scholarly journals Labour sharing promotes coexistence in atrazine degrading bacterial communities

2019 ◽  
Author(s):  
Loren Billet ◽  
Marion Devers ◽  
Nadine Rouard ◽  
Fabrice Martin-Laurent ◽  
Aymé Spor
Keyword(s):  
Gene Loss ◽  
Bacterial Species ◽  
Single Species ◽  
Microbial Consortia ◽  
Future Research ◽  
The Public ◽  
Herbicide Atrazine ◽  
Set Up ◽  
Multiple Species

SUMMARYMicrobial communities exert a pivotal role in the biodegradation of xenobiotics including pesticides1. In the case of atrazine, multiple studies have shown that its degradation involved a consortia rather than a single species2,3,4,5, but little is known about how interdependency between the species composing the consortium is set up. The Black Queen Hypothesis (BQH) formalized theoretically the conditions leading to the evolution of dependency between species6: members of the community called ‘helpers’ provide publicly common goods obtained from the costly degradation of a compound, while others called ‘beneficiaries’ take advantage of the public goods, but lose access to the primary resource through adaptive degrading gene loss. Here, we test whether liquid media supplemented with the herbicide atrazine could support coexistence of bacterial species through BQH mechanisms. We observed the establishment of dependencies between species through atrazine degrading gene loss. Labour sharing between members of the consortium led to coexistence of multiple species on a single resource and improved atrazine degradation potential. Until now, pesticide degradation has not been approached from an evolutionary perspective under the BQH framework. We provide here an evolutionary explanation that might invite researchers to consider microbial consortia, rather than single isolated species, as an optimal strategy for isolation of xenobiotics degraders. Also, we anticipate that future research should focus on the bioaugmentation with stabilized and tightly structured microbial degrading consortia as an effective solution forin situbioremediation of sites polluted with recalcitrant compounds.

scholarly journals Labour sharing promotes coexistence in atrazine degrading bacterial communities

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Loren Billet ◽  
Marion Devers ◽  
Nadine Rouard ◽  
Fabrice Martin-Laurent ◽  
Aymé Spor
Keyword(s):  
Bacterial Communities ◽  
Gene Loss ◽  
Bacterial Species ◽  
Single Species ◽  
Microbial Consortia ◽  
The Public ◽  
Herbicide Atrazine ◽  
Set Up ◽  
Multiple Species ◽  
Isolated Species

AbstractMicrobial communities are pivotal in the biodegradation of xenobiotics including pesticides. In the case of atrazine, multiple studies have shown that its degradation involved a consortia rather than a single species, but little is known about how interdependency between the species composing the consortium is set up. The Black Queen Hypothesis (BQH) formalized theoretically the conditions leading to the evolution of dependency between species: members of the community called ‘helpers’ provide publicly common goods obtained from the costly degradation of a compound, while others called ‘beneficiaries’ take advantage of the public goods, but lose access to the primary resource through adaptive degrading gene loss. Here, we test whether liquid media supplemented with the herbicide atrazine could support coexistence of bacterial species through BQH mechanisms. We observed the establishment of dependencies between species through atrazine degrading gene loss. Labour sharing between members of the consortium led to coexistence of multiple species on a single resource and improved atrazine degradation potential. Until now, pesticide degradation has not been approached from an evolutionary perspective under the BQH framework. We provide here an evolutionary explanation that might invite researchers to consider microbial consortia, rather than single isolated species, as an optimal strategy for isolation of xenobiotics degraders.

scholarly journals CRISPRbuilder-TB: “CRISPR-builder for tuberculosis”. Exhaustive reconstruction of the CRISPR locus in mycobacterium tuberculosis complex using SRA

2021 ◽  
Vol 17 (3) ◽  
pp. e1008500
Author(s):  
Christophe Guyeux ◽  
Christophe Sola ◽  
Camille Noûs ◽  
Guislaine Refrégier
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Bacterial Species ◽  
Direct Repeats ◽  
Crispr Locus ◽  
The Public ◽  
Whole Process ◽  
General Rules ◽  
Genetic Mechanisms ◽  
Set Up

