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https://www.readbyqxmd.com/read/29778159/effects-of-1-octyl-3-methylimidazolium-nitrate-on-the-microbes-in-brown-soil
#1
Cheng Zhang, Jun Wang, Lusheng Zhu, Zhongkun Du, Jinhua Wang, Xi Sun, Tongtong Zhou
The toxicity of ionic liquids (ILs) on soil organisms has aroused wide attention due to their high-solubility. The present investigation focused on the toxicity of 1-octyl-3-methylimidazolium nitrate ([C8 mim]NO3 ) on the microbial populations (bacteria, fungi, and actinomycetes), soil enzyme (urease, dehydrogenase, acid phosphatase, and β-glucosidase) activities, microbial community diversity using terminal restriction fragment length polymorphism (T-RFLP), and abundance of the ammonia monooxygenase (amoA) genes of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) using quantitative real-time polymerase chain reaction (q-PCR) in brown soil at each trial with doses of 0, 1...
May 2018: Journal of Environmental Sciences (China)
https://www.readbyqxmd.com/read/29778154/effects-of-chlortetracycline-cu-and-their-combination-on-the-performance-and-microbial-community-dynamics-in-swine-manure-anaerobic-digestion
#2
Rui Wang, Junya Zhang, Jibao Liu, Dawei Yu, Hui Zhong, Yawei Wang, Meixue Chen, Juan Tong, Yuansong Wei
Swine manure was typical for the combined pollution of heavy metals and antibiotics. The effects of widely used veterinary antibiotic chlortetracycline (CTC), Cu and their combination on swine manure anaerobic digestion performance and microbial community have never been investigated. Thus, four 2L anaerobic digestion reactors were established including reactor A (control), B (CTC spiked by 0.5g/kg dry weight, dw), C (Cu spiked by 5g/kg dw) and D (combination of CTC, 0.5g/kg dw, and Cu, 5g/kg dw), and dynamics of bacterial and archaeal community structure was investigated using high throughput sequencing method...
May 2018: Journal of Environmental Sciences (China)
https://www.readbyqxmd.com/read/29777997/rumen-fluid-fermentation-for-enhancement-of-hydrolysis-and-acidification-of-grass-clipping
#3
Siqi Wang, Guangming Zhang, Panyue Zhang, Xiaowen Ma, Fan Li, Haibo Zhang, Xue Tao, Junpei Ye, Mohammad Nabi
Rumen fluid, formed in rumen of ruminants, includes a complex microbial population of bacteria, protozoa, fungi and archaea, and has high ability to degrade lignocellulosic biomass. In this study, rumen fluid was used to ferment grass clipping for enhancing the hydrolysis and acidification of organic matters. Results showed that strict anaerobic condition, higher grass clipping content and smaller particle size of grass clipping were beneficial to the hydrolysis and acidification of organics. The increase of SCOD and total VFA concentration respectively reached 24...
May 16, 2018: Journal of Environmental Management
https://www.readbyqxmd.com/read/29776729/effect-of-enhancing-nutrient-balance-in-anaerobic-digester-feedstock-by-co-substrate-addition-on-the-microbial-diversity-and-energy-production-from-municipal-sewage-sludge
#4
Amel Farhat, Imène Manai, Maher Gtari, Hassib Bouallagui
Enhancement of methane production during anaerobic digestion of waste activated sludge (WAS) could improve the energy self sufficiency of the municipal wastewater treatment plants (WWTPs). Therefore, mixing WAS with organic wastes improved process performance and stability. In this work, the anaerobic co-digestion of WAS combined with the olive processing wastewater (OPW) was investigated and associated with the energetic benefits and microbial populations shifts. The bio-methane potential (BMP) of various WAS and OPW mixtures corresponding to increased phenols concentrations were tested...
May 16, 2018: Journal of Bioscience and Bioengineering
https://www.readbyqxmd.com/read/29774508/the-bacterial-and-archaeal-community-structures-and-methanogenic-potential-of-the-cecal-microbiota-of-goats-fed-with-hay-and-high-grain-diets
#5
Wei Jin, Yin Li, Yanfen Cheng, Shengyong Mao, Weiyun Zhu
The cecum plays an important role in the feed fermentation of ruminants. However, information is very limited regarding the cecal microbiota and their methane production. In the present study, the cecal content from twelve local Chinese goats, fed with either a hay diet (0% grain) or a high-grain diet (71.5% grain), were used to investigate the bacterial and archaeal community and their methanogenic potential. Microbial community analysis was determined using high-throughput sequencing of 16S rRNA genes and real-time PCR, and the methanogenesis potential was assessed by in vitro fermentation with ground corn or hay as substrates...
