Svetlana Yurgel | Dalhousie University (original) (raw)

Papers by Svetlana Yurgel

Research paper thumbnail of Microbial Consortium Associated with Crustacean Shells Composting

Microorganisms

Soil microbes play an essential role in the biodegradation of crustacean shells, which is the pro... more Soil microbes play an essential role in the biodegradation of crustacean shells, which is the process of sustainable bioconversion to chitin derivatives ultimately resulting in the promotion of plant growth properties. While a number of microorganisms with chitinolytic properties have been characterized, little is known about the microbial taxa that participate in this process either by active chitin degradation or by facilitation of this activity through nutritional cooperation and composting with the chitinolytic microorganisms. In this study, we evaluated the transformation of the soil microbiome triggered by close approximation to the green crab shell surface. Our data indicate that the microbial community associated with green crab shell matter undergoes significant specialized changes, which was reflected in a decreased fungal and bacterial Shannon diversity and evenness and in a dramatic alteration in the community composition. The relative abundance of several bacterial and ...

Research paper thumbnail of A Characterization of a Cool-Climate Organic Vineyard’s Microbiome

Phytobiomes Journal

The microbiome, an influential factor affecting plant health and growth, is attracting increasing... more The microbiome, an influential factor affecting plant health and growth, is attracting increasing interest with respect to wine grape production. The purpose of this study was to characterize the microbiome (fungi and bacteria) of the soil, cover crop roots, and grape (Vitis spp.) roots across rootstock and depth in a cool-climate, organic vineyard. The cover crop consisted of a fescue (Festuca sp.) grass, while grape roots were sampled from New York Muscat, a cool-climate hybrid, across three root types (ungrafted, 3309C and Riparia Gloire) at three root depths (0 to 15, 15 to 30, and 30 to 50 cm). The grape root microbiome was more specialized, with fewer observed amplicon sequence variants for both bacteria (16S) and fungi (internal transcribe spacer) than found in the cover crop and the surrounding soil. Grape roots were dominated by bacterial genera Pseudomonas, Niastella, and Rhizobium; most prominent fungal genera were Plectosphaerella, Trichosporon, and Ilyonectria. Although...

Research paper thumbnail of Effect of Fungicide Application on Lowbush Blueberries Soil Microbiome

Microorganisms

Lowbush blueberries (Vaccinium sp.) are perennial crops produced throughout eastern Canada and Ma... more Lowbush blueberries (Vaccinium sp.) are perennial crops produced throughout eastern Canada and Maine through management of wild populations. Given the constraints of this cropping system, the application of fungicides is critical to reducing disease pressure and ensuring consistent yields. However, as plant health is intertwined with soil health, it is important to consider the impact of fungicides on microbial communities. To understand the effects of fungicides in this context, bacterial and fungal microbial communities from fungicide-treated plots, as well as untreated control plots (UTG) were analyzed using amplicon sequencing. The fungicides, considered collectively as a combined treatment group (CTG), lead to a loss in fungal richness. One family, Clavariaceae, had an increased abundance under prothioconazole relative to UTG. This finding may be significant as taxa in Clavariaceae have been thought to potentially form ericoid mycorrhizae with Vaccinium. Five functional pathway...

Research paper thumbnail of Response of Plant-Associated Microbiome to Plant Root Colonization by Exogenous Bacterial Endophyte in Perennial Crops

Frontiers in Microbiology

The application of bacterial inoculums for improving plant growth and production is an important ... more The application of bacterial inoculums for improving plant growth and production is an important component of sustainable agriculture. However, the efficiency of perennial crop inoculums depends on the ability of the introduced endophytes to exert an impact on the host-plant over an extended period of time. This impact might be evaluated by the response of plant-associated microbiome to the inoculation. In this study, we monitored the effect of a single bacterial strain inoculation on the diversity, structure, and cooperation in plant-associated microbiome over 1-year period. An endophyte (RF67) isolated from Vaccinium angustifolium (wild blueberry) roots and annotated as Rhizobium was used for the inoculation of 1-year-old Lonicera caerulea (Haskap) plants. A significant level of bacterial community perturbation was detected in plant roots after 3 months post-inoculation. About 23% of root-associated community variation was correlated with an application of the inoculant, which was...

