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Microbial Ecology

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https://www.readbyqxmd.com/read/28808742/a-more-comprehensive-community-of%C3%A2-ammonia-oxidizing-archaea-aoa-revealed-by-genomic-dna-and-rna-analyses-of-amoa-gene-in-subtropical-acidic-forest-soils
#1
Ruo-Nan Wu, Han Meng, Yong-Feng Wang, Wensheng Lan, Ji-Dong Gu
Ammonia-oxidizing bacteria (AOB) and archaea (AOA) are the main nitrifiers which are well studied in natural environments, and AOA frequently outnumber AOB by orders especially in acidic conditions, making AOA the most promising ammonia oxidizers. The phylogeny of AOA revealed in related studies, however, often varied and hardly reach a consensus on functional phylotypes. The objective of this study was to compare ammonia-oxidizing communities by amoA gene and transcript based on both genomic DNA and RNA in extremely acidic forest soils (pH <4...
August 14, 2017: Microbial Ecology
https://www.readbyqxmd.com/read/28803409/comparative-16srdna-gene-based-microbiota-profiles-of-the-pacific-oyster-crassostrea-gigas-and-the-mediterranean-mussel-mytilus-galloprovincialis-from-a-shellfish-farm-ligurian-sea-italy
#2
Luigi Vezzulli, L Stagnaro, C Grande, G Tassistro, L Canesi, C Pruzzo
The pacific oyster Crassostrea gigas and the Mediterranean mussel Mytilus galloprovincialis are two widely farmed bivalve species which show contrasting behaviour in relation to microbial diseases, with C. gigas being more susceptible and M. galloprovincialis being generally resistant. In a recent study, we showed that different susceptibility to infection exhibited by these two bivalve species may depend on their different capability to kill invading pathogens (e.g., Vibrio spp.) through the action of haemolymph components...
August 12, 2017: Microbial Ecology
https://www.readbyqxmd.com/read/28791467/banana-fusarium-wilt-disease-incidence-is-influenced-by-shifts-of-soil-microbial-communities-under-different-monoculture-spans
#3
Zongzhuan Shen, C Ryan Penton, Nana Lv, Chao Xue, Xianfu Yuan, Yunze Ruan, Rong Li, Qirong Shen
The continuous cropping of banana in the same field may result in a serious soil-borne Fusarium wilt disease and a severe yield decline, a phenomenon known as soil sickness. Although soil microorganisms play key roles in maintaining soil health, the alternations of soil microbial community and relationship between these changes and soil sickness under banana monoculture are still unclear. Bacterial and fungal communities in the soil samples collected from banana fields with different monoculture spans were profiled by sequencing of the 16S rRNA genes and internal transcribed spacer using the MiSeq platform to explore the relationship between banana monoculture and Fusarium wilt disease in the present study...
August 8, 2017: Microbial Ecology
https://www.readbyqxmd.com/read/28791465/fungal-decision-to-exploit-or-explore-depends-on-growth-rate
#4
Stavros D Veresoglou, Dongwei Wang, Diana R Andrade-Linares, Stefan Hempel, Matthias C Rillig
No abstract text is available yet for this article.
August 8, 2017: Microbial Ecology
https://www.readbyqxmd.com/read/28785816/season-long-experimental-drought-alters-fungal-community-composition-but-not-diversity-in-a-grassland-soil
#5
Philipp-André Schmidt, Imke Schmitt, Jürgen Otte, Cornelia Bandow, Jörg Römbke, Miklós Bálint, Gregor Rolshausen
Using terrestrial model ecosystems (TMEs), we investigated how reduced moisture conditions impact soil fungal communities from a temperate grassland over the course of an entire season. Starting at about 65% of the soil's maximum water holding capacity (WHCmax), TME soils were adjusted to three moisture levels for 15 weeks: 70% WHCmax, approximating starting conditions, 50% WHCmax, and 30% WHCmax, representing reduced moisture conditions. Diversity and abundances of soil fungi at the start and at the end of the experiment were characterized using Illumina meta-barcoding...
