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https://www.readbyqxmd.com/read/28943875/chasing-after-non-cyanobacterial-nitrogen-fixation-in-marine-pelagic-environments
#1
Pia H Moisander, Mar Benavides, Sophie Bonnet, Ilana Berman-Frank, Angelicque E White, Lasse Riemann
Traditionally, cyanobacterial activity in oceanic photic layers was considered responsible for the marine pelagic dinitrogen (N2) fixation. Other potentially N2-fixing bacteria and archaea have also been detected in the pelagic water column, however, the activity and importance of these non-cyanobacterial diazotrophs (NCDs) remain poorly constrained. In this perspective we summarize the N2 fixation rates from recently published studies on photic and aphotic layers that have been attributed to NCD activity via parallel molecular measurements, and discuss the status, challenges, and data gaps in estimating non-cyanobacterial N2 fixation NCNF in the ocean...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28942710/deuterium-incorporation-experiments-from-3r-and-3s-3-2-h-leucine-into-characteristic-isoprenoidal-lipid-core-of-halophilic-archaea-suggests-the-involvement-of-isovaleryl-coa-dehydrogenase
#2
Noriaki Yamauchi, Ryo Tanoue
The stereochemical reaction course for the two C-3 hydrogens of leucine to produce a characteristic isoprenoidal lipid in halophilic archaea was observed using incubation experiments with whole cell Halobacterium salinarum. Deuterium-labeled (3R)- and (3S)-[3-(2)H]leucine were freshly prepared as substrates from 2,3-epoxy-4-methyl-1-pentanol. Incorporation of deuterium from (3S)-[3-(2)H]leucine and loss of deuterium from (3R)-[3-(2)H]leucine in the lipid-core of H. salinarum was observed. Taken together with the results of our previous report, involving the incubation of chiral-labeled [5-(2)H]leucine, these results strongly suggested an involvement of isovaleryl-CoA dehydrogenase in leucine conversion to isoprenoid lipid in halophilic archaea...
September 25, 2017: Bioscience, Biotechnology, and Biochemistry
https://www.readbyqxmd.com/read/28941336/-the-new-generation-tool-for-crispr-genome-editing-crispr-cpf1
#3
Fan Yang, Yin Li
Almost all archaea and many bacteria achieve adaptive immunity through a diverse set of CRISPR-Cas systems. From 2012, Cas9 has been harnessed by thousands of laboratories for genome editing applications in a variety of experimental model systems. Cas9 is driving innovative applications from basic biology to biotechnology and medicine. However, numerous challenges still remain, such as limited targeting range, toxicity, and potential for off-target mutagenesis. Cpf1 represents a class 2/type V CRISPR RNA-guided endonuclease that is distinct from the type II CRISPR Cas9 nuclease...
March 25, 2017: Sheng Wu Gong Cheng Xue Bao, Chinese Journal of Biotechnology
https://www.readbyqxmd.com/read/28939246/co-digestion-of-chicken-manure-and-microalgae-chlorella-1067-grown-in-the-recycled-digestate-nutrients-reuse-and-biogas-enhancement
#4
Ruirui Li, Na Duan, Yuanhui Zhang, Zhidan Liu, Baoming Li, Dongming Zhang, Haifeng Lu, Taili Dong
The present investigation targeted on a sustainable co-digestion system: microalgae Chlorella 1067 (Ch. 1067) was cultivated in chicken manure (CM) based digestate and then algae biomass was used as co-substrate for anaerobic digestion with CM. About 91% of the total nitrogen and 86% of the soluble organics in the digestate were recycled after the microalgae cultivation. The methane potential of co-digestion was evaluated by varying CM to Ch. 1067 ratios (0:10, 2:8, 4:6, 6:4, 8:2, 10:0 based on the volatile solids (VS))...
September 19, 2017: Waste Management
https://www.readbyqxmd.com/read/28938870/evaluation-of-prokaryotic-diversity-of-five-hot-springs-in-eritrea
#5
Amanuel M Ghilamicael, Nancy L M Budambula, Sylvester E Anami, Tadesse Mehari, Hamadi I Boga
BACKGROUND: Total community rDNA was used to determine the diversity of bacteria and archaea from water, wet sediment and microbial mats samples of hot springs in the Eastern lowlands of Eritrea. The temperatures of the springs range from 49.5 °C to 100 °C while pH levels varied from 6.97 to 7.54. Akwar and Maiwooi have high carbonate levels. The springs near the seashore, Garbanabra and Gelti, are more saline with higher levels of sodium and chlorides. Elegedi, situated in the Alid volcanic area, has the highest temperature, iron and sulfate concentrations...
