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Microbial Ecology

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https://www.readbyqxmd.com/read/30413836/variations-in-microbial-diversity-and-metabolite-profiles-of-the-tropical-marine-sponge-xestospongia-muta-with-season-and-depth
#1
Marcela Villegas-Plazas, Melissa L Wos-Oxley, Juan A Sanchez, Dietmar H Pieper, Olivier P Thomas, Howard Junca
Xestospongia muta is among the most emblematic sponge species inhabiting coral reefs of the Caribbean Sea. Besides being the largest sponge species growing in the Caribbean, it is also known to produce secondary metabolites. This study aimed to assess the effect of depth and season on the symbiotic bacterial dynamics and major metabolite profiles of specimens of X. muta thriving in a tropical marine biome (Portobelo Bay, Panamá), which allow us to determine whether variability patterns are similar to those reported for subtropical latitudes...
November 10, 2018: Microbial Ecology
https://www.readbyqxmd.com/read/30411190/detecting-associations-between-ciliated-protists-and-prokaryotes-with-culture-independent-single-cell-microbiomics-a-proof-of-concept-study
#2
Alessia Rossi, Alessio Bellone, Sergei I Fokin, Vittorio Boscaro, Claudia Vannini
Symbioses between prokaryotes and microbial eukaryotes, particularly ciliated protists, have been studied for a long time. Nevertheless, researchers have focused only on a few host genera and species, mainly due to difficulties in cultivating the hosts, and usually have considered a single symbiont at a time. Here, we present a pilot study using a single-cell microbiomic approach to circumvent these issues. Unicellular ciliate isolation followed by simultaneous amplification of eukaryotic and prokaryotic markers was used...
November 8, 2018: Microbial Ecology
https://www.readbyqxmd.com/read/30411189/core-and-dynamic-microbial-communities-of-two-invasive-ascidians-can-host-symbiont-dynamics-plasticity-affect-invasion-capacity
#3
Hila Dror, Lion Novak, James S Evans, Susanna López-Legentil, Noa Shenkar
Ascidians (Chordata, Ascidiacea) are considered to be prominent marine invaders, able to tolerate highly polluted environments and fluctuations in salinity and temperature. Here, we examined the seasonal and spatial dynamics of the microbial communities in the inner-tunic of two invasive ascidians, Styela plicata (Lesueur 1823) and Herdmania momus (Savigny 1816), in order to investigate the changes that occur in the microbiome of non-indigenous ascidians in different environments. Microbial communities were characterized using next-generation sequencing of partial (V4) 16S rRNA gene sequences...
November 8, 2018: Microbial Ecology
https://www.readbyqxmd.com/read/30411188/variations-in-gut-microbiota-of-siberian-flying-squirrels-correspond-to-seasonal-phenological-changes-in-their-hokkaido-subarctic-forest-ecosystem
#4
Po-Yu Liu, An-Chi Cheng, Shiao-Wei Huang, Hao-Wei Chang, Tatsuo Oshida, Hon-Tsen Yu
Gut microbial communities of animals are influenced by diet and seasonal weather changes. Since foraging strategies of wild animals are affected by phenological changes, gut microbial communities would differ among seasons. However, interactions of plant-animal-microbiota with seasonal changes have not been well characterized. Here, we surveyed gut microbial diversity of Siberian flying squirrels (Pteromys volans orii) from a natural forest in Hokkaido during spring and summer of 2013 and 2014. Additionally, we compared microbial diversity to temperature changes and normalized difference vegetation index (NDVI)...
November 8, 2018: Microbial Ecology
https://www.readbyqxmd.com/read/30402724/arbuscular-mycorrhizal-fungi-alter-the-community-structure-of-ammonia-oxidizers-at-high-fertility-via-competition-for-soil-nh-4
#5
Stavros D Veresoglou, Erik Verbruggen, Olga Makarova, India Mansour, Robin Sen, Matthias C Rillig
Nitrification represents a central process in the cycling of nitrogen (N) which in high-fertility habitats can occasionally be undesirable. Here, we explore how arbuscular mycorrhiza (AM) impacts nitrification when N availability is not limiting to plant growth. We wanted to test which of the mechanisms that have been proposed in the literature best describes how AM influences nitrification. We manipulated the growth settings of Plantago lanceolata so that we could control the mycorrhizal state of our plants...
