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Microbial Ecology

Yan Zhang, Stephanie E Simon, Jeff A Johnson, Michael S Allen
Gastrointestinal microbiota is increasingly recognized as an important component of individual health, and therefore, our ability to quantify its diversity accurately is central for exploring different ways to improve health. Non-invasive sampling methods, such as cloaca swabs, are often used to measure gastrointestinal microbiota diversity within an individual. However, few studies have addressed to what degree differences exist in microbial community composition along the gastrointestinal tract, and measures obtained from the cloaca may not actually represent the diversity present elsewhere in the gastrointestinal tract...
October 18, 2016: Microbial Ecology
Ahmed Abdelfattah, Santa O Cacciola, Saveria Mosca, Rocco Zappia, Leonardo Schena
Citrus greasy spot (CGS) is a disease of citrus with worldwide distribution and recent surveys have revealed a high level of incidence and severity of symptoms of the disease in Sicily, southern Italy. Although Mycosphaerel la citri (anamorph Zasmidium citri-griseum) and other related species are generally considered as causal agents, the etiology of CGS is still unclear. Here, we report the use of an amplicon metagenomic approach to investigate the fungal communities on citrus leaves symptomatic or asymptomatic for CGS from an orchard in Sicily showing typical CGS symptoms...
October 18, 2016: Microbial Ecology
Asma Asemaninejad, R Greg Thorn, Zoë Lindo
Peatlands play an important role in global climate change through sequestration of atmospheric CO2. Climate-driven changes in the structure of fungal communities in boreal peatlands that favor saprotrophic fungi can substantially impact carbon dynamics and nutrient cycling in these crucial ecosystems. In a mesocosm study using a full factorial design, 100 intact peat monoliths, complete with living Sphagnum and above-ground vascular vegetation, were subjected to three climate change variables (increased temperature, reduced water table, and elevated CO2 concentrations)...
October 15, 2016: Microbial Ecology
Xiao-Ming Lu, Chang Chen, Tian-Ling Zheng
Pyrosequencing and metagenomic profiling were used to assess the phylogenetic and functional characteristics of microbial communities residing in sediments collected from the estuaries of Rivers Oujiang (OS) and Jiaojiang (JS) in the western region of the East China Sea. Another sediment sample was obtained from near the shore far from estuaries, used for contrast (CS). Characterization of estuary sediment bacterial communities showed that toxic chemicals potentially reduced the natural variability in microbial communities, while they increased the microbial metabolic enzymes and pathways...
October 15, 2016: Microbial Ecology
Kashif Rahim, Shamim Saleha, Xudong Zhu, Liang Huo, Abdul Basit, Octavio Luiz Franco
A wound is damage of a tissue usually caused by laceration of a membrane, generally the skin. Wound healing is accomplished in three stages in healthy individuals, including inflammatory, proliferative, and remodeling stages. Healing of wounds normally starts from the inflammatory phase and ends up in the remodeling phase, but chronic wounds remain in an inflammatory stage and do not show progression due to some specific reasons. Chronic wounds are classified in different categories, such as diabetic foot ulcer (DFU), venous leg ulcers (VLU) and pressure ulcer (PU), surgical site infection (SSI), abscess, or trauma ulcers...
October 14, 2016: Microbial Ecology
Dorsaf Kerfahi, Ryunosuke Tateno, Koichi Takahashi, HyunJun Cho, Hyoki Kim, Jonathan M Adams
There is considerable interest in understanding the processes of microbial development in volcanic ash. We tested the predictions that there would be (1) a distinctive bacterial community associated with soil development on volcanic ash, including groups previously implicated in weathering studies; (2) a slower increase in bacterial abundance and soil C and N accumulation in cooler climates; and (3) a distinct communities developing on the same substrate in different climates. We set up an experiment, taking freshly fallen, sterilized volcanic ash from Sakurajima volcano, Japan...
October 12, 2016: Microbial Ecology
Jan Hubert, Martina Bicianova, Ondrej Ledvinka, Martin Kamler, Philip J Lester, Marta Nesvorna, Jan Kopecky, Tomas Erban
The honey bee, Apis mellifera, is a globally important species that suffers from a variety of pathogens and parasites. These parasites and pathogens may have sublethal effects on their bee hosts via an array of mechanisms, including through a change in symbiotic bacterial taxa. Our aim was to assess the influence of four globally widespread parasites and pathogens on the honey bee bacteriome. We examined the effects of the ectoparasitic mite Varroa destructor, the fungal pathogens Nosema apis and Nosema ceranae, and the trypanosome Lotmaria passim...
