scholarly journals Absence of Genome Reduction In Diverse, Facultative Endohyphal Bacteria

2016 ◽  
Author(s):  
David A. Baltrus ◽  
Kevin Dougherty ◽  
Kayla R. Arendt ◽  
Marcel Huntemann ◽  
Alicia Clum ◽  
...  
Keyword(s):  
Growth Promotion ◽  
Fungal Endophytes ◽  
Phenotypic Traits ◽  
Bacterial Strains ◽  
Genomic Features ◽  
Fungal Life Cycle ◽  
Living Tissues ◽  
Fungal Interactions ◽  
Reproductive Phases ◽  
Shed Light

AbstractFungi interact closely with bacteria both on the surfaces of hyphae, and within their living tissues (i.e., endohyphal bacteria, EHB). These EHB can be obligate or facultative symbionts, and can mediate a diverse phenotypic traits in their hosts. Although EHB have been observed in many major lineages of fungi, it remains unclear how widespread and general these associations are, and whether there are unifying ecological and genomic features found across all EHB strains. We cultured 11 bacterial strains after they emerged from the hyphae of diverse Ascomycota that were isolated as foliar endophytes of cupressaceous trees, and generated nearly complete genome sequences for all. Unlike the genomes of largely obligate EHB, genomes of these facultative EHB resemble those of closely related strains isolated from environmental sources. Although all analyzed genomes encode structures that can be used to interact with eukaryotic hosts, we find no known pathways that facilitate intimate EHB-fungal interactions in all strains. We isolated two strains with nearly identical genomes from different classes of fungi, consistent with previous suggestions of horizontal transfer of EHB across endophytic hosts. Because bacteria are differentially present during the fungal life cycle, these genomes could shed light on the mechanisms of plant growth promotion by fungal endophytes during the symbiotic phase as well as degradation of plant material during saprotrophic and reproductive phases. Given the capacity of EHB to influence fungal phenotypes, these findings illuminate a new dimension of fungal biodiversity.

scholarly journals Genomic diversity of Mycobacterium avium subsp. paratuberculosis: pangenomic approach for highlighting unique genomic features with newly constructed complete genomes

2021 ◽  
Vol 52 (1) ◽  
Author(s):  
Jaewon Lim ◽  
Hong-Tae Park ◽  
Seyoung Ko ◽  
Hyun-Eui Park ◽  
Gyumin Lee ◽  
...  
Keyword(s):  
Mycobacterium Avium ◽  
Phenotypic Diversity ◽  
Control Strategies ◽  
Genomic Diversity ◽  
Phenotypic Traits ◽  
Whole Genome ◽  
Genomic Features ◽  
Phenotypic Differences ◽  
Mycobacterium Avium Subsp Paratuberculosis ◽  
Type Strains

AbstractMycobacterium avium subsp. paratuberculosis (MAP) is a causative agent of Johne’s disease, which is a chronic granulomatous enteropathy in ruminants. Determining the genetic diversity of MAP is necessary to understand the epidemiology and biology of MAP, as well as establishing disease control strategies. In the present study, whole genome-based alignment and comparative analysis were performed using 40 publicly available MAP genomes, including newly sequenced Korean isolates. First, whole genome-based alignment was employed to identify new genomic structures in MAP genomes. Second, the genomic diversity of the MAP population was described by pangenome analysis. A phylogenetic tree based on the core genome and pangenome showed that the MAP was differentiated into two major types (C- and S-type), which was in keeping with the findings of previous studies. However, B-type strains were discriminated from C-type strains. Finally, functional analysis of the pangenome was performed using three virulence factor databases (i.e., PATRIC, VFDB, and Victors) to predict the phenotypic diversity of MAP in terms of pathogenicity. Based on the results of the pangenome analysis, we developed a real-time PCR technique to distinguish among S-, B- and C-type strains. In conclusion, the results of our study suggest that the phenotypic differences between MAP strains can be explained by their genetic polymorphisms. These results may help to elucidate the diversity of MAP, extending from genomic features to phenotypic traits.

