scholarly journals A New Niche for Anoxygenic Phototrophs as Endoliths

2017 ◽  
Vol 84 (4) ◽  
Author(s):  
Daniel Roush ◽  
Estelle Couradeau ◽  
Brandon Guida ◽  
Susanne Neuer ◽  
Ferran Garcia-Pichel
Keyword(s):  
High Throughput Sequencing ◽  
Microbial Mats ◽  
Hot Springs ◽  
Significant Proportion ◽  
Anoxygenic Phototrophic Bacteria ◽  
Major Type ◽  
Carbonate Platforms ◽  
Content Type ◽  
Wide Range ◽  
Isla De Mona

ABSTRACTAnoxygenic phototrophic bacteria (APBs) occur in a wide range of aquatic habitats, from hot springs to freshwater lakes and intertidal microbial mats. Here, we report the discovery of a novel niche for APBs: endoliths within marine littoral carbonates. In a study of 40 locations around Isla de Mona, Puerto Rico, and Menorca, Spain, 16S rRNA high-throughput sequencing of endolithic community DNA revealed the presence of abundant phylotypes potentially belonging to well-known APB clades. Anad hocphylogenetic classification of these sequences enabled us to refine the assignments more stringently. Even then, all locations contained such putative APBs, often reaching a significant proportion of all phototrophic sequences. In fact, in some 20% of samples, their contribution exceeded that of oxygenic phototrophs, previously regarded as the major type of endolithic microbe in carbonates. The communities contained representatives of APBs in theChloroflexales, various proteobacterial groups, andChlorobi. The most abundant phylotypes varied with geography: on Isla de Mona,RoseiflexusandChlorothrix-related phylotypes dominated, whereas those related toErythrobacterwere the most common in Menorca. The presence of active populations of APBs was corroborated through an analysis of photopigments: bacteriochlorophylls were detected in all samples, bacteriochlorophyllcandabeing most abundant. We discuss the potential metabolism and geomicrobial roles of endolithic APBs. Phylogenetic inference suggests that APBs may be playing a role as photoheterotrophs, adding biogeochemical complexity to our understanding of such communities. Given the global extent of coastal carbonate platforms, they likely represent a very large and unexplored habitat for APBs.IMPORTANCEEndolithic microbial communities from carbonates, which have been explored for over 2 centuries in predominantly naturalistic studies, were thought to be primarily composed of eukaryotic algae and cyanobacteria. Our report represents a paradigm shift in this regard, at least for the marine environment, demonstrating the presence of ubiquitous and abundant populations of APBs in this habitat. It raises questions about the role of these organisms in the geological dynamics of coastal carbonates, including coral reefs.

scholarly journals Caldichromatium japonicum gen. nov., sp. nov., a novel thermophilic phototrophic purple sulphur bacterium of the Chromatiaceae isolated from Nakabusa hot springs, Japan

2020 ◽  
Vol 70 (11) ◽  
pp. 5701-5710 ◽  
Author(s):  
Mohit Kumar Saini ◽  
Weng ChihChe ◽  
Nathan Soulier ◽  
Aswathy Sebastian ◽  
Istvan Albert ◽  
...  
Keyword(s):  
Type Species ◽  
Microbial Mats ◽  
Hot Springs ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Sequence Comparisons ◽  
Circular Chromosome ◽  
Content Type ◽  
Link Type ◽  
Purple Sulphur Bacterium

