| 1. |
- Alström, Sadhna, et al.
(författare)
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Chromatographic profiling of hydrophilic metabolites from tubers of different potato cultivars
- 2009
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Konferensbidrag (refereegranskat)abstract
- Potato is an important source of nutrients and bioactive compounds with profitable effect for health, such as antioxidants, vitamins and essential amino acids. The knowledge about metabolite composition of various potato cultivars is necessary to facilitate development of new cultivars with desirable properties. In the present study, the hydrophilic metabolite composition of six potato cultivars with different resistance against potato late blight disease was analyzed. For this, an HPLC-based method was developed and used for the analysis of water-ethanol extracts of freeze-dried potato tubers. Significant differences in concentrations of adenosine, chlorogenic acid, and rutin were revealed. Some other metabolites were found to be cultivar-specific
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| 2. |
- Alström, Sadhna, et al.
(författare)
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Straw microorganisms with combined cellulolytic and chitinolytic activities drive decomposition of rice straw and antagonism against Rhizoctonia solani causing rice sheath blight
- 2023
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Ingår i: International Journal of Agricultural Technology. - 2630-0192. ; 19, s. 833-848
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Tidskriftsartikel (refereegranskat)abstract
- Decomposition of cellulose and chitin substrates plays an important role in ecosystem functions. The relationships between the microbial diversity and the ecosystem functions of decomposition and antagonistic processes were examined using rice straw. A microcosm was designed for investigating complexity in microbial interactions of 16 different microorganisms belonging to 6 different functional groups and were designated as generalists or specialists depending on the number of hydrolases produced. Multiple regression analysis showed that increasing number of isolates, the presence of three fungal and one bacterial isolate and two fungal isolates degraded significantly to the decomposition process of rice straw. Straw was decomposed by one fungus and one bacterium, three fungal and two bacterial isolates and the 16-isolates mixture were significantly inhibited growth of the phytopathogenic Rhizoctonia solani causing rice sheath blight on the decomposed straw.The growth of R. solani was reduced significantly by 62% - 93% compared to the non-inoculated controls. There was a negative correlation between rice straw weight loss and the growth of R. solani. It is suggested that the specific isolates may play an important role in ecosystem functions of decomposition and antagonistic processes.
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| 3. |
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| 4. |
- Do Thi, Xuan, et al.
(författare)
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Different crop rotation systems as drivers of change in soil bacterial community structure and yield of rice, Oryza sativa
- 2011
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Ingår i: Biology and Fertility of Soils. - : Springer Science and Business Media LLC. - 0178-2762 .- 1432-0789. ; 48, s. 1-9
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Tidskriftsartikel (refereegranskat)abstract
- Intensive cropping, especially of rice, is considered to contribute to negative effects not only on soil chemical and biological properties but also on long-term grain yield. Appropriate crop rotation is often practiced as an alternative strategy to overcome the negative side effects of intensive cropping. Although soil microbial diversity and community structure have been shown to respond differently to altered agricultural management practices, little is known about possible links between crop rotation and grain yield on bacterial communities in rice paddy soil. In this study, we investigated the impact of specific rotational crops and compared it with intensive rice cultivation. The main crop rice (Oryza sativa) was rotated with maize (Zea mays) and mungbean (Phaseolus aureus) in different combinations in a system cultivating three crops per year. Soil bacterial communities were studied in two different cropping periods using pyrosequencing of the variable V4 region of the 16s rRNA. Our results showed that rotation with alternative crops increased rice yield by 24- 46% depending on rotation structure and that bacterial community structure was altered in the presence of mungbean and/or maize compared to that in rice monoculture. In the crop rotation systems, composition, abundance, and diversity of soil bacterial communities were significantly different and higher than those in rice monoculture. Our results show that effects of crop rotation relate to changes in soil bacterial community structure suggesting that appropriate crop rotations provide a feasible practice to maintain the equilibrium in soil microbial environment for sustainable rice cultivation
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| 5. |
- Finlay, Roger, et al.
