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Li S, Dong L, Lian WH, Lin ZL, Lu CY, Xu L, Li L, Hozzein WN, Li WJ. Exploring untapped potential of Streptomyces spp. in Gurbantunggut Desert by use of highly selective culture strategy. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 790:148235. [PMID: 34380255 DOI: 10.1016/j.scitotenv.2021.148235] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/28/2021] [Accepted: 05/28/2021] [Indexed: 06/13/2023]
Abstract
Streptomycetes have been, for over 70 years, one of the most abundant sources for the discovery of new antibiotics and clinic drugs. However, in recent decades, it has been more and more difficult to obtain new phylotypes of the genus Streptomyces by using conventional samples and culture strategies. In this study, we combined culture-dependent and culture-independent approaches to better explore the Streptomyces communities in desert sandy soils. Moreover, two different culture strategies termed Conventional Culture Procedure (CCP) and Streptomycetes Culture Procedure (SCP) were employed to evaluate the isolation efficiency of Streptomyces spp. with different intensities of selectivity. The 16S rRNA gene amplicon analysis revealed a very low abundance (0.04-0.37%, average 0.22%) of Streptomyces in all the desert samples, conversely the percentage of Streptomyces spp. obtained by the culture-dependent method was very high (5.20-39.57%, average 27.76%), especially in the rhizospheric sand soils (38.40-39.57%, average 38.99%). Meanwhile, a total of 1589 pure cultures were isolated successfully, dominated by Streptomyces (29.52%), Microvirga (8.06%) and Bacillus (7.68%). In addition, 400 potential new species were obtained, 48 of which belonged to the genus Streptomyces. More importantly, our study demonstrated the SCP strategy which had highly selectivity could greatly expand the number and phylotypes of Streptomyces spp. by almost 4-fold than CCP strategy. These results provide insights on the diversity investigation of desert Streptomyces, and it could be reference for researchers to bring more novel actinobacteria strains from the environment into culture.
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Affiliation(s)
- Shuai Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Lei Dong
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China.
| | - Wen-Hui Lian
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Zhi-Liang Lin
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Chun-Yan Lu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Lu Xu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Li Li
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, PR China
| | - Wael N Hozzein
- Zoology Department, College of Science, King Saud University, Riyadh 999088, Saudi Arabia; Botany and Microbiology Department, Faculty of Science, Beni-Suef University, Beni-Suef 62511, Egypt
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China; State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, PR China.
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Climatic Zone and Soil Properties Determine the Biodiversity of the Soil Bacterial Communities Associated to Native Plants from Desert Areas of North-Central Algeria. Microorganisms 2021; 9:microorganisms9071359. [PMID: 34201731 PMCID: PMC8303931 DOI: 10.3390/microorganisms9071359] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 06/16/2021] [Accepted: 06/17/2021] [Indexed: 12/15/2022] Open
Abstract
Algeria is the largest country in Africa characterized by semi-arid and arid sites, located in the North, and hypersaline zones in the center and South of the country. Several autochthonous plants are well known as medicinal plants, having in common tolerance to aridity, drought and salinity. In their natural environment, they live with a great amount of microbial species that altogether are indicated as plant microbiota, while the plants are now viewed as a “holobiont”. In this work, the microbiota of the soil associated to the roots of fourteen economically relevant autochthonous plants from Algeria have been characterized by an innovative metagenomic approach with a dual purpose: (i) to deepen the knowledge of the arid and semi-arid environment and (ii) to characterize the composition of bacterial communities associated with indigenous plants with a strong economic/commercial interest, in order to make possible the improvement of their cultivation. The results presented in this work highlighted specific signatures which are mainly determined by climatic zone and soil properties more than by the plant species.
