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https://www.readbyqxmd.com/read/28538201/effects-of-adding-trace-elements-on-rice-straw-anaerobic-mono-digestion-focus-on-changes-in-microbial-communities-using-high-throughput-sequencing
#1
Yafan Cai, Binbin Hua, Lijuan Gao, Yuegao Hu, Xufeng Yuan, Zongjun Cui, Wanbin Zhu, Xiaofen Wang
Although trace elements are known to aid anaerobic digestion, their mechanism of action is still unclear. High-throughput sequencing was used to reveal the mechanism by which adding trace elements affects microbial communities and their action. The results showed that the highest methane yields, with addition of Fe, Mo, Se and Mn were 289.2, 289.6, 285.3, 293.0mL/g volatile solids (VS), respectively. The addition of Fe, Mo, Se and Mn significantly (P<0.05) reduced the level of volatile fatty acids (VFAs)...
April 21, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/28535195/presence-of-type-i-f-crispr-cas-systems-is-associated-with-antimicrobial-susceptibility-in-escherichia-coli
#2
Seyid Aydin, Yoann Personne, Enas Newire, Rebecca Laverick, Oliver Russell, Adam P Roberts, Virve I Enne
Background: Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and their associated cas genes are sequence-specific DNA nuclease systems found in bacteria and archaea. CRISPR/Cas systems use RNA transcripts of previously acquired DNA (spacers) to target invading genetic elements with the same sequence, including plasmids. In this research we studied the relationship between CRISPR/Cas systems and multidrug resistance in Escherichia coli . Methods: The presence of Type I-E and Type I-F CRISPR systems was investigated among 82 antimicrobial-susceptible and 96 MDR clinical E...
May 23, 2017: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/28533768/novel-large-sulfur-bacteria-in-the-metagenomes-of-groundwater-fed-chemosynthetic-microbial-mats-in-the-lake-huron-basin
#3
Allison M Sharrar, Beverly E Flood, Jake V Bailey, Daniel S Jones, Bopaiah A Biddanda, Steven A Ruberg, Daniel N Marcus, Gregory J Dick
Little is known about large sulfur bacteria (LSB) that inhabit sulfidic groundwater seeps in large lakes. To examine how geochemically relevant microbial metabolisms are partitioned among community members, we conducted metagenomic analysis of a chemosynthetic microbial mat in the Isolated Sinkhole, which is in a deep, aphotic environment of Lake Huron. For comparison, we also analyzed a white mat in an artesian fountain that is fed by groundwater similar to Isolated Sinkhole, but that sits in shallow water and is exposed to sunlight...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28533395/integrative-modeling-of-gene-and-genome-evolution-roots-the-archaeal-tree-of-life
#4
Tom A Williams, Gergely J Szöllősi, Anja Spang, Peter G Foster, Sarah E Heaps, Bastien Boussau, Thijs J G Ettema, T Martin Embley
A root for the archaeal tree is essential for reconstructing the metabolism and ecology of early cells and for testing hypotheses that propose that the eukaryotic nuclear lineage originated from within the Archaea; however, published studies based on outgroup rooting disagree regarding the position of the archaeal root. Here we constructed a consensus unrooted archaeal topology using protein concatenation and a multigene supertree method based on 3,242 single gene trees, and then rooted this tree using a recently developed model of genome evolution...
May 22, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28531860/boosting-biomethane-yield-and-production-rate-with-graphene-the-potential-of-direct-interspecies-electron-transfer-in-anaerobic-digestion
#5
Richen Lin, Jun Cheng, Jiabei Zhang, Junhu Zhou, Kefa Cen, Jerry D Murphy
Interspecies electron transfer between bacteria and archaea plays a vital role in enhancing energy efficiency of anaerobic digestion (AD). Conductive carbon materials (i.e. graphene nanomaterial and activated charcoal) were assessed to enhance AD of ethanol (a key intermediate product after acidogenesis of algae). The addition of graphene (1.0g/L) resulted in the highest biomethane yield (695.0±9.1mL/g) and production rate (95.7±7.6mL/g/d), corresponding to an enhancement of 25.0% in biomethane yield and 19...