Research paper thumbnail of Content Alerts

This article cites 20 articles, 11 of which can be accessed free

Research paper thumbnail of Specialization in a Nitrogen-Fixing Symbiosis: Proteome Differences Between Sinorhizobium medicae Bacteria and Bacteroids

Molecular Plant-Microbe Interactions®, 2021

Using tandem mass spectrometry (MS/MS), we analyzed the proteome of Sinorhizobium medicae WSM419 ... more Using tandem mass spectrometry (MS/MS), we analyzed the proteome of Sinorhizobium medicae WSM419 growing as free-living cells and in symbiosis with Medicago truncatula. In all, 3,215 proteins were identified, over half of the open reading frames predicted from the genomic sequence. The abundance of 1,361 proteins displayed strong lifestyle bias. In total, 1,131 proteins had similar levels in bacteroids and free-living cells, and the low levels of 723 proteins prevented statistically significant assignments. Nitrogenase subunits comprised approximately 12% of quantified bacteroid proteins. Other major bacteroid proteins included symbiosis-specific cytochromes and FixABCX, which transfer electrons to nitrogenase. Bacteroids had normal levels of proteins involved in amino acid biosynthesis, glycolysis or gluconeogenesis, and the pentose phosphate pathway; however, several amino acid degradation pathways were repressed. This suggests that bacteroids maintain a relatively independent ana...

Research paper thumbnail of Respiratory activity and symbiotic effectiveness in the nodule bacterium Rhizobium meliloti

Research paper thumbnail of A Novel Protein from Ectocarpus sp. Improves Salinity and High Temperature Stress Tolerance in Arabidopsis thaliana

International Journal of Molecular Sciences, 2021

Brown alga Ectocarpus sp. belongs to Phaeophyceae, a class of macroalgae that evolved complex mul... more Brown alga Ectocarpus sp. belongs to Phaeophyceae, a class of macroalgae that evolved complex multicellularity. Ectocarpus sp. is a dominant seaweed in temperate regions, abundant mostly in the intertidal zones, an environment with high levels of abiotic stresses. Previous transcriptomic analysis of Ectocarpus sp. revealed several genes consistently induced by various abiotic stresses; one of these genes is Esi0017_0056, which encodes a protein with unknown function. Bioinformatics analyses indicated that the protein encoded by Esi0017_0056 is soluble and monomeric. The protein was successfully expressed in Escherichia coli,Arabidopsis thaliana and Nicotiana benthamiana. In A. thaliana the gene was expressed under constitutive and stress inducible promoters which led to improved tolerance to high salinity and temperature stresses. The expression of several key abiotic stress-related genes was studied in transgenic and wild type A. thaliana by qPCR. Expression analysis revealed that ...

Research paper thumbnail of Molecular Plant-Microbe Interactions Journal

Research paper thumbnail of A portal for rhizobial genomes: RhizoGATE integrates a Sinorhizobium meliloti genome annotation update with postgenome data

Journal of Biotechnology, 2009

Sinorhizobium meliloti is a symbiotic soil bacterium of the alphaproteobacterial subdivision. Lik... more Sinorhizobium meliloti is a symbiotic soil bacterium of the alphaproteobacterial subdivision. Like other rhizobia, S. meliloti induces nitrogen-fixing root nodules on leguminous plants. This is an ecologically and economically important interaction, because plants engaged in symbiosis with rhizobia can grow without exogenous nitrogen fertilizers. The S. meliloti-Medicago truncatula (barrel medic) association is an important symbiosis model. The S. meliloti genome was published in 2001, and the M. truncatula genome currently is being sequenced. Many new resources and data have been made available since the original S. meliloti genome annotation and an update was needed. In June 2008, we submitted our annotation update to the EMBL and NCBI databases. Here we describe this new annotation and a new webbased portal RhizoGATE. About 1000 annotation updates were made; these included assigning functions to 313 putative proteins, assigning EC numbers to 431 proteins, and identifying 86 new putative genes. RhizoGATE incorporates the new annotion with the S. meliloti GenDB project, a platform that allows annotation updates in real time. Locations of transposon insertions, plasmid integrations, and array probe sequences are available in the GenDB project. RhizoGATE employs the EMMA platform for management and analysis of transcriptome data and the IGetDB data warehouse to integrate a variety of heterogeneous external data sources.