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Guo YH, Tang XK, Hu SR, Zhou ML, Gao J. Streptomyces liangshanensis sp. nov., a novel actinomycete isolated from rhizosphere soil of Fagopyrum tataricum. Arch Microbiol 2021; 203:3055-3059. [PMID: 33783591 DOI: 10.1007/s00203-021-02294-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 02/22/2021] [Accepted: 03/18/2021] [Indexed: 11/24/2022]
Abstract
A novel actinomycete strain, designated strain QMT-12T, was isolated from the rhizospheric soils of Fagopyrum tataricum and characterized using a polyphasic approach. Strain QMT-12T was found to have morphological features typical of the genus Streptomyces. The predominant fatty acids included C18:1 cis9 (35.9%), Summed feature 6 (C18:2 cis9, 12/C18:0 a or C18:0 anteiso/C18:2 c) (30.6%) and C16:0 (16.3%). The whole-cell sugars were arabinose and glucose. The whole-cell-wall amino acids included alanine, aspartate, glutamic acid, glycine and LL-diaminopimelic acid. The menaquinones were MK-9, MK-9(H2), MK-9(H4), MK-9(H6) and MK-9(H8). The diagnostic phospholipids consisted of diphosphatidyl glycerol, phosphatidylethanolamine, phosphatidyl methyl ethanolamine, phospholipids, phosphotidyl inositol, phosphotidylinositol mannosides, and phospholipids of unknown structure containing glucosamine. The full-length 16S rRNA gene sequence analysis showed that strain QMT-12T belonged to the genus Streptomyces and had 98.2, 98.1, 98.1 and ≤ 98.0% similarities to Streptomyces camponoticapitis 2H-TWYE14T, Streptomyces scopuliridis NRRL B-24574T, Streptomyces inhibens NEAU-D10T and other Streptomyces species with validly published and correct names, respectively. Phylogenetic analysis indicated that strain QMT-12T was closely related to Streptomyces inhibens NEAU-D10T. However, the average nucleotide identity value and the digital DNA-DNA hybridization value between strain QMT-12T and S. inhibens NEAU-D10T were 85.0 and 22.3%, respectively, well below 95-96% and 70% cut-off point recommended for delineating species. Based on its phenotypic and genotypic characteristics, strain QMT-12T (= CICC 11056T = JCM 33963T) represents the type strain of a novel species, for which the name Streptomyces liangshanensis sp. nov. is proposed.
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Affiliation(s)
- Yi-Hui Guo
- School of Life Science, Hunan University of Science and Technology, Xiangtan, 411201, People's Republic of China
| | - Xin-Ke Tang
- School of Life Science, Hunan University of Science and Technology, Xiangtan, 411201, People's Republic of China
| | - Si-Ren Hu
- School of Life Science, Hunan University of Science and Technology, Xiangtan, 411201, People's Republic of China
| | - Mei-Liang Zhou
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China.
| | - Jian Gao
- School of Life Science, Hunan University of Science and Technology, Xiangtan, 411201, People's Republic of China. .,Key Laboratory of Ecological Remediation and Safe Utilization of Heavy Metal-Polluted Soils, College of Hunan Province, Xiangtan, 411201, People's Republic of China.
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Saline and Arid Soils: Impact on Bacteria, Plants, and their Interaction. BIOLOGY 2020; 9:biology9060116. [PMID: 32498442 PMCID: PMC7344409 DOI: 10.3390/biology9060116] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/26/2020] [Accepted: 05/29/2020] [Indexed: 12/11/2022]
Abstract
Salinity and drought are the most important abiotic stresses hampering crop growth and yield. It has been estimated that arid areas cover between 41% and 45% of the total Earth area worldwide. At the same time, the world’s population is going to soon reach 9 billion and the survival of this huge amount of people is dependent on agricultural products. Plants growing in saline/arid soil shows low germination rate, short roots, reduced shoot biomass, and serious impairment of photosynthetic efficiency, thus leading to a substantial loss of crop productivity, resulting in significant economic damage. However, plants should not be considered as single entities, but as a superorganism, or a holobiont, resulting from the intimate interactions occurring between the plant and the associated microbiota. Consequently, it is very complex to define how the plant responds to stress on the basis of the interaction with its associated plant growth-promoting bacteria (PGPB). This review provides an overview of the physiological mechanisms involved in plant survival in arid and saline soils and aims at describing the interactions occurring between plants and its bacteriome in such perturbed environments. The potential of PGPB in supporting plant survival and fitness in these environmental conditions has been discussed.
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Suleiman MK, Dixon K, Commander L, Nevill P, Quoreshi AM, Bhat NR, Manuvel AJ, Sivadasan MT. Assessment of the Diversity of Fungal Community Composition Associated With Vachellia pachyceras and Its Rhizosphere Soil From Kuwait Desert. Front Microbiol 2019; 10:63. [PMID: 30766519 PMCID: PMC6365840 DOI: 10.3389/fmicb.2019.00063] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 01/15/2019] [Indexed: 11/13/2022] Open
Abstract
This research examined the general soil fungi and AM fungal communities associated with a Lonely Tree species (Vachellia pachyceras) existing in the Sabah Al-Ahmad Natural Reserve located at the Kuwait desert. The goals of the study were to describe the general fungal and AM fungal communities present in the rhizospheric, non-rhizospheric soils and roots of V. pachyceras, respectively, as well as local and non-local V. pachyceras seedlings when grown under standard nursery growing environments. Soil and root samples were analyzed for an array of characteristics including soil physicochemical composition, and culture-independent method termed PCR-cloning, intermediate variable region of rDNA, the large subunit (LSU) and internal transcribed spacer (ITS) region sequence identifications. The results reveal that the fungal phylotypes were classified in four major fungal phyla namely Ascomycota, Basidiomycota, Chytridiomycota, and Zygomycota. The largest assemblage of fungal analyses showed communities dominated by members of the phylum Ascomycota. The assays also revealed a wealth of incertae sedis fungi, mostly affiliated to uncultured fungi from diverse environmental conditions. Striking difference between rhizosphere and bulk soils communities, with more fungal diversities and Operational Taxonomic Units (OTUs) richness associated with both the field and nursery rhizosphere soils. In contrast, a less diverse fungal community was found in the bulk soil samples. The characterization of AM fungi from the root system demonstrated that the most abundant and diversified group belongs to the family Glomeraceae, with the common genus Rhizophagus (5 phylotypes) and another unclassified taxonomic group (5 phylotypes). Despite the harsh climate that prevails in the Kuwait desert, studied roots displayed the existence of considerable number of AM fungal biota. The present work thus provides a baseline of the fungal and mycorrhizal community associated with rhizosphere and non-rhizosphere soils and roots of only surviving V. pachyceras tree from the Kuwaiti desert and seedlings under nursery growing environments.
