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Microbial Ecology

Mariana L Lyra, Molly C Bletz, Célio F B Haddad, Miguel Vences
Bacterial communities associated to eukaryotes play important roles in the physiology, development, and health of their hosts. Here, we examine the intestinal microbiota in tadpoles and aquatic invertebrates (insects and gastropods) to better understand the degree of specialization in the tadpole microbiotas. Samples were collected at the same time in one pond, and the V4 region of the bacterial 16S rRNA gene was sequenced with Illumina amplicon sequencing. We found that bacterial richness and diversity were highest in two studied snail individuals, intermediate in tadpoles, and lowest in the four groups of aquatic insects...
November 20, 2017: Microbial Ecology
J H Baumann, S W Davies, H E Aichelman, K D Castillo
The authors regret that acknowledgment for Dr. Adrian Marchetti was omitted from the manuscript. The correct acknowledgment is written below.
November 17, 2017: Microbial Ecology
Thiago R Schlemper, Johannes A van Veen, Eiko E Kuramae
Rhizosphere microbial community composition can be influenced by different biotic and abiotic factors. We investigated the composition and co-variation of rhizosphere bacterial and fungal communities from two sorghum genotypes (BRS330 and SRN-39) in three different plant growth stages (emergence of the second leaf, (day10), vegetative to reproductive differentiation point (day 35), and at the last visible emerged leaf (day 50)) in two different soil types, Clue field (CF) and Vredepeel (VD). We observed that either bacterial or fungal community had its composition stronger influenced by soil followed by plant growth stage and cultivar...
November 16, 2017: Microbial Ecology
Zhanshan Sam Ma
The original version of this article unfortunately contained a missing image. The flowchart was not captured in PDF version. The original article was corrected.
November 13, 2017: Microbial Ecology
Brodie Sutcliffe, Anthony A Chariton, Andrew J Harford, Grant C Hose, Sarah Stephenson, Paul Greenfield, David J Midgley, Ian T Paulsen
Elevated uranium dose (4 g kg(-1)) causes a shift in billabong sediment communities that result in the enrichment of five bacterial species. These taxa include Geobacter, Geothrix and Dyella species, as well as a novel-potentially predatory-Bacteroidetes species, and a new member of class Anaerolineae (Chloroflexi). Additionally, a population of methanogenic Methanocella species was also identified. Genomic reconstruction and metabolic examination of these taxa reveal a host of divergent life strategies and putative niche partitioning...
November 11, 2017: Microbial Ecology
C S Schmidt, P Lovecká, L Mrnka, A Vychodilová, M Strejček, M Fenclová, K Demnerová
Numerous studies demonstrated that endophytic microbes can promote plant growth and increase plant stress resistance. We aimed at isolating poplar endophytes able to increase their hosts' fitness both in nutrient-limited and polluted environments. To achieve this goal, endophytic bacteria and fungi were isolated from roots and leaves of hybrid poplars (Populus nigra × P. maximowiczii clone Max-4) on an unpolluted and a risk element-polluted site in the Czech Republic and subsequently screened by a number of in vitro tests...
November 10, 2017: Microbial Ecology
Andreas H Keller, Sabine Kleinsteuber, Carsten Vogt
Benzene mineralization under nitrate-reducing conditions was successfully established in an on-site reactor continuously fed with nitrate and sulfidic, benzene-containing groundwater extracted from a contaminated aquifer. Filling material from the reactor columns was used to set up anoxic enrichment cultures in mineral medium with benzene as electron donor and sole organic carbon source and nitrate as electron acceptor. Benzene degradation characteristics and community composition under nitrate-reducing conditions were monitored and compared to those of a well-investigated benzene-mineralizing consortium enriched from the same column system under sulfate-reducing conditions...
November 9, 2017: Microbial Ecology
Jun Zeng, Ju-Pei Shen, Jun-Tao Wang, Hang-Wei Hu, Cui-Jing Zhang, Ren Bai, Li-Mei Zhang, Ji-Zheng He
Climate change is projected to have impacts on precipitation and temperature regimes in drylands of high elevation regions, with especially large effects in the Qinghai-Tibetan Plateau. However, there was limited information about how the projected climate change will impact on the soil microbial community and their activity in the region. Here, we present results from a study conducted across 72 soil samples from 24 different sites along a temperature and precipitation gradient (substituted by aridity index ranging from 0...