May 17, 2018: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/29773905/establishing-anaerobic-hydrocarbon-degrading-enrichment-cultures-of-microorganisms-under-strictly-anoxic-conditions
#6
Rafael Laso-Pérez, Viola Krukenberg, Florin Musat, Gunter Wegener
Traditionally, the description of microorganisms starts with their isolation from an environmental sample. Many environmentally relevant anaerobic microorganisms grow very slowly, and often they rely on syntrophic interactions with other microorganisms. This impedes their isolation and characterization by classic microbiological techniques. We developed and applied an approach for the successive enrichment of syntrophic hydrocarbon-degrading microorganisms from environmental samples. We collected samples from microbial mat-covered hydrothermally heated hydrocarbon-rich sediments of the Guaymas Basin and mixed them with synthetic mineral medium to obtain sediment slurries...
June 2018: Nature Protocols
https://www.readbyqxmd.com/read/29773659/modeling-leaderless-transcription-and-atypical-genes-results-in-more-accurate-gene-prediction-in-prokaryotes
#7
Alexandre Lomsadze, Karl Gemayel, Shiyuyun Tang, Mark Borodovsky
In a conventional view of the prokaryotic genome organization, promoters precede operons and RBS sites with Shine-Dalgarno consensus precede genes. However, recent experimental research suggesting a more diverse view motivated us to develop an algorithm with improved gene-finding accuracy. We describe GeneMarkS 2, an ab initio algorithm that uses a model derived by self-training for finding species-specific (native) genes, along with an array of pre-computed "heuristic" models designed to identify harder-to-detect genes (likely horizontally transferred)...
May 17, 2018: Genome Research
https://www.readbyqxmd.com/read/29771354/methylation-guide-rna-evolution-in-archaea-structure-function-and-genomic-organization-of-110-c-d-box-srna-families-across-six-pyrobaculum-species
#8
Lauren M Lui, Andrew V Uzilov, David L Bernick, Andrea Corredor, Todd M Lowe, Patrick P Dennis
Archaeal homologs of eukaryotic C/D box small nucleolar RNAs (C/D box sRNAs) guide precise 2'-O-methyl modification of ribosomal and transfer RNAs. Although C/D box sRNA genes constitute one of the largest RNA gene families in archaeal thermophiles, most genomes have incomplete sRNA gene annotation because reliable, fully automated detection methods are not available. We expanded and curated a comprehensive gene set across six species of the crenarchaeal genus Pyrobaculum, particularly rich in C/D box sRNA genes...
May 16, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29769540/different-clusters-of-candidatus-methanoperedens-nitroreducens-like-archaea-as-revealed-by-high-throughput-sequencing-with-new-primers
#9
Sai Xu, Chen Cai, Jianhua Guo, Wenjing Lu, Zhiguo Yuan, Shihu Hu
The newly discovered Candidatus 'Methanoperedens nitroreducens' (M. nitroreducens), mediating nitrate-dependent anaerobic oxidation of methane, is an important microorganism in linking carbon and nitrogen cycles. In order to explore the diversity of M. nitroreducens-like archaea in various environmental niches with advanced high-throughput sequencing, new primers based on alpha subunit of methyl-coenzyme M reductase gene were designed. The PCR results demonstrated that the new primers could effectively detect M...
May 16, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29766233/environmental-drivers-controlling-bacterial-and-archaeal-abundance-in-the-sediments-of-a-mediterranean-lagoon-ecosystem
#10
Claudia Pala, Massimiliano Molari, Daniele Nizzoli, Marco Bartoli, Pierluigi Viaroli, Elena Manini
The environmental factors controlling the abundance of Bacteria and Archaea in lagoon ecosystems are poorly understood. Here, an integrated physico-chemical, biogeochemical, and microbiological survey was applied in the Sacca di Goro lagoon (Po River Delta, Italy) to investigate the variation of bacterial and archaeal abundance, as assessed by Fluorescence In Situ Hybridization, along winter and summer environmental gradients. We hypothesised that bacterial and archaeal cells respond differentially to physico-chemical parameters of the sediment, which can be manifested in variations of total cells number...