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Affiliation(s)
- Majda K. Suleiman
- Environment and Life Sciences Research Center, Desert Agriculture and Ecosystems Program, Kuwait Institute for Scientific Research, Kuwait City, Kuwait
| | - Kingsley Dixon
- ARC Centre for Mine Site Restoration, Department of Environment and Agriculture, Curtin University, Perth, WA, Australia
| | - Lucy Commander
- School of Biological Sciences, The University of Western Australia, Perth, WA, Australia
| | - Paul Nevill
- ARC Centre for Mine Site Restoration, Department of Environment and Agriculture, Curtin University, Perth, WA, Australia
| | - Ali M. Quoreshi
- Environment and Life Sciences Research Center, Desert Agriculture and Ecosystems Program, Kuwait Institute for Scientific Research, Kuwait City, Kuwait
| | - Narayana R. Bhat
- Environment and Life Sciences Research Center, Desert Agriculture and Ecosystems Program, Kuwait Institute for Scientific Research, Kuwait City, Kuwait
| | - Anitha J. Manuvel
- Environment and Life Sciences Research Center, Desert Agriculture and Ecosystems Program, Kuwait Institute for Scientific Research, Kuwait City, Kuwait
| | - Mini T. Sivadasan
- Environment and Life Sciences Research Center, Desert Agriculture and Ecosystems Program, Kuwait Institute for Scientific Research, Kuwait City, Kuwait
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Lauer A, Baal JD, Mendes SD, Casimiro KN, Passaglia AK, Valenzuela AH, Guibert G. Valley Fever on the Rise-Searching for Microbial Antagonists to the Fungal Pathogen Coccidioides immitis. Microorganisms 2019; 7:E31. [PMID: 30682831 PMCID: PMC6406340 DOI: 10.3390/microorganisms7020031] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 01/10/2019] [Accepted: 01/18/2019] [Indexed: 11/16/2022] Open
Abstract
The incidence of coccidioidomycosis, also known as Valley Fever, is increasing in the Southwestern United States and Mexico. Despite considerable efforts, a vaccine to protect humans from this disease is not forthcoming. The aim of this project was to isolate and phylogenetically compare bacterial species that could serve as biocontrol candidates to suppress the growth of Coccidioides immitis, the causative agent of coccidioidomycosis, in eroded soils or in areas close to human settlements that are being developed. Soil erosion in Coccidioides endemic areas is leading to substantial emissions of fugitive dust that can contain arthroconidia of the pathogen and thus it is becoming a health hazard. Natural microbial antagonists to C. immitis, that are adapted to arid desert soils could be used for biocontrol attempts to suppress the growth of the pathogen in situ to reduce the risk for humans and animals of contracting coccidioidomycosis. Bacteria were isolated from soil samples obtained near Bakersfield, California. Subsequently, pairwise challenge assays with bacterial pure cultures were initially performed against Uncinocarpus reesii, a non-pathogenic relative of C. immitis on media plates. Bacterial isolates that exhibited strongly antifungal properties were then re-challenged against C. immitis. Strongly anti-C. immitis bacterial isolates related to Bacillus subtilis and Streptomyces spp. were isolated, and their antifungal spectrum was investigated using a selection of environmental fungi.
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Affiliation(s)
- Antje Lauer
- Department of Biology, California State University Bakersfield, 9001 Stockdale Highway, Bakersfield, CA 93311-1022, USA.
| | - Joe Darryl Baal
- Department of Biology, California State University Bakersfield, 9001 Stockdale Highway, Bakersfield, CA 93311-1022, USA.
| | - Susan D Mendes
- Department of Biology, California State University Bakersfield, 9001 Stockdale Highway, Bakersfield, CA 93311-1022, USA.
| | - Kayla Nicole Casimiro
- Department of Biology, California State University Bakersfield, 9001 Stockdale Highway, Bakersfield, CA 93311-1022, USA.
| | - Alyce Kayes Passaglia
- Department of Biology, California State University Bakersfield, 9001 Stockdale Highway, Bakersfield, CA 93311-1022, USA.
| | - Alex Humberto Valenzuela
- Department of Biology, California State University Bakersfield, 9001 Stockdale Highway, Bakersfield, CA 93311-1022, USA.
| | - Gerry Guibert
- Monterey County Health Department, 1270 Natividad, Salinas, CA 93906, USA.
