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"Microbial ecology"

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https://www.readbyqxmd.com/read/29330649/growth-of-leptospirillum-ferriphilum-in-sulfur-medium-in-co-culture-with-acidithiobacillus-caldus
#1
Sarah L Smith, D Barrie Johnson
Leptospirillum ferriphilum and Acidithiobacillus caldus are both thermotolerant acidophilic bacteria that frequently co-exist in natural and man-made environments, such as biomining sites. Both are aerobic chemolithotrophs; L. ferriphilum is known only to use ferrous iron as electron donor, while A. caldus can use zero-valent and reduced sulfur, and also hydrogen, as electron donors. It has recently been demonstrated that A. caldus reduces ferric iron to ferrous when grown aerobically on sulfur. Experiments were carried out which demonstrated that this allowed L...
January 12, 2018: Extremophiles: Life Under Extreme Conditions
https://www.readbyqxmd.com/read/29324293/biofilms-active-substrata-and-me
#2
REVIEW
Bruce E Rittmann
Having worked with biofilms since the 1970s, I know that they are ubiquitous in nature, of great value in water technology, and scientifically fascinating. Biofilms are naturally able to remove BOD, transform N, generate methane, and biodegrade micropollutants. What I also discovered is that biofilms can do a lot more for us in terms of providing environmental services if we give them a bit of help. Here, I explore how we can use active substrata to enable our biofilm partners to provide particularly challenging environmental services...
December 28, 2017: Water Research
https://www.readbyqxmd.com/read/29318631/early-life-gut-microbiome-and-egg-allergy
#3
Mina Fazlollahi, Yoojin Chun, Alexander Grishin, Robert A Wood, A Wesley Burks, Peter Dawson, Stacie M Jones, Donald Y M Leung, Hugh A Sampson, Scott H Sicherer, Supinda Bunyavanich
BACKGROUND: Gut microbiota may play a role in egg allergy. We sought to examine the association between early-life gut microbiota and egg allergy. METHODS: We studied 141 children with egg allergy and controls from the multi-center Consortium of Food Allergy Research study. At enrollment (age 3 to 16 months), fecal samples were collected and clinical evaluation, egg specific IgE measurement, and egg skin prick test were performed. Gut microbiome was profiled by 16S rRNA sequencing...
January 10, 2018: Allergy
https://www.readbyqxmd.com/read/29314490/a-mixture-of-lactobacillus-species-isolated-from-traditional-fermented-foods-promote-recovery-from-antibiotic-induced-intestinal-disruption-in-mice
#4
Ying Shi, Xi Zhao, Zhao Jianxin, Zhang Hao, Qixiao Zhai, Arjan Narbad, Wei Chen
AIMS: This study evaluated the antibiotic-induced changes in microbial ecology, intestinal dysbiosis and low-grade inflammation; and the combined effect of four different Lactobacillus species on recovery of microbiota composition and improvement of gut barrier function in mice. METHODS AND RESULTS: Administration of the antibiotic ampicillin for 2 weeks decreased microbial community diversity, induced caecum tumefaction and increased gut permeability in mice. Application of a probiotic cocktail of four Lactobacillus species (JUP-Y4) modulated the microbiota community structure and promoted the abundance of potentially beneficial bacteria such as Akkermansia...
January 3, 2018: Journal of Applied Microbiology
https://www.readbyqxmd.com/read/29306132/operation-optimization-of-a-photo-sequencing-batch-reactor-for-wastewater-treatment-study-on-influencing-factors-and-impact-on-symbiotic-microbial-ecology
#5
Jianfeng Ye, Junyu Liang, Liang Wang, Giorgos Markou, Qilong Jia
Wastewater treatment technology with better energy efficiency and recyclability is in urgent demand. Photo-Sequencing batch reactor (SBR), which introduces microalgae into conventional SBR, is considered to have more potential for resource recycling. In this study, a photo-SBR was evaluated through the manipulation of several key operational parameters, i.e., aeration strength, light supply intensity and time per cycle, and solid retention time (SRT). The algal-bacterial symbiotic system had the potential of removing COD, NH4+-N and TN with limited aeration, representing the advantage of energy-saving by low aeration requirement...