September 22, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/28934399/methane-metabolizing-microbial-communities-in-sediments-of-the-haima-cold-seep-area-northwest-slope-of-the-south-china-sea
#6
Mingyang Niu, Xibei Fan, Guangchao Zhuang, Qianyong Liang, Fengping Wang
Cold seeps are widespread chemosynthetic ecosystems in the deep-sea environment, and cold seep microbial communities of the South China Sea are poorly constrained. Here we report on the archaeal communities, particularly those involved in methane metabolization, in sediments of a newly discovered cold seep (named 'Haima') on the northwest slope of the South China Sea. Archaeal diversity, abundance and distribution were investigated in two piston cores collected from a seep area (QDN-14B) and a non-seep control site (QDN-31B)...
September 1, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28932741/efficacies-of-various-anaerobic-starter-seeds-for-biogas-production-from-different-types-of-wastewater
#7
Pawinee Chaiprasert, Nasrul Hudayah, Chompoonut Auphimai
Various anaerobic starter seeds from different sources were investigated for their efficacies in treatment of different types of wastewater. Six combinations of starter seeds and wastewaters were selected out of 25 combination batch experiments and operated in semicontinuous reactors. It was noticed that the efficacies of various anaerobic starter seeds for biogas production from different types of wastewater in terms of reactor performance and stability were depended on wastewater characteristics and F/M ratio affecting microbial community and their microbial activities...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28930187/viruses-of-microbes
#8
EDITORIAL
Laurent Debarbieux, Matthias Fischer, Tessa E F Quax
Viruses of microbes encompass all viruses that infect archaea, bacteria, and single-celled eukaryotes, especially algae and protozoa [...].
September 20, 2017: Viruses
https://www.readbyqxmd.com/read/28930182/microbial-community-structure-and-functions-in-ethanol-fed-sulfate-removal-bioreactors-for-treatment-of-mine-water
#9
Malin Bomberg, Jarno Mäkinen, Marja Salo, Mona Arnold
Sulfate-rich mine water must be treated before it is released into natural water bodies. We tested ethanol as substrate in bioreactors designed for biological sulfate removal from mine water containing up to 9 g L(-1) sulfate, using granular sludge from an industrial waste water treatment plant as inoculum. The pH, redox potential, and sulfate and sulfide concentrations were measured twice a week over a maximum of 171 days. The microbial communities in the bioreactors were characterized by qPCR and high throughput amplicon sequencing...
September 20, 2017: Microorganisms
https://www.readbyqxmd.com/read/28929202/intestinal-microbiota-of-white-shrimp-penaeus-vannamei-under-intensive-cultivation-conditions-in-ecuador
#10
Oreste Gainza, Carolina Ramírez, Alfredo Salinas Ramos, Jaime Romero
The goal of the study was to characterize the intestinal tract bacterial microbiota composition of Penaeus vannamei in intensive commercial ponds in Ecuador, comparing two shrimp-farming phases: nursery and harvest. Bacterial microbiota was examined by sequencing amplicons V2-V3 of the 16S rRNA using Ion Torrent technology. Archaea sequences were detected in both phases. Sequence analyses revealed quantitative and qualitative differences between the nursery phase and the harvest phase in shrimp intestinal microbiota composition...
September 20, 2017: Microbial Ecology
https://www.readbyqxmd.com/read/28928457/methanogens-predominate-in-natural-corrosion-protective-layers-on-metal-sheet-piles
#11
Nardy Kip, Stefan Jansen, Marcio F A Leite, Mattias de Hollander, Michael Afanasyev, Eiko E Kuramae, Johannes A Van Veen
Microorganisms are able to cause, but also to inhibit or protect against corrosion. Corrosion inhibition by microbial processes may be due to the formation of mineral deposition layers on metal objects. Such deposition layers have been found in archaeological studies on ancient metal objects, buried in soil, which were hardly corroded. Recent field investigations showed that natural mineral deposition layers can be found on sheet piles in soil. We investigated the microbial communities of these deposition layers and the adjacent soil...
September 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28928211/the-crispr-spacer-space-is-dominated-by-sequences-from-species-specific-mobilomes
#12
Sergey A Shmakov, Vassilii Sitnik, Kira S Makarova, Yuri I Wolf, Konstantin V Severinov, Eugene V Koonin
Clustered regularly interspaced short palindromic repeats and CRISPR-associated protein (CRISPR-Cas) systems store the memory of past encounters with foreign DNA in unique spacers that are inserted between direct repeats in CRISPR arrays. For only a small fraction of the spacers, homologous sequences, called protospacers, are detectable in viral, plasmid, and microbial genomes. The rest of the spacers remain the CRISPR "dark matter." We performed a comprehensive analysis of the spacers from all CRISPR-cas loci identified in bacterial and archaeal genomes, and we found that, depending on the CRISPR-Cas subtype and the prokaryotic phylum, protospacers were detectable for 1% to about 19% of the spacers (~7% global average)...