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Simon Sola MZ, Pérez Visñuk D, Benimeli CS, Polti MA, Alvarez A. Cr(VI) and lindane removal by Streptomyces
M7 is improved by maize root exudates. J Basic Microbiol 2017; 57:1037-1044. [DOI: 10.1002/jobm.201700324] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 08/14/2017] [Accepted: 08/17/2017] [Indexed: 11/12/2022]
Affiliation(s)
- María Z. Simon Sola
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET); Tucumán Argentina
| | | | - Claudia S. Benimeli
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET); Tucumán Argentina
| | - Marta Alejandra Polti
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET); Tucumán Argentina
- Facultad de Ciencias Naturales e Instituto Miguel Lillo; Universidad Nacional de Tucumán; Tucumán Argentina
| | - Analia Alvarez
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET); Tucumán Argentina
- Facultad de Ciencias Naturales e Instituto Miguel Lillo; Universidad Nacional de Tucumán; Tucumán Argentina
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Matsumoto A, Takahashi Y. Endophytic actinomycetes: promising source of novel bioactive compounds. J Antibiot (Tokyo) 2017; 70:514-519. [PMID: 28270688 DOI: 10.1038/ja.2017.20] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 12/26/2016] [Accepted: 01/26/2017] [Indexed: 12/20/2022]
Abstract
Endophytic actinomycetes associated with plant roots are a relatively untapped source of potential new bioactive compounds. This is becoming increasingly important, as the returns from discovery research on soil-dwelling microbes, have been continuously diminishing. We have isolated more than 1000 strains of actinomycetes from plant roots in our search for novel bioactive compounds, identified and assayed their bioactive metabolites, as well as investigated their biosynthetic genes for generating secondary metabolites. This has resulted in the discovery of several interesting compounds. Creation of plant root clone libraries enabled us to confirm that we had, indeed, isolated endophytes. In this paper, we introduce our approach to this promising line of research, incorporating data from other publications, and illustrate the potential that endophytic actinomycetes offer as a new source of novel lead compounds.
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Affiliation(s)
- Atsuko Matsumoto
- Kitasato Institute for Life Sciences, Laboratory of Microbial Functions, Kitasato University, Tokyo, Japan
| | - Yōko Takahashi
- Kitasato Institute for Life Sciences, Laboratory of Microbial Functions, Kitasato University, Tokyo, Japan
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Alvarez A, Saez JM, Davila Costa JS, Colin VL, Fuentes MS, Cuozzo SA, Benimeli CS, Polti MA, Amoroso MJ. Actinobacteria: Current research and perspectives for bioremediation of pesticides and heavy metals. CHEMOSPHERE 2017; 166:41-62. [PMID: 27684437 DOI: 10.1016/j.chemosphere.2016.09.070] [Citation(s) in RCA: 269] [Impact Index Per Article: 38.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 09/15/2016] [Accepted: 09/16/2016] [Indexed: 05/03/2023]
Abstract
Actinobacteria exhibit cosmopolitan distribution since their members are widely distributed in aquatic and terrestrial ecosystems. In the environment they play relevant ecological roles including recycling of substances, degradation of complex polymers, and production of bioactive molecules. Biotechnological potential of actinobacteria in the environment was demonstrated by their ability to remove organic and inorganic pollutants. This ability is the reason why actinobacteria have received special attention as candidates for bioremediation, which has gained importance because of the widespread release of contaminants into the environment. Among organic contaminants, pesticides are widely used for pest control, although the negative impact of these chemicals in the environmental balance is increasingly becoming apparent. Similarly, the extensive application of heavy metals in industrial processes lead to highly contaminated areas worldwide. Several studies focused in the use of actinobacteria for cleaning up the environment were performed in the last 15 years. Strategies such as bioaugmentation, biostimulation, cell immobilization, production of biosurfactants, design of defined mixed cultures and the use of plant-microbe systems were developed to enhance the capabilities of actinobacteria in bioremediation. In this review, we compiled and discussed works focused in the study of different bioremediation strategies using actinobacteria and how they contributed to the improvement of the already existing strategies. In addition, we discuss the importance of omic studies to elucidate mechanisms and regulations that bacteria use to cope with pollutant toxicity, since they are still little known in actinobacteria. A brief account of sources and harmful effects of pesticides and heavy metals is also given.
