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  1. AU="Michael J. Sadowsky"
  2. AU=Jatt Lauren P
  3. AU=Couser W G
  4. AU="Yingjie Xiao"
  5. AU="Hyunghee Lee"
  6. AU=Seif Sherif AU=Seif Sherif
  7. AU=Rajput Dinesh Vijay
  8. AU="Nilsson, Lovisa"
  9. AU="Wijns, Julie"
  10. AU="Gutiérrez Tolentino, Rey"
  11. AU="Reuss, Annette"
  12. AU=Cook Rebecca
  13. AU="Zhu, Tianhui"
  14. AU=Li Liwu
  15. AU="Akamine, Yuko"
  16. AU=Pereira Carlos
  17. AU=Roosa Kimberlyn
  18. AU=Rodrguez-Garca-de-Cortzar Ainhoa AU=Rodrguez-Garca-de-Cortzar Ainhoa
  19. AU="Eltan, Sevgi Bilgic"
  20. AU=Shibley I A Jr
  21. AU="Shin Ohta"
  22. AU="Herrera, José M."
  23. AU="Bolanle, Ogunyemi Folasade"
  24. AU="Spezialetti, Matteo"
  25. AU=Rosas Lucia E
  26. AU="Spadotto, Valeria"
  27. AU="Jimenez-Macias, Jorge L"

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  1. Artikel ; Online: Herbicide bioremediation

    Marcos Pileggi / Sônia A.V. Pileggi / Michael J. Sadowsky

    Heliyon, Vol 6, Iss 12, Pp e05767- (2020)

    from strains to bacterial communities

    2020  

    Abstract: There is high demand for herbicides based on the necessity to increase crop production to satisfy world-wide demands. Nevertheless, there are negative impacts of herbicide use, manifesting as selection for resistant weeds, production of toxic metabolites ...

    Abstract There is high demand for herbicides based on the necessity to increase crop production to satisfy world-wide demands. Nevertheless, there are negative impacts of herbicide use, manifesting as selection for resistant weeds, production of toxic metabolites from partial degradation of herbicides, changes in soil microbial communities and biogeochemical cycles, alterations in plant nutrition and soil fertility, and persistent environmental contamination. Some herbicides damage non-target microorganisms via directed interference with host metabolism and via oxidative stress mechanisms. For these reasons, it is necessary to identify sustainable, efficient methods to mitigate these environmental liabilities. Before the degradation process can be initiated by microbial enzymes and metabolic pathways, microorganisms need to tolerate the oxidative stresses caused by the herbicides themselves. This can be achieved via a complex system of enzymatic and non-enzymatic antioxidative stress systems. Many of these response systems are not herbicide specific, but rather triggered by a variety of substances. Collectively, these nonspecific response systems enhance the survival and fitness potential of microorganisms. Biodegradation studies and remediation approaches have relied on individually selected strains to effectively remediate herbicides in the environment. Nevertheless, it has been shown that microbial communication systems that modulate social relationships and metabolic pathways inside biofilm structures among microorganisms are complex; therefore, use of isolated strains for xenobiotic degradation needs to be enhanced using a community-based approach with biodegradation pathway integration. Bioremediation efforts can use omics-based technologies to gain a deeper understanding of the molecular complexes of bacterial communities to achieve to more efficient elimination of xenobiotics.With this knowledge, the possibility of altering microbial communities is increased to improve the potential for bioremediation without ...
    Schlagwörter Environmental microbiology ; Analytical chemistry ; DNA analyses ; Metabolic pathways ; Cell communication ; Science (General) ; Q1-390 ; Social sciences (General) ; H1-99
    Thema/Rubrik (Code) 500
    Sprache Englisch
    Erscheinungsdatum 2020-12-01T00:00:00Z
    Verlag Elsevier
    Dokumenttyp Artikel ; Online
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  2. Artikel: Practical considerations for sampling and data analysis in contemporary metagenomics-based environmental studies

    Staley, Christopher / Michael J. Sadowsky

    Journal of microbiological methods. 2018 Nov., v. 154

    2018  

    Abstract: Recent advancements in metagenomic-based studies, especially analyses of amplicon-based DNA sequencing targeting taxonomic marker genes, has led to an unprecedented characterization of microbial communities from diverse ecosystems around the world. While ...

