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Frontiers in Microbiology

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https://www.readbyqxmd.com/read/28804481/the-type-vi-secretion-system-a-dynamic-system-for-bacterial-communication
#1
REVIEW
Mathias Gallique, Mathilde Bouteiller, Annabelle Merieau
Numerous studies in Gram-negative bacteria have focused on the Type VI Secretion Systems (T6SSs), Quorum Sensing (QS), and social behavior, such as in biofilms. These interconnected mechanisms are important for bacterial survival; T6SSs allow bacteria to battle other cells, QS is devoted to the perception of bacterial cell density, and biofilm formation is essentially controlled by QS. Here, we review data concerning T6SS dynamics and T6SS-QS cross-talk that suggest the existence of inter-bacterial communication via T6SSs...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28804480/microbial-community-structure-and-the-persistence-of-cyanobacterial-populations-in-salt-crusts-of-the-hyperarid-atacama-desert-from-genome-resolved-metagenomics
#2
Kari M Finstad, Alexander J Probst, Brian C Thomas, Gary L Andersen, Cecilia Demergasso, Alex Echeverría, Ronald G Amundson, Jillian F Banfield
Although once thought to be devoid of biology, recent studies have identified salt deposits as oases for life in the hyperarid Atacama Desert. To examine spatial patterns of microbial species and key nutrient sources, we genomically characterized 26 salt crusts from three sites along a fog gradient. The communities are dominated by a large variety of Halobacteriales and Bacteroidetes, plus a few algal and Cyanobacterial species. CRISPR locus analysis suggests the distribution of a single Cyanobacterial population among all sites...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28804479/molecular-characterization-of-arbuscular-mycorrhizal-fungi-in-an-agroforestry-system-reveals-the-predominance-of-funneliformis-spp-associated-with-colocasia-esculenta-and-pterocarpus-officinalis-adult-trees-and-seedlings
#3
Alexandre Geoffroy, Hervé Sanguin, Antoine Galiana, Amadou Bâ
Pterocarpus officinalis (Jacq.) is a leguminous forestry tree species endemic to Caribbean swamp forests. In Guadeloupe, smallholder farmers traditionally cultivate flooded taro (Colocasia esculenta) cultures under the canopy of P. officinalis stands. The role of arbuscular mycorrhizal (AM) fungi in the sustainability of this traditional agroforestry system has been suggested but the composition and distribution of AM fungi colonizing the leguminous tree and/or taro are poorly characterized. An in-depth characterization of root-associated AM fungal communities from P...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28804478/the-entomopathogenic-fungi-isaria-fumosorosea-plays-a-vital-role-in-suppressing-the-immune-system-of-plutella-xylostella-rna-seq-and-dge-analysis-of-immunity-related-genes
#4
Jin Xu, Xiaoxia Xu, Muhammad Shakeel, Shuzhong Li, Shuang Wang, Xianqiang Zhou, Jialin Yu, Xiaojing Xu, Xiaoqiang Yu, Fengliang Jin
Most, if not all, entomopathogenic fungi have been used as alternative control agents to decrease the insect resistance and harmful effects of the insecticides on the environment. Among them, Isaria fumosorosea has also shown great potential to control different insect pests. In the present study, we explored the immune response of P. xylostella to the infection of I. fumosorosea at different time points by using RNA-Sequencing and differential gene expression technology at the genomic level. To gain insight into the host-pathogen interaction at the genomic level, five libraries of P...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28804477/glaciers-and-ice-sheets-as-analog-environments-of-potentially-habitable-icy-worlds
#5
REVIEW
Eva Garcia-Lopez, Cristina Cid
Icy worlds in the solar system and beyond have attracted a remarkable attention as possible habitats for life. The current consideration about whether life exists beyond Earth is based on our knowledge of life in terrestrial cold environments. On Earth, glaciers and ice sheets have been considered uninhabited for a long time as they seemed too hostile to harbor life. However, these environments are unique biomes dominated by microbial communities which maintain active biochemical routes. Thanks to techniques such as microscopy and more recently DNA sequencing methods, a great biodiversity of prokaryote and eukaryote microorganisms have been discovered...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28804476/wood-ash-induced-ph-changes-strongly-affect-soil-bacterial-numbers-and-community-composition
