scholarly journals The indole-alkaloid gramine shapes the bacterial communities thriving at the barley root-soil interface

2020 ◽  
Author(s):  
Mauro Maver ◽  
Jenny Morris ◽  
Pete E. Hedley ◽  
Tanja Mimmo ◽  
Davide Bulgarelli
Keyword(s):  
Bacterial Communities ◽  
Soil Bacteria ◽  
Indole Alkaloid ◽  
Significant Component ◽  
Independent Manner ◽  
Bacterial Microbiota ◽  
Plant Allelochemicals ◽  
Breeding Selection ◽  
Soil Interface ◽  
Modern Varieties

AbstractThe biosynthesis of plant allelochemicals underpinning inter-organismal relationships has been moulded by domestication and breeding selection. The indole-alkaloid gramine, whose occurrence in barley (Hordeum vulgare L.) is widespread among wild genotypes but virtually absent from modern varieties, is a paradigmatic example of this phenomenon. This prompted us to investigate how the exogenous application of gramine impacted on the rhizosphere bacterial microbiota of two, gramine-free, elite barley varieties grown in a reference agricultural soil. Our investigation revealed that the application of the indole-alkaloid gramine modulates the proliferation of a subset of soil bacteria with a relatively broad phylogenetic assignment. This effect is two-pronged: a limited, but significant, component of the barley microbiota responds to gramine application in a genotype- and dosage-independent manner while at the highest dosage this secondary metabolite attenuates the host recruitment cues of the barley microbiota. Interestingly, this latter effect displayed a bias for members of the phyla Proteobacteria. These initial observations indicate that gramine can act as a determinant of the bacterial communities inhabiting the root-soil interface.

scholarly journals Applications of the indole-alkaloid gramine modulate the assembly of individual members of the barley rhizosphere microbiota

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12498
Author(s):  
Mauro Maver ◽  
Carmen Escudero-Martinez ◽  
James Abbott ◽  
Jenny Morris ◽  
Pete E. Hedley ◽  
...  
Keyword(s):  
Indole Alkaloid ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Dependent Manner ◽  
Host Genotype ◽  
Independent Manner ◽  
Molecular Determinants ◽  
Breeding Selection ◽  
The Impact ◽  
Soil Interface

Microbial communities proliferating at the root-soil interface, collectively referred to as the rhizosphere microbiota, represent an untapped beneficial resource for plant growth, development and health. Integral to a rational manipulation of the microbiota for sustainable agriculture is the identification of the molecular determinants of these communities. In plants, biosynthesis of allelochemicals is centre stage in defining inter-organismal relationships in the environment. Intriguingly, this process has been moulded by domestication and breeding selection. The indole-alkaloid gramine, whose occurrence in barley (Hordeum vulgare L.) is widespread among wild genotypes but has been counter selected in several modern varieties, is a paradigmatic example of this phenomenon. This prompted us to investigate how exogenous applications of gramine impacted on the rhizosphere microbiota of two, gramine-free, elite barley varieties grown in a reference agricultural soil. High throughput 16S rRNA gene amplicon sequencing revealed that applications of gramine interfere with the proliferation of a subset of soil microbes with a relatively broad phylogenetic assignment. Strikingly, growth of these bacteria appeared to be rescued by barley plants in a genotype- and dosage-independent manner. In parallel, we discovered that host recruitment cues can interfere with the impact of gramine application in a host genotype-dependent manner. Interestingly, this latter effect displayed a bias for members of the phyla Proteobacteria. These initial observations indicate that gramine can act as a determinant of the prokaryotic communities inhabiting the root-soil interface.

scholarly journals Urbanization and Carpobrotus edulis invasion alter the diversity and composition of soil bacterial communities in coastal areas