    Abstract Recent advancements in metagenomic-based studies, especially analyses of amplicon-based DNA sequencing targeting taxonomic marker genes, has led to an unprecedented characterization of microbial communities from diverse ecosystems around the world. While originally constrained by a lack of appropriate analytical tools and sequencing depth, new technologies and computational and statistical algorithms have been developed to handle highly dimensional, next-generation sequencing datasets. Both these tools allow for the robust analysis of structural and distributional patterns of microbiota essential for the understanding of microbial ecology and biogeography. Furthermore, consortia of individual laboratories working on large interdisciplinary research programs, like the Human and Earth Microbiome Projects, have developed standardized protocols for DNA extraction, sequencing pipelines, and bioinformatics. These approaches provide large repositories of publicly available data to serve as references for on-going and future, hypothesis-driven studies to better characterize the roles of microbial communities in diverse ecosystems. In this review, we outline the currently available statistical approaches and tools to aid in statistically powered study designs and analyses. Given what is now known about the enormous diversity and variability of the microbial communities in aquatic and terrestrial habitats, we also discuss practical considerations for sample collection. Due to the extensive advances made in the field of metagenomics over the last decade, rigorous, well replicated, hypothesis-driven studies are: 1) needed, 2) now possible, and 3) essential to make best use of sequencing-based technologies to characterize the roles of microbial communities in the structure and function of diverse ecosystems.
    Schlagwörter DNA ; algorithms ; biogeography ; bioinformatics ; ecosystems ; genetic markers ; habitats ; high-throughput nucleotide sequencing ; interdisciplinary research ; metagenomics ; microbial communities ; microbiome ; microorganisms ; research programs ; statistical analysis ; technology
    Sprache Englisch
    Erscheinungsverlauf 2018-11
    Umfang p. 14-18.
    Erscheinungsort Elsevier B.V.
    Dokumenttyp Artikel
    ZDB-ID 604916-3
    ISSN 1872-8359 ; 0167-7012
    ISSN (online) 1872-8359
    ISSN 0167-7012
    DOI 10.1016/j.mimet.2018.09.020
    Datenquelle NAL Katalog (AGRICOLA)

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  3. Artikel ; Online: CRISPR loci-PCR as Tool for Tracking Azospirillum sp. Strain B510

    Joaquin I. Rilling / Fumito Maruyama / Michael J. Sadowsky / Jacquelinne J. Acuña / Milko A. Jorquera

    Microorganisms, Vol 9, Iss 1351, p

    2021  Band 1351

    Abstract: Azospirillum -based plant and soil inoculants are widely used in agriculture. The inoculated Azospirillum strains are commonly tracked by both culture-dependent and culture-independent methods, which are time-consuming or expensive. In this context, ... ...