August 7, 2017: Microbial Ecology
https://www.readbyqxmd.com/read/28779297/distribution-of-viruses-inhabiting-heterobasidion-annosum-in-a-pine-dominated-forest-plot-in-southern-finland
#6
Rafiqul Hyder, Tuula Piri, Jarkko Hantula, Heikki Nuorteva, Eeva J Vainio
We investigated the diversity and spatial distribution of viruses infecting strains of the root rot fungus Heterobasidion annosum collected from pine stumps at a heavily infected forest site. Four different partitiviruses were detected in 14 H. annosum isolates at the study site, constituting approximately 29% of all Heterobasidion isolates investigated (N = 48). Two of the viruses detected were new partitiviruses designated here as Heterobasidion partitivirus 16 (HetPV16) and HetPV20, and two were previously known partitiviruses: HetPV7 and HetPV13...
August 5, 2017: Microbial Ecology
https://www.readbyqxmd.com/read/28779296/diel-rhythm-does-not-shape-the-vertical-distribution-of-bacterial-and-archaeal-16s-rrna-transcript-diversity-in-intertidal-sediments-a-mesocosm-study
#7
C Lavergne, M Hugoni, C Hubas, D Debroas, C Dupuy, H Agogué
In intertidal sediments, circadian oscillations (i.e., tidal and diel rhythms) and/or depth may affect prokaryotic activity. However, it is difficult to distinguish the effect of each single force on active community changes in these natural and complex intertidal ecosystems. Therefore, we developed a tidal mesocosm to control the tidal rhythm and test whether diel fluctuation or sediment depth influence active prokaryotes in the top 10 cm of sediment. Day- and nighttime emersions were compared as they are expected to display contrasting conditions through microphytobenthic activity in five different sediment layers...
August 4, 2017: Microbial Ecology
https://www.readbyqxmd.com/read/28779295/impact-of-land-use-change-on-vertical-soil-bacterial-communities-in-sabah
#8
Hoe Seng Tin, Kishneth Palaniveloo, Junia Anilik, Mathavan Vickneswaran, Yukihiro Tashiro, Charles S Vairappan, Kenji Sakai
Decline in forest productivity due to forest conversion is defining the Bornean landscape. Responses of bacterial communities due to land-use changes are vital and could define our understanding of ecosystem functions. This study reports the changes in bacterial community structure in organic soil (0-5 cm; O-Horizon) and organic-mineral soil (5-15 cm; A-Horizon) across Maliau Basin Conservation Area old growth forest (MBOG), Fragment E logged forest (FELF) located in Kalabakan Forest Reserve to Benta Wawasan oil palm plantation (BWOP) using two-step PCR amplicon analysis of bacteria DNA on Illumina Miseq next generation sequencing...
August 4, 2017: Microbial Ecology
https://www.readbyqxmd.com/read/28779294/predictors-of-arbuscular-mycorrhizal-fungal-communities-in-the-brazilian-tropical-dry-forest
#9
Natália M F Sousa, Stavros D Veresoglou, Fritz Oehl, Matthias C Rillig, Leonor C Maia
Arbuscular mycorrhizal fungi (AMF) are symbiotic fungi with a broad distribution, and many taxa have physiological and ecological adaptations to specific environments, including semiarid ecosystems. Our aim was to address regional distribution patterns of AMF communities in such semiarid environments based on spore morphological techniques. We assessed AMF spores at the bottom and top of inselbergs distributed throughout the tropical dry forest in the Northeast region of Brazil. Across 10 replicate inselbergs and the surrounding area, spanning a range of altitude between 140 and 2000 m, we scored the AMF soil diversity and properties in 52 plots...
August 4, 2017: Microbial Ecology
https://www.readbyqxmd.com/read/28779293/erratum-to-airborne-bacterial-diversity-from-the-low-atmosphere-of-greater-mexico-city
#10
Jaime García-Mena, Selvasankar Murugesan, Ashael Alfredo Pérez-Muñoz, Matilde García-Espitia, Otoniel Maya, Monserrat Jacinto-Montiel, Giselle Monsalvo-Ponce, Alberto Piña-Escobedo, Lilianha Domínguez-Malfavón, Marlenne Gómez-Ramírez, Elsa Cervantes-Gonzáles, María Teresa Núñez-Cardona
No abstract text is available yet for this article.
August 4, 2017: Microbial Ecology
https://www.readbyqxmd.com/read/28765980/the-aboveground-vegetation-type-and-underground-soil-property-mediate-the-divergence-of-soil-microbiomes-and-the-biological-interactions
#11
Shu-Hong Wu, Bing-Hong Huang, Chia-Lung Huang, Gang Li, Pei-Chun Liao
The composition of the soil microbiome is influenced by environmental (abiotic) variables and biological interactions (biotic factors). To determine whether the aboveground vegetation and soil physicochemical properties were the main determinant of beta-diversity and biological interaction of soil microbial community, we sampled soils from the temperate coniferous forest and grassland. Clustering of operational taxonomic units was conducted using 16S rRNA gene. We found that the microbial composition of the rhizospheres, in which root exudates influence the microbial environment, show lower alpha-diversity than that of nonroot soils...
