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"Microbial ecology"

Yang Song, Yongrong Bian, Fang Wang, Min Xu, Ni Ni, Xinglun Yang, Chenggang Gu, Xin Jiang
The amendment of soil with biochar is an effective soil remediation strategy for organic contaminants. This study investigated the dynamic effects of wheat straw biochar on the bacterial community structure during remediation by high-throughput sequencing. The wheat straw biochar amended into the soil significantly reduced the bioavailability and toxicity of polycyclic aromatic hydrocarbons (PAHs). Biochar amendment helped to maintain the bacterial diversity in the PAH-contaminated soil. The relationship between the immobilization of PAHs and the soil bacterial diversity fit quadratic model...
July 21, 2017: Journal of Agricultural and Food Chemistry
Cristina M Herren, Katherine D McMahon
The ability to predict microbial community dynamics lags behind the quantity of data available in these systems. Most predictive models use only environmental parameters, although a long history of ecological literature suggests that community complexity should also be an informative parameter. Thus, we hypothesize that incorporating information about a community's complexity might improve predictive power in microbial models. Here, we present a new metric, called community 'cohesion,' that quantifies the degree of connectivity of a microbial community...
July 21, 2017: ISME Journal
Conor J Doyle, Paul W O'Toole, Paul D Cotter
Metagenomic-based analyses have the potential to revolutionise our understanding of the microbiology of food production and processing environments. By adopting such approaches it will be possible to more accurately determine sources of microbial contamination, identify critical control points for such contaminants, and select practices that optimise quality and safety. This mini-review will discuss the merits of adopting metagenostic-based approaches, highlight novel insights that they have provided to date and consider how they could be further implemented...
July 20, 2017: Environmental Microbiology
Fabricio Rocha Vieira, John Andrew Pecchia
Substrate preparation (i.e., composting) for Agaricus bisporus cultivation is the most critical point of mushroom production. Among many factors involved in the composting process, the microbial ecology of the system is the underlying drive of composting and can be influenced by composting management techniques. Pasteurization temperature at the beginning of phase II, in theory, may influence the bacterial community and subsequently the "selectivity" and nutrition of the final substrate. Therefore, this hypothesis was tested by simulation in bioreactors under different pasteurization conditions (57 °C/6 h, 60 °C/2 h, and 68 °C/2 h), simulating conditions adopted by many producers...
July 20, 2017: Microbial Ecology
Feifei Wang, Doris van Halem, Gang Liu, Karin Lekkerkerker-Teunissen, Jan Peter van der Hoek
H2O2 residuals from advanced oxidation processes (AOPs) may have critical impacts on the microbial ecology and performance of subsequent biological treatment processes, but little is known. The objective of this study was to evaluate how H2O2 residuals influence sand systems with an emphasis on dissolved organic carbon (DOC) removal, microbial activity change and bacterial community evolution. The results from laboratory batch studies showed that 0.25 mg/L H2O2 lowered DOC removal by 10% while higher H2O2 concentrations at 3 and 5 mg/L promoted DOC removal by 8% and 28%...
July 15, 2017: Chemosphere
Bhagwan N Rekadwad, Chandrahasya N Khobragade
Halophilic bacteria were isolated from oil spill samples collected from West-coast of Goa. Bacteria were isolated from oil studded soil, salt marsh and offshore samples (A, A7, CSM, CB and CM) collected along the West coastline in Goa (India) i.e. Arambol beach, Calanguate beach, Candolim beach and Colva beach on Zobell Marine agar, R2A agar, Mannitol salt agar and Blood agar at temperature 22 to 24 °C. Isolates showed growth in the presence of hydrocarbons (1% phenanthrene and 2% bitumen). Diverse profiles of pigments were observed on different nutrient medium...
August 2017: Data in Brief
Sunayna Dasgupta, Sha Wu, Ramesh Goel
The performance of and the microbial ecology in an integrated lab scale set up comprising of a PN/A bioreactor and an elemental sulfur-supported packed bed autotrophic denitrification (ESSAD) are reported. The PN/A reactor exhibited an average removal rate of 0.56±0.103kgNm(-3)d(-1), whereas the ESSAD reactor removed an average of 0.0018kg NO3(-)-Nm(-3)d(-1). The combined average removal rate was 0.6kgNm(-3)d(-1), yielding an overall total inorganic nitrogen efficiency of 97%. Based on 16S rRNA gene clone libraries from the ESSAD reactor, the extracted Operational Taxonomic Units (OTUs) formed a clade with Thiobacillus denitrificans sp...
