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Microbial Ecology

Irina V Kurina, Hongkai Li
This study focusses on the ecology of testate amoeba species in peatlands of the southern taiga of Western Siberia. To estimate the influence of the trophic state of mires on species optima related to water table depth, a separate study of three calibration datasets including ombrotrophic, minerotrophic and the combined habitats was conducted. In the datasets obtained separately from ombrotrophic and minerotrophic mires, the water table depth was the main factor affecting testate amoeba assemblages. However, the trophic state (specifically pH and ash content) was more important factor in the combined dataset, including all of the studied mires...
May 19, 2018: Microbial Ecology
Erika García-Bonilla, Pedro F B Brandão, Thierry Pérez, Howard Junca
Sponges harbor characteristic microbiomes derived from symbiotic relationships shaping their lifestyle and survival. Haliclona fulva is encrusting marine sponge species dwelling in coralligenous accretions or semidark caves of the Mediterranean Sea and the near Atlantic Ocean. In this work, we characterized the abundance and core microbial community composition found in specimens of H. fulva by means of electron microscopy and 16S amplicon Illumina sequencing. We provide evidence of its low microbial abundance (LMA) nature...
May 15, 2018: Microbial Ecology
Chu Peng, He Wang, Yingying Jiang, Jinhua Yang, Hangxian Lai, Xiaomin Wei
Thus far, no studies have investigated the soil microbial diversity over an elevational gradient in Taibai Mountain, the central massif of the Qinling Mountain Range. Here, we used Illumina sequencing and quantitative PCR of the 16S rRNA gene to assess the diversity and abundance of bacterial communities along an elevational gradient in representative vegetation soils in Taibai Mountain. We identified the soil, climate, and vegetation factors driving the variations in soil bacterial community structure by Pearson correlation and redundancy analysis...
May 10, 2018: Microbial Ecology
Vincent Delafont, Marie-Helene Rodier, Elodie Maisonneuve, Estelle Cateau
Free-living amoebae are protists that are widely distributed in the environment including water, soil, and air. Although the amoebae of the genus Acanthamoeba are still the most studied, other species, such as Vermamoeba vermiformis (formerly Hartmannella vermiformis), are the subject of increased interest. Found in natural or man-made aquatic environments, V. vermiformis can support the multiplication of other microorganisms and is able to harbor and potentially protect pathogenic bacteria or viruses. This feature is to be noted because of the presence of this thermotolerant amoeba in hospital water networks...
May 8, 2018: Microbial Ecology
Nerea Arias-Jayo, Leticia Abecia, Laura Alonso-Sáez, Andoni Ramirez-Garcia, Alfonso Rodriguez, Miguel A Pardo
Energy-dense foods and overnutrition represent major starting points altering lipid metabolism, systemic inflammation and gut microbiota. The aim of this work was to investigate the effects of a high-fat diet (HFD) over a period of 25 days on intestinal microbiota and inflammation in zebrafish. Microbial composition of HFD-fed animals was analysed and compared to controls by 16S rRNA sequencing and quantitative PCR. The expression level on several genes related to inflammation was tested. Furthermore, microscopic assessment of the intestine was performed in both conditions...
May 7, 2018: Microbial Ecology
Baoqin Li, Zhe Li, Xiaoxu Sun, Qi Wang, Enzong Xiao, Weimin Sun
Autotrophs that inhabit soils receive less attention than their counterparts in other ecosystems, such as deep-sea and subsurface sediments, due to the low abundance of autotrophs in soils with high organic contents. However, the karst rocky desertification region is a unique ecosystem that may have a low level of organic compounds. Therefore, we propose that karst rocky desertification ecosystems may harbor diverse autotrophic microbial communities. In this study, DNA-SIP was employed to identify the chemolithoautotrophic bacteria inhabiting three soil types (i...
May 4, 2018: Microbial Ecology
Anne Houles, Bryan Vincent, Magali David, Marc Ducousso, Antoine Galiana, Farid Juillot, Laure Hannibal, Fabian Carriconde, Emmanuel Fritsch, Philippe Jourand
This study aims to characterize the ectomycorrhizal (ECM) communities associated with Acacia spirorbis, a legume tree widely spread in New Caledonia that spontaneously grows on contrasted edaphic constraints, i.e. calcareous, ferralitic and volcano-sedimentary soils. Soil geochemical parameters and diversity of ECM communities were assessed in 12 sites representative of the three mains categories of soils. The ectomycorrhizal status of Acacia spirorbis was confirmed in all studied soils, with a fungal community dominated at 92% by Basidiomycota, mostly represented by/tomentella-thelephora (27...
