scholarly journals Inter-Cluster Competition and Resource Partitioning May Govern the Ecology of Frankia

2021 ◽  
Author(s):  
Indrani Sarkat ◽  
Gargi Sen ◽  
S Bhattacharyya ◽  
Maher Gtari ◽  
Arnab Sen
Keyword(s):  
Resource Partitioning ◽  
Root Nodule ◽  
Habitat Type ◽  
Structural Complexity ◽  
Direct Interaction ◽  
R Package ◽  
Microbial Populations ◽  
Competition Index ◽  
Plant Host ◽  
Metabolic Analysis

Abstract Microbes live in a complex communal ecosystem. The structural complexity of microbial community reflects diversity, functionality as well as habitat type. Delineation of ecologically important microbial populations along with exploration of their roles in environmental adaptation or host-microbe interaction has a crucial role in modern microbiology. In this scenario, reverse ecology (the use of genomics to study ecology) plays a pivotal role. Some studies have reported the presence of other non-Frankia genus from the same root nodule from where the Frankia was isolated. Since co-existance of two different genus in one small niche should maintain a strict direct interaction, it will be interesting to utilize the concept of reverse ecology in this scenario.Here, we exploited an ‘R’ package, the RevEcoR, to resolve the issue of co-existing microbes which are proven to be a crucial tool for identifying the nature of their relationship (competition or complementation) persisting among them. Our target organism here is Frankia, a nitrogen-fixing actinobacterium popular for its genetic and host specificity nature. According to their plant host, Frankia has already been subdivided into four clusters CI, CII, CIII and CIV. Our results revealed a strong competing nature of CI Frankia. The competition index between CI and CIII was greater than other studied Frankia clusters. The other interesting result was the co-occurrence of C-II and C-IV groups. It was revealed that these two groups follow the theory of resource partitioning in their lifestyle. Metabolic analysis along with their differential transporter machinery validated our hypothesis of resource partitioning among C-II and C-IV group.

scholarly journals Viroids: unusual small pathogenic RNAs.

2004 ◽  
Vol 51 (3) ◽  
pp. 587-607 ◽  
Author(s):  
Anna Góra-Sochacka
Keyword(s):  
Secondary Structure ◽  
Hammerhead Ribozyme ◽  
Direct Interaction ◽  
Plant Diseases ◽  
Plant Host ◽  
Rolling Circle ◽  
Rna Molecules ◽  
Viroid Replication ◽  
Plant Genes ◽  
Rolling Circle Mechanism

Viroids are small (about 300 nucleotides), single-stranded, circular, non-encapsidated pathogenic RNA molecules. They do not code for proteins and thus depend on plant host enzymes for their replication and other functions. They induce plant diseases by direct interaction with host factors but the mechanism of pathogenicity is still unknown. They can alter the expression of selected plant genes important for growth and development. Viroids belong to two families, the Avsunviroidae and the Pospiviroidae. Viroids of the Avsunviroidae family adopt a branched or quasi rod-like secondary structure in their native state. Members of the Pospiviroidae family adopt a rod-like secondary structure. In such native structures five structural/functional domains have been identified: central (C), pathogenicity, variable and two terminal domains. The central conserved region (CCR) within the C domain characterizes viroids of the Pospiviroidae. Specific secondary structures of this region play an important role in viroid replication and processing. Viroids of the Avsunviroidae family lack a CCR but possess self-cleaving properties by forming hammerhead ribozyme structures; they accumulate and replicate in chloroplasts, whereas members of the Pospiviroidae family have a nuclear localization. Viroid replication occurs via a rolling circle mechanism using either a symmetric or asymmetric pathway in three steps, RNA transcription, processing and ligation.

scholarly journals T cell–mediated regulation of the microbiota protects against obesity

Science ◽  
2019 ◽  
Vol 365 (6451) ◽  
pp. eaat9351 ◽  
Author(s):  
Charisse Petersen ◽  
Rickesha Bell ◽  
Kendra A. Klag ◽  
Soh-Hyun Lee ◽  
Raymond Soto ◽  
...  
Keyword(s):  
Metabolic Syndrome ◽  
Lipid Metabolism ◽  
T Cell ◽  
Immunoglobulin A ◽  
Lipid Absorption ◽  
Microbial Populations ◽  
Immune Control ◽  
Germ Free ◽  
Metabolic Analysis ◽  
Key Features