November 9, 2017: Microbial Ecology
Patrícia Pereira Gomes, Verónica Ferreira, Alan M Tonin, Adriana Oliveira Medeiros, José Francisco Gonçalves Júnior
Aquatic ecosystems worldwide have been substantially altered by human activities, which often induce changes in multiple factors that can interact to produce complex effects. Here, we evaluated the combined effects of dissolved nutrients (nitrogen [N] and phosphorus [P]; three levels: concentration found in oligotrophic streams in the Cerrado biome, 10× and 100× enriched) and oxygen (O2; three levels: hypoxic [4% O2], depleted [55% O2], and saturated [96% O2]) on plant litter decomposition and associated fungal decomposers in laboratory microcosms simulating stream conditions under distinct scenarios of water quality deterioration...
November 9, 2017: Microbial Ecology
Douglas C Woodhams, Brandon C LaBumbard, Kelly L Barnhart, Matthew H Becker, Molly C Bletz, Laura A Escobar, Sandra V Flechas, Megan E Forman, Anthony A Iannetta, Maureen D Joyce, Falitiana Rabemananjara, Brian Gratwicke, Miguel Vences, Kevin P C Minbiole
Symbiotic bacteria can produce secondary metabolites and volatile compounds that contribute to amphibian skin defense. Some of these symbionts have been used as probiotics to treat or prevent the emerging disease chytridiomycosis. We examined 20 amphibian cutaneous bacteria for the production of prodigiosin or violacein, brightly colored defense compounds that pigment the bacteria and have characteristic spectroscopic properties making them readily detectable, and evaluated the antifungal activity of these compounds...
November 9, 2017: Microbial Ecology
Alina S Grigorescu, François Renoz, Ahmed Sabri, Vincent Foray, Thierry Hance, Philippe Thonart
Microorganism communities that live inside insects can play critical roles in host development, nutrition, immunity, physiology, and behavior. Over the past decade, high-throughput sequencing reveals the extraordinary microbial diversity associated with various insect species and provides information independent of our ability to culture these microbes. However, their cultivation in the laboratory remains crucial for a deep understanding of their physiology and the roles they play in host insects. Aphids are insects that received specific attention because of their ability to form symbiotic associations with a wide range of endosymbionts that are considered as the core microbiome of these sap-feeding insects...
November 9, 2017: Microbial Ecology
John P DeLong, Zeina Al-Ameeli, Shelby Lyon, James L Van Etten, David D Dunigan
Many chloroviruses replicate in endosymbiotic zoochlorellae that are protected from infection by their symbiotic host. To reach the high virus concentrations that often occur in natural systems, a mechanism is needed to release zoochlorellae from their hosts. We demonstrate that the ciliate predator Didinium nasutum foraging on zoochlorellae-bearing Paramecium bursaria can release live zoochlorellae from the ruptured prey cell that can then be infected by chloroviruses. The catalysis process is very effective, yielding roughly 95% of the theoretical infectious virus yield as determined by sonication of P...
November 8, 2017: Microbial Ecology
Santiago Cadena, José Q García-Maldonado, Nguyen E López-Lozano, Francisco J Cervantes
Methanogenesis and sulfate reduction are important microbial processes in hypersaline environments. However, key aspects determining substrate competition between these microbial processes have not been well documented. We evaluated competitive and non-competitive substrates for stimulation of both processes through microcosm experiments of hypersaline microbial mat samples from Guerrero Negro, Baja California Sur, Mexico, and we assessed the effect of these substrates on the microbial community composition...
November 8, 2017: Microbial Ecology
Adriane Clark Jones, K David Hambright, David A Caron
Microbial communities are comprised of complex assemblages of highly interactive taxa. We employed network analyses to identify and describe microbial interactions and co-occurrence patterns between microbial eukaryotes and bacteria at two locations within a low salinity (0.5-3.5 ppt) lake over an annual cycle. We previously documented that the microbial diversity and community composition within Lake Texoma, southwest USA, were significantly affected by both seasonal forces and a site-specific bloom of the harmful alga, Prymnesium parvum...
