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microbial ecology

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https://www.readbyqxmd.com/read/28941348/-application-of-synthetic-biology-in-environmental-remediation
#1
Hongzhi Tang, Weiwei Wang, Lige Zhang, Ling Huang, Xinyu Lu, Ping Xu
Environmental problems are the most serious challenges in the 21st century. With the rapid development of modern industry and agriculture, ecological and environmental deterioration have become the most important factors to restrict the sustainable development of social economy. Microbial cells have strong ability for environmental remediation, but their evolution speed is slower than the speed of emerging pollutants. Therefore, the treatment using the synthetic biology is in urgent need. Full understanding of the microbial degradation characteristics (pathways) of refractory organic pollutants with the help of abundant microbial and gene resources in China is important...
March 25, 2017: Sheng Wu Gong Cheng Xue Bao, Chinese Journal of Biotechnology
https://www.readbyqxmd.com/read/28939605/a-distinctive-and-host-restricted-gut-microbiota-in-populations-of-a-cactophilic-drosophila-species
#2
Vincent G Martinson, Javier Carpinteyro-Ponce, Nancy A Moran, Therese A Markow
Almost all animals possess microbial gut communities, but the nature of these communities varies immensely. For example, in social bees and mammals, composition is relatively constant within species and dominated by specialist bacteria that do not live elsewhere; whereas, in laboratory studies and field surveys of Drosophila melanogaster, gut communities consist of bacteria that are ingested with food and that vary widely among individuals and localities. We addressed whether an ecological specialist in its natural habitat has a microbiota dominated by gut specialists or by environmental bacteria...
September 22, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28938903/metagenomic-characterization-of-ambulances-across-the-usa
#3
Niamh B O'Hara, Harry J Reed, Ebrahim Afshinnekoo, Donell Harvin, Nora Caplan, Gail Rosen, Brook Frye, Stephen Woloszynek, Rachid Ounit, Shawn Levy, Erin Butler, Christopher E Mason
BACKGROUND: Microbial communities in our built environments have great influence on human health and disease. A variety of built environments have been characterized using a metagenomics-based approach, including some healthcare settings. However, there has been no study to date that has used this approach in pre-hospital settings, such as ambulances, an important first point-of-contact between patients and hospitals. RESULTS: We sequenced 398 samples from 137 ambulances across the USA using shotgun sequencing...
September 22, 2017: Microbiome
https://www.readbyqxmd.com/read/28934589/low-dietary-protein-and-high-carbohydrate-infant-formula-affects-the-microbial-ecology-of-the-large-intestine-in-neonatal-rats
#4
Wenguang Fan, Haiwei Ren, Yingying Cao, Yonggang Wang, Guicheng Huo
The aim of this study was to investigate the effects of a low dietary protein and high carbohydrate infant formula on the large intestine of neonatal rats. A total of 24 neonatal SD rats (14d old) were randomly assigned to the low-protein, high-carbohydrate infant formula-fed group (IF group) and a human breast milk-fed group (HF group). After 7 days, we selected 6 rats at random from each group to study. No significantly different microbial colonization patterns were observed in the two groups at the phylum level...
September 21, 2017: Canadian Journal of Microbiology
https://www.readbyqxmd.com/read/28932895/taxonomic-and-functional-analyses-of-the-supragingival-microbiome-from-caries-affected-and-caries-free-hosts
#5
Jinzhi He, Qichao Tu, Yichen Ge, Yujia Qin, Bomiao Cui, Xiaoyu Hu, Yuxia Wang, Ye Deng, Kun Wang, Joy D Van Nostrand, Jiyao Li, Jizhong Zhou, Yan Li, Xuedong Zhou
Caries is one of the most prevalent and costly infectious diseases affecting humans of all ages. It is initiated by cariogenic supragingival dental plaques forming on saliva-coated tooth surfaces, yet the etiology remains elusive. To determine which microbial populations may predispose a patient to caries, we report here an in-depth and comprehensive view of the microbial community associated with supragingival dental plaque collected from the healthy teeth of caries patients and healthy adults. We found that microbial communities from caries patients had a higher evenness and inter-individual variations but simpler ecological networks compared to healthy controls despite the overall taxonomic structure being similar...