(författare)
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Complete genome sequence of Serratia plymuthica strain AS12
- 2012
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Ingår i: Standards in Genomic Sciences. - : Springer Science and Business Media LLC. - 1944-3277. ; 6, s. 165-173
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Tidskriftsartikel (refereegranskat)abstract
- A plant-associated member of the family Enterobacteriaceae, Serratia plymuthica strain AS12 was isolated from rapeseed roots. It is of scientific interest because it promotes plant growth and inhibits plant pathogens. The genome of S. plymuthica AS12 comprises a 5,443,009 bp long circular chromosome, which consists of 4,952 protein-coding genes, 87 tRNA genes and 7 rRNA operons. This genome was sequenced within the 2010 DOE-JGI Community Sequencing Program (CSP2010) as part of the project entitled "Genomics of four rapeseed plant growth promoting bacteria with antagonistic effect on plant pathogens".
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| 6. |
- Gkarmiri, Konstantia, et al.
(författare)
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Identifying the Active Microbiome Associated with Roots and Rhizosphere Soil of Oilseed Rape
- 2017
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Ingår i: Applied and Environmental Microbiology. - : American Society for Microbiology. - 0099-2240 .- 1098-5336. ; 83:22
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Tidskriftsartikel (refereegranskat)abstract
- RNA stable isotope probing and high-throughput sequencing were used to characterize the active microbiomes of bacteria and fungi colonizing the roots and rhizosphere soil of oilseed rape to identify taxa assimilating plant-derived carbon following (13)CO2 labeling. Root- and rhizosphere soil-associated communities of both bacteria and fungi differed from each other, and there were highly significant differences between their DNA- and RNA-based community profiles. Verrucomicrobia, Proteobacteria, Planctomycetes, Acidobacteria, Gemmatimonadetes, Actinobacteria, and Chloroflexi were the most active bacterial phyla in the rhizosphere soil. Bacteroidetes were more active in roots. The most abundant bacterial genera were well represented in both the (13)C- and (12)C-RNA fractions, while the fungal taxa were more differentiated. Streptomyces, Rhizobium, and Flavobacterium were dominant in roots, whereas Rhodoplanes and Sphingomonas (Kaistobacter) were dominant in rhizosphere soil. "Candidatus Nitrososphaera" was enriched in (13)C in rhizosphere soil. Olpidium and Dendryphion were abundant in the (12)C-RNA fraction of roots; Clonostachys was abundant in both roots and rhizosphere soil and heavily (13)C enriched. Cryptococcus was dominant in rhizosphere soil and less abundant, but was (13)C enriched in roots. The patterns of colonization and C acquisition revealed in this study assist in identifying microbial taxa that may be superior competitors for plant-derived carbon in the rhizosphere of Brassica napusIMPORTANCE This microbiome study characterizes the active bacteria and fungi colonizing the roots and rhizosphere soil of Brassica napus using high-throughput sequencing and RNA-stable isotope probing. It identifies taxa assimilating plant-derived carbon following (13)CO2 labeling and compares these with other less active groups not incorporating a plant assimilate. Brassica napus is an economically and globally important oilseed crop, cultivated for edible oil, biofuel production, and phytoextraction of heavy metals; however, it is susceptible to several diseases. The identification of the fungal and bacterial species successfully competing for plant-derived carbon, enabling them to colonize the roots and rhizosphere soil of this plant, should enable the identification of microorganisms that can be evaluated in more detailed functional studies and ultimately be used to improve plant health and productivity in sustainable agriculture.
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| 7. |
- Gkarmiri, Konstantia, et al.