December 28, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/29305503/elucidating-waterborne-pathogen-presence-and-aiding-source-apportionment-in-an-impaired-stream
#6
Jennifer Weidhaas, Angela Anderson, Rubayat Jamal
Fecal indicator bacteria (FIB) are the basis for water quality regulations and are considered proxies for waterborne pathogens when conducting human health risk assessments. Direct detection of pathogens in water and simultaneous identification of the source of fecal contamination is possible with microarrays, circumventing drawbacks to FIB approaches. A multi-gene target microarray was used to assess the prevalence of waterborne pathogens in a fecally impaired, mixed use watershed. Results indicate that fecal coliforms have improved substantially in the watershed since its listing as a 303(d) impaired stream in 2002 and are now near United States recreational water criteria standards...
January 5, 2018: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29305502/how-much-do-rrna-gene-surveys-underestimate-extant-bacterial-diversity
#7
Luis M Rodriguez-R, Juan C Castro, Nikos C Kyrpides, James R Cole, James M Tiedje, Konstantinos T Konstantinidis
The most common practice in studying and cataloguing prokaryotic diversity involves the grouping of sequences into Operational Taxonomic Units (or OTUs) at the 97% 16S rRNA gene sequence identity level, often using partial gene sequences such as PCR-generated amplicons. Due to the high sequence conservation of rRNA genes, organisms belonging to closely related yet distinct species may be grouped under the same OTU. However, it remains unclear how much diversity has been underestimated by this practice. To address this question, we compared OTUs of genomes defined at the 97% or 98...
January 5, 2018: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29304850/metabolic-capability-and-in-situ-activity-of-microorganisms-in-an-oil-reservoir
#8
Yi-Fan Liu, Daniela Domingos Galzerani, Serge Maurice Mbadinga, Livia S Zaramela, Ji-Dong Gu, Bo-Zhong Mu, Karsten Zengler
BACKGROUND: Microorganisms have long been associated with oxic and anoxic degradation of hydrocarbons in oil reservoirs and oil production facilities. While we can readily determine the abundance of microorganisms in the reservoir and study their activity in the laboratory, it has been challenging to resolve what microbes are actively participating in crude oil degradation in situ and to gain insight into what metabolic pathways they deploy. RESULTS: Here, we describe the metabolic potential and in situ activity of microbial communities obtained from the Jiangsu Oil Reservoir (China) by an integrated metagenomics and metatranscriptomics approach...
January 5, 2018: Microbiome
https://www.readbyqxmd.com/read/29298101/diet-microbiota-and-metabolic-health-trade-off-between-saccharolytic-and-proteolytic-fermentation
#9
Katri Korpela
The intestinal microbiota have emerged as a central regulator of host metabolism and immune function, mediating the effects of diet on host health. However, the large diversity and individuality of the gut microbiota have made it difficult to draw conclusions about microbiota responses to dietary interventions. In the light of recent research, certain general patterns are emerging, revealing how the ecology of the gut microbiota profoundly depends on the quality and quantity of dietary carbohydrates and proteins...
January 3, 2018: Annual Review of Food Science and Technology
https://www.readbyqxmd.com/read/29295915/in-nature-there-is-only-diversity
#10
Michael R McLaren, Benjamin J Callahan
Microbial ecology has been transformed by the advent of high-throughput marker gene and metagenomic sequencing methods. These tools provide expansive descriptions of microbial communities, but the descriptions are framed in terms of molecular objects, such as 97% ribosomal operational taxonomic units (OTUs), rather than biological objects, such as species. A recent study by A. B. Chase and colleagues (mBio 8:e01809-17, 2017, https://doi.org/10.1128/mBio.01809-17) explores the so-called microdiversity within the Curtobacterium OTU, the most abundant OTU in a leaf litter community...