    Abstract Azospirillum -based plant and soil inoculants are widely used in agriculture. The inoculated Azospirillum strains are commonly tracked by both culture-dependent and culture-independent methods, which are time-consuming or expensive. In this context, clustered regularly interspaced short palindromic repeats (CRISPR) loci structure is unique in the bacterial genome, including some Azospirillum species. Here, we investigated the use of CRISPR loci to track specific Azospirillum strains in soils systems by PCR. Primer sets for Azospirillum sp. strain B510 were designed and evaluated by colony and endpoint PCR. The CRISPR loci -PCR approach was standardized for Azospirillum sp. strain B510, and its specificity was observed by testing against 9 different Azospirillum strains, and 38 strains of diverse bacterial genera isolated from wheat plants. The CRISPR loci -PCR approach was validated in assays with substrate and wheat seedlings. Azospirillum sp. strain B510 was detected after of two weeks of inoculation in both sterile and nonsterile substrates as well as rhizosphere grown in sterile substrate. The CRISPR loci -PCR approach was found to be a useful molecular tool for specific tracking of Azospirillum at the strain level. This technique can be easily adapted to other microbial inoculants carrying CRISPR loci and can be used to complement other microbiological techniques.
    Schlagwörter Azospirillum ; microbial inoculants ; strain tracking methods ; CRISPR loci -PCR ; Biology (General) ; QH301-705.5
    Thema/Rubrik (Code) 572
    Sprache Englisch
    Erscheinungsdatum 2021-06-01T00:00:00Z
    Verlag MDPI AG
    Dokumenttyp Artikel ; Online
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  4. Artikel ; Online: Biodegradation of azo dyes by bacterial or fungal consortium and identification of the biodegradation products

    Wafaa M. Abd El-Rahim / Hassan Moawad / Ahmed Z. Abdel Azeiz / Michael J. Sadowsky

    Egyptian Journal of Aquatic Research, Vol 47, Iss 3, Pp 269-

    2021  Band 276

    Abstract: Fifteen azo dyes were subjected to microbial degradation by four fungal strains and their mixtures as well as five bacterial strains and their mixtures. The biodegradation efficiency was determined by LC/MS/MS analysis. The most active bacterial strain ... ...

    Abstract Fifteen azo dyes were subjected to microbial degradation by four fungal strains and their mixtures as well as five bacterial strains and their mixtures. The biodegradation efficiency was determined by LC/MS/MS analysis. The most active bacterial strain was B. subtilis, where it showed the highest biodegradation capacity (71.8% to 100%) of eight azo dyes. Bacterial strain B. brevis came next to it. However, the consortium of the five bacterial strains gave lower degradation percentages. On the other hand, the fungal strains and their consortium were more potent in biodegradation of all tested azo dyes, where ten azo dyes were completely (100%) degraded by the consortium. Two of widely used azo dyes, direct violet and methyl red, were further studied in relation to the intermediate biodegradation products by each of the tested fungi and bacteria as well as the bacterial and fungal consortia using GC/MS/MS. The major biodegradation product of methyl red was 2-amino benzoic acid by all of the tested bacterial strains and A. niger, while the major biodegradation products of direct violet by both bacteria and fungi were ethanol, 2(2-butyxyethoxy), followed by 4- methyl benzoic acid and phenol, 2,4-bis (1,1-dimethyl ethyl). The results of this study suggest the successful use of the four fungal consortium for the biodegradation of the azo dyes. These findings are important to design bioremediation technology for treating the azo dye residues.
    Schlagwörter Azo dyes ; Biodegradation ; Bacterial consortium ; Fungal consortium ; Aquaculture. Fisheries. Angling ; SH1-691 ; Environmental sciences ; GE1-350
    Thema/Rubrik (Code) 630
    Sprache Englisch
    Erscheinungsdatum 2021-09-01T00:00:00Z
    Verlag Elsevier
    Dokumenttyp Artikel ; Online
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  5. Artikel ; Online: Rhizobacteria from ‘flowering desert’ events contribute to the mitigation of water scarcity stress during tomato seedling germination and growth

    Marcia Astorga-Eló / Susett Gonzalez / Jacquelinne J. Acuña / Michael J. Sadowsky / Milko A. Jorquera

    Scientific Reports, Vol 11, Iss 1, Pp 1-

    2021  Band 12

    Abstract: Abstract Tomato (Solanum lycopersicum L.) is an important vegetable cultivated around the world. Under field conditions, tomato can be negatively affected by water scarcity in arid and semiarid regions. The application of native plant growth-promoting ... ...