Research paper thumbnail of Unbalancing Symbiotic Nitrogen Fixation: Can We Make Effectiveness More Effective?

Research paper thumbnail of PICRUSt2 for prediction of metagenome functions

Research paper thumbnail of Microbial co-occurrence network analysis of soils receiving short- and long-term applications of alkaline treated biosolids

Science of The Total Environment

Research paper thumbnail of Low Mannitol Concentrations in Arabidopsis thaliana Expressing Ectocarpus Genes Improve Salt Tolerance

Plants

Mannitol is abundant in a wide range of organisms, playing important roles in biotic and abiotic ... more Mannitol is abundant in a wide range of organisms, playing important roles in biotic and abiotic stress responses. Nonetheless, mannitol is not produced by a vast majority of plants, including many important crop plants. Mannitol-producing transgenic plants displayed improved tolerance to salt stresses though mannitol production was rather low, in the µM range, compared to mM range found in plants that innately produce mannitol. Little is known about the molecular mechanisms underlying salt tolerance triggered by low concentrations of mannitol. Reported here is the production of mannitol in Arabidopsis thaliana, by expressing two mannitol biosynthesis genes from the brown alga Ectocarpus sp. strain Ec32. To date, no brown algal genes have been successfully expressed in land plants. Expression of mannitol-1-phosphate dehydrogenase and mannitol-1-phosphatase genes was associated with the production of 42.3–52.7 nmol g−1 fresh weight of mannitol, which was sufficient to impart salinity...

Research paper thumbnail of Combination of Ascophyllum nodosum Extract and Humic Acid Improve Early Growth and Reduces Post-Harvest Loss of Lettuce and Spinach

Agriculture

Leafy vegetables like lettuce and spinach are prone to significant post-harvest losses during han... more Leafy vegetables like lettuce and spinach are prone to significant post-harvest losses during handling and storage. The pre-harvest treatment of crops with biostimulants offers a sustainable strategy for reducing post-harvest losses. Earlier studies focused on the effect of plant biostimulants applied individually. In this study, we studied the efficacy of a combined application of two commonly used plant biostimulants: Ascophyllum nodosum extract (ANE) and humic acid (HA). Interestingly, the combination of both biostimulants improved early growth of lettuce and spinach compared to ANE and HA alone. Among the combinations used in this study, 0.25% ANE + 0.2% HA produced significantly higher fresh and dry biomass in lettuce and spinach compared to the other treatments and the control. Pre-harvest treatment of combination of 0.25% ANE and 0.2% HA significantly reduced the loss of fresh biomass during post-harvest storage. The combination of 0.25% ANE and 0.2% HA reduced lipid peroxida...

Research paper thumbnail of Estabelecimento de sistema bacteriano de expressão de peptídeos derivados da enzima vegetal RuBisCO

Brazilian Journal of Food Technology

Resumo O objetivo do presente estudo foi estabelecer um sistema bacteriano de expressão de peptíd... more Resumo O objetivo do presente estudo foi estabelecer um sistema bacteriano de expressão de peptídeos derivados da proteólise simulada in silico da enzima ribulose-1,5-bisfosfato carboxilase oxigenase (RuBisCO), proveniente de soja, visando viabilizar um método sustentável de produção dessas moléculas para futura aplicação industrial. Inicialmente, foi conferida à cepa Escherichia coli S17-1 cálcio-competência para propagação do plasmídeo de expressão pET-30a(+) contendo o inserto codificante da sequência peptídica GSIKAFKEATKVDKVVVLWTALVPR. Após extração de DNA plasmidial, o material foi transformado em células de alto rendimento E. coli Rosetta™(DE3)pLysS. As células Rosetta portando o plasmídeo de expressão foram induzidas e a produção dos peptídeos foi verificada por meio de eletroforese em gel vertical, confirmando o estabelecimento de um sistema de expressão viável para peptídeos heterólogos. Assim, a produção em maior escala de peptídeos derivados de RuBisCO – associando-se fu...