(författare)
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Transcriptomic changes in the plant pathogenic fungus Rhizoctonia solani AG-3 in response to the antagonistic bacteria Serratia proteamaculans and Serratia plymuthica
- 2015
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Ingår i: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 16
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Tidskriftsartikel (refereegranskat)abstract
- Background: Improved understanding of bacterial-fungal interactions in the rhizosphere should assist in the successful application of bacteria as biological control agents against fungal pathogens of plants, providing alternatives to chemicals in sustainable agriculture. Rhizoctonia solani is an important soil-associated fungal pathogen and its chemical treatment is not feasible or economic. The genomes of the plant-associated bacteria Serratia proteamaculans S4 and Serratia plymuthica AS13 have been sequenced, revealing genetic traits that may explain their diverse plant growth promoting activities and antagonistic interactions with R. solani. To understand the functional response of this pathogen to different bacteria and to elucidate whether the molecular mechanisms that the fungus exploits involve general stress or more specific responses, we performed a global transcriptome profiling of R. solani Rhs1AP anastomosis group 3 (AG-3) during interaction with the S4 and AS13 species of Serratia using RNA-seq.Results: Approximately 104,504 million clean 75-100 bp paired-end reads were obtained from three libraries, each in triplicate (AG3-Control, AG3-S4 and AG3-AS13). Transcriptome analysis revealed that approximately 10 % of the fungal transcriptome was differentially expressed during challenge with Serratia. The numbers of S4- and AS13-specific differentially expressed genes (DEG) were 866 and 292 respectively, while there were 1035 common DEGs in the two treatment groups. Four hundred and sixty and 242 genes respectively had values of log(2) fold-change > 3 and for further analyses this cut-off value was used. Functional classification of DEGs based on Gene Ontology enrichment analysis and on KEGG pathway annotations revealed a general shift in fungal gene expression in which genes related to xenobiotic degradation, toxin and antioxidant production, energy, carbohydrate and lipid metabolism and hyphal rearrangements were subjected to transcriptional regulation.Conclusions: This RNA-seq profiling generated a novel dataset describing the functional response of the phytopathogen R. solani AG3 to the plant-associated Serratia bacteria S4 and AS13. Most genes were regulated in the same way in the presence of both bacterial isolates, but there were also some strain-specific responses. The findings in this study will be beneficial for further research on biological control and in depth exploration of bacterial-fungal interactions in the rhizosphere.
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| 8. |
- Nallanchakravarthula, Srivathsa, et al.
(författare)
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Changes in the root fungal microbiome of strawberry following application of residues of the biofumigant oilseed radish
- 2021
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Ingår i: Applied Soil Ecology. - : Elsevier BV. - 0929-1393 .- 1873-0272. ; 168
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Tidskriftsartikel (refereegranskat)abstract
- Biofumigation has been proposed as an environmentally friendly method of plant protection against soil-borne pathogens, but its effects on microbial communities are still incompletely understood. Using high throughput DNA sequencing, we investigated the effects of oilseed radish residues on the root fungal microbiome of strawberry in the presence of a soil-borne fungal pathogen, Verticillium dahliae. Results of our greenhouse study show that early flowering occurred in response to residue addition, suggesting a plant stress-response and there was a significant decrease in berry yield. The fungal microbiome of roots was significantly restructured by both biofumigation and inoculation with Verticillium. In particular, the abundance of root endophyte- and arbuscular mycorrhizal functional guilds was reduced significantly as a result of biofumigant and V. dahliae addition, whereas the abundance of saprotrophs increased significantly when both treatments were applied together. Alpha diversity analyses of fungi associated with roots indicated a significant increase in species richness following Verticillium inoculation, whereas the biofumigant alone or in the presence of V. dahliae resulted in no significant effect, suggesting that apparently some rare taxa may have been enriched/stimulated in the presence of the pathogen. Further investigations should reveal whether negative effects of biofumigation on potentially beneficial root associated endophytes and arbuscular mycorrhizal fungi are host genotype- or soil-dependent.
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| 9. |
- Nallanchakravarthula, Srivathsa, et al.
(författare)
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Influence of Soil Type, Cultivar and Verticillium dahliae on the Structure of the Root and Rhizosphere Soil Fungal Microbiome of Strawberry
- 2014
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Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 9, s. 1-10
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Tidskriftsartikel (refereegranskat)abstract
- Sustainable management of crop productivity and health necessitates improved understanding of the ways in which rhizosphere microbial populations interact with each other, with plant roots and their abiotic environment. In this study we examined the effects of different soils and cultivars, and the presence of a soil-borne fungal pathogen, Verticillium dahliae, on the fungal microbiome of the rhizosphere soil and roots of strawberry plants, using high-throughput pyrosequencing. Fungal communities of the roots of two cultivars, Honeoye and Florence, were statistically distinct from those in the rhizosphere soil of the same plants, with little overlap. Roots of plants growing in two contrasting field soils had high relative abundance of Leptodontidium sp. C2 BESC 319 g whereas rhizosphere soil was characterised by high relative abundance of Trichosporon dulcitum or Cryptococcus terreus, depending upon the soil type. Differences between different cultivars were not as clear. Inoculation with the pathogen V. dahliae had a significant influence on community structure, generally decreasing the number of rhizosphere soil- and root-inhabiting fungi. Leptodontidium sp. C2 BESC 319 g was the dominant fungus responding positively to inoculation with V. dahliae. The results suggest that 1) plant roots select microorganisms from the wider rhizosphere pool, 2) that both rhizosphere soil and root inhabiting fungal communities are influenced by V. dahliae and 3) that soil type has a stronger influence on both of these communities than cultivar.