May 1, 2018: Microbial Ecology
Attila D Sándor, Mihály Földvári, Aleksandra I Krawczyk, Hein Sprong, Alexandra Corduneanu, Levente Barti, Tamás Görföl, Péter Estók, Dávid Kováts, Sándor Szekeres, Zoltán László, Sándor Hornok, Gábor Földvári
Bats are important zoonotic reservoirs for many pathogens worldwide. Although their highly specialized ectoparasites, bat flies (Diptera: Hippoboscoidea), can transmit Bartonella bacteria including human pathogens, their eco-epidemiology is unexplored. Here, we analyzed the prevalence and diversity of Bartonella strains sampled from 10 bat fly species from 14 European bat species. We found high prevalence of Bartonella spp. in most bat fly species with wide geographical distribution. Bat species explained most of the variance in Bartonella distribution with the highest prevalence of infected flies recorded in species living in dense groups exclusively in caves...
April 29, 2018: Microbial Ecology
Faizan Saleem, Atif Mustafa, Junaid Ahmed Kori, Muhammad Saad Hussain, M Kamran Azim
Supplying safe water to consumers is vital for protection of public health. With population of > 15 million, Karachi is the main economical hub of Pakistan. Lake Keenjhar serves as the main source of fresh water while Hub dam is the secondary water reservoir for Karachi. In this study, bacterial community of the drinking water supply system (DWSS) of Karachi was studied from source to tap using metagenomics approach. For this purpose, we collected 41 water samples from different areas of the city (n = 38) and water reservoirs (n = 3)...
April 24, 2018: Microbial Ecology
Giorgia Gioacchini, Elia Ciani, Andrea Pessina, Cinzia Cecchini, Stefania Silvi, Ana Rodiles, Daniel L Merrifield, Ike Olivotto, Oliana Carnevali
The original version of this article unfortunately contained mistakes in Authors First name/Family name order. Please refer to this paper as Gioacchini et al. and not as Giorgia et al.
April 23, 2018: Microbial Ecology
Marta A Moitinho, Laura Bononi, Danilo T Souza, Itamar S Melo, Rodrigo G Taketani
In this study, 16S rRNA gene amplicon sequencing was used to assess bacterial diversity and dynamics throughout different stages of leaves decomposition of three plant species (Rhizophora mangle, Laguncularia racemosa, and Avicennia schaueriana) in three distinct mangroves of São Paulo state, Brazil. The experiments were conducted in microcosms. Phylogenetic diversity (Faiths' PD) index showed differences between samples and suggested that some treatments like R. mangle increased their bacterial diversity through time...
April 23, 2018: Microbial Ecology
Erica B Young, Jessica Sielicki, Jacob J Grothjan
Carnivorous pitcher plants Sarracenia purpurea host diverse eukaryotic and bacterial communities which aid in insect prey digestion, but little is known about the functional processes mediated by the microbial communities. This study aimed to connect pitcher community diversity with functional nutrient transformation processes, identifying bacterial taxa, and measuring regulation of hydrolytic enzyme activity in response to prey and alternative nutrient sources. Genetic analysis identified diverse bacterial taxa known to produce hydrolytic enzyme activities...
April 20, 2018: Microbial Ecology
Jiarui Zeng, Ting Xu, Lidan Cao, Chunyi Tong, Xuan Zhang, Dingyi Luo, Shuping Han, Pei Pang, Weibin Fu, Jindong Yan, Xuanming Liu, Yonghua Zhu
Rice blast caused by Magnaporthe oryzae severely impacts global rice yield stability. The rice endophyte Streptomyces sporocinereus OsiSh-2, with strong antagonistic activity towards M. oryzae, has been reported in our previous study. To decipher the model of the antagonistic action of OsiSh-2 towards M. oryzae, we compared the iron-capturing abilities of these two strains. The cultivation of OsiSh-2 and a M. oryzae strain under iron-rich and iron-starved conditions showed that M. oryzae depended more on iron supplementation for growth and development than did OsiSh-2...