May 5, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/28529503/response-of-methanogenic-microbial-communities-to-desiccation-stress-in-flooded-and-rain-fed-paddy-soil-from-thailand
#6
Andreas Reim, Marcela Hernández, Melanie Klose, Amnat Chidthaisong, Monthira Yuttitham, Ralf Conrad
Rice paddies in central Thailand are flooded either by irrigation (irrigated rice) or by rain (rain-fed rice). The paddy soils and their microbial communities thus experience permanent or arbitrary submergence, respectively. Since methane production depends on anaerobic conditions, we hypothesized that structure and function of the methanogenic microbial communities are different in irrigated and rain-fed paddies and react differently upon desiccation stress. We determined rates and relative proportions of hydrogenotrophic and aceticlastic methanogenesis before and after short-term drying of soil samples from replicate fields...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28528947/syntrophic-association-of-termite-gut-bacterial-symbionts-with-bifunctional-characteristics-of-cellulose-degrading-and-polyhydroxyalkanoate-producing-bacteria
#7
Balasubramanian Cibichakravarthy, Subramani Abinaya, Solai Ramatchandirane Prabagaran
The guild between higher termites and their partnership with the diverse community of bacteria and archaea in their gut is a marvel evolutionary achievement. Sustained attempts were made worldwide with a quest for identifying viable important biological macromolecule polyhydroxyalkanoate (PHA) accumulating bacteria. Termite gut serve as a novel source for bacteria with dual properties like PHA production as well as cellulose degradation. Among 40 isolates cultivated, 32.5% turned positive for PCR based screening of PhaC gene...
May 18, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/28526980/a-multiomics-approach-to-study-the-microbiome-response-to-phytoplankton-blooms
#8
REVIEW
Liyan Song
Phytoplankton blooms are predictable features of marine and freshwater habitats. Despite a good knowledge base of the environmental factors controlling blooms, complex interactions between the bacterial and archaeal communities and phytoplankton bloom taxa are only now emerging. Here, the current research on bacterial community's structural and functional response to phytoplankton blooms is reviewed and discussed and further research is proposed. More attention should be paid on structure and function of autotrophic bacteria and archaea during phytoplankton blooms...
May 19, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28523826/occurrence-and-abundance-of-ammonia-oxidizing-archaea-and-bacteria-from-the-surface-to-below-the-water-table-in-deep-soil-and-their-contributions-to-nitrification
#9
Lei Zheng, Xue Zhao, Guibing Zhu, Wei Yang, Chao Xia, Tao Xu
Using molecular biology methods (qualitative and quantitative PCR), we determined the occurrence and abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) from a dry inland soil in Basel, Switzerland, and from the riparian zone of Baiyangdian Lake, China. We also determined the contributions of these microorganisms to ammonia oxidization at different depths based on the nitrification rate. The number of archaeal amoA genes (the key functional gene in AOA) was larger than the number of bacterial amoA genes in each sample, suggesting a dominant role for the AOA amoA gene in environments with a low ammonium concentration...
May 19, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28521159/distribution-and-genetic-diversity-of-microbial-populations-in-the-pilot-scale-biofilter-for-simultaneous-removal-of-ammonia-iron-and-manganese-from-real-groundwater
#10
Qingfeng Cheng, Lichao Nengzi, Linlin Bao, Yang Huang, Shengyu Liu, Xiuwen Cheng, Bo Li, Jie Zhang
A pilot-scale biofilter treating real groundwater was developed in this study, which showed that ammonia, iron and manganese were mainly removed at 0.4, 0.4 and 0.8 m of the filter bed, respectively, and the corresponding removal efficiencies were 90.82%, 95.48% and 95.90% in steady phase, respectively. The variation of microbial populations in the biofilter during start-up process was also investigated using high-throughput pyrosequencing (HTP). Results indicated that the main functional microbes for ammonia, iron and manganese removal were Nitrosomonas, Crenothrix and Crenothrix, respectively, which was mainly distributed at 0...