#6
Toke Bang-Andreasen, Jeppe T Nielsen, Jana Voriskova, Janine Heise, Regin Rønn, Rasmus Kjøller, Hans C B Hansen, Carsten S Jacobsen
Recirculation of wood ash from energy production to forest soil improves the sustainability of this energy production form as recycled wood ash contains nutrients that otherwise would be lost at harvest. In addition, wood-ash is beneficial to many soils due to its inherent acid-neutralizing capabilities. However, wood ash has several ecosystem-perturbing effects like increased soil pH and pore water electrical conductivity both known to strongly impact soil bacterial numbers and community composition. Studies investigating soil bacterial community responses to wood ash application remain sparse and the available results are ambiguous and remain at a general taxonomic level...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28798742/preservation-and-significance-of-extracellular-dna-in-ferruginous-sediments-from-lake-towuti-indonesia
#7
Aurèle Vuillemin, Fabian Horn, Mashal Alawi, Cynthia Henny, Dirk Wagner, Sean A Crowe, Jens Kallmeyer
Extracellular DNA is ubiquitous in soil and sediment and constitutes a dominant fraction of environmental DNA in aquatic systems. In theory, extracellular DNA is composed of genomic elements persisting at different degrees of preservation produced by processes occurring on land, in the water column and sediment. Extracellular DNA can be taken up as a nutrient source, excreted or degraded by microorganisms, or adsorbed onto mineral matrices, thus potentially preserving information from past environments. To test whether extracellular DNA records lacustrine conditions, we sequentially extracted extracellular and intracellular DNA from anoxic sediments of ferruginous Lake Towuti, Indonesia...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28798741/deinococcus-radiodurans-toxin-antitoxin-mazef-dr-mediates-cell-death-in-response-to-dna-damage-stress
#8
Tao Li, Yulan Weng, Xiaoqiong Ma, Bing Tian, Shang Dai, Ye Jin, Mengjia Liu, Jiulong Li, Jiangliu Yu, Yuejin Hua
Here we identified a functional MazEF-dr system in the exceptionally stress-resistant bacterium D. radiodurans. We showed that overexpression of the toxin MazF-dr inhibited the growth of Escherichia coli. The toxic effect of MazF-dr was due to its sequence-specific endoribonuclease activity on RNAs containing a consensus 5'ACA3', and it could be neutralized by MazE-dr. The MazF-dr showed a special cleavage preference for the nucleotide present before the ACA sequence with the order by U>A>G>C. MazEF-dr mediated the death of D...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28798740/smrt-sequencing-revealed-mitogenome-characteristics-and-mitogenome-wide-dna-modification-pattern-in-ophiocordyceps-sinensis
#9
Xincong Kang, Liqin Hu, Pengyuan Shen, Rui Li, Dongbo Liu
Single molecule, real-time (SMRT) sequencing was used to characterize mitochondrial (mt) genome of Ophiocordyceps sinensis and to analyze the mt genome-wide pattern of epigenetic DNA modification. The complete mt genome of O. sinensis, with a size of 157,539 bp, is the fourth largest Ascomycota mt genome sequenced to date. It contained 14 conserved protein-coding genes (PCGs), 1 intronic protein rps3, 27 tRNAs and 2 rRNA subunits, which are common characteristics of the known mt genomes in Hypocreales. A phylogenetic tree inferred from 14 PCGs in Pezizomycotina fungi supports O...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28798739/comprehensive-analysis-of-codon-usage-bias-in-seven-epichlo%C3%A3-species-and-their-peramine-coding-genes
#10
Hui Song, Jing Liu, Qiuyan Song, Qingping Zhang, Pei Tian, Zhibiao Nan
Codon usage bias plays an important role in shaping genomes and genes in unicellular species and multicellular species. Here, we first analyzed codon usage bias in seven Epichloë species and their peramine-coding genes. Our results showed that both natural selection and mutation pressure played a role in forming codon usage bias in seven Epichloë species. All seven Epichloë species contained a peramine-coding gene cluster. Interestingly, codon usage bias of peramine-coding genes were not affected by natural selection or mutation pressure...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28798738/zika-virus-an-emerging-worldwide-threat
