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"Microbial ecology"

Isabelle Laforest-Lapointe, Marie-Claire Arrieta
Human-associated microbial communities include prokaryotic and eukaryotic organisms across high-level clades of the tree of life. While advances in high-throughput sequencing technology allow for the study of diverse lineages, the vast majority of studies are limited to bacteria, and very little is known on how eukaryote microbes fit in the overall microbial ecology of the human gut. As recent studies consider eukaryotes in their surveys, it is becoming increasingly clear that eukaryotes play important ecological roles in the microbiome as well as in host health...
March 2018: MSystems
Laura A Hug, Rebecca Co
An enduring theme in microbial ecology is the interdependence of microbial community members. Interactions between community members include provision of cofactors, establishment of redox gradients, and turnover of key nutrients to drive biogeochemical cycles. Pathways canonically conducted by isolated organisms in laboratory cultures are instead collective products of diverse and interchangeable microbes in the environment. Current sequence-based methods provide unprecedented access to uncultivated microorganisms, allowing prediction of previously cryptic roles in biogeochemical cycles and interactions within communities...
March 2018: MSystems
John A Handley, Si Hong Park, Sun Ae Kim, Steven C Ricke
Commercial poultry abattoirs were evaluated to determine the efficacy of the multi-hurdle antimicrobial strategy employed to reduce the microbial load present on incoming broilers from the farm. As next generation sequencing (NGS) has been recently employed to characterize the poultry production system, this study utilized 16S High throughput sequencing (HTS) and quantitative plating data to profile the microbiota of chicken carcasses and determine the efficacy of the multi-hurdle antimicrobial system. Aerobic plate count (APC) and Enterobacteriaceae (EB) microbial counts were quantified from whole bird carcass rinsates (WBCR)...
2018: Frontiers in Microbiology
Yu Xia, Xianghua Wen, Bing Zhang, Yunfeng Yang
Understanding diversity and assembly patterns of microbial communities in activated sludge (AS) is pivotal for addressing fundamental ecological questions and wastewater treatment engineering. Recent applications of molecular methods especially next generation sequencing (NGS) have led to the explosion of information about AS community diversity, including the identification of uncultured taxa, and characterization of low-abundance but environmentally important populations such as antibiotic resistant bacteria and pathogens...
March 15, 2018: Biotechnology Advances
Joseph P Receveur, Jennifer L Pechal, M Eric Benbow, Gary Donato, Tadhgh Rainey, John R Wallace
Ephemeral aquatic habitats and their associated microbial communities (microbiomes) play important roles in the growth and development of numerous aquatic insects, including mosquitoes (Diptera). Biological control agents, such as Bacillus thuringiensis israelensis (Bti) or insect growth regulators (e.g., methoprene), are commonly used to control mosquitoes in these habitats. However, it is unknown how commonly used control compounds affect the mosquito internal microbiome and potentially alter their life history traits...
March 17, 2018: Microbial Ecology
Marie-Cécilia Duvernoy, Thierry Mora, Maxime Ardré, Vincent Croquette, David Bensimon, Catherine Quilliet, Jean-Marc Ghigo, Martial Balland, Christophe Beloin, Sigolène Lecuyer, Nicolas Desprat
Surface colonization underpins microbial ecology on terrestrial environments. Although factors that mediate bacteria-substrate adhesion have been extensively studied, their spatiotemporal dynamics during the establishment of microcolonies remains largely unexplored. Here, we use laser ablation and force microscopy to monitor single-cell adhesion during the course of microcolony formation. We find that adhesion forces of the rod-shaped bacteria Escherichia coli and Pseudomonas aeruginosa are polar. This asymmetry induces mechanical tension, and drives daughter cell rearrangements, which eventually determine the shape of the microcolonies...
March 16, 2018: Nature Communications
Rebekah C Kennedy, Russell R Fling, Michael S Robeson, Arnold M Saxton, Liesel G Schneider, John L Darcy, David A Bemis, Ling Zhao, Jiangang Chen
Widely used as an antimicrobial in antibacterial bar soaps, triclocarban (3,4,4'-trichlorocarbanilide; TCC) is effective against Gram-positive bacteria but shows little efficacy against Gram-negative strains, potentially altering the composition of indigenous microflora within and on the human body. To date, the consequence of continuous or previous nonprescription antimicrobial exposure from compounds in personal care products on commensal microflora is still elusive. Previous research has shown that TCC exposure during gestation and lactation induced dysbiosis of gut microbial communities among exposed dams and neonates...