2020 ◽  
Vol 96 (7) ◽  
Author(s):  
Ana Novoa ◽  
Jan-Hendrik Keet ◽  
Yaiza Lechuga-Lago ◽  
Petr Pyšek ◽  
Johannes J Le Roux
Keyword(s):  
Community Composition ◽  
Bacterial Communities ◽  
Soil Bacteria ◽  
Coastal Dunes ◽  
Coastal Dune ◽  
Western Coast ◽  
Carpobrotus Edulis ◽  
Soil Bacterial Communities ◽  
Soil Bacterial ◽  
The Impact

ABSTRACT Coastal dunes are ecosystems of high conservation value that are strongly impacted by human disturbances and biological invasions in many parts of the world. Here, we assessed how urbanization and Carpobrotus edulis invasion affect soil bacterial communities on the north-western coast of Spain, by comparing the diversity, structure and composition of soil bacterial communities in invaded and uninvaded soils from urban and natural coastal dune areas. Our results suggest that coastal dune bacterial communities contain large numbers of rare taxa, mainly belonging to the phyla Actinobacteria and Proteobacteria. We found that the presence of the invasive C. edulis increased the diversity of soil bacteria and changed community composition, while urbanization only influenced bacterial community composition. Furthermore, the effects of invasion on community composition were conditional on urbanization. These results were contrary to predictions, as both C. edulis invasion and urbanization have been shown to affect soil abiotic conditions of the studied coastal dunes in a similar manner, and therefore were expected to have similar effects on soil bacterial communities. Our results suggest that other factors (e.g. pollution) might be influencing the impact of urbanization on soil bacterial communities, preventing an increase in the diversity of soil bacteria in urban areas.

scholarly journals Contrasting microbiota profiles observed in children carrying either Blastocystis spp. or the commensal amoebas Entamoeba coli or Endolimax nana

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Juan F. Alzate ◽  
Miguel Toro-Londoño ◽  
Felipe Cabarcas ◽  
Gisela Garcia-Montoya ◽  
Ana Galvan-Diaz
Keyword(s):  
Bacterial Communities ◽  
Intestinal Parasites ◽  
Intestinal Lumen ◽  
Bacterial Populations ◽  
Microbial Competition ◽  
E Coli ◽  
Daycare Centers ◽  
Microbial Profile ◽  
Bacterial Microbiota ◽  
Bacterial Richness

Abstract Recent studies have shown how intestinal parasites can modulate gut microbiota. This observation is not surprising since the human intestinal lumen, like any other niche, is a battlefield of microbial competition, and Eukaryotes can affect bacterial populations. Intestinal pathogenic protist has been associated with reshaping the microbial community structure; however, the interactions between the colonic bacterial communities and parasites like Blastocystis spp., Entamoeba coli, and Endolimax nana have been poorly studied. In this work, we studied the distal intestinal bacterial microbiota of 49 children attending 7 public daycare centers in Medellin, Colombia, and compared the bacterial microbiota structure in the presence or absence of the protists Blastocystis spp., E. coli, and E. nana. Parasite colonization was associated with an increase in bacterial richness. Moreover, Blastocystis spp. presented a positive relationship with Prevotella, since this bacterium was selectively enriched in children carrying it. Remarkably, the E. coli colonized children showed a microbial profile that was closer to uninfected controls, although some bacterial taxa displayed to be enriched. This is the case for Akkermansia, which showed to be favored in E. coli colonized individuals, while notably reduced in the Blastocystis spp. parasitized group.

scholarly journals Genetic Diversity of Soil Bacteria

Diversity ◽  
2020 ◽  
Vol 12 (11) ◽  
pp. 414
Author(s):  
Carmine Crecchio
Keyword(s):  
Genetic Diversity ◽  
Bacterial Communities ◽  
Soil Bacteria ◽  
Agricultural Soils ◽  
Field Trials ◽  
Laboratory Scale ◽  
Special Issue ◽  
Soil Bacterial Communities ◽  
Review Articles ◽  
Different Types

The Special Issue “Genetic Diversity of Soil Bacterial Communities” collected research and review articles addressing some relevant and unclear aspects of the composition and functioning of bacterial communities in rich or marginal agricultural soils, in field trials as well as in laboratory-scale experiments, at different latitudes and under different types of management.