Research paper thumbnail of Metagenomic Functional Shifts to Plant Induced Environmental Changes

Frontiers in Microbiology

The Vaccinium angustifolium (wild blueberry) agricultural system involves transformation of the e... more The Vaccinium angustifolium (wild blueberry) agricultural system involves transformation of the environment surrounding the plant to intensify plant propagation and to improve fruit yield, and therefore is an advantageous model to study the interaction between soil microorganisms and plant-host interactions. We studied this system to address the question of a trade-off between microbial adaptation to a plant-influenced environment and its general metabolic capabilities. We found that many basic metabolic functions were similarly represented in bulk soil and rhizosphere microbiomes overall. However, we identified a niche-specific difference in functions potentially beneficial for microbial survival in the rhizosphere but that might also reduce the ability of microbes to withstand stresses in bulk soils. These functions could provide the microbiome with additional capabilities to respond to environmental fluctuations in the rhizosphere triggered by changes in the composition of root exudates. Based on our analysis we hypothesize that the rhizosphere-specific pathways involved in xenobiotics biodegradation could provide the microbiome with functional flexibility to respond to plant stress status.

Research paper thumbnail of PICRUSt2: An improved and extensible approach for metagenome inference

One major limitation of microbial community marker gene sequencing is that it does not provide di... more One major limitation of microbial community marker gene sequencing is that it does not provide direct information on the functional composition of sampled communities. Here, we present PICRUSt2, which expands the capabilities of the original PICRUSt method to predict approximate functional potential of a community based on marker gene sequencing profiles. This updated method and implementation includes several improvements over the previous algorithm: an expanded database of gene families and reference genomes, a new approach now compatible with any OTU-picking or denoising algorithm, novel phenotype predictions, and novel fungal reference databases that enable predictions from 18S rRNA gene and internal transcribed spacer amplicon data. Upon evaluation, PICRUSt2 was more accurate than PICRUSt1 and other current approaches and also more flexible to allow the addition of custom reference databases. Last, we demonstrate the utility of PICRUSt2 by identifying potential disease-associat...

Research paper thumbnail of Exploring the long-term effect of plastic on compost microbiome

PLOS ONE

Little is known about the ecology of microbial plastic degradation. In this study, we employed ne... more Little is known about the ecology of microbial plastic degradation. In this study, we employed next generation amplicon sequencing to assess the effect of low-density polyethylene (LDPE) films on the structure of bacterial and fungal communities in four mature compost piles with age ranging between 2 and 10 years. While, bacterial Proteobacteria, Bacteroidetes, Actinobacteria and fungi Ascomycota were most abundant across all facilities, our data indicated significant differences in compost microbiomes between compost facilities, which might be related to compost chemical parameters, age of piles and characteristics of the feedstock. In addition, a substantial shift in the interaction pattern within microbial communities from bulk and plastic-associated (PA) compost was detected. For example, cooperation between Firmicutes Bacillaceae and Thermoactinomycetaceae was detected only in PA compost. However, based on the analysis of the diversity indices and the relative abundances of microbial taxa we can conclude that the presence of plastics in compost had no significant effect on the structure of microbial community.

Research paper thumbnail of Dissecting Community Structure in Wild Blueberry Root and Soil Microbiome

Frontiers in Microbiology

A complex network of functions and symbiotic interactions between a eukaryotic host and its micro... more A complex network of functions and symbiotic interactions between a eukaryotic host and its microbiome is a the foundation of the ecological unit holobiont. However, little is known about how the non-fungal eukaryotic microorganisms fit in this complex network of host-microbiome interactions. In this study, we employed a unique wild blueberry ecosystem to evaluate plant-associated microbiota, encompassing both eukaryotic and bacterial communities. We found that, while soil microbiome serves as a foundation for root microbiome, plant-influenced species sorting had stronger effect on eukaryotes than on bacteria. Our study identified several fungal and protist taxa, which are correlated with decreased fruit production in wild blueberry agricultural ecosystems. The specific effect of species sorting in root microbiome resulted in an increase in relative abundance of fungi adapted to plant-associated life-style, while the relative abundance of non-fungal eukaryotes was decreased along the soil-endosphere continuum in the root, probably because of low adaptation of these microorganisms to hostplant defense responses. Analysis of community correlation networks indicated that bacterial and eukaryotic interactions became more complex along the soil-endosphere continuum and, in addition to extensive mutualistic interactions, co-exclusion also played an important role in shaping wild blueberry associated microbiome. Our study identified several potential hub taxa with important roles in soil fertility and/or plantmicrobe interaction, suggesting the key role of these taxa in the interconnection between soils and plant health and overall microbial community structure. This study also provides a comprehensive view of the role of non-fungal eukaryotes in soil ecosystem.