November 7, 2017: Microbial Ecology
Jiayan Li, Daiwen Chen, Bing Yu, Jun He, Ping Zheng, Xiangbing Mao, Jie Yu, Junqiu Luo, Gang Tian, Zhiqing Huang, Yuheng Luo
Fungi are often ignored in studies on gut microbes because of their low level of presence (making up only 0.1% of the total microorganisms) in the gastrointestinal tract (GIT) of monogastric animals. Recent studies using novel technologies such as next generation sequencing have expanded our understanding on the importance of intestinal fungi in humans and animals. Here, we provide a comprehensive review on the fungal community, the so-called mycobiome, and their functions from recent studies in humans and mice...
November 6, 2017: Microbial Ecology
Divyashri Baraniya, Paolo Nannipieri, Susanne Kublik, Gisle Vestergaard, Michael Schloter, Anne Schöler
While root exudation follows diurnal rhythms, little is known about the consequences for the microbiome of the rhizosphere. In this study, we used a metatranscriptomic approach to analyze the active microbial communities, before and after sunrise, in the rhizosphere of barley. We detected increased activities of many prokaryotic microbial taxa and functions at the pre-dawn stage, compared to post-dawn. Actinomycetales, Planctomycetales, Rhizobiales, and Burkholderiales were the most abundant and therefore the most active orders in the barley rhizosphere...
November 6, 2017: Microbial Ecology
J H Baumann, S W Davies, H E Aichelman, K D Castillo
Reef-building corals maintain a symbiotic relationship with dinoflagellate algae of the genus Symbiodinium, and this symbiosis is vital for the survival of the coral holobiont. Symbiodinium community composition within the coral host has been shown to influence a coral's ability to resist and recover from stress. A multitude of stressors including ocean warming, ocean acidification, and eutrophication have been linked to global scale decline in coral health and cover in recent decades. Three distinct thermal regimes (highTP, modTP, and lowTP) following an inshore-offshore gradient of declining average temperatures and thermal variation were identified on the Belize Mesoamerican Barrier Reef System (MBRS)...
November 2, 2017: Microbial Ecology
Nina V Kulakova, Maria V Sakirko, Renat V Adelshin, Igor V Khanaev, Ivan A Nebesnykh, Thierry Pérez
Mass mortality events have led to a collapse of the sponge fauna of Lake Baikal. We describe a new Brown Rot Syndrome affecting the endemic species Lubomirskia baicalensis. The main symptoms are the appearance of brown patches at the sponge surface, necrosis, and cyanobacterial fouling. 16S rRNA gene sequencing was used to characterize the bacterial community of healthy versus diseased sponges, in order to identify putative pathogens. The relative abundance of 89 eubacterial OTUs out of 340 detected has significantly changed between healthy and diseased groups...
November 2, 2017: Microbial Ecology
Corey D Russo, David W Weller, Karen E Nelson, Susan J Chivers, Manolito Torralba, D Jay Grimes
The dermis of cetaceans is in constant contact with microbial species. Although the skin of the bottlenose dolphin provides adequate defense against most disease-causing microbes, it also provides an environment for microbial community development. Microbial community uniqueness and richness associated with bottlenose dolphin skin is a function of varying habitats and changing environmental conditions. The current study uses ribosomal DNA as a marker to identify bacteria found on the skin of coastal and offshore bottlenose dolphins off of Southern California...
October 28, 2017: Microbial Ecology
Alexandra Schwarz, Eric M Adetutu, Albert L Juhasz, Arturo Aburto-Medina, Andrew S Ball, Esmaeil Shahsavari
Phenanthrene mineralisation studies in both pristine and contaminated sandy soils were undertaken through detailed assessment of the activity and diversity of the microbial community. Stable isotope probing (SIP) was used to assess and identify active (13)C-labelled phenanthrene degraders. Baseline profiling indicated that there was little difference in fungal diversity but a significant difference in bacterial diversity dependent on contamination history. Identification of dominant fungal and bacterial species highlighted the presence of organisms capable of degrading various petroleum-based compounds together with other anthropogenic compounds, regardless of contamination history...
October 27, 2017: Microbial Ecology
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