June 27, 2017: Bioresource Technology
Marie C Lewis, Claire A Merrifield, Bernard Berger, Olivier Cloarec, Swantje Duncker, Annick Mercenier, Jeremy K Nicholson, Elaine Holmes, Mick Bailey
Inflammatory and metabolic diseases can originate during early-life and have been correlated with shifts in intestinal microbial ecology. Here we demonstrate that minor environmental fluctuations during the early neonatal period had sustained effects on the developing porcine microbiota and host-microbe interface. These inter-replicate effects appear to originate during the first day of life, and are likely to reflect very early microbiota acquisition from the environment. We statistically link early systemic inflammation with later local increases in inflammatory cytokine (IL-17) production, which could have important enteric health implications...
July 13, 2017: Scientific Reports
Roo Vandegrift, Ashley C Bateman, Kyla N Siemens, May Nguyen, Hannah E Wilson, Jessica L Green, Kevin G Van Den Wymelenberg, Roxana J Hickey
The concept of hygiene is rooted in the relationship between cleanliness and the maintenance of good health. Since the widespread acceptance of the germ theory of disease, hygiene has become increasingly conflated with sterilization. In reviewing studies across the hygiene literature (most often hand hygiene), we found that nearly all studies of hand hygiene utilize bulk reduction in bacterial load as a proxy for reduced transmission of pathogenic organisms. This treatment of hygiene may be insufficient in light of recent microbial ecology research, which has demonstrated that humans have intimate and evolutionarily significant relationships with a diverse assemblage of microorganisms (our microbiota)...
July 14, 2017: Microbiome
Toby J Wilkinson, A A Cowan, H E Vallin, L A Onime, Linda B Oyama, S J Cameron, Charlotte Gonot, J M Moorby, K Waddams, V J Theobald, D Leemans, S Bowra, C Nixey, Sharon A Huws
The turkey microbiome is largely understudied, despite its relationship with bird health and growth, and the prevalence of human pathogens such as Campylobacter spp. In this study we investigated the microbiome within the small intestine (SI), caeca (C), large intestine (LI), and cloaca (CL) of turkeys at 6, 10, and 16 weeks of age. Eight turkeys were dissected within each age category and the contents of the SI, C, LI, and CL were harvested. 16S rDNA based QPCR was performed on all samples and samples for the four locations within three birds/age group were sequenced using ion torrent-based sequencing of the 16S rDNA...
2017: Frontiers in Microbiology
Lucas William Mendes, Lucas Peres Palma Braga, Acacio Aparecido Navarrete, Dennis Goss de Souza, Genivaldo Gueiros Zacarias Silva, Siu Mui Tsai
Microbes constitute about a third of the Earth's biomass and are composed by an enormous genetic diversity. In a majority of environments the microbial communities play crucial roles for the ecosystem functioning, where a drastic biodiversity alteration or loss could lead to negative effects on the environment and sustainability. A central goal in microbiome studies is to elucidate the relation between microbial diversity to functions. A better understanding of the relation diversity-function would increase the ability to manipulate that diversity to improve plant and animal health and also setting conservation priorities...
July 6, 2017: Current Issues in Molecular Biology
Alexandra M Linz, Benjamin C Crary, Ashley Shade, Sarah Owens, Jack A Gilbert, Rob Knight, Katherine D McMahon
Bacteria play a key role in freshwater biogeochemical cycling, but long-term trends in freshwater bacterial community composition and dynamics are not yet well characterized. We used a multiyear time series of 16S rRNA gene amplicon sequencing data from eight bog lakes to census the freshwater bacterial community and observe annual and seasonal trends in abundance. The sites that we studied encompassed a range of water column mixing frequencies, which we hypothesized would be associated with trends in alpha and beta diversity...
May 2017: MSphere
Guanghuan Cheng, Mingyang Sun, Jingrang Lu, Xinlei Ge, Huihui Zhang, Xinhua Xu, Liping Lou, Qi Lin
The observed strong sorption of hydrophobic organic contaminants (HOCs) to biochar presents potential implications for HOCs bioavailability and bioaccessibility in sediments, while biochar could impact sediment microbial ecology. However, the comprehensive study on the effects of biochar on HOC biodegradation coupled with bioavailability and microbial ecology are rarely documented. In this paper, the effects of biochar on the biodegradation of nonylphenol (NP) were investigated using 3 different NP concentrations (20, 50 and 500 mg/Kg) in sediments amended with different percentage of rice straw biochar (RC)...