Research paper thumbnail of Microbial Consortium Associated with Crustacean Shells Composting

Microorganisms

Soil microbes play an essential role in the biodegradation of crustacean shells, which is the pro... more Soil microbes play an essential role in the biodegradation of crustacean shells, which is the process of sustainable bioconversion to chitin derivatives ultimately resulting in the promotion of plant growth properties. While a number of microorganisms with chitinolytic properties have been characterized, little is known about the microbial taxa that participate in this process either by active chitin degradation or by facilitation of this activity through nutritional cooperation and composting with the chitinolytic microorganisms. In this study, we evaluated the transformation of the soil microbiome triggered by close approximation to the green crab shell surface. Our data indicate that the microbial community associated with green crab shell matter undergoes significant specialized changes, which was reflected in a decreased fungal and bacterial Shannon diversity and evenness and in a dramatic alteration in the community composition. The relative abundance of several bacterial and ...

Research paper thumbnail of A Characterization of a Cool-Climate Organic Vineyard’s Microbiome

Phytobiomes Journal

The microbiome, an influential factor affecting plant health and growth, is attracting increasing... more The microbiome, an influential factor affecting plant health and growth, is attracting increasing interest with respect to wine grape production. The purpose of this study was to characterize the microbiome (fungi and bacteria) of the soil, cover crop roots, and grape (Vitis spp.) roots across rootstock and depth in a cool-climate, organic vineyard. The cover crop consisted of a fescue (Festuca sp.) grass, while grape roots were sampled from New York Muscat, a cool-climate hybrid, across three root types (ungrafted, 3309C and Riparia Gloire) at three root depths (0 to 15, 15 to 30, and 30 to 50 cm). The grape root microbiome was more specialized, with fewer observed amplicon sequence variants for both bacteria (16S) and fungi (internal transcribe spacer) than found in the cover crop and the surrounding soil. Grape roots were dominated by bacterial genera Pseudomonas, Niastella, and Rhizobium; most prominent fungal genera were Plectosphaerella, Trichosporon, and Ilyonectria. Although...

Research paper thumbnail of Effect of Fungicide Application on Lowbush Blueberries Soil Microbiome

Microorganisms

Lowbush blueberries (Vaccinium sp.) are perennial crops produced throughout eastern Canada and Ma... more Lowbush blueberries (Vaccinium sp.) are perennial crops produced throughout eastern Canada and Maine through management of wild populations. Given the constraints of this cropping system, the application of fungicides is critical to reducing disease pressure and ensuring consistent yields. However, as plant health is intertwined with soil health, it is important to consider the impact of fungicides on microbial communities. To understand the effects of fungicides in this context, bacterial and fungal microbial communities from fungicide-treated plots, as well as untreated control plots (UTG) were analyzed using amplicon sequencing. The fungicides, considered collectively as a combined treatment group (CTG), lead to a loss in fungal richness. One family, Clavariaceae, had an increased abundance under prothioconazole relative to UTG. This finding may be significant as taxa in Clavariaceae have been thought to potentially form ericoid mycorrhizae with Vaccinium. Five functional pathway...

Research paper thumbnail of Response of Plant-Associated Microbiome to Plant Root Colonization by Exogenous Bacterial Endophyte in Perennial Crops

Frontiers in Microbiology

The application of bacterial inoculums for improving plant growth and production is an important ... more The application of bacterial inoculums for improving plant growth and production is an important component of sustainable agriculture. However, the efficiency of perennial crop inoculums depends on the ability of the introduced endophytes to exert an impact on the host-plant over an extended period of time. This impact might be evaluated by the response of plant-associated microbiome to the inoculation. In this study, we monitored the effect of a single bacterial strain inoculation on the diversity, structure, and cooperation in plant-associated microbiome over 1-year period. An endophyte (RF67) isolated from Vaccinium angustifolium (wild blueberry) roots and annotated as Rhizobium was used for the inoculation of 1-year-old Lonicera caerulea (Haskap) plants. A significant level of bacterial community perturbation was detected in plant roots after 3 months post-inoculation. About 23% of root-associated community variation was correlated with an application of the inoculant, which was...

