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microbial ecology

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https://www.readbyqxmd.com/read/28637304/effects-of-alternative-electron-acceptors-on-the-activity-and-community-structure-of-methane-producing-and-consuming-microbes-in-the-sediments-of-two-shallow-boreal-lakes
#1
Antti J Rissanen, Anu Karvinen, Hannu Nykänen, Sari Peura, Marja Tiirola, Anita Mäki, Paula Kankaala
The role of anaerobic CH4 oxidation in controlling lake sediment CH4 emissions remains unclear. Therefore, we tested how relevant EAs (SO42-, NO3-, Fe3+, Mn4+, O2) affect CH4 production and oxidation in the sediments of two shallow boreal lakes. The changes induced to microbial communities by the addition of Fe3+ and Mn4+ were studied using next-generation sequencing targeting the 16S rRNA and methyl-coenzyme M reductase (mcrA) genes and mcrA transcripts. Putative anaerobic CH4 oxidizing archaea (ANME-2D) and bacteria (NC 10) were scarce (up to 3...
June 15, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28637301/eden-evolutionary-dynamics-within-environments
#2
Philipp C Münch, Bärbel Stecher, Alice C McHardy
Summary: Metagenomics revolutionized the field of microbial ecology, giving access to Gb-sized datasets of microbial communities under natural conditions. This enables fine-grained analyses of the functions of community members, studies of their association with phenotypes and environments, as well as of their microevolution and adaptation to changing environmental conditions. However, phylogenetic methods for studying adaptation and evolutionary dynamics are not able to cope with big data...
June 16, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28637162/response-of-antimicrobial-nitrofurazone-degrading-biocathode-communities-to-different-cathode-potentials
#3
Deyong Kong, Hui Yun, Dan Cui, Mengyuan Qi, Chunyan Shao, Dichen Cui, Nanqi Ren, Bin Liang, Aijie Wang
Bioelectrodegradation of various organic pollutants has been extensively studied. However, whether different cathode potentials could alter the antimicrobial-degrading biocathode community structure and composition remain poorly understood. Here, the microbial community structure and composition of the nitrofurans nitrofurazone (NFZ) degrading biocathode in response to different cathode potentials (-0.45±0.01, -0.65±0.01 and -0.86±0.05V vs standard hydrogen electrode, with applied cell voltages of 0.2, 0...
June 13, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/28633514/metagenomic-smrt-sequencing-based-exploration-of-novel-lignocellulose-degrading-capability-in-wood-detritus-from-torreya-nucifera-in-bija-forest-on-jeju-island
#4
Han Na Oh, Tae Kwon Lee, Jae Wan Park, Jee Hyun No, Dockyu Kim, Woo Jun Sul
Lignocellulose, mostly composed of cellulose, hemicellulose and lignin generated through secondary growth of woody plant, is considered as promising resources for bio-fuel. In order to use lignocellulose as a biofuel, the biodegradation besides high-cost chemical treatments were applied, but its knowledge on decomposition of lignocellulose occurring in a natural environment were insufficient. We analyzed 16S rRNA gene and metagenome to understand how the lignocellulose are decomposed naturally in decayed Torreya nucifera (L) of Bija forest (Bijarim) in Gotjawal, an ecologically distinct environment...
June 21, 2017: Journal of Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28631411/function-of-bacterial-community-dynamics-in-the-formation-of-cadaveric-semiochemicals-during-in-situ-carcass-decomposition
#5
Javier Pascual, Christian von Hoermann, Ann-Marie Rottler-Hoermann, Omer Nevo, Alicia Geppert, Johannes Sikorski, Katharina J Huber, Sandra Steiger, Manfred Ayasse, Jörg Overmann
The decomposition of dead mammalian tissue involves a complex temporal succession of epinecrotic bacteria. Microbial activity may release different cadaveric volatile organic compounds which in turn attract other key players of carcass decomposition such as scavenger insects. To elucidate the dynamics and potential functions of epinecrotic bacteria on carcasses, we monitored bacterial communities developing on still-born piglets incubated in different forest ecosystems by combining high-throughput Illumina 16S rRNA sequencing with gas chromatography-mass spectrometry of volatiles...
June 19, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28630293/a-null-model-for-microbial-diversification
#6
Timothy J Straub, Olga Zhaxybayeva
Whether prokaryotes (Bacteria and Archaea) are naturally organized into phenotypically and genetically cohesive units comparable to animal or plant species remains contested, frustrating attempts to estimate how many such units there might be, or to identify the ecological roles they play. Analyses of gene sequences in various closely related prokaryotic groups reveal that sequence diversity is typically organized into distinct clusters, and processes such as periodic selection and extensive recombination are understood to be drivers of cluster formation ("speciation")...
June 19, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28625991/different-amplicon-targets-for-sequencing-based-studies-of-fungal-diversity
#7
Francesca De Filippis, Manolo Laiola, Giuseppe Blaiotta, Danilo Ercolini
Target-gene amplicon sequencing is the most exploited high-throughput sequencing application in microbial ecology. The targets are taxonomically relevant genes with the 16S rRNA being the gold standard for bacteria. As for Fungi, the most commonly used target is the internal transcribed spacer (ITS). However, the uneven ITS length among species may promote preferential amplification and sequencing and incorrect estimation of their abundance. Therefore, the use of different targets is desirable. We evaluated the use of three different target amplicons for the characterization of fungal diversity...
