an increasing population (Niinemets &... more
Spring 2015 tree vigor and increase susceptibility to pests and diseases (Tubby & Webber 20 0). Restricted and limited water will lead to tradeoffs between conserving water and meeting the demands of an increasing population (Niinemets & Penuelas 2008). Tree species with high water needs will be vulnerable in the changing conditions and the use of saline reclaimed water will adversely impact the health of sensitive trees. The goal of this study is to evaluate the growth and survival of climate-ready trees in the Central Valley. By identifying trees that perform best under stressors associated with climate change, we can help shift the palette of trees commonly planted to species that will provide the most
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Research Interests: Landscape Ecology, Geography, Earth Sciences, Environmental Management, China, and 12 moreIntelligent Transport System, Landscape, Urban Development, Biological Sciences, Environmental Sciences, Nature Conservation, Species Diversity, Threatened Species, Institute of Transportation Studies 50th Anniversary, Landscape Fragmentation, Urban Area, and transport system
Research Interests: Engineering, Geography, Decision Making, Landscape, Urban Development, and 15 moreRegional Planning, Environmental Sciences, Land Development, Road Ecology, Habitat, Case Study, Transportation Planning, Fragmentation, Spatial Scale, Habitat fragmentation, Landscape connectivity, Transport Infrastructure, Landscape Fragmentation, Urban Area, and Cumulant
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Identifying orthologous genes is an initial step required for phylogenetics, and it is also a common strategy employed in functional genetics to find candidates for functionally equivalent genes across multiple species. At the same time,... more
Identifying orthologous genes is an initial step required for phylogenetics, and it is also a common strategy employed in functional genetics to find candidates for functionally equivalent genes across multiple species. At the same time, in silico orthology prediction tools often require large computational resources only available on computing clusters. Here we present OrthoReD, an open-source orthology prediction tool with accuracy comparable to published tools that requires only a desktop computer. The low computational resource requirement of OrthoReD is achieved by repeating orthology searches on one gene of interest at a time, thereby generating a reduced dataset to limit the scope of orthology search for each gene of interest. The output of OrthoReD was highly similar to the outputs of two other published orthology prediction tools, OrthologID and/or OrthoDB, for the three dataset tested, which represented three phyla with different ranges of species diversity and different n...
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Research Interests: Botany, Plant Biology, Symbiosis, Biology, Medicine, and 4 moreNitrogen metabolism, Defensin, Frankia, and Rhamnaceae
Research Interests: Botany, Plant Biology, Symbiosis, Biology, Medicine, and 6 moreActinorhizal, Frankia, Rhizobia, Legume, Flavonoid, and Phenylpropanoid
Plants are associated with a complex microbiota that contributes to nutrient acquisition, plant growth, and plant defense. Nitrogen-fixing microbial associations are efficient and well characterized in legumes but are limited in cereals,... more
Plants are associated with a complex microbiota that contributes to nutrient acquisition, plant growth, and plant defense. Nitrogen-fixing microbial associations are efficient and well characterized in legumes but are limited in cereals, including maize. We studied an indigenous landrace of maize grown in nitrogen-depleted soils in the Sierra Mixe region of Oaxaca, Mexico. This landrace is characterized by the extensive development of aerial roots that secrete a carbohydrate-rich mucilage. Analysis of the mucilage microbiota indicated that it was enriched in taxa for which many known species are diazotrophic, was enriched for homologs of genes encoding nitrogenase subunits, and harbored active nitrogenase activity as assessed by acetylene reduction and 15N2 incorporation assays. Field experiments in Sierra Mixe using 15N natural abundance or 15N-enrichment assessments over 5 years indicated that atmospheric nitrogen fixation contributed 29%-82% of the nitrogen nutrition of Sierra Mi...