September 20, 2017: Microbial Ecology
https://www.readbyqxmd.com/read/28930642/microbial-complexes-and-caries-in-17-year-olds-with-and-without-streptococcus-mutans
#6
L Eriksson, P Lif Holgerson, A Esberg, I Johansson
Streptococcus mutans is a key bacterial species in the caries process, which affects >90% of the population worldwide. However, other acidogenic and aciduric/acidophilic species may contribute to disease development. In Sweden, a country with low prevalences of caries and S. mutans, a significant portion of caries-affected adolescents lack detectable levels of S. mutans. The objectives of the present study were 1) to characterize the tooth biofilm and saliva microbiota of adolescents with caries disease, with or without detectable S...
September 1, 2017: Journal of Dental Research
https://www.readbyqxmd.com/read/28929990/microbial-composition-affects-the-performance-of-an-artificial-tephritid-larval-diet
#7
P Rempoulakis, S Sela Saldinger, E Nemny-Lavy, R Pinto, A Birke, D Nestel
The present study investigated the patterns of microorganisms in an artificial larval diet during Dacus ciliatus (Diptera; Tephritidae) larval development. Microbial population contents in the diet of total heterotrophic bacteria, yeast and molds, coliform and lactobacilli, and their dynamics during development, were monitored. Initially, the microbial composition in diet trays failing to produce viable pupae and in trays successfully producing pupae and adult flies was characterized. The failing diet trays contained large populations of lactobacilli that increased during larval development, and low populations of coliforms...
September 20, 2017: Bulletin of Entomological Research
https://www.readbyqxmd.com/read/28929212/an-insight-into-phage-diversity-at-environmental-habitats-using-comparative-metagenomics-approach
#8
Krupa Parmar, Nishant Dafale, Rajesh Pal, Hitesh Tikariha, Hemant Purohit
Bacteriophages play significant role in driving microbial diversity; however, little is known about the diversity of phages in different ecosystems. A dynamic predator-prey mechanism called "kill the winner" suggests the elimination of most active bacterial populations through phages. Thus, interaction between phage and host has an effect on the composition of microbial communities in ecosystems. In this study, secondary phage metagenome data from aquatic habitats: wastewater treatment plant (WWTP), fresh, marine, and hot water spring habitat were analyzed using MG-RAST and STAMP tools to explore the diversity of the viruses...
September 19, 2017: Current Microbiology
https://www.readbyqxmd.com/read/28928718/analysing-microbial-community-composition-through-amplicon-sequencing-from-sampling-to-hypothesis-testing
#9
REVIEW
Luisa W Hugerth, Anders F Andersson
Microbial ecology as a scientific field is fundamentally driven by technological advance. The past decade's revolution in DNA sequencing cost and throughput has made it possible for most research groups to map microbial community composition in environments of interest. However, the computational and statistical methodology required to analyse this kind of data is often not part of the biologist training. In this review, we give a historical perspective on the use of sequencing data in microbial ecology and restate the current need for this method; but also highlight the major caveats with standard practices for handling these data, from sample collection and library preparation to statistical analysis...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28928063/trends-in-the-biomanufacture-of-polyhydroxyalkanoates-with-focus-on-downstream-processing
#10
REVIEW
Maria R Kosseva, Edy Rusbandi
The aim of the current review is to analyze trends in development of an efficient technology for polyhydroxyalkanoate (PHA) biomanufacture highlighting the up-to-date progress on PHA biosynthesis and focusing on the downstream processing. Three main production pathways were identified: through microbial, enzymic, or plant routes. Microbial fermentation processes were predominant, with a wide range of microorganisms, starting materials and culture conditions reported. Largely, two schemes for recovering PHAs from the reaction medium post fermentation were identified: dissolving biomass to separate PHAs granules with strong oxidants, and extracting PHAs directly from the biomass using suitable solvents...