A novel thermophilic phototrophic purple sulphur bacterium was isolated from microbial mats (56 °C) at Nakabusa hot springs, Nagano prefecture, Japan. Cells were motile, rod-shaped, stain Gram-negative and stored sulphur globules intracellularly. Bacteriochlorophyll a and carotenoids of the normal spirilloxanthin series were the major pigments. Dense liquid cultures were red in colour. Strain No.7T was able to grow photoautotrophically using sulfide, thiosulfate, sulfite and hydrogen (in the presence of sulfide) as electron donors and bicarbonate as the sole carbon source. Optimum growth occurred under anaerobic conditions in the light at 50 °C (range, 40–56 °C) and pH 7.2 (range, pH 7–8). Major fatty acids were C16 : 0 (46.8 %), C16 : 1 ω7c (19.9 %), C18 : 1 ω7c (21.1 %), C14 : 0 (4.6 %) and C18 : 0 (2.4 %). The polar lipid profile showed phosphatidylglycerol and unidentified aminophospholipids to be the major lipids. The only quinone detected was ubiquinone-8. 16S rRNA gene sequence comparisons indicated that the novel bacterium is only distantly related to Thermochromatium tepidum with a nucleotide identity of 90.4 %. The phylogenetic analysis supported the high novelty of strain No.7T with a long-branching phylogenetic position within the Chromatiaceae next to Thermochromatium tepidum . The genome comprised a circular chromosome of 2.99 Mbp (2 989 870 bp), included no plasmids and had a DNA G+C content of 61.2 mol%. Polyphasic taxonomic analyses of the isolate suggested strain No.7T is a novel genus within the Chromatiaceae . The proposed genus name of the second truly thermophilic purple sulphur bacterium is Caldichromatium gen. nov. with the type species Caldichromatium japonicum sp. nov. (DSM 110881=JCM 39101).

scholarly journals Genomic Insights into Intrinsic and Acquired Drug Resistance Mechanisms in Achromobacter xylosoxidans

2014 ◽  
Vol 59 (2) ◽  
pp. 1152-1161 ◽  
Author(s):  
Yongfei Hu ◽  
Yuying Zhu ◽  
Yanan Ma ◽  
Fei Liu ◽  
Na Lu ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Clinical Isolate ◽  
Resistance Genes ◽  
Type Strain ◽  
High Throughput Sequencing ◽  
Resistance Mechanisms ◽  
Achromobacter Xylosoxidans ◽  
Content Type ◽  
Acquired Drug Resistance ◽  
Wide Range

ABSTRACTAchromobacter xylosoxidansis an opportunistic pathogen known to be resistant to a wide range of antibiotics; however, the knowledge about the drug resistance mechanisms is limited. We used a high-throughput sequencing approach to sequence the genomes of theA. xylosoxidanstype strain ATCC 27061 and a clinical isolate,A. xylosoxidansX02736, and then we used different bioinformatics tools to analyze the drug resistance genes in these bacteria. We obtained the complete genome sequence forA. xylosoxidansATCC 27061 and the draft sequence for X02736. We predicted a total of 50 drug resistance-associated genes in the type strain, including 5 genes for β-lactamases and 17 genes for efflux pump systems; these genes are also conserved among otherA. xylosoxidansgenomes. In the clinical isolate, except for the conserved resistance genes, we also identified several acquired resistance genes carried by a new transposon embedded in a novel integrative and conjugative element. Our study provides new insights into the intrinsic and acquired drug resistance mechanisms inA. xylosoxidans, which will be helpful for better understanding the physiology ofA. xylosoxidansand the evolution of antibiotic resistance in this bacterium.

scholarly journals RpoN-Dependent Direct Regulation of Quorum Sensing and the Type VI Secretion System inPseudomonas aeruginosaPAO1

2018 ◽  
Vol 200 (16) ◽  
Author(s):  
Xiaolong Shao ◽  
Xiaoning Zhang ◽  
Yingchao Zhang ◽  
Miao Zhu ◽  
Pan Yang ◽  
...  
Keyword(s):  
Quorum Sensing ◽  
High Throughput Sequencing ◽  
Functional Characterization ◽  
Secretion System ◽  
Global Regulator ◽  
Type Vi Secretion System ◽  
Related Factors ◽  
Content Type ◽  
Type Vi Secretion ◽  
Wide Range