May 15, 2018: Current Microbiology
https://www.readbyqxmd.com/read/29760463/marsarchaeota-are-an-aerobic-archaeal-lineage-abundant-in-geothermal-iron-oxide-microbial-mats
#11
Zackary J Jay, Jacob P Beam, Mensur Dlakić, Douglas B Rusch, Mark A Kozubal, William P Inskeep
The discovery of archaeal lineages is critical to our understanding of the universal tree of life and evolutionary history of the Earth. Geochemically diverse thermal environments in Yellowstone National Park provide unprecedented opportunities for studying archaea in habitats that may represent analogues of early Earth. Here, we report the discovery and characterization of a phylum-level archaeal lineage proposed and herein referred to as the 'Marsarchaeota', after the red planet. The Marsarchaeota contains at least two major subgroups prevalent in acidic, microaerobic geothermal Fe(III) oxide microbial mats across a temperature range from ~50-80 °C...
May 14, 2018: Nature Microbiology
https://www.readbyqxmd.com/read/29758429/microbial-ecology-of-two-hot-springs-of-sikkim-predominate-population-and-geochemistry
#12
Ishfaq Nabi Najar, Mingma Thundu Sherpa, Sayak Das, Saurav Das, Nagendra Thakur
Northeastern regions of India are known for their floral and faunal biodiversity. Especially the state of Sikkim lies in the eastern Himalayan ecological hotspot region. The state harbors many sulfur rich hot springs which have therapeutic and spiritual values. However, these hot springs are yet to be explored for their microbial ecology. The development of neo generation techniques such as metagenomics has provided an opportunity for inclusive study of microbial community of different environment. The present study describes the microbial diversity in two hot springs of Sikkim that is Polok and Borong with the assist of culture dependent and culture independent approaches...
May 11, 2018: Science of the Total Environment
https://www.readbyqxmd.com/read/29758420/assessment-of-the-impact-of-three-pesticides-on-microbial-dynamics-and-functions-in-a-lab-to-field-experimental-approach
#13
P A Karas, C Baguelin, G Pertile, E S Papadopoulou, S Nikolaki, V Storck, F Ferrari, M Trevisan, A Ferrarini, F Fornasier, S Vasileiadis, G Tsiamis, F Martin-Laurent, D G Karpouzas
The toxicity of pesticides on soil microorganisms is as an emerging area of concern. Novel and well-standardized tools could be now used to provide a robust assessment of the ecotoxicity of pesticides on soil microorganisms. We followed a tiered lab-to-field approach to assess the toxicity of three pesticides, widely used at EU level, (chlorpyrifos (CHL), isoproturon (IPU) and tebuconazole (TBZ)) on (i) the abundance of 11 microbial taxa and 8 functional microbial groups via q-PCR and (ii) the activity of enzymes involved in biogeochemical cycles via fluorometric analysis...
May 11, 2018: Science of the Total Environment
https://www.readbyqxmd.com/read/29757234/effect-of-uvc-radiation-on-hydrated-and-desiccated-cultures-of-slightly-halophilic-and-non-halophilic-methanogenic-archaea-implications-for-life-on-mars
#14
Navita Sinha, Timothy A Kral
Methanogens have been considered models for life on Mars for many years. In order to survive any exposure at the surface of Mars, methanogens would have to endure Martian UVC radiation. In this research, we irradiated hydrated and desiccated cultures of slightly halophilic Methanococcus maripaludis and non-halophilic Methanobacterium formicicum for various time intervals with UVC (254 nm) radiation. The survivability of the methanogens was determined by measuring methane concentrations in the headspace gas samples of culture tubes after re-inoculation of the methanogens into their growth-supporting media following exposure to UVC radiation...
May 12, 2018: Microorganisms
https://www.readbyqxmd.com/read/29753224/diversity-and-distribution-of-archaea-in-global-estuarine-ecosystems
#15
Xiaobo Liu, Jie Pan, Yang Liu, Meng Li, Ji-Dong Gu
Estuarine ecosystem is a unique geographical transitional zone between freshwater and seawater, harboring a wide range of microbial communities including Archaea. Although a large number of Archaea have been detected in such ecosystem, the global patterns in archaeal diversity and distribution are extremely scarce. To bridge this gap, we carried out a comprehensive survey of archaeal communities using ca. 4000 publicly available archaeal 16S rRNA gene sequences (>300 bp) collected from 24 estuaries in different latitude regions...