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Affiliation(s)
- Analia Alvarez
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), Avenida Belgrano y Pasaje Caseros, Tucumán 4000, Argentina; Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán (UNT), Miguel Lillo 205, Tucumán 4000, Argentina.
| | - Juliana Maria Saez
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), Avenida Belgrano y Pasaje Caseros, Tucumán 4000, Argentina.
| | - José Sebastian Davila Costa
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), Avenida Belgrano y Pasaje Caseros, Tucumán 4000, Argentina.
| | - Veronica Leticia Colin
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), Avenida Belgrano y Pasaje Caseros, Tucumán 4000, Argentina.
| | - María Soledad Fuentes
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), Avenida Belgrano y Pasaje Caseros, Tucumán 4000, Argentina.
| | - Sergio Antonio Cuozzo
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), Avenida Belgrano y Pasaje Caseros, Tucumán 4000, Argentina; Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán (UNT), Miguel Lillo 205, Tucumán 4000, Argentina.
| | - Claudia Susana Benimeli
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), Avenida Belgrano y Pasaje Caseros, Tucumán 4000, Argentina.
| | - Marta Alejandra Polti
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), Avenida Belgrano y Pasaje Caseros, Tucumán 4000, Argentina; Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán (UNT), Miguel Lillo 205, Tucumán 4000, Argentina.
| | - María Julia Amoroso
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), Avenida Belgrano y Pasaje Caseros, Tucumán 4000, Argentina.
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Jorquera MA, Maruyama F, Ogram AV, Navarrete OU, Lagos LM, Inostroza NG, Acuña JJ, Rilling JI, de La Luz Mora M. Rhizobacterial Community Structures Associated with Native Plants Grown in Chilean Extreme Environments. MICROBIAL ECOLOGY 2016; 72:633-646. [PMID: 27406732 DOI: 10.1007/s00248-016-0813-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 06/29/2016] [Indexed: 06/06/2023]
Abstract
Chile is topographically and climatically diverse, with a wide array of diverse undisturbed ecosystems that include native plants that are highly adapted to local conditions. However, our understanding of the diversity, activity, and role of rhizobacteria associated with natural vegetation in undisturbed Chilean extreme ecosystems is very poor. In the present study, the combination of denaturing gradient gel electrophoresis and 454-pyrosequencing approaches was used to describe the rhizobacterial community structures of native plants grown in three representative Chilean extreme environments: Atacama Desert (ATA), Andes Mountains (AND), and Antarctic (ANT). Both molecular approaches revealed the presence of Proteobacteria, Bacteroidetes, and Actinobacteria as the dominant phyla in the rhizospheres of native plants. Lower numbers of operational taxonomic units (OTUs) were observed in rhizosphere soils from ATA compared with AND and ANT. Both approaches also showed differences in rhizobacterial community structures between extreme environments and between plant species. The differences among plant species grown in the same environment were attributed to the higher relative abundance of classes Gammaproteobacteria and Alphaproteobacteria. However, further studies are needed to determine which environmental factors regulate the structures of rhizobacterial communities, and how (or if) specific bacterial groups may contribute to the growth and survival of native plants in each Chilean extreme environments.
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Affiliation(s)
- Milko A Jorquera
- Center of Plant, Soil Interaction, and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Ave. Francisco Salazar, 01145, Temuco, Chile.
| | - Fumito Maruyama
- Section of Microbiology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Andrew V Ogram
- Soil and Water Science Department, University of Florida, 2181 McCarty Hall, PO Box 110290, Gainesville, FL, 32611, USA
| | - Oscar U Navarrete
- Center of Plant, Soil Interaction, and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Ave. Francisco Salazar, 01145, Temuco, Chile
| | - Lorena M Lagos
- Programa de Doctorado en Ciencias de Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
| | - Nitza G Inostroza
- Center of Plant, Soil Interaction, and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Ave. Francisco Salazar, 01145, Temuco, Chile
| | - Jacquelinne J Acuña
- Center of Plant, Soil Interaction, and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Ave. Francisco Salazar, 01145, Temuco, Chile
| | - Joaquín I Rilling
- Programa de Doctorado en Ciencias de Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
| | - María de La Luz Mora
- Center of Plant, Soil Interaction, and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Ave. Francisco Salazar, 01145, Temuco, Chile
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11
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Chessa L, Pusino A, Garau G, Mangia NP, Pinna MV. Soil microbial response to tetracycline in two different soils amended with cow manure. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:5807-17. [PMID: 26590057 DOI: 10.1007/s11356-015-5789-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 11/09/2015] [Indexed: 05/16/2023]
Abstract
High amounts of antibiotics are introduced in the soil environment by manure amendment, which is the most important spreading route in soil, with a potential ecotoxicological impact on the environment. The objectives of this study were (a) to assess the tetracycline (Tc) bioavailability in a clay and in a sandy soil, and (b) to evaluate the effects of the Tc and cow manure on the structure and function of soil microbial communities. Clay and sandy soils were spiked with Tc at the concentrations of 100 and 500 mg Tc kg(-1) soil, and were amended or not with cow manure. The clay soil showed greater Tc sorption capacity and bioavailable Tc was between 0.157 and 4.602 mg kg(-1) soil. Tc dose and time-dependent effects on soil microbial communities were investigated by fluorescein diacetate activity, phospholipid fatty acids analysis, as well as by Biolog community level physiological profile and microbial counts at 2, 7 and 60 days after Tc and/or manure addition. The added Tc caused detrimental effect on the microbial activity and structure, particularly in the short term at the highest concentrations. However, the Tc effect was transient' it decreased after 7 days and totally disappeared within 60 days. Cow manure shifted the bacterial structure in both soils, increased the microbial activity in clay soil and contributed to recover the microbial structure in Tc-spiked manure treatments.