August 1, 2017: Microbial Ecology
https://www.readbyqxmd.com/read/28755027/genetic-structure-of-the-rice-blast-pathogen-magnaporthe-oryzae-over-a-decade-in-north-central-california-rice-fields
#12
Deborah Pagliaccia, Ryan Z Urak, Frank Wong, LeAnn I Douhan, Christopher A Greer, Georgios Vidalakis, Greg W Douhan
Rice blast, caused by the ascomycete Magnaporthe oryzae, is one of the most destructive rice diseases worldwide. Even though the disease has been present in California since 1996, there is no data for the pathogen population biology in the state. Using amplified fragment length polymorphisms and mating-type markers, the M. oryzae population diversity was investigated using isolates collected when the disease was first established in California and isolates collected a decade later. While in the 1990 samples, a single multilocus genotype (MLG) was identified (MLG1), over a decade later, we found 14 additional MLGs in the 2000 isolates...
July 28, 2017: Microbial Ecology
https://www.readbyqxmd.com/read/28741266/effect-of-simulated-climate-warming-on-the-ectomycorrhizal-fungal-community-of-boreal-and-temperate-host-species-growing-near-their-shared-ecotonal-range-limits
#13
Joanna Mucha, Kabir G Peay, Dylan P Smith, Peter B Reich, Artur Stefański, Sarah E Hobbie
Ectomycorrhizal (ECM) fungi can influence the establishment and performance of host species by increasing nutrient and water absorption. Therefore, understanding the response of ECM fungi to expected changes in the global climate is crucial for predicting potential changes in the composition and productivity of forests. While anthropogenic activity has, and will continue to, cause global temperature increases, few studies have investigated how increases in temperature will affect the community composition of ectomycorrhizal fungi...
July 25, 2017: Microbial Ecology
https://www.readbyqxmd.com/read/28736793/bacterial-and-archaeal-diversity-in-hypersaline-cyanobacterial-mats-along-a-transect-in-the-intertidal-flats-of-the-sultanate-of-oman
#14
Janina C Vogt, Raeid M M Abed, Dirk C Albach, Katarzyna A Palinska
Hypersaline intertidal zones are highly dynamic ecosystems that are exposed to multiple extreme environmental conditions including rapidly and frequently changing parameters (water, nutrients, temperature) as well as highly elevated salinity levels often caused by high temperatures and evaporation rates. Microbial mats in most extreme settings, as found at the coastline of the subtropical-arid Arabian Peninsula, have been relatively less studied compared to their counterparts around the world. We report, here, for the first time on the diversity of the bacterial and archaeal communities of marine microbial mats along an intertidal transect in a wide salt flat with strongly increased salinity employing Illumina MiSeq technology for amplicon sequencing of 16S rRNA gene fragments...
July 24, 2017: Microbial Ecology
https://www.readbyqxmd.com/read/28735426/diet-versus-phylogeny-a-comparison-of-gut-microbiota-in-captive-colobine-monkey-species
#15
Vanessa L Hale, Chia L Tan, Kefeng Niu, Yeqin Yang, Rob Knight, Qikun Zhang, Duoying Cui, Katherine R Amato
Both diet and host phylogeny shape the gut microbial community, and separating out the effects of these variables can be challenging. In this study, high-throughput sequencing was used to evaluate the impact of diet and phylogeny on the gut microbiota of nine colobine monkey species (N = 64 individuals). Colobines are leaf-eating monkeys that fare poorly in captivity-often exhibiting gastrointestinal (GI) problems. This study included eight Asian colobines (Rhinopithecus brelichi, Rhinopithecus roxellana, Rhinopithecus bieti, Pygathrix nemaeus, Nasalis larvatus, Trachypithecus francoisi, Trachypithecus auratus, and Trachypithecus vetulus) and one African colobine (Colobus guereza)...