May 13, 2017: Chemosphere
https://www.readbyqxmd.com/read/28520982/genome-wide-mrna-processing-in-methanogenic-archaea-reveals-post-transcriptional-regulation-of-ribosomal-protein-synthesis
#11
Lei Qi, Lei Yue, Deqin Feng, Fengxia Qi, Jie Li, Xiuzhu Dong
Unlike stable RNAs that require processing for maturation, prokaryotic cellular mRNAs generally follow an 'all-or-none' pattern. Herein, we used a 5΄ monophosphate transcript sequencing (5΄P-seq) that specifically captured the 5΄-end of processed transcripts and mapped the genome-wide RNA processing sites (PSSs) in a methanogenic archaeon. Following statistical analysis and stringent filtration, we identified 1429 PSSs, among which 23.5% and 5.4% were located in 5΄ untranslated region (uPSS) and intergenic region (iPSS), respectively...
May 18, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28520934/the-smap1-2-proteins-of-the-crenarchaeon-sulfolobus-solfataricus-interact-with-the-exosome-and-stimulate-a-rich-tailing-of-transcripts
#12
Birgit Märtens, Linlin Hou, Fabian Amman, Michael T Wolfinger, Elena Evguenieva-Hackenberg, Udo Bläsi
The conserved Sm and Sm-like proteins are involved in different aspects of RNA metabolism. Here, we explored the interactome of SmAP1 and SmAP2 of the crenarchaeon Sulfolobus solfataricus (Sso) to shed light on their physiological function(s). Both, SmAP1 and SmAP2 co-purified with several proteins involved in RNA-processing/modification, translation and protein turnover as well as with components of the exosome involved in 3΄ to 5΄ degradation of RNA. In follow-up studies a direct interaction with the poly(A) binding and accessory exosomal subunit DnaG was demonstrated...
May 18, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28520472/a-study-of-the-microbial-spatial-heterogeneity-of-bahamian-thrombolites-using-molecular-biochemical-and-stable-isotope-analyses
#13
Artemis S Louyakis, Jennifer M Mobberley, Brooke E Vitek, Pieter T Visscher, Paul D Hagan, R Pamela Reid, Reinhard Kozdon, Ian J Orland, John W Valley, Noah J Planavsky, Giorgio Casaburi, Jamie S Foster
Thrombolites are buildups of carbonate that exhibit a clotted internal structure formed through the interactions of microbial mats and their environment. Despite recent advances, we are only beginning to understand the microbial and molecular processes associated with their formation. In this study, a spatial profile of the microbial and metabolic diversity of thrombolite-forming mats of Highborne Cay, The Bahamas, was generated by using 16S rRNA gene sequencing and predictive metagenomic analyses. These molecular-based approaches were complemented with microelectrode profiling and in situ stable isotope analysis to examine the dominant taxa and metabolic activities within the thrombolite-forming communities...
May 2017: Astrobiology
https://www.readbyqxmd.com/read/28516862/non-essential-mcm-related-proteins-mediate-a-response-to-dna-damage-in-the-archaeon-methanococcus-maripaludis
#14
Alison D Walters, James P J Chong
The single minichromosome maintenance (MCM) protein found in most archaea has been widely studied as a simplified model for the MCM complex that forms the catalytic core of the eukaryotic replicative helicase. Organisms of the order Methanococcales are unusual in possessing multiple MCM homologues. The Methanococcus maripaludis S2 genome encodes four MCM homologues, McmA-McmD. DNA helicase assays reveal that the unwinding activity of the three MCM-like proteins is highly variable despite sequence similarities and suggests additional motifs that influence MCM function are yet to be identified...
May 18, 2017: Microbiology
https://www.readbyqxmd.com/read/28516483/capabilities-and-limitations-of-dgge-for-the-analysis-of-hydrocarbonoclastic-prokaryotic-communities-directly-in-environmental-samples
#15
Dina M Al-Mailem, Mayada K Kansour, Samir S Radwan
Prokaryotic communities in pristine and oil-contaminated desert soil, seawater, and hypersaline coastal soil were analyzed using culture-dependent and culture-independent approaches. The former technique was the dilution-plating method. For the latter, total genomic DNA was extracted and the 16S rRNA genes were amplified using a universal bacterial primer pair and primer pairs specific for Actinobacteria, Gammaproteobacteria, and Archaea. The amplicons were resolved using denaturing gradient gel electrophoresis (DGGE) and sequenced, and the sequences were compared to those in GenBank...