June 16, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28622287/a-niche-for-cyanobacteria-producing-chlorophyll-f-within-a-microbial-mat
#8
Satoshi Ohkubo, Hideaki Miyashita
Acquisition of additional photosynthetic pigments enables photosynthetic organisms to survive in particular niches. To reveal the ecological significance of chlorophyll (Chl) f, we investigated the distribution of Chl and cyanobacteria within two microbial mats. In a 7-mm-thick microbial mat beneath the running water of the Nakabusa hot spring, Japan, Chl f was only distributed 4.0-6.5 mm below the surface, where the intensity of far-red light (FR) was higher than that of photosynthetically active radiation (PAR)...
June 16, 2017: ISME Journal
https://www.readbyqxmd.com/read/28621836/-dietary-advanced-glycation-end-products-modify-gut-microbial-composition-and-partially-increase-colon-permeability-in-rats
#9
Wanting Qu, Xiaojin Yuan, Jinsong Zhao, Yingxiao Zhang, Jing Hu, Jiawei Wang, Juxiu Li
SCOPE: The adverse impacts of dietary advanced glycation end products (AGEs) on health are currently of interest. These compounds are inevitably formed during thermal food processing and make foods less digestible because of protein cross-linking. This study examined not only whether dietary AGEs alter cecal microbiota and their metabolites but also their effects on colon permeability. METHODS AND RESULTS: Sprague-Dawley rats were exposed to a high-AGEs diet (AGEs content was increased by heating food at 125°C/3 h) for 6, 12, or 18 weeks...
June 16, 2017: Molecular Nutrition & Food Research
https://www.readbyqxmd.com/read/28620748/diversity-of-the-most-commonly-reported-facultative-symbionts-in-two-closely-related-aphids-with-different-host-ranges
#10
A S Guidolin, F L Cônsoli
Richness and abundance of facultative symbionts vary strongly with aphid species and genotype, symbiont strain, host plant, biogeography, and a number of abiotic factors. Despite indications that aphids in the same ecological niche show similar levels of facultative symbiont richness, existing reports do not consider the potential role of host plants on aphid microbial community. Little is known about how oligophagy and polyphagy may be influenced by secondary symbiont distribution, mainly because studies on secondary symbiont diversity are biased towards polyphagous aphids from the Northern Hemisphere...
June 15, 2017: Neotropical Entomology
https://www.readbyqxmd.com/read/28620188/ecological-diversity-and-co-occurrence-patterns-of-bacterial-community-through-soil-profile-in-response-to-long-term-switchgrass-cultivation
#11
Shubin He, Lixiang Guo, Mengying Niu, Fuhong Miao, Shuo Jiao, Tianming Hu, Mingxiu Long
Switchgrass (Panicum virgatum L.) is a cellulosic biofuel feedstock and their effects on bacterial communities in deep soils remain poorly understood. To reveal the responses of bacterial communities to long-term switchgrass cultivation through the soil profile, we examined the shift of soil microbial communities with depth profiles of 0-60 cm in five-year switchgrass cultivation and fallow plots. The Illumina sequencing of the 16S rRNA gene showed that switchgrass cultivation significantly increased microbial OTU richness, rather than microbial Shannon diversity; however, there was no significant difference in the structure of microbial communities between switchgrass cultivation and fallow soils...
June 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28618144/thermal-barriers-constrain-microbial-elevational-range-size-via-climate-variability
#12
Jianjun Wang, Janne Soininen
Range size is invariably limited and understanding range size variation is an important objective in ecology. However, microbial range size across geographical gradients remains understudied, especially on mountainsides. Here, we examined patterns of range size of stream microbes (i.e., bacteria and diatoms) and macroorganisms (i.e., macroinvertebrates) along elevational gradients in Asia and Europe. In bacteria, elevational range size showed non-significant phylogenetic signals. In all taxa, there was a positive relationship between niche breadth and species elevational range size, driven by local environmental and climatic variables...
June 15, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28618126/temporal-scale-dependent-interactions-between-multiple-environmental-disturbances-in-microcosm-ecosystems
#13
Aurélie Garnier, Frank Pennekamp, Mélissa Lemoine, Owen L Petchey
Global environmental change has negative impacts on ecological systems, impacting the stable provision of functions, goods and services. Whereas effects of individual environmental changes (e.g. temperature change or change in resource availability) are reasonably well understood, we lack information about if and how multiple changes interact. We examined interactions among four types of environmental disturbance (temperature, nutrient ratio, carbon enrichment, and light) in a fully factorial design using a microbial aquatic ecosystem and observed responses of dissolved oxygen saturation at three temporal scales (resistance, resilience and return time)...