November 6, 2018: Microbial Ecology
https://www.readbyqxmd.com/read/30397796/temporal-development-of-the-culturable-endophytic-fungal-community-in-healthy-grapevine-branches-and-occurrence-of-gtd-associated-fungi
#6
Christian Kraus, Ralf T Voegele, Michael Fischer
Endophytic fungi play an important role in the life of grapevine, either as beneficial microorganisms or as pathogens. Many surveys concerning the fungal grapevine community have been conducted. Nevertheless, exactly how the fungal community arises within the plant and develops from young shoots to mature vines is still unknown. Therefore, it was the aim of this study to investigate the early development of endophytic fungal communities in healthy grapevine branches from 2 months to 8 years old. More than 3800 fungi belonging to 86 operational taxonomic units (OTUs) were isolated from wood samples and assigned to eight age groups...
November 5, 2018: Microbial Ecology
https://www.readbyqxmd.com/read/30397795/early-changes-in-nutritional-conditions-affect-formation-of-synthetic-mutualism-between-chlorella-sorokiniana-and-the-bacterium-azospirillum-brasilense
#7
Oskar A Palacios, Blanca R Lopez, Yoav Bashan, Luz E de-Bashan
The effect of three different nutritional conditions during the initial 12 h of interaction between the microalgae Chlorella sorokiniana UTEX 2714 and the plant growth-promoting bacterium Azospirillum brasilense Cd on formation of synthetic mutualism was assessed by changes in population growth, production of signal molecules tryptophan and indole-3-acetic acid, starch accumulation, and patterns of cell aggregation. When the interaction was supported by a nutrient-rich medium, production of both signal molecules was detected, but not when this interaction began with nitrogen-free (N-free) or carbon-free (C-free) media...
November 5, 2018: Microbial Ecology
https://www.readbyqxmd.com/read/30397794/diversity-and-coding-potential-of-the-microbiota-in-the-photic-and-aphotic-zones-of-tropical-man-made-lake-with-intensive-aquaculture-activities-a-case-study-on-temengor-lake-malaysia
#8
Nyok-Sean Lau, Kamarul Zaman Zarkasi, Amir Shah Ruddin Md Sah, Alexander Chong Shu-Chien
Although freshwater biomes cover less than 1% of the Earth's surface, they have disproportionate ecological significances. Attempts to study the taxonomy and function of freshwater microbiota are currently limited to samples collected from temperate lakes. In this study, we investigated samples from the photic and aphotic of an aquaculture site (disturbed) of Temengor Lake, a tropical lake in comparison with the undisturbed site of the lake using 16S rRNA amplicon and shotgun metagenomic approaches. Vertical changes in bacterial community composition and function of the Temengor Lake metagenomes were observed...
November 5, 2018: Microbial Ecology
https://www.readbyqxmd.com/read/30357428/a-survey-on-plant-viruses-in-natural-brassicaceae-communities-using-rna-seq
#9
Mari Kamitani, Atsushi J Nagano, Mie N Honjo, Hiroshi Kudoh
Studies on plant viruses are biased towards crop diseases and little is known about viruses in natural vegetation. We conducted extensive surveys of plant viruses in wild Brassicaceae plants occurring in three local plant communities in central Japan. We applied RNA-Seq with selective depletion of rRNA, which allowed us to detect infections of all genome-reported viruses simultaneously. Infections of Turnip mosaic virus (TuMV), Cucumber mosaic virus (CMV), Brassica yellows virus, Pelargonium zonate spot virus, and Arabidopsis halleri partitivirus 1 were detected from the two perennial species, Arabidopsis halleri subsp...
October 24, 2018: Microbial Ecology
https://www.readbyqxmd.com/read/30357425/titanium-ions-inhibit-the-bacteria-in-vase-solutions-of-freshly-cut-gerbera-jamesonii-and-extend-the-flower-longevity
#10
Cai-Xia Li, Yan-Fen Fan, Wei Luan, Ya Dai, Ming-Xiu Wang, Chun-Mei Wei, Yan Wang, Xiang Tao, Ping Mao, Xin-Rong Ma
Titanium ions significantly promote plant growth, but the mechanism is still unclear. Cut flowers are ideal materials for the study of plant growth and senescence. In this study, freshly cut Gerbera jamesonii were used to study the effects of titanium ions (8 mg/L) on the flower longevity. Flowering observation showed that the gerbera vase life was significantly prolonged in the presence of titanium ions. Plate colony counts showed that the amounts of bacteria in the vase solution of the control group were approximately 1700 times more than that of titanium ion treatment group...