scholarly journals The Effects of Plant Growth-Promoting Bacteria with Biostimulant Features on the Growth of a Local Onion Cultivar and a Commercial Zucchini Variety

Agronomy ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 888
Author(s):  
Giorgia Novello ◽  
Patrizia Cesaro ◽  
Elisa Bona ◽  
Nadia Massa ◽  
Fabio Gosetti ◽  
...  
Keyword(s):  
Plant Growth ◽  
Growth Promotion ◽  
Global Market ◽  
Plant Growth Promoting Bacteria ◽  
Bacterial Strains ◽  
Mineral Concentration ◽  
Positive Effects ◽  
Plant Growth Promoting ◽  
Onion Cultivar ◽  
Growth Promoting

The reduction of chemical inputs due to fertilizer and pesticide applications is a target shared both by farmers and consumers in order to minimize the side effects for human and environmental health. Among the possible strategies, the use of biostimulants has become increasingly important as demonstrated by the fast growth of their global market and by the increased rate of registration of new products. In this work, we assessed the effects of five bacterial strains (Pseudomonas fluorescens Pf4, P. putida S1Pf1, P. protegens Pf7, P. migulae 8R6, and Pseudomonas sp. 5Vm1K), which were chosen according to their previously reported plant growth promotion traits and their positive effects on fruit/seed nutrient contents, on a local onion cultivar and on zucchini. The possible variations induced by the inoculation with the bacterial strains on the onion nutritional components were also evaluated. Inoculation resulted in significant growth stimulation and improvement of the mineral concentration of the onion bulb, induced particularly by 5Vm1K and S1Pf1, and in different effects on the flowering of the zucchini plants according to the bacterial strain. The present study provides new information regarding the activity of the five plant growth-promoting bacteria (PGPB) strains on onion and zucchini, two plant species rarely considered by the scientific literature despite their economic relevance.

scholarly journals Draft Genome Sequence of Plant Growth-Promoting Drought-Tolerant Bacillus sp. Strain CMAA 1363 Isolated from the Brazilian Caatinga Biome

2017 ◽  
Vol 5 (5) ◽  
Author(s):  
Vanessa Nessner Kavamura ◽  
Suikinai Nobre Santos ◽  
Rodrigo Gouvêa Taketani ◽  
Rafael Leandro Figueiredo Vasconcellos ◽  
Itamar Soares Melo
Keyword(s):  
Plant Growth ◽  
Growth Promotion ◽  
Draft Genome ◽  
Negative Effects ◽  
Genomic Features ◽  
Drought Tolerant ◽  
Caatinga Biome ◽  
Plant Growth Promoting ◽  
Growth Promoting ◽  
Plant Growth Promoting Traits

ABSTRACT The strain of Bacillus sp. CMAA 1363 was isolated from the Brazilian Caatinga biome and showed plant growth-promoting traits and ability to promote maize growth under drought stress. Sequencing revealed genes involved in stress response and plant growth promotion. These genomic features might aid in the protection of plants against the negative effects imposed by drought.

scholarly journals New complete genome sequences of human rhinoviruses shed light on their phylogeny and genomic features

BMC Genomics ◽  
2007 ◽  
Vol 8 (1) ◽  
pp. 224 ◽  
Author(s):  
Caroline Tapparel ◽  
Thomas Junier ◽  
Daniel Gerlach ◽  
Samuel Cordey ◽  
Sandra Van Belle ◽  
...  
Keyword(s):  
Complete Genome ◽  
Genome Sequences ◽  
Genomic Features ◽  
Shed Light

scholarly journals Antibiotics create a shift from mutualism to competition in human gut communities with a longer-lasting impact on fungi than bacteria