Mycobacterium tuberculosis complex (MTC) CRISPR locus diversity has long been studied solely investigating the presence/absence of a known set of spacers. Unveiling the genetic mechanisms of its evolution requires a more exhaustive reconstruction in a large amount of representative strains. In this article, we point out and resolve, with a new pipeline, the problem of CRISPR reconstruction based directly on short read sequences in M. tuberculosis. We first show that the process we set up, that we coin as “CRISPRbuilder-TB” (https://github.com/cguyeux/CRISPRbuilder-TB), allows an efficient reconstruction of simulated or real CRISPRs, even when including complex evolutionary steps like the insertions of mobile elements. Compared to more generalist tools, the whole process is much more precise and robust, and requires only minimal manual investigation. Second, we show that more than 1/3 of the currently complete genomes available for this complex in the public databases contain largely erroneous CRISPR loci. Third, we highlight how both the classical experimental in vitro approach and the basic in silico spoligotyping provided by existing analytic tools miss a whole diversity of this locus in MTC, by not capturing duplications, spacer and direct repeats variants, and IS6110 insertion locations. This description is extended in a second article that describes MTC-CRISPR diversity and suggests general rules for its evolution. This work opens perspectives for an in-depth exploration of M. tuberculosis CRISPR loci diversity and of mechanisms involved in its evolution and its functionality, as well as its adaptation to other CRISPR locus-harboring bacterial species.

scholarly journals In situ imaging of bacterial outer membrane projections and associated protein complexes using electron cryo-tomography

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Mohammed Kaplan ◽  
Georges Chreifi ◽  
Lauren Ann Metskas ◽  
Janine Liedtke ◽  
Cecily R Wood ◽  
...  
Keyword(s):  
Outer Membrane ◽  
Protein Complexes ◽  
Bacterial Species ◽  
Membrane Vesicles ◽  
Future Research ◽  
The Past ◽  
Widespread Phenomenon ◽  
Bacterial Outer Membrane ◽  
Uniform Diameter

The ability to produce outer membrane projections in the form of tubular membrane extensions (MEs) and membrane vesicles (MVs) is a widespread phenomenon among diderm bacteria. Despite this, our knowledge of the ultrastructure of these extensions and their associated protein complexes remains limited. Here, we surveyed the ultrastructure and formation of MEs and MVs, and their associated protein complexes, in tens of thousands of electron cryo-tomograms of ~90 bacterial species that we have collected for various projects over the past 15 years (Jensen lab database), in addition to data generated in the Briegel lab. We identified outer MEs and MVs in 13 diderm bacterial species and classified several major ultrastructures: (1) tubes with a uniform diameter (with or without an internal scaffold), (2) tubes with irregular diameter, (3) tubes with a vesicular dilation at their tip, (4) pearling tubes, (5) connected chains of vesicles (with or without neck-like connectors), (6) budding vesicles and nanopods. We also identified several protein complexes associated with these MEs and MVs which were distributed either randomly or exclusively at the tip. These complexes include a secretin-like structure and a novel crown-shaped structure observed primarily in vesicles from lysed cells. In total, this work helps to characterize the diversity of bacterial membrane projections and lays the groundwork for future research in this field.

scholarly journals Spatial and Temporal Population Dynamics of a Naturally Occurring Two-Species Microbial Community inside the Digestive Tract of the Medicinal Leech

2007 ◽  
Vol 73 (6) ◽  
pp. 1984-1991 ◽  
Author(s):  
Yoshitomo Kikuchi ◽  
Joerg Graf
Keyword(s):  
Population Dynamics ◽  
Digestive Tract ◽  
Bacterial Species ◽  
Single Species ◽  
Medicinal Leech ◽  
Aeromonas Veronii ◽  
Lectin Staining ◽  
Naturally Occurring ◽  
Hirudo Verbana

ABSTRACT The medicinal leech, Hirudo verbana, is one of the simplest naturally occurring models for digestive-tract symbioses, where only two bacterial species, Aeromonas veronii bv. sobria (γ-Proteobacteria) and a Rikenella-like bacterium (Bacteroidetes), colonize the crop, the largest compartment of the leech digestive tract. In this study, we investigated spatial and temporal changes of the localization and microcolony structure of the native symbionts in the crop, after ingestion of a sterile blood meal, by fluorescence in situ hybridization. The population dynamics differed between the two symbiotic bacteria. A. veronii was detected mainly as individual cells inside the intraluminal fluid (ILF) during 14 days after feeding (daf) unless it was found in association with Rikenella microcolonies. The Rikenella-like bacteria were observed not only inside the ILF but also in association with the luminal surface of the crop epithelium. The sizes of Rikenella microcolonies changed dynamically through the 14-day period. From 3 daf onward, mixed microcolonies containing both species were frequently observed, with cells of both species tightly associating with each other. The sizes of the mixed microcolonies were consistently larger than the size of either single-species microcolony, suggesting a synergistic interaction of the symbionts. Lectin staining with succinylated wheat germ agglutinin revealed that the planktonic microcolonies present in the ILF were embedded in a polysaccharide matrix containing N-acetylglucosamine. The simplicity, symbiont-symbiont interaction, and mixed microcolonies of this naturally occurring, digestive-tract symbiosis lay the foundation for understanding the more complex communities residing in most animals.