ABSTRACTPseudomonas aeruginosais a Gram-negative opportunistic pathogen of humans, particularly those with cystic fibrosis. As a global regulator, RpoN controls a group of virulence-related factors and quorum-sensing (QS) genes inP. aeruginosa. To gain further insights into the direct targets of RpoNin vivo, the present study focused on identifying the direct targets of RpoN regulation in QS and the type VI secretion system (T6SS). We performed chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq) that identified 1,068 binding sites of RpoN, mostly including metabolic genes, a group of genes in QS (lasI,rhlI, andpqsR) and the T6SS (hcpAandhcpB). The direct targets of RpoN have been verified by electrophoretic mobility shifts assays (EMSA),luxreporter assay, reverse transcription-quantitative PCR, and phenotypic detection. TheΔrpoN::Tc mutant resulted in the reduced production of pyocyanin, motility, and proteolytic activity. However, the production of rhamnolipids and biofilm formation were higher in theΔrpoN::Tc mutant than in the wild type. In summary, the results indicated that RpoN had direct and profound effects on QS and the T6SS.IMPORTANCEAs a global regulator, RpoN controls a wide range of biological pathways, including virulence inP. aeruginosaPAO1. This work shows that RpoN plays critical and global roles in the regulation of bacterial pathogenicity and fitness. ChIP-seq provided a useful database to characterize additional functions and targets of RpoN in the future. The functional characterization of RpoN-mediated regulation will improve the current understanding of the regulatory network of quorum sensing and virulence inP. aeruginosaand other bacteria.

scholarly journals Exploring industry priorities regarding customer satisfaction and implications for event evaluation

2018 ◽  
Vol 9 (1) ◽  
pp. 51-66 ◽  
Author(s):  
Dewi Jaimangal-Jones ◽  
Jonathan Fry ◽  
Claire Haven-Tang
Keyword(s):  
Customer Satisfaction ◽  
Consumer Satisfaction ◽  
Significant Proportion ◽  
Evaluation Criteria ◽  
Future Research ◽  
Content Type ◽  
Wide Range ◽  
Research Findings ◽  
Customer Satisfaction Evaluation ◽  
Satisfaction Evaluation

Purpose The purpose of this paper is to explore the priorities of event organisers (EOs) and venue managers (VM) in terms of evaluation criteria and avenues for advancing the development and implementation of banks of questions regarding customer satisfaction evaluation. Design/methodology/approach The results presented are based on a questionnaire distributed to a sample of EOs and VM which sought to identify their priorities with regard to customer satisfaction feedback. Findings The findings show that a significant proportion of respondents had never undertaken formal evaluation, citing time and resources as the key barriers. In addition, a wide range of satisfaction-related criteria were rated as important, with the most valued criteria often related to generalised areas, but failing to consider the motivations of individuals for event attendance, which also appears as a gap within evaluation literature. The research findings indicate that developing banks of evaluation questions is a complex task, due to the number of potential variables in terms of events and audiences. Originality/value In linking the priority areas identified by the respondents with evaluation literature and event attendee motivations, this paper proposes alternative ways of structuring and utilising banks of evaluation questions linked to attendee profiles and motivations. Its central premise is that evaluation of consumer satisfaction should be led by consumer motivations and expectations if it is to be viable, meaningful and aid future event development and enhancement. This raises many questions and avenues for future research, to progress the area of logistically feasible evaluation, which generates rich and meaningful data.

scholarly journals Cell Size Distributions of Soil Bacterial and Archaeal Taxa

2013 ◽  
Vol 79 (24) ◽  
pp. 7610-7617 ◽  
Author(s):  
Maria C. Portillo ◽  
Jonathan W. Leff ◽  
Christian L. Lauber ◽  
Noah Fierer
Keyword(s):  
Life History ◽  
Cell Size ◽  
High Throughput Sequencing ◽  
Size Fraction ◽  
Life History Strategies ◽  
Rrna Gene ◽  
Average Cell ◽  
Content Type ◽  
Size Fractions ◽  
Wide Range