October 24, 2018: Microbial Ecology
https://www.readbyqxmd.com/read/30349964/changes-in-the-microbial-community-of-pinus-arizonica-saplings-after-being-colonized-by-the-bark-beetle-dendroctonus-rhizophagus-curculionidae-scolytinae
#11
Roman Gonzalez-Escobedo, Carlos I Briones-Roblero, María Fernanda López, Flor N Rivera-Orduña, Gerardo Zúñiga
The death of trees is an ecological process that promotes regeneration, organic matter recycling, and the structure of communities. However, diverse biotic and abiotic factors can disturb this process. Dendroctonus bark beetles (Curculionidae: Scolytinae) are natural inhabitants of pine forests, some of which produce periodic outbreaks, killing thousands of trees in the process. These insects spend almost their entire life cycle under tree bark, where they reproduce and feed on phloem. Tunneling and feeding of the beetles result in the death of the tree and an alteration of the resident microbiota as well as the introduction of microbes that the beetles vector...
October 22, 2018: Microbial Ecology
https://www.readbyqxmd.com/read/30343437/adaptation-to-fasting-in-crucian-carp-carassius-auratus-gut-microbiota-and-its-correlative-relationship-with-immune-function
#12
Tongtong Li, Mengting Qi, François-Joël Gatesoupe, Dongcan Tian, Weihua Jin, Jun Li, Qiang Lin, Shijin Wu, Huan Li
Fasting influences the overall physiology of fish, and the knowledge how the gut microbiota, growth performances, and immune function in response to intermittent and long-term fasting is still insufficient. Here, we characterized the effects of fasting on the host-gut microbiota in crucian carp, which would enhance our insight into physiological adaptation to fasting. To achieve this, we investigated the gut microbial communities of crucian carp with different fasting stress, and corresponding immune and growth parameters...
October 21, 2018: Microbial Ecology
https://www.readbyqxmd.com/read/30341500/comamonadaceae-otu-as-a-remnant-of-an-ancient-microbial-community-in-sulfidic-waters
#13
Edyta Deja-Sikora, Marcin Gołębiewski, Agnieszka Kalwasińska, Arkadiusz Krawiec, Przemysław Kosobucki, Maciej Walczak
Intraterrestrial waters harbor microbial communities being extensively studied to understand microbial processes underlying subsurface ecosystem functioning. This paper provides the results of an investigation on the microbiomes of unique, subsurface sulfidic waters associated with Upper Jurassic, Cretaceous, and Miocene sediments. We used high-throughput 16S rDNA amplicon sequencing to reveal the structure of bacterial and archaeal communities in water samples differing in sulfide content (20-960 mg/dm3 ), salinity (1...
October 19, 2018: Microbial Ecology
https://www.readbyqxmd.com/read/30327827/rickettsiales-occurrence-and-co-occurrence-in-ixodes-ricinus-ticks-in-natural-and-urban-areas
#14
Maciej Kowalec, Tomasz Szewczyk, Renata Welc-Falęciak, Edward Siński, Grzegorz Karbowiak, Anna Bajer
Bacteria of Rickettsiaceae and Anaplasmataceae families include disease agents spread by Ixodes ricinus ticks, the most common tick vector in Europe. The aim of the study was to compare the prevalence and co-infection prevalence of particular tick-transmitted Rickettsiales members: Rickettsia spp. (further referred as Rs), Anaplasma phagocytophilum (Ap), and "Candidatus Neoehrlichia mikurensis" (CNM) in I. ricinus ticks in two types of areas, different in terms of human impact: natural and urban. Using additional data, we aimed at investigating co-occurrence of these Rickettsiales with Borreliella spp...
October 16, 2018: Microbial Ecology
https://www.readbyqxmd.com/read/30317429/prokaryotic-diversity-and-distribution-in-different-habitats-of-an-alpine-rock-glacier-pond-system
#15
I Mania, R Gorra, N Colombo, M Freppaz, M Martin, A M Anesio
Rock glaciers (RG) are assumed to influence the biogeochemistry of downstream ecosystems because of the high ratio of rock:water in those systems, but no studies have considered the effects of a RG inflow on the microbial ecology of sediments in a downstream pond. An alpine RG-pond system, located in the NW Italian Alps has been chosen as a model, and Bacteria and Archaea 16S rRNA genes abundance, distribution and diversity have been assessed by qPCR and Illumina sequencing, coupled with geochemical analyses on sediments collected along a distance gradient from the RG inflow...