January 2, 2018: MBio
https://www.readbyqxmd.com/read/29273717/strain-profiling-and-epidemiology-of-bacterial-species-from-metagenomic-sequencing
#11
Davide Albanese, Claudio Donati
Microbial communities are often composed by complex mixtures of multiple strains of the same species, characterized by a wide genomic and phenotypic variability. Computational methods able to identify, quantify and classify the different strains present in a sample are essential to fully exploit the potential of metagenomic sequencing in microbial ecology, with applications that range from the epidemiology of infectious diseases to the characterization of the dynamics of microbial colonization. Here we present a computational approach that uses the available genomic data to reconstruct complex strain profiles from metagenomic sequencing, quantifying the abundances of the different strains and cataloging them according to the population structure of the species...
December 22, 2017: Nature Communications
https://www.readbyqxmd.com/read/29250049/using-click-chemistry-for-visualizing-in-situ-changes-of-translational-activity-in-planktonic-marine-bacteria
#12
Ainara Leizeaga, Margarita Estrany, Irene Forn, Marta Sebastián
A major challenge in microbial ecology is linking diversity and function to determine which microbes are actively contributing to processes occurring in situ. Bioorthogonal non-canonical amino acid tagging (BONCAT) is a promising technique for detecting and quantifying translationally active bacteria in the environment. This technique consists of incubating a bacterial sample with an analog of methionine and using click-chemistry to identify the cells that have incorporated the substrate. Here, we established an optimized protocol for the visualization of protein-synthesizing cells in oligotrophic waters that can be coupled with taxonomic identification using Catalyzed Reporter Deposition Fluorescent in Situ Hybridization...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29247239/biogas-production-from-food-waste-via-co-digestion-and-digestion-effects-on-performance-and-microbial-ecology
#13
Mirzaman Zamanzadeh, Live Heldal Hagen, Kine Svensson, Roar Linjordet, Svein Jarle Horn
In this work, performance and microbial structure of a digestion (food waste-only) and a co-digestion process (mixture of cow manure and food waste) were studied at mesophilic (37 °C) and thermophilic (55 °C) temperatures. The highest methane yield (480 mL/g VS) was observed in the mesophilic digester (MDi) fed with food waste alone. The mesophilic co-digestion of food waste and manure (McoDi) yielded 26% more methane than the sum of individual digestions of manure and food waste. The main volatile fatty acid (VFA) in the mesophilic systems was acetate, averaging 93 and 172 mg/L for McoDi and MDi, respectively...
December 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29237993/-eukaryotic-microbiomes-of-membrane-attached-biofilms-in-membrane-bioreactors-analyzed-by-high-throughput-sequencing-and-microscopic-observations
#14
Tomohiro Inaba, Tomoyuki Hori, Yuya Sato, Tomo Aoyagi, Dai Hanajima, Atsushi Ogata, Hiroshi Habe
Limited information is currently available on the contribution of eukaryotes to the reactor performance of membrane bioreactors (MBRs). Using high-throughput Illumina sequencing of 18S rRNA genes and microscopic observations, we investigated eukaryotic microbiomes in membrane-attached biofilms in MBRs treating piggery wastewater. Protozoa preying on bacteria were frequently detected under stable conditions when membrane clogging was suppressed. However, the eukaryotes preying upon protozoa became predominant in biofilms when membrane fouling rapidly progressed...
December 12, 2017: Microbes and Environments
https://www.readbyqxmd.com/read/29235707/tales-from-the-tomb-the-microbial-ecology-of-exposed-rock-surfaces
#15
Tess E Brewer, Noah Fierer
Although a broad diversity of eukaryotic and bacterial taxa reside on rock surfaces where they can influence the weathering of rocks and minerals, these communities and their contributions to mineral weathering remain poorly resolved. To build a more comprehensive understanding of the diversity, ecology, and potential functional attributes of microbial communities living on rock, we sampled 149 tombstones across three continents and analyzed their bacterial and eukaryotic communities via marker gene and shotgun metagenomic sequencing...