Research paper thumbnail of Content Alerts

This article cites 20 articles, 11 of which can be accessed free

Research paper thumbnail of Specialization in a Nitrogen-Fixing Symbiosis: Proteome Differences Between Sinorhizobium medicae Bacteria and Bacteroids

Molecular Plant-Microbe Interactions®, 2021

Using tandem mass spectrometry (MS/MS), we analyzed the proteome of Sinorhizobium medicae WSM419 ... more Using tandem mass spectrometry (MS/MS), we analyzed the proteome of Sinorhizobium medicae WSM419 growing as free-living cells and in symbiosis with Medicago truncatula. In all, 3,215 proteins were identified, over half of the open reading frames predicted from the genomic sequence. The abundance of 1,361 proteins displayed strong lifestyle bias. In total, 1,131 proteins had similar levels in bacteroids and free-living cells, and the low levels of 723 proteins prevented statistically significant assignments. Nitrogenase subunits comprised approximately 12% of quantified bacteroid proteins. Other major bacteroid proteins included symbiosis-specific cytochromes and FixABCX, which transfer electrons to nitrogenase. Bacteroids had normal levels of proteins involved in amino acid biosynthesis, glycolysis or gluconeogenesis, and the pentose phosphate pathway; however, several amino acid degradation pathways were repressed. This suggests that bacteroids maintain a relatively independent ana...

Research paper thumbnail of Respiratory activity and symbiotic effectiveness in the nodule bacterium Rhizobium meliloti

Research paper thumbnail of A Novel Protein from Ectocarpus sp. Improves Salinity and High Temperature Stress Tolerance in Arabidopsis thaliana

International Journal of Molecular Sciences, 2021

Brown alga Ectocarpus sp. belongs to Phaeophyceae, a class of macroalgae that evolved complex mul... more Brown alga Ectocarpus sp. belongs to Phaeophyceae, a class of macroalgae that evolved complex multicellularity. Ectocarpus sp. is a dominant seaweed in temperate regions, abundant mostly in the intertidal zones, an environment with high levels of abiotic stresses. Previous transcriptomic analysis of Ectocarpus sp. revealed several genes consistently induced by various abiotic stresses; one of these genes is Esi0017_0056, which encodes a protein with unknown function. Bioinformatics analyses indicated that the protein encoded by Esi0017_0056 is soluble and monomeric. The protein was successfully expressed in Escherichia coli,Arabidopsis thaliana and Nicotiana benthamiana. In A. thaliana the gene was expressed under constitutive and stress inducible promoters which led to improved tolerance to high salinity and temperature stresses. The expression of several key abiotic stress-related genes was studied in transgenic and wild type A. thaliana by qPCR. Expression analysis revealed that ...

Research paper thumbnail of Molecular Plant-Microbe Interactions Journal

Research paper thumbnail of A portal for rhizobial genomes: RhizoGATE integrates a Sinorhizobium meliloti genome annotation update with postgenome data

Journal of Biotechnology, 2009

Sinorhizobium meliloti is a symbiotic soil bacterium of the alphaproteobacterial subdivision. Lik... more Sinorhizobium meliloti is a symbiotic soil bacterium of the alphaproteobacterial subdivision. Like other rhizobia, S. meliloti induces nitrogen-fixing root nodules on leguminous plants. This is an ecologically and economically important interaction, because plants engaged in symbiosis with rhizobia can grow without exogenous nitrogen fertilizers. The S. meliloti-Medicago truncatula (barrel medic) association is an important symbiosis model. The S. meliloti genome was published in 2001, and the M. truncatula genome currently is being sequenced. Many new resources and data have been made available since the original S. meliloti genome annotation and an update was needed. In June 2008, we submitted our annotation update to the EMBL and NCBI databases. Here we describe this new annotation and a new webbased portal RhizoGATE. About 1000 annotation updates were made; these included assigning functions to 313 putative proteins, assigning EC numbers to 431 proteins, and identifying 86 new putative genes. RhizoGATE incorporates the new annotion with the S. meliloti GenDB project, a platform that allows annotation updates in real time. Locations of transposon insertions, plasmid integrations, and array probe sequences are available in the GenDB project. RhizoGATE employs the EMMA platform for management and analysis of transcriptome data and the IGetDB data warehouse to integrate a variety of heterogeneous external data sources.

Research paper thumbnail of Unbalancing Symbiotic Nitrogen Fixation: Can We Make Effectiveness More Effective?