April 20, 2018: Microbial Ecology
J R Saucedo-Carabez, Randy C Ploetz, J L Konkol, D Carrillo, R Gazis
Nutritional mutualisms that ambrosia beetles have with fungi are poorly understood. Although these interactions were initially thought to be specific associations with a primary symbiont, there is increasing evidence that some of these fungi are associated with, and move among, multiple beetle partners. We examined culturable fungi recovered from mycangia of ambrosia beetles associated with trees of Persea humilis (silk bay, one site) and P. americana (avocado, six commercial orchards) that were affected by laurel wilt, an invasive disease caused by a symbiont, Raffaelea lauricola, of an Asian ambrosia beetle, Xyleborus glabratus...
April 20, 2018: Microbial Ecology
Víctor Hernando-Morales, Marta M Varela, David M Needham, Jacob Cram, Jed A Fuhrman, Eva Teira
Analysis of seasonal patterns of marine bacterial community structure along horizontal and vertical spatial scales can help to predict long-term responses to climate change. Several recent studies have shown predictable seasonal reoccurrence of bacterial assemblages. However, only a few have assessed temporal variability over both horizontal and vertical spatial scales. Here, we simultaneously studied the bacterial community structure at two different locations and depths in shelf waters of a coastal upwelling system during an annual cycle...
April 19, 2018: Microbial Ecology
Alice C Ortmann, Pamela M Brannock, Lei Wang, Kenneth M Halanych
Meiobenthic community structure in the northern Gulf of Mexico has been shown to be driven by geographical differences due to inshore-offshore gradients and location relative to river discharge. Samples collected along three transects spanning Mobile Bay, Alabama, showed significant differences in meiobenthic communities east of the bay compared to those sampled from the west. In contrast, analysis of bacterial and archaeal communities from the same sediment samples shows that the inshore-offshore gradient has minimal impact on their community structure...
April 17, 2018: Microbial Ecology
Lubov B Glukhova, Yulia A Frank, Ehrzena V Danilova, Marat R Avakyan, David Banks, Olli H Tuovinen, Olga V Karnachuk
The role of fungi in metal cycling in acidic environments has been little explored to date. In this study, two acid-tolerant and metal-resistant Penicillium isolates, strains ShG4B and ShG4C, were isolated from a mine site in the Transbaikal area of Siberia (Russia). Waters at the mine site were characterized by extremely high metal concentrations: up to 18 g l-1 Fe and > 2 g l-1 each of Cu, Zn, Al, and As. Both isolates were identified as Penicillium spp. by phylogenetic analyses and they grew well in Czapek medium acidified to pH 2...
April 17, 2018: Microbial Ecology
Christina Birnbaum, Andrew Bissett, Francois P Teste, Etienne Laliberté
Long-term soil age gradients are useful model systems to study how changes in nutrient limitation shape communities of plant root mutualists because they represent strong natural gradients of nutrient availability, particularly of nitrogen (N) and phosphorus (P). Here, we investigated changes in the dinitrogen (N2 )-fixing bacterial community composition and diversity in nodules of a single host legume (Acacia rostellifera) across the Jurien Bay chronosequence, a retrogressive 2 million-year-old sequence of coastal dunes representing an exceptionally strong natural soil fertility gradient...
April 16, 2018: Microbial Ecology
Fei Ye, Mao-Hua Ma, Huub J M Op den Camp, Antonis Chatzinotas, Lei Li, Ming-Quan Lv, Sheng-Jun Wu, Yu Wang
Understanding how microorganisms respond to environmental disturbance is one of the key focuses in microbial ecology. Ammonia-oxidizing bacteria (AOB) and archaea (AOA) are responsible for ammonia oxidation which is a crucial step in the nitrogen cycle. Although the physiology, distribution, and activity of AOA and AOB in soil have been extensively investigated, their recovery from a natural disturbance remains largely unknown. To assess the recovery capacities, including resistance and resilience, of AOA and AOB, soil samples were taken from a reservoir riparian zone which experienced periodically water flooding...
April 11, 2018: Microbial Ecology
Sarah A Knutie, Kiyoko M Gotanda
Over the past few decades, studies have demonstrated that the gut microbiota strongly influences the physiology, behavior, and fitness of its host. Such studies have been conducted primarily in humans and model organisms under controlled laboratory conditions. More recently, researchers have realized the importance of placing host-associated microbiota studies into a more ecological context; however, few non-destructive methods have been established to collect fecal samples from wild birds. Here, we present an inexpensive and easy-to-use kit for the non-invasive collection of feces from small birds...
April 5, 2018: Microbial Ecology
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