#11
Irfan A Rather, Jameel B Lone, Vivek K Bajpai, Woon K Paek, Jeongheui Lim
ZIKA virus (ZIKV) poses a severe threat to the world. Recent outbreaks of ZIKV after 2007 along with its quick transmission have made this virus a matter of international concern. The virus shows symptoms that are similar to those caused in the wake of dengue virus (DENV) and other flaviviruses, which makes it difficult to discern the viral infection. Diagnosis is further complicated as the virus cross-reacts with antibodies of other viruses. Currently, molecular diagnosis of the virus is being performed by RT-PCR and IgM-captured enzyme-linked immunosorbent assay (MAC-ELISA)...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28798737/complete-genome-analysis-of-thermus-parvatiensis-and-comparative-genomics-of-thermus-spp-provide-insights-into-genetic-variability-and-evolution-of-natural-competence-as-strategic-survival-attributes
#12
Charu Tripathi, Harshita Mishra, Himani Khurana, Vatsala Dwivedi, Komal Kamra, Ram K Negi, Rup Lal
Thermophilic environments represent an interesting niche. Among thermophiles, the genus Thermus is among the most studied genera. In this study, we have sequenced the genome of Thermus parvatiensis strain RL, a thermophile isolated from Himalayan hot water springs (temperature >96°C) using PacBio RSII SMRT technique. The small genome (2.01 Mbp) comprises a chromosome (1.87 Mbp) and a plasmid (143 Kbp), designated in this study as pTP143. Annotation revealed a high number of repair genes, a squeezed genome but containing highly plastic plasmid with transposases, integrases, mobile elements and hypothetical proteins (44%)...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28798736/escherichia-coli-o157-h7-acid-sensitivity-correlates-with-flocculation-phenotype-during-nutrient-limitation
#13
Kathryn L Kay, Frederick Breidt, Pina M Fratamico, Gian M Baranzoni, Gwang-Hee Kim, Amy M Grunden, Deog-Hwan Oh
Shiga toxin producing Escherichia coli (STEC) strains vary in acid resistance; however, little is known about the underlying mechanisms that result in strain specific differences. Among 25 STEC O157:H7 strains tested, 7 strains flocculated when grown statically for 18 h in minimal salts medium at 37°C, while 18 strains did not. Interestingly, the flocculation phenotype (cells came out of suspension) was found to correlate with degree of acid sensitivity in an assay with 400 mM acetic acid solution at pH 3...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28798735/phenotypic-heterogeneity-in-attachment-of-marine-bacteria-toward-antifouling-copolymers-unraveled-by-afm
#14
Sofiane El-Kirat-Chatel, Aurore Puymege, The H Duong, Perrine Van Overtvelt, Christine Bressy, Lénaïk Belec, Yves F Dufrêne, Maëlle Molmeret
Up to recent years, bacterial adhesion has mostly been evaluated at the population level. Single cell level has improved in the past few years allowing a better comprehension of the implication of individual behaviors as compared to the one of a whole community. A new approach using atomic force microscopy (AFM) to measure adhesion forces between a live bacterium attached via a silica microbead to the AFM tipless cantilever and the surface has been recently developed. The objectives of this study is to examine the bacterial adhesion to a surface dedicated to ship hulls at the population and the cellular level to understand to what extent these two levels could be correlated...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28798734/mixotrophic-phytoflagellate-bacterivory-field-measurements-strongly-biased-by-standard-approaches-a-case-study
#15
Ruth Anderson, Klaus Jürgens, Per J Hansen
Bacterivory among small (≤20 μm) phytoflagellates (SP) is increasingly recognized as a globally relevant phenomenon, impacting a wide range of aspects from primary production levels to marine fisheries. However, to correctly parametrize mixotrophic SP in biogeochemical and food web models, a better understanding of the magnitude and regulation of in situ SP feeding is urgently needed. Current methods to determine SP bacterivory in the field may introduce biases by treating these organisms as equivalent to heterotrophic nanoflagellates (HNF)...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28798733/beef-chicken-and-soy-proteins-in-diets-induce-different-gut-microbiota-and-metabolites-in-rats
#16