The microbiota influences obesity, yet organisms that protect from disease remain unknown. During studies interrogating host-microbiota interactions, we observed the development of age-associated metabolic syndrome (MetS). Expansion of Desulfovibrio and loss of Clostridia were key features associated with obesity in this model and are present in humans with MetS. T cell–dependent events were required to prevent disease, and replacement of Clostridia rescued obesity. Inappropriate immunoglobulin A targeting of Clostridia and increased Desulfovibrio antagonized the colonization of beneficial Clostridia. Transcriptional and metabolic analysis revealed enhanced lipid absorption in the obese host. Colonization of germ-free mice with Clostridia, but not Desulfovibrio, down-regulated genes that control lipid absorption and reduced adiposity. Thus, immune control of the microbiota maintains beneficial microbial populations that constrain lipid metabolism to prevent MetS.

scholarly journals The Biology of Frankia sp. Strains in the Post-Genome Era

2011 ◽  
Vol 24 (11) ◽  
pp. 1310-1316 ◽  
Author(s):  
David R. Benson ◽  
James M. Brooks ◽  
Ying Huang ◽  
Derek M. Bickhart ◽  
Juliana E. Mastronunzio
Keyword(s):  
Root Nodule ◽  
Root Nodules ◽  
Ammonium Assimilation ◽  
Defense Responses ◽  
Nodule Formation ◽  
Plant Defense Responses ◽  
Plant Host ◽  
Future Studies ◽  
Microbiological Techniques ◽  
Bacterial Genes

Progress in understanding symbiotic determinants involved in the N2-fixing actinorhizal plant symbioses has been slow but steady. Problems persist with studying the bacterial contributions to the symbiosis using traditional microbiological techniques. However, recent years have seen the emergence of several genomes from Frankia sp. strains and the development of techniques for manipulating plant gene expression. Approaches to understanding the bacterial side of the symbiosis have employed a range of techniques that reveal the proteomes and transcriptomes from both cultured and symbiotic frankiae. The picture beginning to emerge provides some perspective on the heterogeneity of frankial populations in both conditions. In general, frankial populations in root nodules seem to maintain a rather robust metabolism that includes nitrogen fixation and substantial biosynthesis and energy-generating pathways, along with a modified ammonium assimilation program. To date, particular bacterial genes have not been implicated in root nodule formation but some hypotheses are emerging with regard to how the plant and microorganism manage to coexist. In particular, frankiae seem to present a nonpathogenic presence to the plant that may have the effect of minimizing some plant defense responses. Future studies using high-throughput approaches will likely clarify the range of bacterial responses to symbiosis that will need to be understood in light of the more rapidly advancing work on the plant host.

scholarly journals Ecological patterns of root nodule diversity in cultivated and wild rooibos populations: a community prediction approach

2020 ◽  
Author(s):  
Josep Ramoneda ◽  
Jaco Le Roux ◽  
Emmanuel Frossard ◽  
Beat Frey ◽  
Hannes Andres Gamper
Keyword(s):  
Bacterial Diversity ◽  
Bacterial Communities ◽  
Root Nodule ◽  
Plant Traits ◽  
Dispersal Limitation ◽  
Soil Conditions ◽  
Plant Host ◽  
Legume Crop ◽  
Population Type ◽  
Prediction Approach

AbstractThere is interest in understanding the factors behind the biogeography of root-associated bacteria due to the joint effects that plant host, climate, and soil conditions can have on bacterial diversity. For legume crops with remaining wild populations, this is of even more importance, because the effects of cropping on undisturbed root-associated bacterial communities can be addressed. Here, we used a community prediction approach to describe the diversity of the root nodule bacterial communities of rooibos (Aspalathus linearis), an endemic legume crop from South Africa. The goal was to reveal whether patterns of root nodule community composition in paired cultivated and wild rooibos populations could be related to geographical distance, plant traits, and plant population type (i.e. cultivated or uncultivated). We identified a core of dominant and widespread Mesorhizobium ZOTUs that each defined one of 4 different root nodule community classes. Rooibos cultivation impacted root nodule bacterial diversity at regional and local scales, while the geographical origin of the root nodule communities was the strongest predictor of root nodule community structure. Beyond impacts of cultivation on root nodule bacterial diversity, this study suggests a mixture of dispersal limitation and ecological drift regionally, and selection by different plant populations locally, define the biogeography of rooibos root nodule bacterial communities.