scholarly journals A Multi–Membrane System to Study the Effects of Physical and Metabolic Interactions in Microbial Co-Cultures and Consortia

Fermentation ◽  
2021 ◽  
Vol 7 (4) ◽  
pp. 206
Author(s):  
Jennifer R. Oosthuizen ◽  
Rene K. Naidoo-Blassoples ◽  
Debra Rossouw ◽  
Robert Pott ◽  
Florian F. Bauer
Keyword(s):  
Bacterial Species ◽  
Single Species ◽  
Membrane System ◽  
Ceramic Membranes ◽  
Physical Contact ◽  
Microbial Consortia ◽  
Cell Contact ◽  
Natural Environments ◽  
Multispecies Systems ◽  
Almost All

Continuous cell-to-cell contact between different species is a general feature of all natural environments. However, almost all research is conducted on single-species cultures, reflecting a biotechnological bias and problems associated with the complexities of reproducibly growing and controlling multispecies systems. Consequently, biotic stress due to the presence of other species remains poorly understood. In this context, understanding the effects of physical contact between species when compared to metabolic contact alone is one of the first steps to unravelling the mechanisms that underpin microbial ecological interactions. The current technologies to study the effects of cell-to-cell contact present disadvantages, such as the inefficient or discontinuous exchange of metabolites when preventing contact between species. This paper presents and characterizes a novel bioreactor system that uses ceramic membranes to create a “multi-membrane” compartmentalized system whereby two or more species can be co-cultured without the mixing of the species, while ensuring the efficient sharing of all of the media components. The system operates continuously, thereby avoiding the discontinuities that characterize other systems, which either have to use hourly backwashes to clean their membranes, or have to change the direction of the flow between compartments. This study evaluates the movement of metabolites across the membrane in co-cultures of yeast, microalgae and bacterial species, and monitors the movement of the metabolites produced during co-culturing. These results show that the multi-membrane system proposed in this study represents an effective system for studying the effects of cell-to-cell contact in microbial consortia. The system can also be adapted for various biotechnological purposes, such as the production of metabolites when more than one species is required for such a process.

scholarly journals A Microbial Metagenome (Leucobacter sp.) in Caenorhabditis Whole Genome Sequences

2013 ◽  
Vol 7 ◽  
pp. BBI.S11064 ◽  
Author(s):  
Riccardo Percudani
Keyword(s):  
Genetic Information ◽  
Bacterial Species ◽  
Draft Genome ◽  
Single Species ◽  
Public Database ◽  
Genome Sequences ◽  
The Public ◽  
Caenorhabditis Remanei ◽  
Insight Into ◽  
Annotation Errors

DNA of apparently recent bacterial origin is found in the genomic sequences of Caenorhabditis angaria and Caenorhabditis remanei. Here we present evidence that the DNA belongs to a single species of the genus Leucobacter (high-GC Gram+Actinobacteria). Metagenomic tools enabled the assembly of the contaminating sequences in a draft genome of 3.2 Mb harboring 2,826 genes. This information provides insight into a microbial organism intimately associated with Caenorhabditis as well as a solid basis for the reassignment of 3,373 metazoan entries of the public database to a novel bacterial species ( Leucobacter sp. AEAR). The application of metagenomic techniques can thus prevent annotation errors and reveal unexpected genetic information in data obtained by conventional genomics.

scholarly journals In situ imaging of bacterial membrane projections and associated protein complexes using electron cryo-tomography

2021 ◽  
Author(s):  
Mohammed Kaplan ◽  
Georges Chreifi ◽  
Lauren Ann Metskas ◽  
Janine Liedtke ◽  
Cecily R Wood ◽  
...  
Keyword(s):  
Protein Complexes ◽  
Bacterial Species ◽  
Membrane Vesicles ◽  
Future Research ◽  
Bacterial Membrane ◽  
Tubular Membrane ◽  
The Past ◽  
Widespread Phenomenon ◽  
Uniform Diameter

The ability to produce membrane projections in the form of tubular membrane extensions (MEs) and membrane vesicles (MVs) is a widespread phenomenon among bacteria. Despite this, our knowledge of the ultrastructure of these extensions and their associated protein complexes remains limited. Here, we surveyed the ultrastructure and formation of MEs and MVs, and their associated protein complexes, in tens of thousands of electron cryo-tomograms of ~ 90 bacterial species that we have collected for various projects over the past 15 years (Jensen lab database), in addition to data generated in the Briegel lab. We identified MEs and MVs in 13 species and classified several major ultrastructures: 1) tubes with a uniform diameter (with or without an internal scaffold), 2) tubes with irregular diameter, 3) tubes with a vesicular dilation at their tip, 4) pearling tubes, 5) connected chains of vesicles (with or without neck-like connectors), 6) budding vesicles and nanopods. We also identified several protein complexes associated with these MEs and MVs which were distributed either randomly or exclusively at the tip. These complexes include a secretin-like structure and a novel crown-shaped structure observed primarily in vesicles from lysed cells. In total, this work helps to characterize the diversity of bacterial membrane projections and lays the groundwork for future research in this field.