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Affiliation(s)
- Luigi Chessa
- Department of Agriculture, University of Sassari, Viale Italia 39, 07100, Sassari, Italy.
| | - Alba Pusino
- Department of Agriculture, University of Sassari, Viale Italia 39, 07100, Sassari, Italy
| | - Giovanni Garau
- Department of Agriculture, University of Sassari, Viale Italia 39, 07100, Sassari, Italy
| | | | - Maria Vittoria Pinna
- Department of Agriculture, University of Sassari, Viale Italia 39, 07100, Sassari, Italy
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Hadizadeh S, Forootanfar H, Shahidi Bonjar GH, Falahati Nejad M, Karamy Robati A, Ayatollahi Mousavi SA, Amirporrostami S. Antifungal activity of terrestrial Streptomyces rochei strain HF391 against clinical azole -resistant Aspergillus fumigatus. Curr Med Mycol 2015; 1:19-24. [PMID: 28680984 PMCID: PMC5490309 DOI: 10.18869/acadpub.cmm.1.2.19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND AND PURPOSE Actinomycetes have been discovered as source of antifungal compounds that are currently in clinical use. Invasive aspergillosis (IA) due to Aspergillus fumigatus has been identified as individual drug-resistant Aspergillus spp. to be an emerging pathogen opportunities a global scale. This paper described the antifungal activity of one terrestrial actinomycete against the clinically isolated azole-resistant A. fumigatus. MATERIALS AND METHODS Soil samples were collected from various locations of Kerman, Iran. Thereafter, the actinomycetes were isolated using starch-casein-nitrate-agar medium and the most efficient actinomycetes (capable of inhibiting A. fumigatus) were screened using agar block method. In the next step, the selected actinomycete was cultivated in starch-casein- broth medium and the inhibitory activity of the obtained culture broth was evaluated using agar well diffusion method. RESULTS The selected actinomycete, identified as Streptomyces rochei strain HF391, could suppress the growth of A. fumigatus isolates which was isolated from the clinical samples of patients treated with azoles. This strain showed higher inhibition zones on agar diffusion assay which was more than 15 mm. CONCLUSION The obtained results of the present study introduced Streptomyces rochei strain HF391 as terrestrial actinomycete that can inhibit the growth of clinically isolated A. fumigatus.
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Affiliation(s)
- S Hadizadeh
- Department of Medical Mycology & Parasitology, Faculty of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - H Forootanfar
- Herbal and Traditional Medicines Research Center, Kerman University of Medical Sciences, Kerman, Iran
| | - G H Shahidi Bonjar
- Department of Plant Pathology & Biotechnology, College of Agriculture, Bahonar University of Kerman, Iran
| | - M Falahati Nejad
- Student Research Committee, Mazandaran University of Medical Sciences, Sari, Iran
| | - A Karamy Robati
- Department of Medical Mycology & Parasitology, Faculty of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - S A Ayatollahi Mousavi
- Department of Medical Mycology & Parasitology, Faculty of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - S Amirporrostami
- Department of Medical Mycology & Parasitology, Faculty of Medicine, Kerman University of Medical Sciences, Kerman, Iran
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13
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Kaplan D, Maymon M, Agapakis CM, Lee A, Wang A, Prigge BA, Volkogon M, Hirsch AM. A survey of the microbial community in the rhizosphere of two dominant shrubs of the Negev Desert highlands, Zygophyllum dumosum (Zygophyllaceae) and Atriplex halimus (Amaranthaceae), using cultivation-dependent and cultivation-independent methods. AMERICAN JOURNAL OF BOTANY 2013; 100:1713-25. [PMID: 23975635 DOI: 10.3732/ajb.1200615] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
PREMISE OF THE STUDY Plant roots comprise more than 50% of the plant's biomass. Part of that biomass includes the root microbiome, the assemblage of bacteria and fungi living in the 1-3 mm region adjacent to the external surface of the root, the rhizosphere. We hypothesized that the microorganisms living in the rhizosphere and in bulk soils of the harsh environment of the Negev Desert of Israel had potential for use as plant-growth-promoting bacteria (PGPB) to improve plant productivity in nutrient-poor, arid soils that are likely to become more common as the climate changes. • METHODS We used cultivation-dependent methods including trap experiments with legumes to find nitrogen-fixing rhizobia, specialized culture media to determine iron chelation via siderophores and phosphate-solubilizing and cellulase activities; cultivation-independent methods, namely 16S rDNA cloning and sequencing; and also community-level physiological profiling to discover soil microbes associated with the Negev desert perennials Zygophyllum dumosum and Atriplex halimus during the years 2009-2010. • KEY RESULTS We identified a number of PGPB, both epiphytes and endophytes, which fix nitrogen, chelate iron, solubilize phosphate, and secrete cellulase, as well as many other bacteria and some fungi, thereby providing a profile of the microbiomes that support the growth of two desert perennials. • CONCLUSION We generated a snapshot of the microbial communities in the Negev Desert, giving us an insight in its natural state. This desert, like many arid environments, is vulnerable to exploitation for other purposes, including solar energy production and dry land farming.