scholarly journals Effects of structural complexity and habitat type on the gall distribution of Jatrophobia brasiliensis (Rübsaamen, 1907) (Diptera, Cecidomyiidae) in two host-species of Manihot (Euphorbiaceae)

2020 ◽  
Vol 2 ◽  
pp. ec02003
Author(s):  
Mariane D. Scarcela ◽  
Walter S de Araújo
Keyword(s):  
Host Plant ◽  
Plant Height ◽  
Host Species ◽  
Habitat Type ◽  
Structural Complexity ◽  
Minas Gerais ◽  
Plant Structure ◽  
Extrinsic Factors ◽  
Crown Diameter ◽  
Number Of Leaves

In the present study, we evaluate the distribution of galls induced by Jatrophobia brasiliensis (Rübsaamen, 1907) in two species of Manihot (Manihot caerulescens Pohl and Manihot sp.). The study was performed in two Cerrado phytophysiognomies (typical savannah and rocky savannah) in Jequitaí municipality, Minas Gerais, Brazil. A total of 1,157 galls of Jatrophobia brasiliensis were analyzed, of which 459 galls in Manihot sp. and 698 galls in Manihot caerulescens. We found that plant height, crown diameter and number of leaves per branch positively influenced the number of galled leaves. Our results also showed that habitat type influenced the number of galled leaves and the gall size, with the rocky savannah presenting more and larger galls than the typical savannah. Our findings demonstrate that both intrinsic (related to host plant structure) and extrinsic factors (related to habitat type) influence the distribution of the galls induced by Jatrophobia brasiliensis on Manihot.

scholarly journals Habitat niche community-level analysis of an amphibian assemblage at Lake Nabugabo, Uganda

Web Ecology ◽  
2008 ◽  
Vol 8 (1) ◽  
pp. 125-134 ◽  
Author(s):  
M. Behangana ◽  
L. Luiselli
Keyword(s):  
Community Structure ◽  
Relative Abundance ◽  
Resource Partitioning ◽  
Community Organization ◽  
Habitat Type ◽  
Niche Overlap ◽  
Seasonal Effects ◽  
Wet Season ◽  
Swamp Forest ◽  
Score Analysis

Abstract. Community structure was studied across six different habitat types in an amphibian assemblage constituted by 24 species belonging to five families, from Lake Nabugabo, Uganda. We employed a suite of different statistical methods, including univariate, multivariate, and Monte Carlo procedures to investigate the randomness/nonrandomness and the seasonal effects (wet versus dry season) of the community assembly. We calculated for each species in each habitat type an index of relative abundance by using a time constrained counting technique, with 48 1-h counts for each habitat type. Co-occurrence was analysed by C score with 30 000 simulations; resource partitioning patterns by RA2 and RA3 algorithms with 30 000 simulations; and apparent dissimilarity among species in terms of habitat use by UPGMA dendrograms. After pooling data from wet and dry seasons, it resulted that the amphibian community was non-randomly assembled according to C-score analyses, but both RA2 and RA3 were unable to uncover any competitive structure for the dataset. Seasonal effects were evident, and although C score analyses confirmed a nonrandom structure for the community under study (particularly in wet season), RA3 showed that species with high relative abundance tended to significantly concentrate in one habitat type (swamp forest) rather than to partition the habitat resource. UPGMA dendrograms grouped the species differently in dry versus wet seasons. Overall, the comparative evidence of 1) non-random community structure according to C-score analysis, and 2) absence of resource partitioning according to niche overlap null models analysis, suggests that community organization in Lake Nabugabo amphibians is generated by habitat affinities rather than by interspecific competition.

Microhabitat separation among diurnal saxicolous lizards in Zimbabwe

1999 ◽  
Vol 15 (3) ◽  
pp. 367-378 ◽  
Author(s):  
Karen E. Howard ◽  
Adrian Hailey
Keyword(s):  
Rock Slope ◽  
Granitic Rock ◽  
Slope Angle ◽  
Habitat Type ◽  
Structural Complexity ◽  
Niche Overlap ◽  
Niche Separation ◽  
Lizard Species ◽  
High Degree ◽  
Dimensions Of Space