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| 10. |
- Neupane, Saraswoti, et al.
(författare)
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Complete genome sequence of the plant-associated Serratia plymuthica strain AS13
- 2012
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Ingår i: Standards in Genomic Sciences. - : Springer Science and Business Media LLC. - 1944-3277. ; 7, s. 22-30
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Tidskriftsartikel (refereegranskat)abstract
- Serratia plymuthica AS13 is a plant-associated Gammaproteobacteria, isolated from rapeseed roots. It is of special interest because of its ability to inhibit fungal pathogens of rapeseed and to promote plant growth. The complete genome of S. plymuthica AS13 consists of a 5,442,549 bp circular chromosome. The chromosome contains 4,951 protein-coding genes, 87 tRNA genes and 7 rRNA operons. This genome was sequenced as part of the project entitled "Genomics of four rapeseed plant growth promoting bacteria with antagonistic effect on plant pathogens" within the 2010 DOE-JGI Community Sequencing Program (CSP2010).
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| 11. |
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| 12. |
- Neupane, Saraswoti, et al.
(författare)
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Fungal communities associated with field grown oilseed rape (Brassica napus L.) - their possible role in early crop establishment
- 2013
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Ingår i: Acta Agriculturae Scandinavica, Section B - Soil and Plant Science. - : Informa UK Limited. - 0906-4710 .- 1651-1913. ; 63, s. 241-252
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Tidskriftsartikel (refereegranskat)abstract
- Problems with patchiness due to delay in emergence or poor crop establishment are not uncommon in oilseed rape cultivation. Our aim was to study the fungal communities associated with field grown oilseed rape and to explore their role in emergence and early crop establishment. This study was carried out by characterising the fungal communities in roots and rhizosphere soils of both spring and winter oilseed rape. The fungal communities were analysed using both culture-dependent and culture-independent approaches. Sampling was carried out in field plots with clear differences in crop establishment. Phylogenetic comparison of the fungal communities in different environments revealed significant differences between roots and rhizosphere soils. In winter rape, the fungal communities in the poor-emergence plots differed significantly from that found in normal-emergence plots, while in spring rape this difference was less prominent. However, in a combined statistical analysis of data from both winter and spring rape, the fungal communities in poor- and normal-emergence plots differed significantly. In follow-up studies, putatively pathogenic fungi were isolated from poor-emergence plots. Their effects on emergence and seedling growth were evaluated in the two crop types in greenhouse experiments. Rhizoctonia solani was found only in roots from poor-emergence plots, and was also demonstrated to be highly pathogenic on oilseed rape independent of cultivars when tested in greenhouse trials. The results from the fungal community analysis and from the greenhouse experiments are discussed in relation to their role in crop establishment related problems in oilseed rape.
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| 13. |
- Neupane, Saraswoti, et al.
(författare)
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Non-contiguous finished genome sequence of plant-growth promoting Serratia proteamaculans S4
- 2013
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Ingår i: Standards in Genomic Sciences. - : Springer Science and Business Media LLC. - 1944-3277. ; 8, s. 441-449
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Tidskriftsartikel (refereegranskat)abstract
- Serratia proteamaculans S4 (previously Serratia sp. S4), isolated from the rhizosphere of wild Equisetum sp., has the ability to stimulate plant growth and to suppress the growth of several soil-borne fungal pathogens of economically important crops. Here we present the non-contiguous, finished genome sequence of S. proteamaculans S4, which consists of a 5,324,944 bp circular chromosome and a 129,797 bp circular plasmid. The chromosome contains 5,008 predicted genes while the plasmid comprises 134 predicted genes. In total, 4,993 genes are assigned as protein-coding genes. The genome consists of 22 rRNA genes, 82 tRNA genes and 58 pseudogenes. This genome is a part of the project "Genomics of four rapeseed plant growth-promoting bacteria with antagonistic effect on plant pathogens" awarded through the 2010 DOE-JGI's Community Sequencing Program.