scholarly journals Characterization of bacterial communities of rhizosphere and rhizoplane of Early Zhukovsky potato

2020 ◽  
Vol 222 ◽  
pp. 02050
Author(s):  
Marat Lutfulin ◽  
Darya Zaripova ◽  
Oksana Moiseeva ◽  
Semen Vologin ◽  
Ayslu Mardanova
Keyword(s):  
Bacterial Communities ◽  
Functional Role ◽  
Agricultural Crop ◽  
Potato Root ◽  
Bacterial Microbiota ◽  
16S R Rna ◽  
Significant Difference ◽  
Dominant Bacteria

Identification of patterns of formation of bacterial communities of the rhizosphere and rhizoplane of potato (Solanum tuberosum L.), the most important agricultural crop, is necessary for the introduction and maintenance of sustainable organic farming. The purpose of this work was the study of the biodiversity of the bacterial microbiota of the rhizosphere and rhizoplane of Early Zhukovsky potato, cultivated on gray forest soils. Comparative analysis based on sequencing of the 16S R RNA gene showed a significant difference in the representation of different groups of bacteria in these potato root compartments. Thus, the proportions of the dominant bacteria in the rhizosphere and rhizoplane of the Proteobacteria phylum reach 47.66% ± 7.22 % and 86.35 % ± 0.53%, respectively (P < 0.05). In contrast, the representation of phylum Bacteroidetes and Firmicutes in the rhizosphere is significantly higher and reaches 41.45 % ± 10.42% and 6.49 % ± 3.23%, respectively, compared to the rhizoplane (7.84 % ± 1.24 % and 0.43 % ± 0.48 %, (P < 0.05). At the same time, Actinobacteria phylum bacteria are present in both compartments in approximately equal amounts (4.40 % ± 1.81% in the rhizosphere and 5.37 % ± 1.42% in the rhizoplane). Thus, it was found that potato forms different bacterial communities in the rhizosphere and rhizoplane in quantitative proportions, which is probably determined by the functional role of these microorganisms in the plant physiology.

scholarly journals Impact of Logging and Forest Conversion to Oil Palm Plantations on Soil Bacterial Communities in Borneo

2013 ◽  
Vol 79 (23) ◽  
pp. 7290-7297 ◽  
Author(s):  
Larisa Lee-Cruz ◽  
David P. Edwards ◽  
Binu M. Tripathi ◽  
Jonathan M. Adams
Keyword(s):  
Forest Soil ◽  
Oil Palm ◽  
Bacterial Communities ◽  
Soil Bacteria ◽  
Forest Conversion ◽  
Soil Bacterial Communities ◽  
Oil Palm Plantation ◽  
Β Diversity ◽  
Logged Forest ◽  
Soil Bacterial

ABSTRACTTropical forests are being rapidly altered by logging and cleared for agriculture. Understanding the effects of these land use changes on soil bacteria, which constitute a large proportion of total biodiversity and perform important ecosystem functions, is a major conservation frontier. Here we studied the effects of logging history and forest conversion to oil palm plantations in Sabah, Borneo, on the soil bacterial community. We used paired-end Illumina sequencing of the 16S rRNA gene, V3 region, to compare the bacterial communities in primary, once-logged, and twice-logged forest and land converted to oil palm plantations. Bacteria were grouped into operational taxonomic units (OTUs) at the 97% similarity level, and OTU richness and local-scale α-diversity showed no difference between the various forest types and oil palm plantations. Focusing on the turnover of bacteria across space, true β-diversity was higher in oil palm plantation soil than in forest soil, whereas community dissimilarity-based metrics of β-diversity were only marginally different between habitats, suggesting that at large scales, oil palm plantation soil could have higher overall γ-diversity than forest soil, driven by a slightly more heterogeneous community across space. Clearance of primary and logged forest for oil palm plantations did, however, significantly impact the composition of soil bacterial communities, reflecting in part the loss of some forest bacteria, whereas primary and logged forests did not differ in composition. Overall, our results suggest that the soil bacteria of tropical forest are to some extent resilient or resistant to logging but that the impacts of forest conversion to oil palm plantations are more severe.