October 13, 2018: Microbial Ecology
https://www.readbyqxmd.com/read/30288545/fungal-bacterial-and-archaeal-diversity-in-soils-beneath-native-and-introduced-plants-in-fiji-south-pacific
#16
Gian Maria Niccolò Benucci, Victor Bonito, Gregory Bonito
The Fiji Islands is an archipelago of more than 330 islands located in the tropics of the South Pacific Ocean. Microbial diversity and biogeography in this region is still not understood. Here, we present the first molecular characterization of fungal, bacterial, and archaeal communities in soils from different habitats within the largest Fijian island, Viti Levu. Soil samples were collected from under native vegetation in maritime-, forest-, stream-, grassland-, and casuarina-dominated habitats, as well as from under the introduced agricultural crops sugarcane, cassava, pine, and mahogany...
October 4, 2018: Microbial Ecology
https://www.readbyqxmd.com/read/30288544/genetic-and-genome-analyses-reveal-genetically-distinct-populations-of-the-bee-pathogen-nosema-ceranae-from-thailand
#17
Melissa J Peters, Guntima Suwannapong, Adrian Pelin, Nicolas Corradi
The recent global decline in Western honeybee (Apis mellifera) populations is of great concern for pollination and honey production worldwide. Declining honeybee populations are frequently infected by the microsporidian pathogen Nosema ceranae. This species was originally described in the Asiatic honeybee (Apis cerana), and its identification in global A. mellifera hives could result from a recent host transfer. Recent genome studies have found that global populations of this parasite are polyploid and that humans may have fueled their global expansion...
October 4, 2018: Microbial Ecology
https://www.readbyqxmd.com/read/30284602/mangrove-sediment-microbiome-adaptive-microbial-assemblages-and-their-routed-biogeochemical-processes-in-yunxiao-mangrove-national-nature-reserve-china
#18
Xiaolan Lin, Buce Hetharua, Lian Lin, Hong Xu, Tianling Zheng, Zhili He, Yun Tian
Microorganisms play important roles in mangrove ecosystems. However, we know little about the ecological implications of mangrove microbiomes for high productivity and the efficient circulation of elements in mangrove ecosystems. Here, we focused on mangrove sediments located at the Yunxiao National Mangrove Reserve in southeast China, uncovering the mangrove microbiome using the 16S rRNA gene and shotgun metagenome sequencing approaches. Physicochemical assays characterized the Yunxiao mangrove sediments as carbon (C)-rich, sulfur (S)-rich, and nitrogen (N)-limited environment...
October 4, 2018: Microbial Ecology
https://www.readbyqxmd.com/read/30280234/phenotyping-thermal-responses-of-yeasts-and-yeast-like-microorganisms-at-the-individual-and-population-levels-proof-of-concept-development-and-application-of-an-experimental-framework-to-a-plant-pathogen
#19
Anne-Lise Boixel, Ghislain Delestre, Jean Legeay, Michaël Chelle, Frédéric Suffert
Deciphering the responses of microbial populations to spatiotemporal changes in their thermal environment is instrumental in improving our understanding of their eco-evolutionary dynamics. Recent studies have shown that current phenotyping protocols do not adequately address all dimensions of phenotype expression. Therefore, these methods can give biased assessments of sensitivity to temperature, leading to misunderstandings concerning the ecological processes underlying thermal plasticity. We describe here a new robust and versatile experimental framework for the accurate investigation of thermal performance and phenotypic diversity in yeasts and yeast-like microorganisms, at the individual and population levels...
October 2, 2018: Microbial Ecology
https://www.readbyqxmd.com/read/30276419/evidence-for-gut-associated-serratia-symbiotica-in-wild-aphids-and-ants-provides-new-perspectives-on-the-evolution-of-bacterial-mutualism-in-insects
#20
François Renoz, Inès Pons, Alain Vanderpoorten, Gwennaël Bataille, Christine Noël, Vincent Foray, Valentin Pierson, Thierry Hance
Many insects engage in symbiotic associations with diverse assemblages of bacterial symbionts that can deeply impact on their ecology and evolution. The intraspecific variation of symbionts remains poorly assessed while phenotypic effects and transmission behaviors, which are key processes for the persistence and evolution of symbioses, may differ widely depending on the symbiont strains. Serratia symbiotica is one of the most frequent symbiont species in aphids and a valuable model to assess this intraspecific variation since it includes both facultative and obligate symbiotic strains...
October 1, 2018: Microbial Ecology
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