    Abstract Abstract Tomato (Solanum lycopersicum L.) is an important vegetable cultivated around the world. Under field conditions, tomato can be negatively affected by water scarcity in arid and semiarid regions. The application of native plant growth-promoting rhizobacteria (PGPR) isolated from arid environments has been proposed as an inoculant to mitigate abiotic stresses in plants. In this study, we evaluated rhizobacteria from Cistanthe longiscapa (syn Calandrinia litoralis and Calandrinia longiscapa), a representative native plant of flowering desert (FD) events (Atacama Desert, Chile), to determine their ability to reduce water scarcity stress on tomato seedlings. The isolated bacterial strains were characterized with respect to their PGPR traits, including P solubilization, 1-aminocyclopropane-1-carboxylate deaminase activity, and tryptophan-induced auxin and exopolysaccharide production. Three PGPR consortia were formulated with isolated Bacillus strains and then applied to tomato seeds, and then, the seedlings were exposed to different levels of water limitations. In general, tomato seeds and seedlings inoculated with the PGPR consortia presented significantly (P ≤ 0.05) greater plant growth (48 to 60 cm of height and 171 to 214 g of weight) and recovery rates (88 to 100%) compared with those without inoculation (37 to 51 cm of height; 146 to 197 g of fresh weight; 54 to 92% of recovery) after exposure to a lack of irrigation over different time intervals (24, 72 and 120 h) before transplantation. Our results revealed the effectiveness of the formulated PGPR consortia from FD to improve the performance of inoculated seeds and seedlings subjected to water scarcity; thus, the use of these consortia can represent an alternative approach for farmers facing drought events and water scarcity associated with climate change in semiarid and arid regions worldwide.
    Schlagwörter Medicine ; R ; Science ; Q
    Thema/Rubrik (Code) 580
    Sprache Englisch
    Erscheinungsdatum 2021-07-01T00:00:00Z
    Verlag Nature Portfolio
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  6. Artikel ; Online: Climate Change Impacts on Microbiota in Beach Sand and Water

    João Brandão / Chelsea Weiskerger / Elisabete Valério / Tarja Pitkänen / Päivi Meriläinen / Lindsay Avolio / Christopher D. Heaney / Michael J. Sadowsky

    International Journal of Environmental Research and Public Health, Vol 19, Iss 1444, p

    Looking Ahead

    2022  Band 1444

    Abstract: Beach sand and water have both shown relevance for human health and their microbiology have been the subjects of study for decades. Recently, the World Health Organization recommended that recreational beach sands be added to the matrices monitored for ... ...

    Abstract Beach sand and water have both shown relevance for human health and their microbiology have been the subjects of study for decades. Recently, the World Health Organization recommended that recreational beach sands be added to the matrices monitored for enterococci and Fungi. Global climate change is affecting beach microbial contamination, via changes to conditions like water temperature, sea level, precipitation, and waves. In addition, the world is changing, and humans travel and relocate, often carrying endemic allochthonous microbiota. Coastal areas are amongst the most frequent relocation choices, especially in regions where desertification is taking place. A warmer future will likely require looking beyond the use of traditional water quality indicators to protect human health, in order to guarantee that waterways are safe to use for bathing and recreation. Finally, since sand is a complex matrix, an alternative set of microbial standards is necessary to guarantee that the health of beach users is protected from both sand and water contaminants. We need to plan for the future safer use of beaches by adapting regulations to a climate-changing world.
    Schlagwörter climate change ; global warming ; beach sand ; FIB ; sand ; recreational water ; Medicine ; R
    Thema/Rubrik (Code) 333
    Sprache Englisch
    Erscheinungsdatum 2022-01-01T00:00:00Z
    Verlag MDPI AG
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  7. Artikel ; Online: Convenient Protocol for Production and Purification of Clostridioides difficile Spores for Germination Studies

    Melissa Weldy / Clayton Evert / Peter I. Dosa / Alexander Khoruts / Michael J. Sadowsky

    STAR Protocols, Vol 1, Iss 2, Pp 100071- (2020)

    2020  

    Abstract: Summary: Clostridioides difficile, an obligate anaerobic bacterium, causes infections leading to prolonged diarrhea. The bacterium produces dormant spores that can withstand an aerobic environment, resulting in easy environmental transfer. Here, we ... ...