Research paper thumbnail of PICRUSt2 for prediction of metagenome functions

Research paper thumbnail of Microbial co-occurrence network analysis of soils receiving short- and long-term applications of alkaline treated biosolids

Science of The Total Environment

Research paper thumbnail of Low Mannitol Concentrations in Arabidopsis thaliana Expressing Ectocarpus Genes Improve Salt Tolerance

Plants

Mannitol is abundant in a wide range of organisms, playing important roles in biotic and abiotic ... more Mannitol is abundant in a wide range of organisms, playing important roles in biotic and abiotic stress responses. Nonetheless, mannitol is not produced by a vast majority of plants, including many important crop plants. Mannitol-producing transgenic plants displayed improved tolerance to salt stresses though mannitol production was rather low, in the µM range, compared to mM range found in plants that innately produce mannitol. Little is known about the molecular mechanisms underlying salt tolerance triggered by low concentrations of mannitol. Reported here is the production of mannitol in Arabidopsis thaliana, by expressing two mannitol biosynthesis genes from the brown alga Ectocarpus sp. strain Ec32. To date, no brown algal genes have been successfully expressed in land plants. Expression of mannitol-1-phosphate dehydrogenase and mannitol-1-phosphatase genes was associated with the production of 42.3–52.7 nmol g−1 fresh weight of mannitol, which was sufficient to impart salinity...

Research paper thumbnail of Combination of Ascophyllum nodosum Extract and Humic Acid Improve Early Growth and Reduces Post-Harvest Loss of Lettuce and Spinach

Agriculture

Leafy vegetables like lettuce and spinach are prone to significant post-harvest losses during han... more Leafy vegetables like lettuce and spinach are prone to significant post-harvest losses during handling and storage. The pre-harvest treatment of crops with biostimulants offers a sustainable strategy for reducing post-harvest losses. Earlier studies focused on the effect of plant biostimulants applied individually. In this study, we studied the efficacy of a combined application of two commonly used plant biostimulants: Ascophyllum nodosum extract (ANE) and humic acid (HA). Interestingly, the combination of both biostimulants improved early growth of lettuce and spinach compared to ANE and HA alone. Among the combinations used in this study, 0.25% ANE + 0.2% HA produced significantly higher fresh and dry biomass in lettuce and spinach compared to the other treatments and the control. Pre-harvest treatment of combination of 0.25% ANE and 0.2% HA significantly reduced the loss of fresh biomass during post-harvest storage. The combination of 0.25% ANE and 0.2% HA reduced lipid peroxida...

Research paper thumbnail of Estabelecimento de sistema bacteriano de expressão de peptídeos derivados da enzima vegetal RuBisCO

Brazilian Journal of Food Technology

Resumo O objetivo do presente estudo foi estabelecer um sistema bacteriano de expressão de peptíd... more Resumo O objetivo do presente estudo foi estabelecer um sistema bacteriano de expressão de peptídeos derivados da proteólise simulada in silico da enzima ribulose-1,5-bisfosfato carboxilase oxigenase (RuBisCO), proveniente de soja, visando viabilizar um método sustentável de produção dessas moléculas para futura aplicação industrial. Inicialmente, foi conferida à cepa Escherichia coli S17-1 cálcio-competência para propagação do plasmídeo de expressão pET-30a(+) contendo o inserto codificante da sequência peptídica GSIKAFKEATKVDKVVVLWTALVPR. Após extração de DNA plasmidial, o material foi transformado em células de alto rendimento E. coli Rosetta™(DE3)pLysS. As células Rosetta portando o plasmídeo de expressão foram induzidas e a produção dos peptídeos foi verificada por meio de eletroforese em gel vertical, confirmando o estabelecimento de um sistema de expressão viável para peptídeos heterólogos. Assim, a produção em maior escala de peptídeos derivados de RuBisCO – associando-se fu...