October 11, 2016: Microbial Ecology
Patricia M Valdespino-Castillo, Rocío J Alcántara-Hernández, Martín Merino-Ibarra, Javier Alcocer, Miroslav Macek, Octavio A Moreno-Guillén, Luisa I Falcón
Microbes can modulate ecosystem function since they harbor a vast genetic potential for biogeochemical cycling. The spatial and temporal dynamics of this genetic diversity should be acknowledged to establish a link between ecosystem function and community structure. In this study, we analyzed the genetic diversity of bacterial phosphorus utilization genes in two microbial assemblages, microbialites and bacterioplankton of Lake Alchichica, a semiclosed (i.e., endorheic) system with marked seasonality that varies in nutrient conditions, temperature, dissolved oxygen, and water column stability...
October 10, 2016: Microbial Ecology
Yuyin Yang, Yu Dai, Ningning Li, Bingxin Li, Shuguang Xie, Yong Liu
Anaerobic ammonium-oxidizing (anammox) process can play an important role in freshwater nitrogen cycle. However, the distribution of anammox bacteria in freshwater lake and the associated environmental factors remain essentially unclear. The present study investigated the temporal and spatial dynamics of sediment anammox bacterial populations in eutrotrophic Dianchi Lake and mesotrophic Erhai Lake on the Yunnan Plateau (southwestern China). The remarkable spatial change of anammox bacterial abundance was found in Dianchi Lake, while the relatively slight spatial shift occurred in Erhai Lake...
October 10, 2016: Microbial Ecology
Jeroen A J M van de Water, Rémy Melkonian, Christian R Voolstra, Howard Junca, Eric Beraud, Denis Allemand, Christine Ferrier-Pagès
Gorgonians are key habitat-forming species of Mediterranean benthic communities, but their populations have suffered from mass mortality events linked to high summer seawater temperatures and microbial disease. However, our knowledge on the diversity, dynamics and function of gorgonian-associated microbial communities is limited. Here, we analysed the spatial variability of the microbiomes of five sympatric gorgonian species (Eunicella singularis, Eunicella cavolini, Eunicella verrucosa, Leptogorgia sarmentosa and Paramuricea clavata), collected from the Mediterranean Sea over a scale of ∼1100 km, using next-generation amplicon sequencing of the 16S rRNA gene...
October 10, 2016: Microbial Ecology
Jessica A Lee, Christopher A Francis
Denitrifying bacteria play a critical role in the estuarine nitrogen cycle. Through the transformation of nitrate into nitrogen gas, these organisms contribute to the loss of bioavailable (i.e., fixed) nitrogen from low-oxygen environments such as estuary sediments. Denitrifiers have been shown to vary in abundance and diversity across the spatial environmental gradients that characterize estuaries, such as salinity and nitrogen availability; however, little is known about how their communities change in response to temporal changes in those environmental properties...
October 5, 2016: Microbial Ecology
Débora Farage Knupp Dos Santos, Paula Istvan, Betania Ferraz Quirino, Ricardo Henrique Kruger
Antibiotic resistance has become a major concern for human and animal health, as therapeutic alternatives to treat multidrug-resistant microorganisms are rapidly dwindling. The problem is compounded by low investment in antibiotic research and lack of new effective antimicrobial drugs on the market. Exploring environmental antibiotic resistance genes (ARGs) will help us to better understand bacterial resistance mechanisms, which may be the key to identifying new drug targets. Because most environment-associated microorganisms are not yet cultivable, culture-independent techniques are essential to determine which organisms are present in a given environmental sample and allow the assessment and utilization of the genetic wealth they represent...
October 5, 2016: Microbial Ecology
Antonino Malacrinò, Leonardo Schena, Orlando Campolo, Francesca Laudani, Saveria Mosca, Giulia Giunti, Cinzia Patricia Strano, Vincenzo Palmeri
The occurrence of interaction between insects and fungi is interesting from an ecological point of view, particularly when these interactions involve insect pests and plant pathogens within an agroecosystem. In this study, we aimed to perform an accurate analysis on the fungal microbiota associated to Bactrocera oleae (Rossi) through a metabarcoding approach based on 454 pyrosequencing. From this analysis, we retrieved 43,549 reads that clustered into 128 operational taxonomic units (OTUs), of which 29 resulted in the "core" associate fungi of B...