    Abstract Summary: Clostridioides difficile, an obligate anaerobic bacterium, causes infections leading to prolonged diarrhea. The bacterium produces dormant spores that can withstand an aerobic environment, resulting in easy environmental transfer. Here, we present a convenient sporulation and purification protocol that can be practiced in any lab setting using a portable anaerobic glove bag. This protocol also optimizes existing cell growth methods and presents a detailed trouble shooting guide.This protocol is a modification of those previously reported by Edwards and McBride (2016) and Shen et al. (2016).
    Schlagwörter Science (General) ; Q1-390
    Sprache Englisch
    Erscheinungsdatum 2020-09-01T00:00:00Z
    Verlag Elsevier
    Dokumenttyp Artikel ; Online
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  8. Artikel ; Online: Bacterial community composition in agricultural soils under long‐term organic and conventional management

    Adria L. Fernandez / Craig C. Sheaffer / Donald L. Wyse / Michael J. Sadowsky

    Agrosystems, Geosciences & Environment, Vol 3, Iss 1, Pp n/a-n/a (2020)

    2020  

    Abstract: Abstract Organic row cropping systems utilize diverse management regimes, but share required practices, including biological fertility sources, diverse rotations, incorporation of organic matter, and lack of synthetic pesticides. The practices can alter ... ...

    Abstract Abstract Organic row cropping systems utilize diverse management regimes, but share required practices, including biological fertility sources, diverse rotations, incorporation of organic matter, and lack of synthetic pesticides. The practices can alter the composition of functionally significant soil microbes relative to conventional practices. We used 16S rRNA sequencing to profile soil bacterial communities at five locations where long‐term organic and conventional row cropping were practiced in close proximity on the same underlying soil type. Location effects, reflecting soil characteristics, were stronger than effects of organic vs. conventional management or corn (Zea mays L.) vs. soybean [Glycine max (L.) Merr.] cropping on the relative abundance of bacterial taxa. A core subset of 1,300 operational taxonomic units (OTUs) were detected in all sampled soils. Firmicutes made up a smaller portion of core OTUs than total OTUs, indicating that taxa in this group were more likely to be found only in specific environments. Conversely, Actinobacteria OTUs were more highly represented in the core than the full OTU set, indicating wide distribution of these taxa across environments. The genus Streptomyces comprised a five‐fold–greater proportion of core OTUs than of total OTUs. We identified 303 OTUs whose abundance differed with management system. Of those, members of the phyla Bacteroidetes and Planctomycetes tended to be more abundant under organic management, whereas members of the Actinobacteria and Verrucomicrobia tended to be more abundant in conventional. This multi‐site study contributes to identification of bacterial community members most affected by organic practice adoption across soil types and practices.
    Schlagwörter Agriculture ; S ; Environmental sciences ; GE1-350
    Thema/Rubrik (Code) 630
    Sprache Englisch
    Erscheinungsdatum 2020-01-01T00:00:00Z
    Verlag Wiley
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  9. Artikel ; Online: Engineering Multigenerational Host-Modulated Microbiota against Soilborne Pathogens in Response to Global Climate Change

    Paola Durán / Gonzalo Tortella / Michael J. Sadowsky / Sharon Viscardi / Patricio Javier Barra / Maria de la Luz Mora

    Biology, Vol 10, Iss 865, p

    2021  Band 865

    Abstract: Crop migration caused by climatic events has favored the emergence of new soilborne diseases, resulting in the colonization of new niches (emerging infectious diseases, EIDs). Soilborne pathogens are extremely persistent in the environment. This is in ... ...