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Affiliation(s)
- Drora Kaplan
- Department of Environmental Hydrology and Microbiology, Zuckerberg Institute for Water Research, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus Midreshet Ben-Gurion 84990, Israel
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Antifungal and antifeedant activities of extracellular product of Streptomyces spp. ERI-04 isolated from Western Ghats of Tamil Nadu. J Mycol Med 2010. [DOI: 10.1016/j.mycmed.2010.09.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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15
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Chowdhury SP, Schmid M, Hartmann A, Tripathi AK. Identification of diazotrophs in the culturable bacterial community associated with roots of Lasiurus sindicus, a perennial grass of Thar Desert, India. MICROBIAL ECOLOGY 2007; 54:82-90. [PMID: 17264993 DOI: 10.1007/s00248-006-9174-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2006] [Revised: 09/18/2006] [Accepted: 09/26/2006] [Indexed: 05/13/2023]
Abstract
Lasiurus sindicus is a highly nutritive, drought-tolerant, perennial grass that is endemic to the Thar Desert of Rajasthan, India. Analysis of 16S rRNA coding genes of the bacterial isolates enriched in nitrogen-free semisolid medium, from the surface-sterilized roots of L. sindicus, showed predominance of Gram-negative over Gram-positive bacteria. According to comparative sequence analysis of 16S rDNA sequence data, Gram-positive bacteria with low GC content (Staphylococcus warneri and Bacillus sp.) and high GC content (Micrococcus luteus, Microbacterium sp.) were identified. Gram-negative bacteria included Azospirillum sp., Rhizobium sp., Agrobacterium tumefaciens, and Inquilinus limosus (alpha-proteobacteria); Ralstonia sp., Variovorax paradoxus, and Bordetella petrii (beta-proteobacteria); and Pseudomonas pseudoalcaligenes, Stenotrophomonas sp. (gamma-proteobacteria). The occurrence of nifH sequences in Azospirillum sp., Rhizobium sp., and P. pseudoalcaligenes showed the possibility of supplying biologically fixed nitrogen by the root-associated diazotrophs to the host plant.
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Benli M, Kaya I, Yigit N. Screening antimicrobial activity of various extracts ofArtemisia dracunculus L. Cell Biochem Funct 2007; 25:681-6. [PMID: 16986171 DOI: 10.1002/cbf.1373] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The antimicrobial activities of chloroform, acetone and two different concentrations of methanol extracts of Artemisia dracunculus L. were studied. These extracts were tested against nine bacteria and four yeasts strains by the disc diffusion method. The results indicated that the methanol extract of A. dracunculus is more effective against tested microorganisms than chloroform or acetone extracts. The chloroform and acetone extracts were inhibitory only towards Pseudomonas aeruginosa (ATCC 27853). While the methanol extract that was diluted with 10 ml distilled water showed inhibition zones against Shigella (RSHI), Listeria monocytogenes ATCC 7644, P. aeruginosa (ATCC 27853), the methanol extract that was diluted with 5 ml distilled water showed inhibition zones against two different strains of Escherichia coli (RSHI, ATCC 25922), Shigella (RSHI), L. monocytogenes (ATCC 7644), and P. aeruginosa ATCC 27853. The cells of microorganisms treated with plant extracts and normal microorganism cells were observed by scanning electron microscope. It was apparent that cells are damaged after treatment with A. dracunculus.
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Affiliation(s)
- Mehlika Benli
- Department of Biology, Faculty of Science, University of Ankara, Ankara, Turkey.