May 18, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28515720/computational-exploration-of-putative-luxr-solos-in-archaea-and-their-functional-implications-in-quorum-sensing
#16
Akanksha Rajput, Manoj Kumar
LuxR solos are unexplored in Archaea, despite their vital role in the bacterial regulatory network. They assist bacteria in perceiving acyl homoserine lactones (AHLs) and/or non-AHLs signaling molecules for establishing intraspecies, interspecies, and interkingdom communication. In this study, we explored the potential LuxR solos of Archaea from InterPro v62.0 meta-database employing taxonomic, probable function, distribution, and evolutionary aspects to decipher their role in quorum sensing (QS). Our bioinformatics analyses showed that putative LuxR solos of Archaea shared few conserved domains with bacterial LuxR despite having less similarity within proteins...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28515389/ca-2-in-hybridization-solutions-for-fluorescence-in-situ-hybridization-facilitates-the-detection-of-enterobacteriaceae
#17
Shin Haruta, Takao Iino, Moriya Ohkuma, Ken-Ichiro Suzuki, Yasuo Igarashi
Fluorescence in situ hybridization (FISH) has been employed to identify microorganisms at the single cell level under a microscope. Extensive efforts have been made to improve and extend the FISH technique; however, the development of a widely applicable protocol is a continuing challenge. The present study evaluated the effects of divalent cations in the hybridization solution on the FISH-based detection of various species of bacteria and archaea with rRNA-targeted probes. A flow cytometric analysis after FISH with a standard hybridization buffer detected positive signals from less than 30% of Escherichia coli IAM 1264 cells...
May 18, 2017: Microbes and Environments
https://www.readbyqxmd.com/read/28514846/natural-mutagenesis-enabled-global-proteomic-study-of-metabolic-and-carbon-source-implications-in-mutant-thermoacidophillic-archaeon-sulfolobus-solfataricus-pbl2025
#18
Wen Qiu, Trong Khoa Pham, Xin Zou, Saw Yen Ow, Phillip C Wright
The thermoacidophilic crenarchaeon Sulfolobus solfataricus has been widely used as a model organism for archaeal systems biology research. Investigation using its spontaneous mutant PBL2025 provides an effective metabolic baseline to study subsequent mutagenesis-induced process shifts as well as changes in feedback inhibitions. Here, an untargeted metabolic investigation using quantitative proteomics and metabolomics was performed to correlate changes in S. solfataricus strains P2 against PBL2025 and under both glucose and tryptone...
May 17, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28514840/plastics-in-the-north-atlantic-garbage-patch-a-boat-microbe-for-hitchhikers-and-plastic-degraders
#19
Debroas Didier, Mone Anne, Ter Halle Alexandra
Plastic is a broad name given to different polymers with high molecular weight that impact wildlife. Their fragmentation leads to a continuum of debris sizes (meso to microplastics) entrapped in gyres and colonized by microorganisms. In the present work, the structure of eukaryotes, bacteria and Archaea was studied by a metabarcoding approach, and statistical analysis associated with network building was used to define a core microbiome at the plastic surface. Most of the bacteria significantly associated with the plastic waste originated from non-marine ecosystems, and numerous species can be considered as hitchhikers, whereas others act as keystone species (e...
May 13, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28512453/alterations-in-the-rumen-liquid-particle-and-epithelium-associated-microbiota-of-dairy-cows-during-the-transition-from-a-silage-and-concentrate-based-ration-to-pasture-in-spring
#20
Melanie Schären, Kerstin Kiri, Susanne Riede, Mark Gardener, Ulrich Meyer, Jürgen Hummel, Tim Urich, Gerhard Breves, Sven Dänicke
In spring dairy cows are often gradually transitioned from a silage- and concentrate-based ration (total mixed ration, TMR) to pasture. Rumen microbiota adaptability is a key feature of ruminant survival strategy. However, only little is known on the temporal and spatial microbial alterations involved. This study aims to investigate how the rumen liquid (LAAB), particle (PAAB), and epithelium (EAAB) associated archaea and bacteria are influenced by this nutritional change. A 10-wk trial was performed, including 10 rumen-fistulated dairy cows, equally divided into a pasture- and a confinement- group (PG and CG)...
2017: Frontiers in Microbiology
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