Research paper thumbnail of Metagenomic Functional Shifts to Plant Induced Environmental Changes

Frontiers in Microbiology

The Vaccinium angustifolium (wild blueberry) agricultural system involves transformation of the e... more The Vaccinium angustifolium (wild blueberry) agricultural system involves transformation of the environment surrounding the plant to intensify plant propagation and to improve fruit yield, and therefore is an advantageous model to study the interaction between soil microorganisms and plant-host interactions. We studied this system to address the question of a trade-off between microbial adaptation to a plant-influenced environment and its general metabolic capabilities. We found that many basic metabolic functions were similarly represented in bulk soil and rhizosphere microbiomes overall. However, we identified a niche-specific difference in functions potentially beneficial for microbial survival in the rhizosphere but that might also reduce the ability of microbes to withstand stresses in bulk soils. These functions could provide the microbiome with additional capabilities to respond to environmental fluctuations in the rhizosphere triggered by changes in the composition of root exudates. Based on our analysis we hypothesize that the rhizosphere-specific pathways involved in xenobiotics biodegradation could provide the microbiome with functional flexibility to respond to plant stress status.

Research paper thumbnail of PICRUSt2: An improved and extensible approach for metagenome inference

One major limitation of microbial community marker gene sequencing is that it does not provide di... more One major limitation of microbial community marker gene sequencing is that it does not provide direct information on the functional composition of sampled communities. Here, we present PICRUSt2, which expands the capabilities of the original PICRUSt method to predict approximate functional potential of a community based on marker gene sequencing profiles. This updated method and implementation includes several improvements over the previous algorithm: an expanded database of gene families and reference genomes, a new approach now compatible with any OTU-picking or denoising algorithm, novel phenotype predictions, and novel fungal reference databases that enable predictions from 18S rRNA gene and internal transcribed spacer amplicon data. Upon evaluation, PICRUSt2 was more accurate than PICRUSt1 and other current approaches and also more flexible to allow the addition of custom reference databases. Last, we demonstrate the utility of PICRUSt2 by identifying potential disease-associat...

Research paper thumbnail of Exploring the long-term effect of plastic on compost microbiome

PLOS ONE

Little is known about the ecology of microbial plastic degradation. In this study, we employed ne... more Little is known about the ecology of microbial plastic degradation. In this study, we employed next generation amplicon sequencing to assess the effect of low-density polyethylene (LDPE) films on the structure of bacterial and fungal communities in four mature compost piles with age ranging between 2 and 10 years. While, bacterial Proteobacteria, Bacteroidetes, Actinobacteria and fungi Ascomycota were most abundant across all facilities, our data indicated significant differences in compost microbiomes between compost facilities, which might be related to compost chemical parameters, age of piles and characteristics of the feedstock. In addition, a substantial shift in the interaction pattern within microbial communities from bulk and plastic-associated (PA) compost was detected. For example, cooperation between Firmicutes Bacillaceae and Thermoactinomycetaceae was detected only in PA compost. However, based on the analysis of the diversity indices and the relative abundances of microbial taxa we can conclude that the presence of plastics in compost had no significant effect on the structure of microbial community.

Research paper thumbnail of Dissecting Community Structure in Wild Blueberry Root and Soil Microbiome

Frontiers in Microbiology

A complex network of functions and symbiotic interactions between a eukaryotic host and its micro... more A complex network of functions and symbiotic interactions between a eukaryotic host and its microbiome is a the foundation of the ecological unit holobiont. However, little is known about how the non-fungal eukaryotic microorganisms fit in this complex network of host-microbiome interactions. In this study, we employed a unique wild blueberry ecosystem to evaluate plant-associated microbiota, encompassing both eukaryotic and bacterial communities. We found that, while soil microbiome serves as a foundation for root microbiome, plant-influenced species sorting had stronger effect on eukaryotes than on bacteria. Our study identified several fungal and protist taxa, which are correlated with decreased fruit production in wild blueberry agricultural ecosystems. The specific effect of species sorting in root microbiome resulted in an increase in relative abundance of fungi adapted to plant-associated life-style, while the relative abundance of non-fungal eukaryotes was decreased along the soil-endosphere continuum in the root, probably because of low adaptation of these microorganisms to hostplant defense responses. Analysis of community correlation networks indicated that bacterial and eukaryotic interactions became more complex along the soil-endosphere continuum and, in addition to extensive mutualistic interactions, co-exclusion also played an important role in shaping wild blueberry associated microbiome. Our study identified several potential hub taxa with important roles in soil fertility and/or plantmicrobe interaction, suggesting the key role of these taxa in the interconnection between soils and plant health and overall microbial community structure. This study also provides a comprehensive view of the role of non-fungal eukaryotes in soil ecosystem.