May 9, 2018: Science of the Total Environment
https://www.readbyqxmd.com/read/29745187/-type-and-key-drivers-of-nitrification-for-an-acidic-peat-soil-in-xiaoxing-an-mountain-china
#16
Zhi Hui Wang, Jing Su, Xian Jun Jiang
Acidic forest peat soil in Xiaoxing'an Mountain was used to investigate the type and key drivers of nitrification by carrying out nitrification incubation after adding 10 mL·L-1 C2 H2 and different amounts of (NH4 )2 SO4 (0, 1.2, 6.0 mmol N·kg-1 ). Results showed that strong mineralization (0.9-1.4 mg N·kg-1 ·d-1 ) and nitrification (0.4-0.6 mg N·kg-1 ·d-1 ) after 2 weeks of incubation were observed for both nitrogen and no nitrogen treatments, and no significant difference was observed for different (NH4 )2 SO4 application treatments...
May 18, 2017: Ying Yong Sheng Tai Xue Bao, the Journal of Applied Ecology
https://www.readbyqxmd.com/read/29744521/impact-of-heavy-metal-pollution-on-ammonia-oxidizers-in-soils-in-the-vicinity-of-a-tailings-dam-baotou-china
#17
Jumei Liu, Weiwei Cao, Haiming Jiang, Jing Cui, Chunfang Shi, Xiaohui Qiao, Ji Zhao, Wantong Si
Soil heavy metal pollution has received increasing attention due to their toxicity to soil microorganisms. We have analyzed the effects of heavy metal pollution on ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in soils in the vicinity of a tailings dam of Baotou region, China. Results showed that AOB were dominated with Nitrosomonas-like clusters, while AOA was dominated by group1.1b (Nitrososphaera cluster). Single Cd and Cr contents, as well as compound heavy metal pollution levels, had a significant negative impact on soil potential nitrification rate and both diversities of AOA and AOB...
May 9, 2018: Bulletin of Environmental Contamination and Toxicology
https://www.readbyqxmd.com/read/29743201/what-is-the-role-of-archaea-in-plants-new-insights-from-the-vegetation-of-alpine-bogs
#18
Julian Taffner, Armin Erlacher, Anastasia Bragina, Christian Berg, Christine Moissl-Eichinger, Gabriele Berg
The Archaea represent a significant component of the plant microbiome, whereas their function is still unclear. Different plant species representing the natural vegetation of alpine bogs harbor a substantial archaeal community originating from five phyla, 60 genera, and 334 operational taxonomic units (OTUs). We identified a core archaeome for all bog plants and ecosystem-specific, so far unclassified Archaea In the metagenomic data set, Archaea were found to have the potential to interact with plants by (i) possible plant growth promotion through auxin biosynthesis, (ii) nutrient supply, and (iii) protection against abiotic (especially oxidative and osmotic) stress...
June 27, 2018: MSphere
https://www.readbyqxmd.com/read/29741662/physical-and-functional-interplay-between-pcna-dna-clamp-and-mre11-rad50-complex-from-the-archaeon-pyrococcus-furiosus
#19
Gaëlle Hogrel, Yang Lu, Sébastien Laurent, Etienne Henry, Clarisse Etienne, Duy Khanh Phung, Rémi Dulermo, Audrey Bossé, Pierre-François Pluchon, Béatrice Clouet-d'Orval, Didier Flament
Several archaeal species prevalent in extreme environments are particularly exposed to factors likely to cause DNA damages. These include hyperthermophilic archaea (HA), living at temperatures >70°C, which arguably have efficient strategies and robust genome guardians to repair DNA damage threatening their genome integrity. In contrast to Eukarya and other archaea, homologous recombination appears to be a vital pathway in HA, and the Mre11-Rad50 complex exerts a broad influence on the initiation of this DNA damage response process...
May 8, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29741625/dna-repair-in-the-archaea-an-emerging-picture
#20
Malcolm F White, Thorsten Allers
There has long been a fascination in the DNA Repair pathways of archaea, for two main reasons. Firstly, many archaea inhabit extreme environments where the rate of physical damage to DNA is accelerated. These archaea might reasonably be expected to have particularly robust or novel DNA repair pathways to cope with this. Secondly, the archaea have long been understood to be a lineage distinct from the bacteria, and to share a close relationship with the eukarya, particularly in their information processing systems...
May 5, 2018: FEMS Microbiology Reviews
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