July 5, 2017: Scientific Reports
Naresh S Redhu, Vasudevan Bakthavatchalu, Evan A Conaway, Dror S Shouval, Amy M Tsou, Jeremy A Goettel, Amlan Biswas, Chuanwu Wang, Michael Field, Werner Muller, Andre Bleich, Ning Li, Georg K Gerber, Lynn Bry, James G Fox, Scott B Snapper, Bruce H Horwitz
Infants with defects in the interleukin 10 receptor (IL10R) develop very early onset inflammatory bowel disease. Whether IL10R regulates lamina propria macrophage function during infant development in mice and whether macrophage-intrinsic IL10R signaling is required to prevent colitis in infancy is unknown. Here we show that although signs of colitis are absent in IL10R-deficient mice during the first 2 weeks of life, intestinal inflammation and macrophage dysfunction begin during the 3(rd) week of life, concomitant with weaning and accompanying diversification of the intestinal microbiota...
July 5, 2017: ELife
Sami Ben Said, Dani Or
The metabolic diversity present in microbial communities enables cooperation toward accomplishing more complex tasks than possible by a single organism. Members of a consortium communicate by exchanging metabolites or signals that allow them to coordinate their activity through division of labor. In contrast with monocultures, evidence suggests that microbial consortia self-organize to form spatial patterns, such as observed in biofilms or in soil aggregates, that enable them to respond to gradient, to improve resource interception and to exchange metabolites more effectively...
2017: Frontiers in Microbiology
Junshi Shen, Zhuang Liu, Zhongtang Yu, Weiyun Zhu
Nisin, a bacteriocin, is a potential alternative to antibiotics to modulate rumen fermentation. However, little is known about its impacts on rumen microbes. This study evaluated the effects of nisin (1 and 5 μM) on in vitro rumen fermentation characteristics, microbiota, and select groups of rumen microbes in comparison with monensin (5 μM), one of the most commonly used ionophores in ruminants. Nisin had greater effects than monensin in inhibiting methane production and decreasing acetate/propionate ratio...
2017: Frontiers in Microbiology
Xabier Vázquez-Campos, Andrew S Kinsela, Mark W Bligh, Jennifer J Harrison, Timothy E Payne, T David Waite
During the 1960s, small quantities of radioactive materials were co-disposed with chemical waste at the Little Forest Legacy Site (Sydney, Australia) in three-metre-deep, unlined trenches. Chemical and microbial analyses, including functional and taxonomic information derived from shotgun metagenomics, were collected across a six-week period immediately after a prolonged rainfall event to assess how changing water levels impact upon the microbial ecology and contaminant mobility. Collectively, results demonstrated that oxygen-laden rainwater rapidly altered the redox balance in the trench water, strongly impacting microbial functioning as well as the radiochemistry...
June 30, 2017: Applied and Environmental Microbiology
Siele Ceuppens, Dieter De Coninck, Nadine Bottledoorn, Filip Van Nieuwerburgh, Mieke Uyttendaele
Application of 16S rRNA (gene) amplicon sequencing on food samples is increasingly applied for assessing microbial diversity but may as unintended advantage also enable simultaneous detection of any human pathogens without a priori definition. In the present study high-throughput next-generation sequencing (NGS) of the V1-V2-V3 regions of the 16S rRNA gene was applied to identify the bacteria present on fresh basil leaves. However, results were strongly impacted by variations in the bioinformatics analysis pipelines (MEGAN, SILVAngs, QIIME and MG-RAST), including the database choice (Greengenes, RDP and M5RNA) and the annotation algorithm (best hit, representative hit and lowest common ancestor)...
June 17, 2017: International Journal of Food Microbiology
Erica E Alexeev, Xuan He, Carolyn M Slupsky, Bo Lönnerdal
BACKGROUND: Iron deficiency is common during infancy and therefore iron supplementation is recommended. Recent reports suggest that iron supplementation in already iron replete infants may adversely affect growth, cognitive development, and morbidity. METHODS: Normal and growth restricted rat pups were given iron daily (30 or 150 μg/d) from birth to postnatal day (PD) 20, and followed to PD56. At PD20, hematology, tissue iron, and the hepatic metabolome were measured...
2017: PloS One
Christine Sambles, Karen Moore, Thomas M Lux, Katy Jones, George R Littlejohn, João D Gouveia, Stephen J Aves, David J Studholme, Rob Lee, John Love
Microalgae are widely viewed as a promising and sustainable source of renewable chemicals and biofuels. Botryococcus braunii synthesizes and secretes significant amounts of long-chain (C30 -C40 ) hydrocarbons that can be subsequently converted into gasoline, diesel, and aviation fuel. B. braunii cultures are not axenic and the effects of co-cultured microorganisms on B. braunii growth and hydrocarbon yield are important, but sometimes contradictory. To understand the composition of the B. braunii microbial consortium, we used high throughput Illumina sequencing of metagenomic DNA to profile the microbiota within a well established, stable B...
June 28, 2017: MicrobiologyOpen
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