June 15, 2017: Global Change Biology
https://www.readbyqxmd.com/read/28614743/impacts-of-biostimulation-and-bioaugmentation-on-the-performance-and-microbial-ecology-in-methanogenic-reactors-treating-purified-terephthalic-acid-wastewater
#14
Miaomiao Liu, Shanquan Wang, Masaru Konishi Nobu, Benjamin T W Bocher, Scott A Kaley, Wen-Tso Liu
Up-flow anaerobic sludge blanket (UASB) processes treating purified terephthalic acid (PTA) wastewater often face challenges associated with biomass loss. As excessive biomass loss could lead to deterioration of PTA removal, biostimulation and bioaugmentation were often practiced without understanding the microbial impact in UASB. Three laboratory-scale UASB reactors were operated with synthetic PTA wastewater as the feed, with two added with co-substrate (glucose or molasses) on Day 170 for 90 days, and one with external granules on Day 118...
June 4, 2017: Water Research
https://www.readbyqxmd.com/read/28611749/sustaining-rare-marine-microorganisms-macroorganisms-as-repositories-and-dispersal-agents-of-microbial-diversity
#15
Marc Troussellier, Arthur Escalas, Thierry Bouvier, David Mouillot
Recent analyses revealed that most of the biodiversity observed in marine microbial communities is represented by organisms with low abundance but, nonetheless essential for ecosystem dynamics and processes across both temporal and spatial scales. Surprisingly, few studies have considered the effect of macroorganism-microbe interactions on the ecology and distribution dynamics of rare microbial taxa. In this review, we synthesize several lines of evidence that these relationships cannot be neglected any longer...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28611747/microbial-community-and-functional-structure-significantly-varied-among-distinct-types-of-paddy-soils-but-responded-differently-along-gradients-of-soil-depth-layers
#16
Ren Bai, Jun-Tao Wang, Ye Deng, Ji-Zheng He, Kai Feng, Li-Mei Zhang
Paddy rice fields occupy broad agricultural area in China and cover diverse soil types. Microbial community in paddy soils is of great interest since many microorganisms are involved in soil functional processes. In the present study, Illumina Mi-Seq sequencing and functional gene array (GeoChip 4.2) techniques were combined to investigate soil microbial communities and functional gene patterns across the three soil types including an Inceptisol (Binhai), an Oxisol (Leizhou), and an Ultisol (Taoyuan) along four profile depths (up to 70 cm in depth) in mesocosm incubation columns...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28609134/relationships-among-microbial-communities-maternal-cells-oligosaccharides-and-macronutrients-in-human-milk
#17
Janet E Williams, William J Price, Bahman Shafii, Katherine M Yahvah, Lars Bode, Mark A McGuire, Michelle K McGuire
BACKGROUND: Human milk provides all essential nutrients necessary for early life and is rich in nonnutrients, maternally derived (host) cells, and bacteria, but almost nothing is known about the interplay among these components. Research aim: The primary objective of this research was to characterize relationships among macronutrients, maternal cells, and bacteria in milk. METHODS: Milk samples were collected from 16 women and analyzed for protein, lipid, fatty acid, lactose, and human milk oligosaccharide concentrations...
June 1, 2017: Journal of Human Lactation: Official Journal of International Lactation Consultant Association
https://www.readbyqxmd.com/read/28607347/living-microorganisms-change-the-information-shannon-content-of-a-geophysical-system
#18
Fiona H M Tang, Federico Maggi
The detection of microbial colonization in geophysical systems is becoming of interest in various disciplines of Earth and planetary sciences, including microbial ecology, biogeochemistry, geomicrobiology, and astrobiology. Microorganisms are often observed to colonize mineral surfaces, modify the reactivity of minerals either through the attachment of their own biomass or the glueing of mineral particles with their mucilaginous metabolites, and alter both the physical and chemical components of a geophysical system...
June 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28604679/a-stabilized-microbial-ecosystem-of-self-limiting-bacteria-using-synthetic-quorum-regulated-lysis
#19
Spencer R Scott, M Omar Din, Philip Bittihn, Liyang Xiong, Lev S Tsimring, Jeff Hasty
Microbial ecologists are increasingly turning to small, synthesized ecosystems(1-5) as a reductionist tool to probe the complexity of native microbiomes(6,7). Concurrently, synthetic biologists have gone from single-cell gene circuits(8-11) to controlling whole populations using intercellular signalling(12-16). The intersection of these fields is giving rise to new approaches in waste recycling(17), industrial fermentation(18), bioremediation(19) and human health(16,20). These applications share a common challenge(7) well-known in classical ecology(21,22)-stability of an ecosystem cannot arise without mechanisms that prohibit the faster-growing species from eliminating the slower...
June 12, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/28602403/panacea-in-progress-crispr-and-the-future-of-its-biological-research-introduction
#20
REVIEW
Michael Carroll, Xiaohui Zhou
The elucidation of the CRISPR (clustered, regularly interspaced, short palindromic repeats) adaptive immune system endogenous to most microbial life has culminated in progress in a diversity of scientific disciplines. The concurrently promising and eccentric nature of its theoretically plausible applications has wrought enthusiasm in the research community globally, potentiating advancements in human and animal health, ecological stability, and economic wellbeing, that would hitherto be considered the unattainable fancies of a futurist...
August 2017: Microbiological Research
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