Assessments of User Comments With “Alternative Views” as a Function of Media Trust

2020 ◽  
pp. 1-12
Author(s):  
Marlene Kunst
Keyword(s):  
Online Discussions ◽  
Future Research ◽  
Political Issues ◽  
Argument Quality ◽  
The Public ◽  
Mainstream Media ◽  
User Comments ◽  
Media Trust ◽  
Heuristic Information Processing

Abstract. Comments sections under news articles have become popular spaces for audience members to oppose the mainstream media’s perspective on political issues by expressing alternative views. This kind of challenge to mainstream discourses is a necessary element of proper deliberation. However, due to heuristic information processing and the public concern about disinformation online, readers of comments sections may be inherently skeptical about user comments that counter the views of mainstream media. Consequently, commenters with alternative views may participate in discussions from a position of disadvantage because their contributions are scrutinized particularly critically. Nevertheless, this effect has hitherto not been empirically established. To address this gap, a multifactorial, between-subjects experimental study ( N = 166) was conducted that investigated how participants assess the credibility and argument quality of media-dissonant user comments relative to media-congruent user comments. The findings revealed that media-dissonant user comments are, indeed, disadvantaged in online discussions, as they are assessed as less credible and more poorly argued than media-congruent user comments. Moreover, the findings showed that the higher the participants’ level of media trust, the worse the assessment of media-dissonant user comments relative to media-congruent user comments. Normative implications and avenues for future research are discussed.

The use of ICT by SMMEs in a Digital Economy: A case study in Buffalo City Metropolitan in South Africa [Abstract]

10.28945/4314 ◽  
2019 ◽  
Keyword(s):  
South Africa ◽  
Technology Acceptance ◽  
21St Century ◽  
Common Knowledge ◽  
Digital Economy ◽  
Future Research ◽  
Wealth Creation ◽  
Underdeveloped Areas ◽  
And Gender ◽  
Set Up

Aim/Purpose: The goal of this study is to advance understanding of ICT utilization by SMMEs by checking access, ability (in terms of technological skills) and usage of ICT among some SMMEs entrepreneurs operating their businesses in an underdeveloped areas to enhance their business activities in order to utilizes the digital opportunities 21st century digital economies present. Background: In today’s world no nation or region is untouched by the forces of globalization and digital economy. One of the key pioneering forces of globalization is the advances of ICT like internet, social networks, etc. In the sphere of business, this pioneering force has also altered the way businesses and organizations communicate and interact with customers and society at large. Such alternation presents obvious opportunities for wealth creation and growth for businesses and organizations that are well-equipped to take advantages of them. But for those that are less-equipped, particularly SMMEs, globalization can easily lead to fore-closures and marginalization. It is a common knowledge that SMMEs entrepreneurs mostly rely on ICT gadgets like mobile phone, Laptops, Tablets to conduct their business activities as many of them don’t have enough capital to set up offices with necessary equipment. Therefore, using various ICT functions/programs on these ICT devices to enhance their business activities are critical to their businesses in the 21st century digital economies. Methodology: Purposeful sampling was used to approach fifty-four SMMEs entrepreneurs operating their businesses in underdeveloped areas locally called Townships in Buffalo City Metropolitan. Microsoft excel was used in the descriptive statistics. Contribution: This research will add to the growing knowledge ICT usage in SMMEs in the 21st century digital economies. Findings: The results indicate that the participating SMMEs entrepreneurs need to be educated, trained and supported in the use of the ICT applicable to enhance their business activities in order for them to take advantages of 21st century digital economies present. Recommendations for Practitioners: The agencies tasked with looking after SMMEs in South Africa needs to consider the lacked of utilisation of ICTs by SMMEs entrepreneurs operating their businesses in underdeveloped areas as one of the barrier to growing of their businesses and take necessary steps to address it. Recommendation for Researchers: Since age and gender have been proven to be key-moderating variables in many technology acceptance models. There is a need to explore in depth whether the factors of gender and age also act as barriers. Impact on Society: The research will assist stakeholders, policy makers and agencies tasked with looking after SMMEs to identify the barriers hindering SMMEs to grow and address them accordingly. Future Research: More work needs to be done to check whether gender, age of the SMMEs entrepreneurs have some effects on their attitude towards the integration of ICT into their business activities.

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