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The genus Frankia comprises a group of nitrogen-fixing actinobacteria that form root-nodule symbioses with perennial dicotyledonous plants in the nitrogen-fixing clade. These bacteria have been characterized phylogenetically and grouped... more
The genus Frankia comprises a group of nitrogen-fixing actinobacteria that form root-nodule symbioses with perennial dicotyledonous plants in the nitrogen-fixing clade. These bacteria have been characterized phylogenetically and grouped into four clusters (clusters 1-4). Cluster 2 contains mostly uncultured strains that induce nodules on species of the genera Datisca (Datiscaceae), Coriaria (Coriariaceae), Ceanothus (Rhamnaceae) and several genera in the family Rosaceae (Cercocarpus, Chamaebatia, Dryas, Purshia), all of which except members of the genus Coriaria are present within the California Floristic Province (CFP) or neighbouring areas of western North America. Those strains occurring in western North America are genetically very closely related to one another, and genetically distinct from strains characterized from other locales. We hereby propose to create a 'Candidatus Frankia californiensis' species for those cluster 2 strains of the genus Frankia with both high g...
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The actinobacterial genus Frankia establishes nitrogen-fixing root nodule symbioses with specific hosts within the nitrogen-fixing plant clade. Of four genetically distinct subgroups of Frankia , cluster I, II, and III strains are capable... more
The actinobacterial genus Frankia establishes nitrogen-fixing root nodule symbioses with specific hosts within the nitrogen-fixing plant clade. Of four genetically distinct subgroups of Frankia , cluster I, II, and III strains are capable of forming effective nitrogen-fixing symbiotic associations, while cluster IV strains generally do not. Cluster II Frankia strains have rarely been detected in soil devoid of host plants, unlike cluster I or III strains, suggesting a stronger association with their host. To investigate the degree of host influence, we characterized the cluster II Frankia strain distribution in rhizosphere soil in three locations in northern California. The presence/absence of cluster II Frankia strains at a given site correlated significantly with the presence/absence of host plants on the site, as determined by glutamine synthetase ( glnA ) gene sequence analysis, and by microbiome analysis (16S rRNA gene) of a subset of host/nonhost rhizosphere soils. However, th...
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The ability to establish root nodule symbioses is restricted to four different plant orders. Soil actinobacteria of the genus Frankia can establish a symbiotic relationship with a diverse group of plants within eight different families... more
The ability to establish root nodule symbioses is restricted to four different plant orders. Soil actinobacteria of the genus Frankia can establish a symbiotic relationship with a diverse group of plants within eight different families from three different orders, the Cucurbitales, Fagales and Rosales. Phylogenetically, Frankia strains can be divided into four clusters, three of which (I, II, III) contain symbiotic strains. Members of Cluster II nodulate the broadest range of host plants with species from four families from two different orders, growing on six continents. Two Cluster II genomes were sequenced thus far, both from Asia. In this paper we present the first Frankia cluster II genome from North America (California), Dg2, which represents a metagenome of two major and one minor strains. A phylogenetic analysis of the core genomes of 16 Frankia strains shows that Cluster II the ancestral group in the genus, also ancestral to the non-symbiotic Cluster IV. Dg2 contains the ca...
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We have isolated a 590-bp full-length cDNA clone designatedDg93, an mRNA that is highly expressed in symbiotic root nodules of the actinorhizal host Datisca glomerata. Dg93mRNA encodes a deduced polypeptide of 105 amino acids with... more
We have isolated a 590-bp full-length cDNA clone designatedDg93, an mRNA that is highly expressed in symbiotic root nodules of the actinorhizal host Datisca glomerata. Dg93mRNA encodes a deduced polypeptide of 105 amino acids with significant identity (74%) to the soybean (Glycine max) early nodulin (ENOD) gene GmENOD93 (Kouchi and Hata, 1993).Dg93 mRNA is abundant in nodules at 4 weeks post inoculation, the earliest time assayed, and steady-state mRNA levels remain elevated 11 weeks after inoculation. Spatial patterns ofDg93 mRNA expression are complex, with transcript accumulation in the nodule lobe meristem, early infection zone, periderm, and cells of the vascular cylinder, but not in the surrounding uninfected cortical cells. Dg93 is encoded by a small gene family in D. glomerata. To our knowledge, this is the first report of a gene from an actinorhizal host that is expressed in the nodule meristem and that shares sequence homology with an early nodulin gene from a legume.