Yingying Zhu, Xuebin Shi, Xisha Lin, Keping Ye, Xinglian Xu, Chunbao Li, Guanghong Zhou
Previous studies have paid much attention to the associations between high intake of meat and host health. Our previous study showed that the intake of meat proteins can maintain a more balanced composition of gut bacteria as compared to soy protein diet. However, the associations between dietary protein source, gut bacteria, and host health were still unclear. In this study, we collected colonic contents from the growing rats fed with casein, beef, chicken or soy proteins for 90 days, and analyzed the compositions of gut microbiota and metabolites...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28798732/activation-of-erk-signaling-via-tlr11-induces-il-12p40-production-in-peritoneal-macrophages-challenged-by-neospora-caninum
#17
Xiaoxia Jin, Pengtao Gong, Xichen Zhang, Guojiang Li, Tao Zhu, Mengge Zhang, Jianhua Li
Neospora caninum, an obligate intracellular protozoan parasite, can infect a large variety of vertebrate hosts including the most economically important cattle. Infection with N. caninum is a main cause of abortion in both dairy and beef cattle, which causes great economic losses worldwide. However, the mechanism of host cell infection by N. caninum has not been fully elucidated, especially in terms of inflammatory responses. In this study, the effect of TLR-ERK signaling pathway on the synthesis of pro-inflammatory interleukin-12p40 in mouse peritoneal macrophages (PMϕ) challenged by N...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28798731/mechanisms-and-regulation-of-extracellular-dna-release-and-its-biological-roles-in-microbial-communities
#18
REVIEW
Alejandra L Ibáñez de Aldecoa, Olga Zafra, José E González-Pastor
The capacity to release genetic material into the extracellular medium has been reported in cultures of numerous species of bacteria, archaea, and fungi, and also in the context of multicellular microbial communities such as biofilms. Moreover, extracellular DNA (eDNA) of microbial origin is widespread in natural aquatic and terrestrial environments. Different specific mechanisms are involved in eDNA release, such as autolysis and active secretion, as well as through its association with membrane vesicles. It is noteworthy that in microorganisms, in which DNA release has been studied in detail, the production of eDNA is coordinated by the population when it reaches a certain cell density, and is induced in a subpopulation in response to the accumulation of quorum sensing signals...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28798730/characterization-of-the-culturable-subpopulations-of-lactobacillus-in-the-chicken-intestinal-tract-as-a-resource-for-probiotic-development
#19
Bishnu Adhikari, Young M Kwon
To gain better understanding of the distributions of the culturable Lactobacillus species in the chicken intestinal tract, we collected ceca, and distal ileum from 10 3-weeks-old broiler chickens. Lactobacillus strains from cecal lumen contents (M-CL), and those associated with mucosa of ceca (M-CM) and ileum (M-IM) were recovered on de Man, Rogosa and Sharpe (MRS) agar plates, and used for microbiota analysis. The total cecal content (T-CL) was also used directly for microbiota analysis. We purposefully focused on MRS-recovered populations to gain understanding of the culturable subpopulations of Lactobacillus, since the culturability is an important phenotype in order to exploit the chicken gut microbiota as a resource for development of probiotics...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28798729/in-silico-evolution-of-lysis-lysogeny-strategies-reproduces-observed-lysogeny-propensities-in-temperate-bacteriophages
#20
Vaibhhav Sinha, Akshit Goyal, Sine L Svenningsen, Szabolcs Semsey, Sandeep Krishna
Bacteriophages are the most abundant organisms on the planet and both lytic and temperate phages play key roles as shapers of ecosystems and drivers of bacterial evolution. Temperate phages can choose between (i) lysis: exploiting their bacterial hosts by producing multiple phage particles and releasing them by lysing the host cell, and (ii) lysogeny: establishing a potentially mutually beneficial relationship with the host by integrating their chromosome into the host cell's genome. Temperate phages exhibit lysogeny propensities in the curiously narrow range of 5-15%...
2017: Frontiers in Microbiology
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