September 16, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/28926606/links-between-plant-and-fungal-diversity-in-habitat-fragments-of-coastal-shrubland
#11
Mia R Maltz, Kathleen K Treseder, Krista L McGuire
Habitat fragmentation is widespread across ecosystems, detrimentally affecting biodiversity. Although most habitat fragmentation studies have been conducted on macroscopic organisms, microbial communities and fungal processes may also be threatened by fragmentation. This study investigated whether fragmentation, and the effects of fragmentation on plants, altered fungal diversity and function within a fragmented shrubland in southern California. Using fluorimetric techniques, we assayed enzymes from plant litter collected from fragments of varying sizes to investigate enzymatic responses to fragmentation...
2017: PloS One
https://www.readbyqxmd.com/read/28926207/seasonal-rather-than-spatial-variability-drives-planktonic-and-benthic-bacterial-diversity-in-a-microtidal-lagoon-and-the-adjacent-open-sea
#12
G M Quero, L Perini, G Pesole, C Manzari, C Lionetti, M Bastianini, M Marini, G M Luna
Coastal lagoons are highly productive ecosystems, which are experiencing a variety of human disturbances at increasing frequency. Bacteria are key ecological players within lagoons, yet little is known about the magnitude, patterns and drivers of diversity in these transitional environments. We carried out a seasonal study in the Venice Lagoon (Italy) and the adjacent sea, to simultaneously explore diversity patterns in different domains (pelagic, benthic) and their spatio-temporal variability, and test the role of environmental gradients in structuring assemblages...
September 19, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28926167/disentangling-environmental-and-host-sources-of-fungal-endophyte-communities-in-an-experimental-beachgrass-study
#13
Aaron S David, Eric W Seabloom, Georgiana May
Disentangling the ecological factors that contribute to the assembly of the microbial symbiont communities within eukaryotic hosts is an ongoing challenge. Broadly speaking, symbiont propagules arrive either from external sources in the environment or from internal sources within the same host individual. To understand the relative importance of these propagule sources to symbiont community assembly, we characterized symbiotic fungal endophyte communities within the roots of three species of beachgrass in a field experiment...
September 19, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28926148/biodiversity-and-species-competition-regulate-the-resilience-of-microbial-biofilm-community
#14
Kai Feng, Zhaojing Zhang, Weiwei Cai, Wenzong Liu, Meiying Xu, Huaqun Yin, Aijie Wang, Zhili He, Ye Deng
The relationship between biodiversity and ecosystem stability is poorly understood in microbial communities. Biofilm communities in small bioreactors called microbial electrolysis cells (MEC) contain moderate species numbers and easy tractable functional traits, thus providing an ideal platform for verifying ecological theories in microbial ecosystems. Here, we investigated the resilience of biofilm communities with a gradient of diversity, and explored the relationship between biodiversity and stability in response to a pH shock...
September 19, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28924189/communication-via-extracellular-vesicles-enhances-viral-infection-of-a-cosmopolitan-alga
#15
Daniella Schatz, Shilo Rosenwasser, Sergey Malitsky, Sharon G Wolf, Ester Feldmesser, Assaf Vardi
Communication between microorganisms in the marine environment has immense ecological impact by mediating trophic-level interactions and thus determining community structure (1) . Extracellular vesicles (EVs) are produced by bacteria (2,3) , archaea (4) , protists (5) and metazoans, and can mediate pathogenicity (6) or act as vectors for intercellular communication. However, little is known about the involvement of EVs in microbial interactions in the marine environment (7) . Here we investigated the signalling role of EVs produced during interactions between the cosmopolitan alga Emiliania huxleyi and its specific virus (EhV, Phycodnaviridae) (8) , which leads to the demise of these large-scale oceanic blooms (9,10) ...