Microbiome ◽  
2020 ◽  
Vol 8 (1) ◽  
Author(s):  
Bastian Seelbinder ◽  
Jiarui Chen ◽  
Sascha Brunke ◽  
Ruben Vazquez-Uribe ◽  
Rakesh Santhaman ◽  
...  
Keyword(s):  
Fungal Community ◽  
Fungal Infections ◽  
Cell Damage ◽  
Fungal Colonization ◽  
Antibiotic Administration ◽  
Bacterial Strains ◽  
Human Gut ◽  
Healthy Human ◽  
Shotgun Metagenomics ◽  
Fungal Interactions

Abstract Background Antibiotic treatment has a well-established detrimental effect on the gut bacterial composition, but effects on the fungal community are less clear. Bacteria in the lumen of the gastrointestinal tract may limit fungal colonization and invasion. Antibiotic drugs targeting bacteria are therefore seen as an important risk factor for fungal infections and induced allergies. However, antibiotic effects on gut bacterial-fungal interactions, including disruption and resilience of fungal community compositions, were not investigated in humans. We analysed stool samples collected from 14 healthy human participants over 3 months following a 6-day antibiotic administration. We integrated data from shotgun metagenomics, metatranscriptomics, metabolomics, and fungal ITS2 sequencing. Results While the bacterial community recovered mostly over 3 months post treatment, the fungal community was shifted from mutualism at baseline to competition. Half of the bacterial-fungal interactions present before drug intervention had disappeared 3 months later. During treatment, fungal abundances were associated with the expression of bacterial genes with functions for cell growth and repair. By extending the metagenomic species approach, we revealed bacterial strains inhibiting the opportunistic fungal pathogen Candida albicans. We demonstrated in vitro how C. albicans pathogenicity and host cell damage might be controlled naturally in the human gut by bacterial metabolites such as propionate or 5-dodecenoate. Conclusions We demonstrated that antibacterial drugs have long-term influence on the human gut mycobiome. While bacterial communities recovered mostly 30-days post antibacterial treatment, the fungal community was shifted from mutualism towards competition.

scholarly journals Host and body site-specific adaptation of Lactobacillus crispatus genomes

2020 ◽  
Vol 2 (1) ◽  
Author(s):  
Meichen Pan ◽  
Claudio Hidalgo-Cantabrana ◽  
Rodolphe Barrangou
Keyword(s):  
Ecological Niches ◽  
Human Gut ◽  
Important Species ◽  
Genomic Features ◽  
Specific Adaptation ◽  
Lactobacillus Crispatus ◽  
Vaginal Tract ◽  
Functional Features ◽  
In Silico Analyses ◽  
Shed Light

Abstract Lactobacillus crispatus is a common inhabitant of both healthy poultry gut and human vaginal tract, and the absence of this species has been associated with a higher risk of developing infectious diseases. In this study, we analyzed 105 L. crispatus genomes isolated from a variety of ecological niches, including the human vaginal tract, human gut, chicken gut and turkey gut, to shed light on the genetic and functional features that drive evolution and adaptation of this important species. We performed in silico analyses to identify the pan and core genomes of L. crispatus, and to reveal the genomic differences and similarities associated with their origins of isolation. Our results demonstrated that, although a significant portion of the genomic content is conserved, human and poultry L. crispatus isolates evolved to encompass different genomic features (e.g. carbohydrate usage, CRISPR–Cas immune systems, prophage occurrence) in order to thrive in different environmental niches. We also observed that chicken and turkey L. crispatus isolates can be differentiated based on their genomic information, suggesting significant differences may exist between these two poultry gut niches. These results provide insights into host and niche-specific adaptation patterns in species of human and animal importance.