September 29, 2016: Microbial Ecology
Martina Hujslová, Alena Kubátová, Petra Bukovská, Milada Chudíčková, Miroslav Kolařík
Highly acidic soils (pH < 3) represent an environment which might potentially offer new biotechnologically interesting fungi. Nevertheless, only little data on fungal communities in highly acidic habitats are available. Here, we focused on the diversity of cultivable filamentous microfungi in highly acidic soils (pH < 3) in the Czech Republic. Altogether, 16 soil samples were collected from four sampling sites and were processed by various approaches. In total, 54 fungal taxa were isolated and identified using classical as well as molecular markers...
September 29, 2016: Microbial Ecology
Eugenia Sanchez, Molly C Bletz, Laura Duntsch, Sabin Bhuju, Robert Geffers, Michael Jarek, Anja B Dohrmann, Christoph C Tebbe, Sebastian Steinfartz, Miguel Vences
Amphibian skin provides a habitat for bacterial communities in its mucus. Understanding the structure and function of this "mucosome" in the European fire salamander (Salamandra salamandra) is critical in the context of novel emerging pathogenic diseases. We compare the cutaneous bacterial communities of this species using amplicon-based sequencing of the 16S rRNA V4 region. Across 290 samples, over 4000 OTUs were identified, four of them consistently present in all samples. Larvae and post-metamorphs exhibited distinct cutaneous microbial communities...
September 27, 2016: Microbial Ecology
Obed Hernández-Gómez, Steven J A Kimble, Jeffrey T Briggler, Rod N Williams
Pathogens currently threaten the existence of many amphibian species. In efforts to combat global declines, researchers have characterized the amphibian cutaneous microbiome as a resource for disease management. Characterization of microbial communities has become useful in studying the links between organismal health and the host microbiome. Hellbender salamanders (Cryptobranchus alleganiensis) provide an ideal system to explore the cutaneous microbiome as this species requires extensive conservation management across its range...
September 27, 2016: Microbial Ecology
Suzanne L Ishaq, Stephen P Johnson, Zach J Miller, Erik A Lehnhoff, Sarah Olivo, Carl J Yeoman, Fabian D Menalled
Farming practices affect the soil microbial community, which in turn impacts crop growth and crop-weed interactions. This study assessed the modification of soil bacterial community structure by organic or conventional cropping systems, weed species identity [Amaranthus retroflexus L. (redroot pigweed) or Avena fatua L. (wild oat)], and living or sterilized inoculum. Soil from eight paired USDA-certified organic and conventional farms in north-central Montana was used as living or autoclave-sterilized inoculant into steam-pasteurized potting soil, planted with Am...
September 27, 2016: Microbial Ecology
Lei Wang, Jing Li, Fang Yang, Yaoyao E, Waseem Raza, Qiwei Huang, Qirong Shen
Application of bioorganic fertilizers has been reported to improve crop yields and change soil bacterial community structure; however, little work has been done in apple orchard soils where the biological properties of the soils are being degraded due to long-term application of chemical fertilizers. In this study, we used Illumina-based sequencing approach to characterize the bacterial community in the 0-60-cm soil profile under different fertilizer regimes in the Loess Plateau. The experiment includes three treatments: (1) control without fertilization (CK); (2) application of chemical fertilizer (CF); and (3) application of bioorganic fertilizer and organic-inorganic mixed fertilizer (BOF)...
September 26, 2016: Microbial Ecology
Sigmund Jensen, Sofia A V Fortunato, Friederike Hoffmann, Solveig Hoem, Hans Tore Rapp, Lise Øvreås, Vigdis L Torsvik
During the last decades, our knowledge about the activity of sponge-associated microorganisms and their contribution to biogeochemical cycling has gradually increased. Functional groups involved in carbon and nitrogen metabolism are well documented, whereas knowledge about microorganisms involved in the sulfur cycle is still limited. Both sulfate reduction and sulfide oxidation has been detected in the cold water sponge Geodia barretti from Korsfjord in Norway, and with specimens from this site, the present study aims to identify extant versus active sponge-associated microbiota with focus on sulfur metabolism...
September 23, 2016: Microbial Ecology
Kevin Panke-Buisse, Stacey Lee, Jenny Kao-Kniffin
The collection of microorganisms found in the root zone of soil, termed the rhizosphere microbiome, has been shown to impact plant growth and development. Here, we tease apart the function of the cultivable portion of the microbiome from the whole microbiome in retaining plant traits modified through artificial selection on flowering time. Specifically, the whole microbiome associated with earlier flowering time of Arabidopsis thaliana was cultivated on four types of solid media to create cultivated fractions of the microbiome...
September 21, 2016: Microbial Ecology
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