March 13, 2018: Environmental Science and Pollution Research International
Kaihui Liu, Xiaowei Ding, Xiaofei Tang, Jianjun Wang, Wenjun Li, Qingyun Yan, Zhenghua Liu
Understanding the effects of environmental factors on microbial communities is critical for microbial ecology, but it remains challenging. In this study, we examined the diversity (alpha diversity) and community compositions (beta diversity) of prokaryotes and fungi in hypersaline sediments and salinized soils from northern China. Environmental variables were highly correlated, but they differed significantly between the sediments and saline soils. The compositions of prokaryotic and fungal communities in the hypersaline sediments were different from those in adjacent saline-alkaline soils, indicating a habitat-specific microbial distribution pattern...
2018: Frontiers in Microbiology
Hye-Jin Kim, Hanbyul Kim, Jin Ju Kim, Nu Ri Myeong, Taeyune Kim, Taehun Park, Eunjoo Kim, Ji-Yei Choi, Johnhwan Lee, Susun An, Woo Jun Sul
Given the higher incidence of skin diseases in more urbanized populations and its association with the skin microbiome, we questioned how the skin microbiome differed depending on the degree of urbanization. Skin microbiomes of 231 healthy subjects in five large cities in China varied mainly with environment and socioeconomic status of the cities in question. The differences among microbiomes could be explained by the predominantly niche-based assembly of microbial communities, which was supported by a dominance test, β-null deviation, and edge-length abundance distribution...
March 2018: Science Advances
Lucinda E Doyle, Enrico Marsili
Electroactivity appears to be a phylogenetically diverse trait independent of cell wall classification, with both Gram-negative and Gram-positive electricigens reported. While numerous electricigens have been observed, the majority of research focuses on a select group of highly electroactive species. Under favorable conditions, many microorganisms can be considered electroactive, either through their own mechanisms or exogenously-added mediators, producing a weak current. Such microbes should not be dismissed based on their modest electroactivity...
February 20, 2018: Bioresource Technology
Diane Plouchart, Kim Milferstedt, Guillaume Guizard, Eric Latrille, Jérôme Hamelin
Continuous cultures in chemostats have proven their value in microbiology, microbial ecology, systems biology and bioprocess engineering, among others. In these systems, microbial growth and ecosystem performance can be quantified under stable and defined environmental conditions. This is essential when linking microbial diversity to ecosystem function. Here, a new system to test this link in anaerobic, methanogenic microbial communities is introduced. Rigorously replicated experiments or a suitable experimental design typically require operating several chemostats in parallel...
2018: PloS One
James C Stegen, Tim Johnson, James K Fredrickson, Michael J Wilkins, Allan E Konopka, William C Nelson, Evan V Arntzen, William B Chrisler, Rosalie K Chu, Sarah J Fansler, Emily B Graham, David W Kennedy, Charles T Resch, Malak Tfaily, John Zachara
The original version of this Article contained an error in Fig. 6e, in which the text in the legend was omitted. This has been corrected in both the PDF and HTML versions of the article.
March 7, 2018: Nature Communications
Ian Pepper, John P Brooks, Charles P Gerba
Recently, there has been increased concern about the presence of antibiotic resistant bacteria (ARB) and antibiotic resistant genes (ARG), in treated domestic wastewaters, animal manures and municipal biosolids. The concern is whether these additional sources of ARB contribute to antibiotic resistance levels in the environment, i.e. "environmental antibiotic resistance." ARB and ARG occur naturally in soil and water, and it remains unclear whether the introduction of ARB in liquid and solid municipal and animal wastes via land application have any significant impact on the background levels of antibiotic resistance in the environment, and whether they affect human exposure to ARB...
March 5, 2018: Environmental Science & Technology
Federica Valeriani, Silvia Crognale, Carmela Protano, Gianluca Gianfranceschi, Massimiliano Orsini, Matteo Vitali, Vincenzo Romano Spica
Several factors influence bacteria biodiversity in hot springs. The impact of biotic and abiotic pathways on travertine deposition plays a key role in microbial ecology and in the final composition of the waterborne microbiota. The metabolism of some bacterial groups such as photoautotrophs or lithoautotrophs influences water chemistry, favoring carbonate precipitation processes. The role of microbial mats in mineral precipitation processes is not fully clarified. For the first time, a comprehensive metagenomic analysis has been undertaken in the historical Bullicame hot spring...