ABSTRACTCell size is a key ecological trait of soil microorganisms that determines a wide range of life history attributes, including the efficiency of nutrient acquisition. However, because of the methodological issues associated with determining cell sizesin situ, we have a limited understanding of how cell abundances vary across cell size fractions and whether certain microbial taxa have consistently smaller cells than other taxa. In this study, we extracted cells from three distinct soils and fractionated them into seven size ranges (5 μm to 0.2 μm) by filtration. Cell abundances in each size fraction were determined by direct microscopy, with the taxonomic composition of each size fraction determined by high-throughput sequencing of the 16S rRNA gene. Most of the cells were smaller than cells typically grown in culture, with 59 to 67% of cells <1.2 μm in diameter. Furthermore, each size fraction harbored distinct bacterial and archaeal communities in each of the three soils, and many of the taxa exhibited distinct size distribution patterns, with the smaller size fractions having higher relative abundances of taxa that are rare or poorly characterized (includingAcidobacteria,Gemmatimonadetes,Crenarchaeota,Verrucomicrobia, andElusimicrobia). In general, there was a direct relationship between average cell size and culturability, with those soil taxa that are poorly represented in culture collections tending to be smaller. Size fractionation not only provides important insight into the life history strategies of soil microbial taxa but also is a useful tool to enable more focused investigations into those taxa that remain poorly characterized.

scholarly journals Endogenous Gibbon Ape Leukemia Virus Identified in a Rodent (Melomys burtoni subsp.) from Wallacea (Indonesia)

2016 ◽  
Vol 90 (18) ◽  
pp. 8169-8180 ◽  
Author(s):  
Niccolò Alfano ◽  
Johan Michaux ◽  
Serge Morand ◽  
Ken Aplin ◽  
Kyriakos Tsangaras ◽  
...  
Keyword(s):  
Southeast Asia ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Leukemia Virus ◽  
Southeast Asian ◽  
Content Type ◽  
Hybridization Capture ◽  
Wide Range ◽  
Gibbon Ape Leukemia Virus ◽  
Koala Retrovirus

ABSTRACTGibbon ape leukemia virus (GALV) and koala retrovirus (KoRV) most likely originated from a cross-species transmission of an ancestral retrovirus into koalas and gibbons via one or more intermediate as-yet-unknown hosts. A virus highly similar to GALV has been identified in an Australian native rodent (Melomys burtoni) after extensive screening of Australian wildlife. GALV-like viruses have also been discovered in several Southeast Asian species, although screening has not been extensive and viruses discovered to date are only distantly related to GALV. We therefore screened 26 Southeast Asian rodent species for KoRV- and GALV-like sequences, using hybridization capture and high-throughput sequencing, in the attempt to identify potential GALV and KoRV hosts. Only the individuals belonging to a newly discovered subspecies ofMelomysburtonifrom Indonesia were positive, yielding an endogenous provirus very closely related to a strain of GALV. The sequence of the critical receptor domain for GALV infection in the IndonesianM. burtonisubsp. was consistent with the susceptibility of the species to GALV infection. The second record of a GALV inM. burtoniprovides further evidence thatM. burtoni, and potentially other lineages within the widespread subfamilyMurinae, may play a role in the spread of GALV-like viruses. The discovery of a GALV in the most western part of the Australo-Papuan distribution ofM. burtoni, specifically in a transitional zone between Asia and Australia (Wallacea), may be relevant to the cross-species transmission to gibbons in Southeast Asia and broadens the known distribution of GALVs in wild rodents.IMPORTANCEGibbon ape leukemia virus (GALV) and the koala retrovirus (KoRV) are very closely related, yet their hosts neither are closely related nor overlap geographically. Direct cross-species infection between koalas and gibbons is unlikely. Therefore, GALV and KoRV may have arisen via a cross-species transfer from an intermediate host whose range overlaps those of both gibbons and koalas. Using hybridization capture and high-throughput sequencing, we have screened a wide range of rodent candidate hosts from Southeast Asia for KoRV- and GALV-like sequences. Only aMelomysburtonisubspecies from Wallacea (Indonesia) was positive for GALV. We report the genome sequence of this newly identified GALV, the critical domain for infection of its potential cellular receptor, and its phylogenetic relationships with the other previously characterized GALVs. We hypothesize thatMelomysburtoni, and potentially related lineages with an Australo-Papuan distribution, may have played a key role in cross-species transmission to other taxa.