scholarly journals Nitrogen Fertilisers Shape the Composition and Predicted Functions of the Microbiota of Field-Grown Tomato Plants

2019 ◽  
Author(s):  
Federica Caradonia ◽  
Domenico Ronga ◽  
Marcello Catellani ◽  
Cleber Vinícius Giaretta Azevedo ◽  
Rodrigo Alegria Terrazas ◽  
...  
Keyword(s):  
Crop Production ◽  
Developmental Stages ◽  
Agricultural Practices ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Two Component System ◽  
Tomato Root ◽  
Bacterial Microbiota ◽  
Rrna Gene Sequencing ◽  
Soil Interface

ABSTRACTThe microbial communities thriving at the root-soil interface have the potential to improve plant growth and sustainable crop production. Yet, how agricultural practices, such as the application of either mineral or organic nitrogen fertilisers, impact on the composition and functions of these communities remains to be fully elucidated. By deploying a two-pronged 16S rRNA gene sequencing and predictive metagenomics approach we demonstrated that the bacterial microbiota of field-grown tomato (Solanum lycopersicum) plants is the product of a selective process that progressively differentiates between rhizosphere and root microhabitats. This process initiates as early as plants are in a nursery stage and it is then more marked at late developmental stages, in particular at harvest. This selection acts on both the bacterial relative abundances and phylogenetic assignments, with a bias for the enrichment of members of the phylum Actinobacteria in the root compartment. Digestate-based and mineral-based nitrogen fertilisers trigger a distinct bacterial enrichment in both rhizosphere and root microhabitats. This compositional diversification mirrors a predicted functional diversification of the root-inhabiting communities, manifested predominantly by the differential enrichment of genes associated to ABC transporters and the two-component system. Together, our data suggest that the microbiota thriving at the tomato root-soil interface is modulated by and in responses to the type of nitrogen fertiliser applied to the field.

scholarly journals The predatory soil bacterium Lysobacter reprograms quorum sensing system to regulate antifungal antibiotic production in a cyclic-di-GMP-independent manner

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Kaihuai Li ◽  
Gaoge Xu ◽  
Bo Wang ◽  
Guichun Wu ◽  
Rongxian Hou ◽  
...  
Keyword(s):  
Quorum Sensing ◽  
Soil Bacteria ◽  
Antibiotic Production ◽  
System Component ◽  
Two Component System ◽  
Interspecies Competition ◽  
Independent Manner ◽  
Sensing System ◽  
Heat Stable

AbstractSoil bacteria often harbour various toxins to against eukaryotic or prokaryotic. Diffusible signal factors (DSFs) represent a unique group of quorum sensing (QS) chemicals that modulate interspecies competition in bacteria that do not produce antibiotic-like molecules. However, the molecular mechanism by which DSF-mediated QS systems regulate antibiotic production for interspecies competition remains largely unknown in soil biocontrol bacteria. In this study, we find that the necessary QS system component protein RpfG from Lysobacter, in addition to being a cyclic dimeric GMP (c-di-GMP) phosphodiesterase (PDE), regulates the biosynthesis of an antifungal factor (heat-stable antifungal factor, HSAF), which does not appear to depend on the enzymatic activity. Interestingly, we show that RpfG interacts with three hybrid two-component system (HyTCS) proteins, HtsH1, HtsH2, and HtsH3, to regulate HSAF production in Lysobacter. In vitro studies show that each of these proteins interacted with RpfG, which reduced the PDE activity of RpfG. Finally, we show that the cytoplasmic proportions of these proteins depended on their phosphorylation activity and binding to the promoter controlling the genes implicated in HSAF synthesis. These findings reveal a previously uncharacterized mechanism of DSF signalling in antibiotic production in soil bacteria.