March 2, 2018: New Microbiologica
Ai-Hua Zhang, Feng-Jie Lei, Jun-Fan Fu, Ru-Jun Zhou, Lian-Xue Zhang
Ginsenosides are the main active ingredient and allelochemicals of Panax ginseng, and they play an important role in ginseng growth and in ecological adaptation. To study the influence of ginsenosides on soil microbial communities, the method of given exogenous total ginsenosides of different concentrations were used to study the influence of ginsenosides on new forest soil microbial community, evaluate the change of metabolic activity of microbial community and investigate the ecological effect of ginsenosides on soil microbial community...
December 2017: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
Benjamin J Thwaites, Ben van den Akker, Petra J Reeve, Michael D Short, Nirmala Dinesh, Juan Pablo Alvarez-Gaitan, Richard Stuetz
The successful development of aerobic granular sludge (AGS) for secondary wastewater treatment has been linked to a dedicated anaerobic feeding phase, which enables key microbes such as poly-phosphate-accumulating organisms (PAOs) and glycogen-accumulating organisms to gain a competitive advantage over floc-forming organisms. The application of AGS to treat high-saline sewage and its subsequent impacts on microbial ecology, however, are less well understood. In this study, the impacts of high-saline sewage on AGS development, performance and ecology were investigated using molecular microbiology methods...
February 2018: Water Science and Technology: a Journal of the International Association on Water Pollution Research
Jennifer L Wood, Caixian Tang, Ashley E Franks
Understanding how biotic and abiotic factors govern the assembly of rhizosphere-microbial communities is a long-standing goal in microbial ecology. In phytoremediation research, where plants are used to remediate heavy metal-contaminated soils, a deeper understanding of rhizosphere-microbial ecology is needed to fully exploit the potential of microbial-assisted phytoremediation. This study investigated whether Grime's competitor/stress-tolerator/ruderal (CSR) theory could be used to describe the impact of cadmium (Cd) and the presence of a Cd-accumulating plant, Carpobrotus rossii (Haw...
2018: Frontiers in Microbiology
Stilianos Louca, Michael Doebeli, Laura Wegener Parfrey
The 16S ribosomal RNA gene is the most widely used marker gene in microbial ecology. Counts of 16S sequence variants, often in PCR amplicons, are used to estimate proportions of bacterial and archaeal taxa in microbial communities. Because different organisms contain different 16S gene copy numbers (GCNs), sequence variant counts are biased towards clades with greater GCNs. Several tools have recently been developed for predicting GCNs using phylogenetic methods and based on sequenced genomes, in order to correct for these biases...
February 26, 2018: Microbiome
Navdeep K Dhami, Abhijit Mukherjee, Elizabeth L J Watkin
Natural mineral formations are a window into important processes leading to carbon storage and mineralized carbonate structures formed through abiotic and biotic processes. In the current study, we made an attempt to undertake a comprehensive approach to characterize the mineralogical, mechanical, and microbial properties of different kinds of speleothems from karstic caves; with an aim to understand the bio-geo-chemical processes in speleothem structures and their impact on nanomechanical properties. We also investigated the biomineralization abilities of speleothem surface associated microbial communities in vitro ...
2018: Frontiers in Microbiology
A Deveau, G Bonito, J Uehling, M Paoletti, M Becker, S Bindschedler, S Hacquard, V Hervé, J Labbé, O A Lastovetsky, S Mieszkin, L J Millet, B Vajna, P Junier, P Bonfante, B P Krom, S Olsson, J D van Elsas, L Y Wick
Fungi and bacteria are found living together in a wide variety of environments. Their interactions are significant drivers of many ecosystem functions and are important for the health of plants and animals. A large number of fungal and bacterial families are engaged in complex interactions that lead to critical behavioural shifts of the microorganisms ranging from mutualism to pathogenicity. The importance of bacterial-fungal interactions (BFI) in environmental science, medicine and biotechnology has led to the emergence of a dynamic and multidisciplinary research field that combines highly diverse approaches including molecular biology, genomics, geochemistry, chemical and microbial ecology, biophysics and ecological modelling...
February 19, 2018: FEMS Microbiology Reviews
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