Screening fungal endophytes from a wild grass for growth promotion in tritordeum, an agricultural cereal

Plant Science ◽  
2021 ◽  
Vol 303 ◽  
pp. 110762
Author(s):  
Beatriz R. Vázquez de Aldana ◽  
Juan B. Arellano ◽  
María José Cuesta ◽  
Elena Mellado-Ortega ◽  
Virginia González ◽  
...  
Keyword(s):  
Growth Promotion ◽  
Fungal Endophytes ◽  
Wild Grass

Evaluation of bacteria isolated from rice for plant growth promotion and biological control of seedling disease of rice

2001 ◽  
Vol 47 (10) ◽  
pp. 916-924 ◽  
Author(s):  
Tika B Adhikari ◽  
C M Joseph ◽  
Guoping Yang ◽  
Donald A Phillips ◽  
Louise M Nelson
Keyword(s):  
Biological Control ◽  
Plant Growth ◽  
Plant Growth Promotion ◽  
Growth Promotion ◽  
Disease Incidence ◽  
Control Plant ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Bacterial Strains ◽  
Seedling Disease

Of 102 rhizoplane and endophytic bacteria isolated from rice roots and stems in California, 37% significantly (P [Formula: see text] 0.05) inhibited the growth in vitro of two pathogens, Achlya klebsiana and Pythium spinosum, causing seedling disease of rice. Four endophytic strains were highly effective against seedling disease in growth pouch assays, and these were identified as Pseudomonas fluorescens (S3), Pseudomonas tolaasii (S20), Pseudomonas veronii (S21), and Sphingomonas trueperi (S12) by sequencing of amplified 16S rRNA genes. Strains S12, S20, and S21 contained the nitrogen fixation gene, nifD, but only S12 was able to reduce acetylene in pure culture. The four strains significantly enhanced plant growth in the absence of pathogens, as evidenced by increases in plant height and dry weight of inoculated rice seedlings relative to noninoculated rice. Three bacterial strains (S3, S20, and S21) were evaluated in pot bioassays and reduced disease incidence by 50%–73%. Strain S3 was as effective at suppressing disease at the lowest inoculum density (106 CFU/mL) as at higher density (108 CFU/mL or undiluted suspension). This study indicates that selected endophytic bacterial strains have potential for control of seedling disease of rice and for plant growth promotion.Key words: biological control, plant growth promotion, endophytes, rice, seedling disease.

scholarly journals Raising Beet Tolerance to Salinity through Bioaugmentation with Halotolerant Endophytes

Agronomy ◽  
2020 ◽  
Vol 10 (10) ◽  
pp. 1571
Author(s):  
Sonia Szymańska ◽  
Jarosław Tyburski ◽  
Agnieszka Piernik ◽  
Marcin Sikora ◽  
Justyna Mazur ◽  
...  
Keyword(s):  
Salt Stress ◽  
Growth Promotion ◽  
Growth Parameters ◽  
Pseudomonas Stutzeri ◽  
Crop Productivity ◽  
Salicornia Europaea ◽  
Bacterial Strains ◽  
New Host ◽  
Potential Applications ◽  
Selection Of

Increasing land salinization in recent decades has led to a decrease in crop productivity worldwide. We hypothesized that bioaugmentation of beetroot (Beta vulgaris) with halotolerant endophytic bacterial strains isolated from the obligatory halophytic plant Salicornia europaea L. may mitigate salt stress in new host plants. Therefore, we investigated the effects of inoculation with Pseudomonas stutzeri ISE12 or Kushneria marisflavi CSE9 on B. vulgaris growth in substrates enriched with various NaCl concentrations (0, 50, 150, 300 mM). The results of this study indicated that bioaugmentation with either bacteria resulted in improved growth parameters and increased chlorophyll content, as well as decreased proline and hydrogen peroxide concentrations, in B. vulgaris organs. However, K. marisflavi CSE9 was more efficient in achieving salt stress mitigation than P. stutzeri ISE12. In conclusion, the range of salinity tolerance seems to be a key parameter in the selection of strains for beet inoculation. The selected halotolerant endophytes (P. stutzeri ISE12 and K. marisflavi CSE9) isolated from the roots of obligatory halophytic S. europaea may be employed for plant growth promotion, especially in saline areas, and have potential applications in sustainable agriculture.

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