scholarly journals Microbiota Dysbiosis in Fungal Rhinosinusitis

2019 ◽  
Vol 8 (11) ◽  
pp. 1973 ◽  
Author(s):  
Yen-Ting Lu ◽  
Shao-Hung Wang ◽  
Ming-Li Liou ◽  
Ting-An Shen ◽  
Ying-Chou Lu ◽  
...  
Keyword(s):  
Bacterial Community ◽  
16S Rrna ◽  
Chronic Rhinosinusitis ◽  
Bacterial Communities ◽  
Middle Meatus ◽  
Fungal Rhinosinusitis ◽  
Bacterial Microbiota ◽  
Histological Characteristics ◽  
Distinct Distribution

Fungal rhinosinusitis is a unique phenotype of chronic rhinosinusitis with unique clinical and histological characteristics. The role of bacterial microbiota in various phenotypes chronic rhinosinusitis is not thoroughly understood. Therefore, we conducted 16s rRNA amplification sequencing to determine differences in bacterial communities between phenotypes (fungal vs. non- fungal) and anatomical sites (middle meatus vs. nasopharynx). Endoscope-guided swabs were used to collect samples from the middle meatus and nasopharynx of seven consecutive patients with fungal and 18 consecutive patients with non-fungal rhinosinusitis. DNA was extracted and investigated through 16S rRNA amplification. Among samples from the middle meatus, Shannon diversity was significantly lower in those from the fungal rhinosinusitis group (p = 0.029). However, no significant differences in diversity were noted between nasopharynx samples (p = 0.85). Fungal rhinosinusitis samples exhibited a distinct distribution of taxon relative abundance, which involved not only the absence of rhinosinusitis-associated commensal Corynebacterium and Fusobacterium in the middle meatus but also a significant increase in Haemophilus prevalence and abundance. This is the first study to compare bacterial communities in fungal and non-fungal rhinosinusitis samples. Our findings demonstrated that bacterial community dysbiosis was more apparent in fungal rhinosinusitis samples and was limited to the middle meatus.

scholarly journals Nitrogen Fertilizers Shape the Composition and Predicted Functions of the Microbiota of Field-Grown Tomato Plants

2019 ◽  
Vol 3 (4) ◽  
pp. 315-325 ◽  
Author(s):  
Federica Caradonia ◽  
Domenico Ronga ◽  
Marcello Catellani ◽  
Cleber Vinícius Giaretta Azevedo ◽  
Rodrigo Alegria Terrazas ◽  
...  
Keyword(s):  
Crop Production ◽  
Developmental Stages ◽  
Agricultural Practices ◽  
16S Rrna Gene Sequencing ◽  
Nitrogen Fertilizers ◽  
Rrna Gene ◽  
Tomato Root ◽  
Bacterial Microbiota ◽  
Rrna Gene Sequencing ◽  
Soil Interface

The microbial communities thriving at the root−soil interface have the potential to improve plant growth and sustainable crop production. Yet, how agricultural practices, such as the application of either mineral or organic nitrogen fertilizers, impact on the composition and functions of these communities remains to be fully elucidated. By deploying a two-pronged 16S rRNA gene sequencing and predictive metagenomics approach, we demonstrated that the bacterial microbiota of field-grown tomato (Solanum lycopersicum) plants is the product of a selective process that progressively differentiates between rhizosphere and root microhabitats. This process initiates as early as plants are in a nursery stage and it is then more marked at late developmental stages, in particular at harvest. This selection acts on both the bacterial relative abundances and phylogenetic assignments, with a bias for the enrichment of members of the phylum Actinobacteria in the root compartment. Digestate-based and mineral-based nitrogen fertilizers trigger a distinct bacterial enrichment in both rhizosphere and root microhabitats. This compositional diversification mirrors a predicted functional diversification of the root-inhabiting communities, manifested predominantly by the differential enrichment of genes associated to ABC transporters and the two-component system. Together, our data suggest that the microbiota thriving at the tomato root−soil interface is modulated by and in responses to the type of nitrogen fertilizer applied to the field. [Formula: see text] Copyright © 2019 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

Sign in / Sign up

Export Citation Format

Share Document