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Vesicles are specific Frankia structures which are produced under nitrogen-limiting culture conditions. Hopanoids are the most abundant lipids in these vesicles and are believed to protect the nitrogenase against oxygen. The amounts and... more
Vesicles are specific Frankia structures which are produced under nitrogen-limiting culture conditions. Hopanoids are the most abundant lipids in these vesicles and are believed to protect the nitrogenase against oxygen. The amounts and quality of each hopanoid were estimated in different Frankia strains cultivated under nitrogen-depleted and nitrogen-replete conditions in order to detect a possible variation. Studied Frankia strains nodulating Eleagnus were phylogenetically characterized by analysis of the nifD-K intergenic region as closely related to genomic species 4 and 5. Phylogenetically different strains belonging to three infectivity groups were cultivated in the same medium with and without nitrogen source for 10 d before hopanoid content analysis by HPLC. Four hopanoids together accounted for 23-87% and 15-87% of the total lipids under nitrogen-replete and nitrogen-depleted culture conditions, respectively. Two of the hopanoids found, bacteriohopanetetrols and their pheny...
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N2-fixing symbiotic root nodules of the actinorhizal host Datisca glomerata express Dgrca(D.glomerataRubisco activase) mRNA, a transcript usually associated with photosynthetic organs or tissues. In northern blots a mature,... more
N2-fixing symbiotic root nodules of the actinorhizal host Datisca glomerata express Dgrca(D.glomerataRubisco activase) mRNA, a transcript usually associated with photosynthetic organs or tissues. In northern blots a mature, 1700-nucleotide Dgrca mRNA was detected in green plant organs (leaves, flowers, and developing fruits) and in nodules but was not detected in roots. A second message of 3000 nucleotides was observed only in nodules. Both size classes of transcripts were polyadenylated. The larger transcript was 2- to 5-fold more abundant than the mature mRNA; it was hybridized to an intronic probe, indicating that a stable, incompletely spliced transcript was accumulating. Treatment with light on excised nodules did not alter the relative abundance of the two species. In in situ hybridizations theDgrca message was expressed intensely in the nuclei of infected cells. The Dgrca transcripts also accumulated at lower levels in uninfected cortical cells adjacent to the periderm and th...
Research Interests: Photosynthesis, Biology, Polyadenylation, Medicine, Gene expression, and 15 moreIn Situ Hybridization, Biological Sciences, Plant Physiology, Bacteria, Plants, Plant Roots, Introns, Frankia, Actinomycetales, Amino Acid Sequence, Base Sequence, Organogenesis, PLANT PROTEINS, Nucleotides, and Molecular Sequence Data
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Phylogenetic analyses suggest that, among the members of the Eurosid I clade, nitrogen-fixing root nodule symbioses developed multiple times independently, four times with rhizobia and four times with the genus Frankia. In order to... more
Phylogenetic analyses suggest that, among the members of the Eurosid I clade, nitrogen-fixing root nodule symbioses developed multiple times independently, four times with rhizobia and four times with the genus Frankia. In order to understand the degree of similarity between symbiotic systems of different phylogenetic subgroups, gene expression patterns were analyzed in root nodules of Datisca glomerata and compared with those in nodules of another actinorhizal plant, Alnus glutinosa, and with the expression patterns of homologous genes in legumes. In parallel, the phylogeny of actinorhizal plants was examined more closely. The results suggest that, although relationships between major groups are difficult to resolve using molecular phylogenetic analysis, the comparison of gene expression patterns can be used to inform evolutionary relationships. In this case, stronger similarities were found between legumes and intracellularly infected actinorhizal plants (Alnus) than between actin...
Research Interests: Botany, Genetics, Microbiology, Phylogenetics, Plant Biology, and 15 moreBiology, Plant Molecular Biology, Medicine, Phylogeny, Plants, Molecular Plant Microbe Interactions, Plant Roots, Frankia, Fabaceae, Phylogenetic Tree, Amino Acid Sequence, Base Sequence, PLANT PROTEINS, Molecular Sequence Data, and Ag
Members of the noncultured clade of Frankia enter into root nodule symbioses with actinorhizal species from the orders Cucurbitales and Rosales. We report the genome sequence of a member of this clade originally from Pakistan but obtained... more
Members of the noncultured clade of Frankia enter into root nodule symbioses with actinorhizal species from the orders Cucurbitales and Rosales. We report the genome sequence of a member of this clade originally from Pakistan but obtained from root nodules of the American plant Datisca glomerata without isolation in culture.