scholarly journals Ecological and biochemical properties of thermophilic bacteria taken from the Dachnie hot springs of Kamchatka (Far East, Russia)

2020 ◽  
Vol 9 (3) ◽  
pp. 79-85
Author(s):  
Elena G. Lebedeva ◽  
Natalya A. Kharitonova
Keyword(s):  
Heavy Metals ◽  
Enzymatic Activity ◽  
Microbial Mats ◽  
Hot Springs ◽  
Heterotrophic Bacteria ◽  
Thermophilic Bacteria ◽  
Far East ◽  
Biochemical Properties ◽  
Thermal Waters ◽  
Wide Range

In this work, we studied some ecological and biochemical characteristics (cultural, morphological, physiological and biochemical properties, extracellular enzymatic activity, bacterial growth in various ranges of temperatures, pH, NaCl concentrations, resistance to heavy metals) of 14 strains of thermophilic bacteria taken from thermal waters and microbial mats of Kamchatka Dachnie springs. On selective environment the strains formed mostly transparent, beige, white-gray, brown, yellow and pink colonies. It was shown that the isolates were represented most of all by asporogenic, catalase-positive and oxidase-positive, mobile, gram-negative rods of various sizes. Most of the cultures were capable of forming exozymes, especially amylases and proteinases. The strains grew in a wide range of temperatures (3550C), pH (58), NaCl concentration (15%) and were characterized by increased resistance to a number of heavy metals. 4 strains of thermophilic heterotrophic bacteria exhibited multiple multidrug resistance to metals. They were identified and it was shown that the isolates were represented by bacteria of the genus Bacillus sp. (№ 19), Thermus sp. (№ 40), Pseudomonas sp. (№ 15), Rhizobium sp. (№ 125). The strains with high enzymatic activity and increased resistance to pollutants are promising for use in the field of ecology for cleaning contaminated environmental objects.

scholarly journals Transfer of Plasmid DNA to Clinical Coagulase-Negative Staphylococcal Pathogens by Using a Unique Bacteriophage

2015 ◽  
Vol 81 (7) ◽  
pp. 2481-2488 ◽  
Author(s):  
Volker Winstel ◽  
Petra Kühner ◽  
Bernhard Krismer ◽  
Andreas Peschel ◽  
Holger Rohde
Keyword(s):  
Plasmid Dna ◽  
Genetic Manipulation ◽  
Current Knowledge ◽  
Virulence Determinants ◽  
Coagulase Negative Staphylococci ◽  
Reliable Technique ◽  
Content Type ◽  
Research Activities ◽  
Wide Range ◽  
Genetic Barriers

ABSTRACTGenetic manipulation of emerging bacterial pathogens, such as coagulase-negative staphylococci (CoNS), is a major hurdle in clinical and basic microbiological research. Strong genetic barriers, such as restriction modification systems or clustered regularly interspaced short palindromic repeats (CRISPR), usually interfere with available techniques for DNA transformation and therefore complicate manipulation of CoNS or render it impossible. Thus, current knowledge of pathogenicity and virulence determinants of CoNS is very limited. Here, a rapid, efficient, and highly reliable technique is presented to transfer plasmid DNA essential for genetic engineering to important CoNS pathogens from a uniqueStaphylococcus aureusstrain via a specificS. aureusbacteriophage, Φ187. Even strains refractory to electroporation can be transduced by this technique once donor and recipient strains share similar Φ187 receptor properties. As a proof of principle, this technique was used to delete the alternative transcription factor sigma B (SigB) via allelic replacement in nasal and clinicalStaphylococcus epidermidisisolates at high efficiencies. The described approach will allow the genetic manipulation of a wide range of CoNS pathogens and might inspire research activities to manipulate other important pathogens in a similar fashion.