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| 14. |
- Neupane, Saraswoti, et al.
(författare)
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Transcriptional responses of the bacterial antagonist Serratia plymuthica to the fungal phytopathogen Rhizoctonia solani
- 2015
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Ingår i: Environmental Microbiology Reports. - : Wiley. - 1758-2229. ; 7, s. 123-127
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Tidskriftsartikel (refereegranskat)abstract
- Rhizobacteria with biocontrol ability exploit a range of mechanisms to compete successfully with other microorganisms and to ensure their growth and survival in the rhizosphere, ultimately promoting plant growth. The rhizobacterium Serratia plymuthicaAS13 is able to promote oilseed rape growth and improve seedling survival in the presence of the fungal pathogen, Rhizoctonia solaniAG 2-1; however, our understanding of the mechanisms underlying the antagonism of Serratia is limited. To elucidate possible mechanisms, genome-wide gene expression profiling of S.plymuthicaAS13 was carried out in the presence or absence of R.solani. We used RNA sequencing methodology to obtain a comprehensive overview of Serratia gene expression in response to R.solani. The differential gene expression profiles of S.plymuthicaAS13 revealed significantly increased expression of genes related to the biosynthesis of the antibiotic pyrrolnitrin (prnABCD), protease production and transporters. The results presented here provide evidence that antibiosis is a major functional mechanism underlying the antagonistic behaviour of S.plymuthicaAS13.
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| 15. |
- Santos-González, Juan, et al.
(författare)
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Soil, But Not Cultivar, Shapes the Structure of Arbuscular Mycorrhizal Fungal Assemblages Associated with Strawberry
- 2011
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Ingår i: Microbial Ecology. - : Springer Science and Business Media LLC. - 0095-3628 .- 1432-184X. ; 62, s. 25-35
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Tidskriftsartikel (refereegranskat)abstract
- Arbuscular mycorrhizal fungi are widespread plant symbionts occurring in most agricultural crops, where they can play key roles in the growth and health of their plant hosts. Plant benefits can depend on the identity of the associated arbuscular mycorrhizal fungi (AMF), but little is known about the identity of the fungal partners in most agricultural systems. In this study, we describe the AMF assemblages associated with four cultivars of strawberry in an outdoor experiment using two field soils with different origin and management history. Assemblages were characterised by clone library sequencing of 18S rRNA gene fragments. Soil dramatically influenced the degree of mycorrhizal colonisation and AMF assemblage structure in the roots. No differences were observed between cultivars. Fungi belonging to the genus Acaulospora dominated the AMF assemblages in one soil, but they were not detected in the other. These results suggest that physicochemical soil characteristics and management can play a role in determining the identity and structure of microbial communities associated with particular hosts in agricultural systems.
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| 16. |
- Yahya, Asha, et al.
(författare)
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Micro-organisms associated with endangered Cordeauxia edulis affect its growth and inhibit pathogens
- 2010
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Ingår i: African Journal of Agricultural Research. - 1991-637X. ; 5, s. 3360-3368
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Tidskriftsartikel (refereegranskat)abstract
- Cordeauxia edulis is an endangered leguminous shrub native to semi-arid border between Ethiopia and Somalia. To enable its successful cultivation in new environment, we investigated the effect of its microbial residents on establishment and growth. Plant growth-affecting bacteria and arbuscular mycorrhizal fungi (AMF) were the focus of this study. Bacteria were isolated from rhizosphere soil and pre-germinated seeds of C. edulis and tested for in vitro inhibition of Aspergillus niger, A. biciliate and A. versicolor. The three aspergilli were found as frequent colonizers of seeds with deteriorating effect on emergence. Six bacteria were further evaluated in greenhouse experiments for their effect on plant growth. The isolates with beneficial effects seemed to belong to Pseudomonas sp., Klebsiella sp. and Pantoea sp. Occurrence and abundance of AMF was determined as spore density and % root colonization in the field samples. Effect of AMF on plant growth was also studied in greenhouse, on seedlings inoculated with its native population and the results compared with those inoculated with a commercial mix, Vaminoc or in vitro cultured Glomus intraradices. Our results show that, C. edulis harbours both AMF and bacteria with plant growth affecting potential and that it responds positively to microbial inoculations in foreign environments.
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