December 13, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/29230650/available-forms-of-nutrients-and-heavy-metals-control-the-distribution-of-microbial-phospholipid-fatty-acids-in-sediments-of-the-three-gorges-reservoir-china
#16
Hongyang Sun, Yanhong Wu, Haijian Bing, Jun Zhou, Na Li
The construction of the Three Gorges Reservoir (TGR) as well as the development of local industry and agriculture not only had tremendous impacts on the environment but also affected human health. Although water, soil, and air in the TGR have been well studied for environmental risk assessment, very little information is available on benthic sediments and microorganisms. In this study, sedimentary samples were collected along the main stream of the TGR to examine microbial phospholipid fatty acids (PLFA) and relevant variables (e...
December 11, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/29230200/from-genes-to-ecosystems-in-microbiology-modeling-approaches-and-the-importance-of-individuality
#17
REVIEW
Jan-Ulrich Kreft, Caroline M Plugge, Clara Prats, Johan H J Leveau, Weiwen Zhang, Ferdi L Hellweger
Models are important tools in microbial ecology. They can be used to advance understanding by helping to interpret observations and test hypotheses, and to predict the effects of ecosystem management actions or a different climate. Over the past decades, biological knowledge and ecosystem observations have advanced to the molecular and in particular gene level. However, microbial ecology models have changed less and a current challenge is to make them utilize the knowledge and observations at the genetic level...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29228191/frogs-find-rapidly-otus-with-galaxy-solution
#18
Frédéric Escudié, Lucas Auer, Maria Bernard, Mahendra Mariadassou, Laurent Cauquil, Katia Vidal, Sarah Maman, Guillermina Hernandez-Raquet, Sylvie Combes, Géraldine Pascal
Motivation: Metagenomics leads to major advances in microbial ecology and biologists need user friendly tools to analyze their data on their own. Results: This Galaxy-supported pipeline, called FROGS, is designed to analyze large sets of amplicon sequences and produce abundance tables of Operational Taxonomic Units (OTUs) and their taxonomic affiliation. The clustering uses Swarm. The chimera removal uses VSEARCH, combined with original cross-sample validation. The taxonomic affiliation returns an innovative multi-affiliation output to highlight databases conflicts and uncertainties...
December 7, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29225380/performance-of-anaerobic-biotrickling-filter-and-its-microbial-diversity-for-the-removal-of-stripped-disinfection-byproducts
#19
Bineyam Mezgebe, George A Sorial, E Sahle-Demessie, Ashraf Aly Hassan, Jingrang Lu
The objective of this research was to evaluate the biodegradation of chloroform by using biotrickling filter (BTF) and determining the dominant bacteria responsible for the degradation. The research was conducted in three phases under anaerobic condition, namely, in the presence of co-metabolite (Phase I), in the presence of co-metabolite and surfactant (Phase II) and in the presence of surfactant but no co-metabolite (Phase III). The results showed that the presence of ethanol as a co-metabolite provided 49% removal efficiency...
November 1, 2017: Water, Air, and Soil Pollution
https://www.readbyqxmd.com/read/29224879/plant-oil-supplements-reduce-methane-emissions-and-improve-milk-fatty-acid-composition-in-dairy-cows-fed-grass-silage-based-diets-without-affecting-milk-yield
#20
A R Bayat, I Tapio, J Vilkki, K J Shingfield, H Leskinen
Four lipid supplements varying in chain length or degree of unsaturation were examined for their effects on milk yield and composition, ruminal CH4 emissions, rumen fermentation, nutrient utilization, and microbial ecology in lactating dairy cows. Five Nordic Red cows fitted with rumen cannulas were used in a 5 × 5 Latin square with five 28-d periods. Treatments comprised total mixed rations based on grass silage with a forage-to-concentrate ratio of 60:40 supplemented with no lipid (CO) or 50 g/kg of diet dry matter (DM) of myristic acid (MA), rapeseed oil (RO), safflower oil (SO), or linseed oil (LO)...
December 7, 2017: Journal of Dairy Science
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