    Abstract Crop migration caused by climatic events has favored the emergence of new soilborne diseases, resulting in the colonization of new niches (emerging infectious diseases, EIDs). Soilborne pathogens are extremely persistent in the environment. This is in large part due to their ability to reside in the soil for a long time, even without a host plant, using survival several strategies. In this regard, disease-suppressive soils, characterized by a low disease incidence due to the presence of antagonist microorganisms, can be an excellent opportunity for the study mechanisms of soil-induced immunity, which can be applied in the development of a new generation of bioinoculants. Therefore, here we review the main effects of climate change on crops and pathogens, as well as the potential use of soil-suppressive microbiota as a natural source of biocontrol agents. Based on results of previous studies, we also propose a strategy for the optimization of microbiota assemblages, selected using a host-mediated approach. This process involves an increase in and prevalence of specific taxa during the transition from a conducive to a suppressive soil. This strategy could be used as a model to engineer microbiota assemblages for pathogen suppression, as well as for the reduction of abiotic stresses created due to global climate change.
    Schlagwörter suppressive soils ; engineering microbiome ; biocontrol ; food security ; sustainability ; Biology (General) ; QH301-705.5
    Sprache Englisch
    Erscheinungsdatum 2021-09-01T00:00:00Z
    Verlag MDPI AG
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  10. Artikel: Recent changes to the classification of symbiotic, nitrogen-fixing, legume-associating bacteria: a review

    Shamseldin, Abdelaal / Ahmed Abdelkhalek / Michael J. Sadowsky

    Symbiosis. 2017 Feb., v. 71, no. 2

    2017  

    Abstract: The Rhizobia are collectively comprised of gram negative soil bacteria that have the ability to form symbiotic nitrogen-fixing root and/or stem nodules in association with leguminous plants. The taxonomy of these bacteria is continually in a state of ... ...

    Abstract The Rhizobia are collectively comprised of gram negative soil bacteria that have the ability to form symbiotic nitrogen-fixing root and/or stem nodules in association with leguminous plants. The taxonomy of these bacteria is continually in a state of flux, in large part due to rapid development of refined molecular biology techniques. The isolation and characterization of new, and often different, legumes-nodulating bacteria on a variety of plant hosts has resulted in the naming of many new rhizobial species. Here we update the taxonomy of the legume-nodulating bacteria and describe newly identified rhizobia capable of nodulating edible legumes and legume trees. In 1990, there was only one bacterial species that was known to nodulate common bean worldwide (Rhizobium leguminosarum sv. phaseoli), one species that nodulated faba bean (Rhizobium leguminosarum sv. viciae), and two species that nodulated soybean (Bradyrhizobium japonicum and Rhizobium fredii). Today, nearly 14, 11, 6, 5, 5, 4, 3 and 2 species have been defined that are capable of nodulating common bean, soybean, cowpea, chickpea, peanut, lentils, faba bean and pea, respectively. The recent use of whole genome based taxonomy (genomotaxonomy) will surely change how we define this important group of bacteria. The identification of several rhizobial species that are able to nodulate and fix nitrogen with edible legumes may enhance the production of these crops and can compensate for worldwide deficiencies in human nutritional needs in the future.
    Schlagwörter Bradyrhizobium japonicum ; Rhizobium leguminosarum ; Sinorhizobium fredii ; chickpeas ; cowpeas ; crops ; faba beans ; genome ; humans ; lentils ; molecular biology ; nitrogen fixation ; nutrient requirements ; peanuts ; peas ; soil bacteria ; soybeans ; stem nodules ; taxonomy ; trees
    Sprache Englisch
    Erscheinungsverlauf 2017-02
    Umfang p. 91-109.
    Erscheinungsort Springer Netherlands
    Dokumenttyp Artikel
    Anmerkung Review
    ZDB-ID 2535332-9
    ISSN 1878-7665 ; 0334-5114
    ISSN (online) 1878-7665
    ISSN 0334-5114
    DOI 10.1007/s13199-016-0462-3
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