Studies of niche overlap within communities of lizards have shown that separation may be along the three major dimensions of space, time and food. Space is usually the most important dimension where a range of habitats are involved; there is less information on the importance of microhabitat separation within a single habitat type. This study investigated microhabitat relationships of small diurnal lizard species occupying granitic rock habitat in Zimbabwe. There was statistically significant niche separation among all species in both the type of rock occupied (size, shape, number of cracks, closeness to other rocks, and vegetation cover) and the position of the lizard in the microhabitat (height on rock, slope angle, and distance to cover). Overlap of microhabitat was lowest between the generalist terrestrial skink Mabuya varia and all other species. The arboreal skink Mabuya striata was found on rocks at one site where the more saxicolous Mabuya quinquetaeniata was absent, due to competitor release. Overlap of microhabitat among rock specialists was lowest between the sit-and-wait foragers Agama kirkii and Platysaurus intermedius, as in other tropical lizard communities. The high degree of microhabitat separation was attributed to the high structural complexity of the granitic rock habitat.

scholarly journals Quantifying vegetation and canopy structural complexity from terrestrial Li DAR data using the forestr r package

2018 ◽  
Vol 9 (10) ◽  
pp. 2057-2066 ◽  
Author(s):  
Jeff W. Atkins ◽  
Gil Bohrer ◽  
Robert T. Fahey ◽  
Brady S. Hardiman ◽  
Timothy H. Morin ◽  
...  
Keyword(s):  
Structural Complexity ◽  
R Package

scholarly journals A Krüppel-like zinc finger protein is involved in nitrogen-fixing root nodule organogenesis

2000 ◽  
Vol 14 (4) ◽  
pp. 475-482
Author(s):  
Florian Frugier ◽  
Simone Poirier ◽  
Béatrice Satiat-Jeunemaître ◽  
Adam Kondorosi ◽  
Martin Crespi
Keyword(s):  
Zinc Finger ◽  
Root Nodule ◽  
Zinc Finger Protein ◽  
Root Nodules ◽  
Yeast Cells ◽  
Bacterial Invasion ◽  
Vascular Bundles ◽  
Nitrogen Fixing ◽  
Plant Host ◽  
Finger Protein

Mechanisms regulating plant host differentiation of the nitrogen-fixing root nodules remain mostly unknown. Sinorhizobium meliloti induces this process in Medicago sativa in which the Mszpt2-1 gene is expressed in vascular bundles of roots and nodules. This gene codes for a Krüppel-like zinc finger protein, a class of transcription factors involved in many animal developmental processes. Expression of Mszpt2-1 in yeast cells conferred osmotic tolerance. Antisense plants grew normally but developed nonfunctional nodules, in which differentiation of the nitrogen-fixing zone and bacterial invasion were arrested. Hence, a vascular bundle-associated Krüppel-like gene is required for the formation of the central nitrogen-fixing zone of the root nodule.

Conformation of eukaryotic ribosomal RNAs

1983 ◽  
Vol 41 ◽  
pp. 592-593
Author(s):  
M. Boublik ◽  
G. Thornton ◽  
G. Oostergetel ◽  
J.F. Hainfeld ◽  
J.S. Wall
Keyword(s):  
Molecular Weight ◽  
Mass Measurement ◽  
Carbon Film ◽  
Structural Complexity ◽  
Scanning Transmission Electron Microscope ◽  
Electron Microscopic ◽  
Pure Nitrogen ◽  
Freeze Dried ◽  
Scanning Transmission ◽  
Partially Unfolded

Understanding the structural complexity of ribosomes and their role in protein synthesis requires knowledge of the conformation of their components - rRNAs and proteins. Application of dedicated scanning transmission electron microscope (STEM), electrical discharge of the support carbon film in an atmosphere of pure nitrogen, and determination of the molecular weight of individual rRNAs enabled us to obtain high resolution electron microscopic images of unstained freeze-dried rRNA molecules from BHK cells in a form suitable for evaluation of their 3-D structure. Preliminary values for the molecular weight of 28S RNA from the large and 18S RNA from the small ribosomal subunits as obtained by mass measurement were 1.84 x 106 and 0.97 x 106, respectively. Conformation of rRNAs consists, in general, of alternating segments of intramolecular hairpin stems and single stranded loops in a proportion which depends on their ionic environment, the Mg++ concentration in particular. Molecules of 28S RNA (Fig. 1) and 18S RNA (not shown) obtained by freeze-drying from a solution of 60 mM NH+4 acetate and 2 mM Mg++ acetate, pH 7, appear as partially unfolded coils with compact cores suggesting a high degree of ordered secondary structure.

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