September 18, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/28918349/inhibition-of-anaerobic-digestion-processes-applications-of-molecular-tools
#16
REVIEW
Yamrot M Amha, Muhammad Zohaib Anwar, Andrew Brower, Carsten S Jacobsen, Lauren B Stadler, Tara M Webster, Adam L Smith
Inhibition of anaerobic digestion (AD) due to perturbation caused by substrate composition and/or operating conditions can significantly reduce performance. Such perturbations could be limited by elucidating microbial community response to inhibitors and devising strategies to increase community resilience. To this end, advanced molecular methods are increasingly being applied to study the AD microbiome, a diverse community of microbial populations with complex interactions. This literature review of AD inhibition studies indicates that inhibitory concentrations are highly variable, likely stemming from differences in community structure or activity profile and previous exposure to inhibitors...
September 4, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/28916990/transformation-of-anaerobic-granules-into-aerobic-granules-and-the-succession-of-bacterial-community
#17
Haohao Sun, Ping Yu, Qiaoling Li, Hongqiang Ren, Bo Liu, Lin Ye, Xu-Xiang Zhang
In this study, we demonstrated that anaerobic granular sludge could be successfully transformed into aerobic granular sludge in a continuous up-flow reactor in 45 days. An aerobic microbial community successfully developed in the granules and high organic matter and nitrogen removal performance was achieved. Under an ammonia nitrogen loading rate of 0.8 kg N/(m(3) day), ammonia nitrogen and the total nitrogen removal efficiency of the reactor reached up to 100 and 93%, respectively. An obvious bacterial community shift in granular sludge was observed during the transformation process...
September 15, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28915336/the-microbiome-associated-with-two-synechococcus-ribotypes-at-different-levels-of-ecological-interaction
#18
Cristiana Callieri, Stefano Amalfitano, Gianluca Corno, Andrea Di Cesare, Roberto Bertoni, Ester Eckert
Planktonic cyanobacteria belonging to the genus Synechococcus are ubiquitously distributed in marine and fresh waters, substantially contributing to total carbon fixation on a global scale. While their ecological relevance is acknowledged, increasing resolution in molecular techniques allows disentangling cyanobacteria's role at the micro-scale, where complex microbial interactions may drive the overall community assembly. The interplay between phylogenetically different Synechococcus clades and their associated bacterial communities can affect their ecological fate and susceptibility to protistan predation...
September 15, 2017: Journal of Phycology
https://www.readbyqxmd.com/read/28911664/smog-induces-oxidative-stress-and-microbiota-disruption
#19
REVIEW
Tit-Yee Wong
Smog is created through the interactions between pollutants in the air, fog, and sunlight. Air pollutants, such as carbon monoxide, heavy metals, nitrogen oxides, ozone, sulfur dioxide, volatile organic vapors, and particulate matters, can induce oxidative stress in human directly or indirectly through the formation of reactive oxygen species. The outermost boundary of human skin and mucous layers are covered by a complex network of human-associated microbes. The relation between these microbial communities and their human host are mostly mutualistic...
April 2017: Journal of Food and Drug Analysis
https://www.readbyqxmd.com/read/28904999/linking-spatial-structure-and-community-level-biotic-interactions-through-cooccurrence-and-time-series-modeling-of-the-human-intestinal-microbiota
#20
Eric J de Muinck, Knut E A Lundin, Pål Trosvik
The gastrointestinal (GI) microbiome is a densely populated ecosystem where dynamics are determined by interactions between microbial community members, as well as host factors. The spatial organization of this system is thought to be important in human health, yet this aspect of our resident microbiome is still poorly understood. In this study, we report significant spatial structure of the GI microbiota, and we identify general categories of spatial patterning in the distribution of microbial taxa along a healthy human GI tract...
September 2017: MSystems
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