July 22, 2017: Microbial Ecology
https://www.readbyqxmd.com/read/28735425/influence-of-host-plant-on-thaumetopoea-pityocampa-gut-bacterial-community
#16
Cinzia P Strano, Antonino Malacrinò, Orlando Campolo, Vincenzo Palmeri
Microbial communities associated to the gut of insects are attracting an increasing interest, mainly because of their role in influencing several host life-traits. The characterization of the gut microbial community is pivotal for understanding insect ecology and, thus, to develop novel pest management strategies. The pine processionary moth, Thaumetopoea pytiocampa (Denis & Schiff.) (Lepidoptera: Thaumetopoeidae), is a severe defoliator of pine forests, able to feed on several pine species. In this work, we performed a metabarcoding analysis to investigate, for the first time, the diversity of the gut bacterial community of pine processionary larvae associated with three different host pine species (Pinus halepensis, Pinus nigra subsp...
July 22, 2017: Microbial Ecology
https://www.readbyqxmd.com/read/28730353/an-exploration-into-the-bacterial-community-under-different-pasteurization-conditions-during-substrate-preparation-composting-phase-ii-for-agaricus-bisporus-cultivation
#17
Fabricio Rocha Vieira, John Andrew Pecchia
Substrate preparation (i.e., composting) for Agaricus bisporus cultivation is the most critical point of mushroom production. Among many factors involved in the composting process, the microbial ecology of the system is the underlying drive of composting and can be influenced by composting management techniques. Pasteurization temperature at the beginning of phase II, in theory, may influence the bacterial community and subsequently the "selectivity" and nutrition of the final substrate. Therefore, this hypothesis was tested by simulation in bioreactors under different pasteurization conditions (57 °C/6 h, 60 °C/2 h, and 68 °C/2 h), simulating conditions adopted by many producers...
July 20, 2017: Microbial Ecology
https://www.readbyqxmd.com/read/28725945/genetic-characteristics-of-coronaviruses-from-korean-bats-in-2016
#18
Saemi Lee, Seong-Deok Jo, Kidong Son, Injung An, Jipseol Jeong, Seung-Jun Wang, Yongkwan Kim, Weonhwa Jheong, Jae-Ku Oem
Bats have increasingly been recognized as the natural reservoir of severe acute respiratory syndrome (SARS), coronavirus, and other coronaviruses found in mammals. However, little research has been conducted on bat coronaviruses in South Korea. In this study, bat samples (332 oral swabs, 245 fecal samples, 38 urine samples, and 57 bat carcasses) were collected at 33 natural bat habitat sites in South Korea. RT-PCR and sequencing were performed for specific coronavirus genes to identify the bat coronaviruses in different bat samples...
July 19, 2017: Microbial Ecology
https://www.readbyqxmd.com/read/28725944/skin-bacterial-community-reorganization-following-metamorphosis-of-the-fire-bellied-toad-bombina-orientalis
#19
Arnaud Bataille, Larisa Lee-Cruz, Binu Tripathi, Bruce Waldman
In organisms with complex life histories, dramatic changes in microbial community structure may occur with host development and immune system maturation. Amphibian host susceptibility to diseases such as chytridiomycosis may be affected by the reorganization of skin microbial community structure that occurs during metamorphosis. We tracked changes in the bacterial communities inhabiting skin of Korean fire-bellied toads (Bombina orientalis) that we infected as tadpoles with different strains of Batrachochytrium dendrobatidis (Bd), the pathogenic fungus that causes chytridiomycosis...
July 19, 2017: Microbial Ecology
https://www.readbyqxmd.com/read/28721506/interaction-between-a-bacterivorous-ciliate-aspidisca-cicada-and-a-rotifer-lecane-inermis-doozers-and-fraggles-in-aquatic-flocs
#20
Aleksandra Walczyńska, Mateusz Sobczyk, Edyta Fiałkowska, Agnieszka Pajdak-Stós, Janusz Fyda, Krzysztof Wiąckowski
Activated sludge is a semi-natural habitat composed of macroaggregates made by flocculating bacteria and inhabited by numerous protozoans and metazoans, creating a complicated interactome. The activated sludge resembles the biological formation of naturally occurring floc habitats, such as "marine snow." So far, these two types of habitat have been analyzed separately, despite their similarities. We examined the effect of a bacterivorous ciliate, Aspidisca cicada, on the quality of the macroaggregate ecosystem by estimating (i) the floc characteristics, (ii) the proliferation of other bacterivores (rotifers), and (iii) the chemical processes...
July 19, 2017: Microbial Ecology
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