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We present here the complete 2.4-Mb genome of the cellulolytic actinobacterial thermophile Acidothermus cellulolyticus 11B. New secreted glycoside hydrolases and carbohydrate esterases were identified in the genome, revealing a diverse... more
We present here the complete 2.4-Mb genome of the cellulolytic actinobacterial thermophile Acidothermus cellulolyticus 11B. New secreted glycoside hydrolases and carbohydrate esterases were identified in the genome, revealing a diverse biomass-degrading enzyme repertoire far greater than previously characterized and elevating the industrial value of this organism. A sizable fraction of these hydrolytic enzymes break down plant cell walls, and the remaining either degrade components in fungal cell walls or metabolize storage carbohydrates such as glycogen and trehalose, implicating the relative importance of these different carbon sources. Several of the A. cellulolyticus secreted cellulolytic and xylanolytic enzymes are fused to multiple tandemly arranged carbohydrate binding modules (CBM), from families 2 and 3. For the most part, thermophilic patterns in the genome and proteome of A. cellulolyticus were weak, which may be reflective of the recent evolutionary history of A. cellulo...
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Nitrogen-fixing root nodules are plant organs specialised for symbiotic transfer of nitrogen and carbon between microsymbiont and host. The organisation of nitrogen assimilation, storage and transport processes is partitioned at the... more
Nitrogen-fixing root nodules are plant organs specialised for symbiotic transfer of nitrogen and carbon between microsymbiont and host. The organisation of nitrogen assimilation, storage and transport processes is partitioned at the subcellular and tissue levels, in distinctive patterns depending on the symbiotic partners. In this review, recent advances in understanding of actinorhizal nodule nitrogen assimilation are presented. New findings indicate that Frankia within nodules of Datisca glomerata (Presl.) Baill. carries out both primary nitrogen assimilation and biosynthesis of arginine, rather than exporting ammonium. Arginine is a typical storage form of nitrogen in plant tissues, but is a novel nitrogen carrier molecule in root nodule symbioses. Thus Frankia within D. glomerata nodules exhibits considerable metabolic independence. Furthermore, nitrogen reassimilation is likely to take place in the host in the uninfected nodule cortical cells of this root nodule symbiosis, befo...
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Structural and cell developmental studies of root hair deformation in Alnus rubra Bong. (Betulaceae) were carried out following inoculation with the soil pseudomonad Pseudomonas cepacia 85, alone or in concert with Frankia, and using... more
Structural and cell developmental studies of root hair deformation in Alnus rubra Bong. (Betulaceae) were carried out following inoculation with the soil pseudomonad Pseudomonas cepacia 85, alone or in concert with Frankia, and using axenically grown seedlings. Deformational changes can be observed in elongating root hairs within 2 h of inoculation with P. cepacia 85. These growing root hairs become branched or multilobed and highly modified from the single-tip growth of axenic root hairs. The cell walls of deformed hairs are histologically distinctive when stained with the fluorochrome acridine orange. Filtrate studies using P. cepacia 85 suggest that the deforming substance is not a low molecular weight compound. Root hair deformation and the associated wall histology are host specific in that Betula root hairs show none of these responses when grown and inoculated in the experimental conditions described. The bacterially induced changes in root hair cell walls during deformation ...
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We cloned and purified the major family 10 xylanase (Xyn10A) from Acidothermus cellulolyticus 11B. Xyn10A was active on oat spelt and birchwood xylans between 60°C and 100°C and between pH 4 and pH 8. The optimal activity was at 90°C and... more
We cloned and purified the major family 10 xylanase (Xyn10A) from Acidothermus cellulolyticus 11B. Xyn10A was active on oat spelt and birchwood xylans between 60°C and 100°C and between pH 4 and pH 8. The optimal activity was at 90°C and pH 6; specific activity and K m for oat spelt xylan were 350 μmol xylose produced min −1 mg of protein −1 and 0.53 mg ml −1 , respectively. Based on xylan cleavage patterns, Xyn10A is an endoxylanase, and its half-life at 90°C was approximately 1.5 h in the presence of xylan.