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Sanguin H, Remenant B, Dechesne A, Thioulouse J, Vogel TM, Nesme X, Moënne-Loccoz Y, Grundmann GL. Potential of a 16S rRNA-based taxonomic microarray for analyzing the rhizosphere effects of maize on Agrobacterium spp. and bacterial communities. Appl Environ Microbiol 2006; 72:4302-12. [PMID: 16751545 PMCID: PMC1489601 DOI: 10.1128/aem.02686-05] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacterial diversity is central to ecosystem sustainability and soil biological function, for which the role of roots is important. The high-throughput analysis potential of taxonomic microarray should match the breadth of bacterial diversity. Here, the power of this technology was evidenced through methodological verifications and analysis of maize rhizosphere effect based on a 16S rRNA-based microarray developed from the prototype of H. Sanguin et al. (Environ. Microbiol. 8:289-307, 2006). The current probe set was composed of 170 probes (41 new probes in this work) that targeted essentially the Proteobacteria. Cloning and sequencing of 16S rRNA amplicons were carried out on maize rhizosphere and bulk soil DNA. All tested clones that had a perfect match with corresponding probes were positive in the hybridization experiment. The hierarchically nested probes were reliable, but the level of taxonomic identification was variable, depending on the probe set specificity. The comparison of experimental and theoretical hybridizations revealed 0.91% false positives and 0.81% false negatives. The microarray detection threshold was estimated at 0.03% of a given DNA type based on DNA spiking experiments. A comparison of the maize rhizosphere and bulk soil hybridization results showed a significant rhizosphere effect, with a higher predominance of Agrobacterium spp. in the rhizosphere, as well as a lower prevalence of Acidobacteria, Bacteroidetes, Verrucomicrobia, and Planctomycetes, a new taxon of interest in soil. In addition, well-known taxonomic groups such as Sphingomonas spp., Rhizobiaceae, and Actinobacteria were identified in both microbial habitats with strong hybridization signals. The taxonomic microarray developed in the present study was able to discriminate and characterize bacterial community composition in related biological samples, offering extensive possibilities for systematic exploration of bacterial diversity in ecosystems.
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Affiliation(s)
- Hervé Sanguin
- UMR CNRS 5557/USC INRA 1193 Ecologie Microbienne, Université Claude Bernard (Lyon 1), 43 bd du 11 Novembre 1918, F-69622 Villeurbanne Cedex, France
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Gunatilaka AAL. Natural products from plant-associated microorganisms: distribution, structural diversity, bioactivity, and implications of their occurrence. JOURNAL OF NATURAL PRODUCTS 2006; 69:509-26. [PMID: 16562864 PMCID: PMC3362121 DOI: 10.1021/np058128n] [Citation(s) in RCA: 531] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
A growing body of evidence suggests that plant-associated microorganisms, especially endophytic and rhizosphere bacteria and fungi, represent a huge and largely untapped resource of natural products with chemical structures that have been optimized by evolution for biological and ecological relevance. A diverse array of bioactive small molecule natural products has been encountered in these microorganisms. The structures of over 230 metabolites isolated and characterized from over 70 plant-associated microbial strains during the past four years are presented with information on their hosts, culture conditions, and biological activities. Some significant biological and ecological implications of their occurrence are also reviewed.
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Affiliation(s)
- A A Leslie Gunatilaka
- Southwest Center for Natural Products Research and Commercialization, Office of Arid Lands Studies, College of Agriculture and Life Sciences, University of Arizona, Tucson, 85706-6800, USA.
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Jiménez-Esquilín AE, Roane TM. Antifungal activities of actinomycete strains associated with high-altitude sagebrush rhizosphere. J Ind Microbiol Biotechnol 2005; 32:378-81. [PMID: 16044290 DOI: 10.1007/s10295-005-0007-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2005] [Accepted: 06/19/2005] [Indexed: 10/25/2022]
Abstract
The antifungal-producing potential of actinomycete populations from the rhizosphere of low-altitude sagebrush, Artemisia tridentata, has been examined. In a continued investigation of new sources of antifungal-producing microorganisms, this study examined the antifungal-producing potential of actinomycetes from the rhizosphere of high-altitude A. tridentata. With high-altitude sagebrush, rhizosphere soil actinomycete numbers were one to four orders of magnitude higher than those found in nonrhizosphere bulk soils and different from those found with the low-altitude plants. A total of 122 actinomycete isolates was screened against nine fungal species and six bacterial species for the production of antimicrobial compounds. Four rhizosphere isolates, Streptomyces amakusaensis, S. coeruleorubidus, S. hawaiiensis and S. scabies, showed broad-spectrum antifungal activity against three or more fungal species in plate assays. In liquid antagonism assays, mycelium production by Aspergillus niger was reduced by up to 50% by two of the actinomycete isolates. These results demonstrate the potential of rhizosphere microbiology in the search for new antimicrobials.
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Affiliation(s)
- A E Jiménez-Esquilín
- Department of Biology, University of Colorado, Campus Box 171, Denver, CO 80217-3364, USA
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