scholarly journals Use of Proteins Identified through a Functional Genomic Screen To Develop a Protein Subunit Vaccine That Provides Significant Protection against Virulent Streptococcus suis in Pigs

2017 ◽  
Vol 86 (3) ◽  
Author(s):  
Susan L. Brockmeier ◽  
Crystal L. Loving ◽  
Tracy L. Nicholson ◽  
Jinhong Wang ◽  
Sarah E. Peters ◽  
...  
Keyword(s):  
Immune Response ◽  
Vaccine Trial ◽  
Streptococcus Suis ◽  
Protein Subunit ◽  
Content Type ◽  
Degree Of Protection ◽  
Wide Range ◽  
Associated Proteins ◽  
Clinical Protection ◽  
Cellular Immune

ABSTRACT Streptococcus suis is a bacterium that is commonly carried in the respiratory tract and that is also one of the most important invasive pathogens of swine, commonly causing meningitis, arthritis, and septicemia. Due to the existence of many serotypes and a wide range of immune evasion capabilities, efficacious vaccines are not readily available. The selection of S. suis protein candidates for inclusion in a vaccine was accomplished by identifying fitness genes through a functional genomics screen and selecting conserved predicted surface-associated proteins. Five candidate proteins were selected for evaluation in a vaccine trial and administered both intranasally and intramuscularly with one of two different adjuvant formulations. Clinical protection was evaluated by subsequent intranasal challenge with virulent S. suis . While subunit vaccination with the S. suis proteins induced IgG antibodies to each individual protein and a cellular immune response to the pool of proteins and provided substantial protection from challenge with virulent S. suis , the immune response elicited and the degree of protection were dependent on the parenteral adjuvant given. Subunit vaccination induced IgG reactive against different S. suis serotypes, indicating a potential for cross protection.

scholarly journals Validation and standardization of DNA extraction and library construction methods for metagenomics-based human fecal microbiome measurements

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Dieter M. Tourlousse ◽  
Koji Narita ◽  
Takamasa Miura ◽  
Mitsuo Sakamoto ◽  
Akiko Ohashi ◽  
...  
Keyword(s):  
Dna Extraction ◽  
High Throughput Sequencing ◽  
Performance Metrics ◽  
Collaborative Study ◽  
Human Microbiome ◽  
Second Phase ◽  
Intermediate Precision ◽  
Fecal Microbiome ◽  
Library Construction ◽  
Wide Range

Abstract Background Validation and standardization of methodologies for microbial community measurements by high-throughput sequencing are needed to support human microbiome research and its industrialization. This study set out to establish standards-based solutions to improve the accuracy and reproducibility of metagenomics-based microbiome profiling of human fecal samples. Results In the first phase, we performed a head-to-head comparison of a wide range of protocols for DNA extraction and sequencing library construction using defined mock communities, to identify performant protocols and pinpoint sources of inaccuracy in quantification. In the second phase, we validated performant protocols with respect to their variability of measurement results within a single laboratory (that is, intermediate precision) as well as interlaboratory transferability and reproducibility through an industry-based collaborative study. We further ascertained the performance of our recommended protocols in the context of a community-wide interlaboratory study (that is, the MOSAIC Standards Challenge). Finally, we defined performance metrics to provide best practice guidance for improving measurement consistency across methods and laboratories. Conclusions The validated protocols and methodological guidance for DNA extraction and library construction provided in this study expand current best practices for metagenomic analyses of human fecal microbiota. Uptake of our protocols and guidelines will improve the accuracy and comparability of metagenomics-based studies of the human microbiome, thereby facilitating development and commercialization of human microbiome-based products.

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