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Gln synthetase (GS) is the key enzyme of primary ammonia assimilation in nitrogen-fixing root nodules of legumes and actinorhizal (Frankia-nodulated) plants. In root nodules of Datisca glomerata (Datiscaceae), transcripts hybridizing to a... more
Gln synthetase (GS) is the key enzyme of primary ammonia assimilation in nitrogen-fixing root nodules of legumes and actinorhizal (Frankia-nodulated) plants. In root nodules of Datisca glomerata (Datiscaceae), transcripts hybridizing to a conserved coding region of the abundant nodule isoform, DgGS1-1, are abundant in uninfected nodule cortical tissue, but expression was not detectable in the infected zone or in the nodule meristem. Similarly, the GS holoprotein is immunolocalized exclusively to the uninfected nodule tissue. Phylogenetic analysis of the full-length cDNA of DgGS1-1 indicates affinities with cytosolic GS genes from legumes, the actinorhizal species Alnus glutinosa, and nonnodulating species, Vitis vinifera and Hevea brasilensis. The D. glomerata nodule GS expression pattern is a new variant among reported root nodule symbioses and may reflect an unusual nitrogen transfer pathway from the Frankia nodule microsymbiont to the plant infected tissue, coupled to a distincti...
Research Interests: Botany, Biology, Nitrogen Cycle, Medicine, Biological Sciences, and 15 morePhylogeny, Plant Physiology, Nitrogen Fixation, Plant, Nitrogen, Phylogenetic analysis, Enzyme, Frankia, Amino Acid Profile, Base Sequence, Glutamine Synthetase, Full Length Movies, Cucurbitaceae, Molecular Sequence Data, and Expression pattern
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Nightcrawler (Lumbricus terrestris L. [Oligochaeta: Lumbricidae]) is an anecic earthworm typically lacking from Persian walnut (Juglans regia L.) orchards in northern California, yet this earthworm may be established by inoculative... more
Nightcrawler (Lumbricus terrestris L. [Oligochaeta: Lumbricidae]) is an anecic earthworm typically lacking from Persian walnut (Juglans regia L.) orchards in northern California, yet this earthworm may be established by inoculative release. Our purpose of was to determine the effect of L. terrestris inoculation on green manure incorporation, in this case woolypod vetch (Vicia villosa Roth ssp. varia [Host] Cabriere), and on the decomposer community. An experiment using controlled-environment microcosms showed that disappearance of surface-applied vetch residue was increased by the addition of L. terrestris compared to a resident earthworm complex consisting of the endogeic Lumbricidae Aporrectodea sp. prob. trapezoides (Dugès) and Allolobophora chlorotica (Savigny) as well as the epigeic Eisenia foetida (Savigny). An experiment conducted in an organic Persian walnut orchard during the spring of 1996 also showed that disappearance of surface-applied vetch residue was increased in plots that had been inoculated with L. terrestris. However, an additional study conducted in the same orchard during the summer of 1998 showed similar rates of vetch biomass disappearance in plots with or without inoculated L. terrestris. Colonization by L. terrestris did not lead to significant differences in densities or live biomass for resident earthworms in this orchard. However, night observations showed significantly greater densities of isopod Crustacea (Isopoda: Oniscidae) in plots without L. terrestris, suggesting possible interference between L. terrestris and the isopods.
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The phylogeny of the class Actinobacteria remains controversial, essentially because it is very sensitive to the choice of dataset and phylogenetic methods. We used a test proposed recently, based on complete genome data, which chooses... more
The phylogeny of the class Actinobacteria remains controversial, essentially because it is very sensitive to the choice of dataset and phylogenetic methods. We used a test proposed recently, based on complete genome data, which chooses among candidate species phylogenies based on the number of lateral gene transfers (LGT) needed to explain the diversity of histories among gene trees for a set of genomes. We used 100 completely sequenced genomes representing 35 families and 17 orders of the class Actinobacteria and evaluated eight different hypotheses for their phylogeny, including one based on a concatenate of 54 conserved proteins present in single copy in all these genomes, trees based on 16S and 23S rRNA gene sequences or their concatenation, and a tree based on the concatenation of MLSA genes (encoding AtpI, GyrA, FtsZ, SecA and DnaK). We used Prunier to infer the number of LGT in 579 proteins (different from those used to build the concatenated tree) present in at least 70 spec...