September 19, 2017: MBio
https://www.readbyqxmd.com/read/28927381/in-defence-of-the-three-domains-of-life-paradigm
#13
REVIEW
P T S van der Gulik, W D Hoff, D Speijer
BACKGROUND: Recently, important discoveries regarding the archaeon that functioned as the "host" in the merger with a bacterium that led to the eukaryotes, its "complex" nature, and its phylogenetic relationship to eukaryotes, have been reported. Based on these new insights proposals have been put forward to get rid of the three-domain Model of life, and replace it with a two-domain model. RESULTS: We present arguments (both regarding timing, complexity, and chemical nature of specific evolutionary processes, as well as regarding genetic structure) to resist such proposals...
September 19, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28926633/effects-of-salinity-on-the-cellular-physiological-responses-of-natrinema-sp-j7-2
#14
Yunjun Mei, Huan Liu, Shunxi Zhang, Ming Yang, Chun Hu, Jian Zhang, Ping Shen, Xiangdong Chen
The halophilic archaea (haloarchaea) live in hyersaline environments such as salt lakes, salt ponds and marine salterns. To cope with the salt stress conditions, haloarchaea have developed two fundamentally different strategies: the "salt-in" strategy and the "compatible-solute" strategy. Although investigation of the molecular mechanisms underlying the tolerance to high salt concentrations has made outstanding achievements, experimental study from the aspect of transcription is rare. In the present study, we monitored cellular physiology of Natrinema sp...
2017: PloS One
https://www.readbyqxmd.com/read/28926282/bacterial-and-archaeal-lipids-recovered-from-subsurface-evaporites-of-dalangtan-playa-on-the-tibetan-plateau-and-their-astrobiological-implications
#15
Ziye Cheng, Long Xiao, Hongmei Wang, Huan Yang, Jingjing Li, Ting Huang, Yi Xu, Nina Ma
Qaidam Basin (Tibetan Plateau) is considered an applicable analogue to Mars with regard to sustained extreme aridity and abundant evaporites. To investigate the possibility of the preservation of microbial lipids under these Mars analog conditions, we conducted a mineralogical and organic geochemistry study on samples collected from two Quaternary sections in Dalangtan Playa, northwestern Qaidam Basin, which will enhance our understanding of the potential preservation of molecular biomarkers on Mars. Two sedimentary units were identified along two profiles: one salt unit characterized by a predominance of gypsum and halite, and one detrital unit with a decrease of gypsum and halite and enrichment in siliciclastic minerals...
September 19, 2017: Astrobiology
https://www.readbyqxmd.com/read/28925557/analysis-of-multiple-haloarchaeal-genomes-suggests-that-the-quinone-dependent-respiratory-nitric-oxide-reductase-is-an-important-source-of-nitrous-oxide-in-hypersaline-environments
#16
Javier Torregrosa-Crespo, Pedro González-Torres, Vanesa Bautista, Julia M Esclapez, Carmen Pire, Mónica Camacho, María José Bonete, David J Richardson, Nicholas J Watmough, Rosa María Martínez-Espinosa
Microorganisms, including Bacteria and Archaea, play a key role in denitrification, which is the major mechanism by which fixed nitrogen returns to the atmosphere from soil and water. Whilst the enzymology of denitrification is well understood in Bacteria, the details of the last two reactions in this pathway, which catalyse the reduction of nitric oxide (NO) via nitrous oxide (N2 O) to nitrogen (N2 ), are little studied in Archaea, and hardly at all in haloarchaea. This work describes an extensive interspecies analysis of both complete and draft haloarchaeal genomes aimed at identifying the genes that encode respiratory nitric oxide reductases (Nors)...
September 19, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28924189/communication-via-extracellular-vesicles-enhances-viral-infection-of-a-cosmopolitan-alga
#17
Daniella Schatz, Shilo Rosenwasser, Sergey Malitsky, Sharon G Wolf, Ester Feldmesser, Assaf Vardi
Communication between microorganisms in the marine environment has immense ecological impact by mediating trophic-level interactions and thus determining community structure (1) . Extracellular vesicles (EVs) are produced by bacteria (2,3) , archaea (4) , protists (5) and metazoans, and can mediate pathogenicity (6) or act as vectors for intercellular communication. However, little is known about the involvement of EVs in microbial interactions in the marine environment (7) . Here we investigated the signalling role of EVs produced during interactions between the cosmopolitan alga Emiliania huxleyi and its specific virus (EhV, Phycodnaviridae) (8) , which leads to the demise of these large-scale oceanic blooms (9,10) ...
September 18, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/28920507/navigating-the-structure-function-evolutionary-relationship-of-csaa-chaperone-in-archaea
#18
Archana Sharma, Shikha Rani, Manisha Goel
CsaA is a protein involved in the post-translational translocation of proteins across the cytoplasmic membrane. It is considered to be a functional homolog of SecB which participates in the Sec-dependent translocation pathway in an analogous manner. CsaA has also been reported to act as a molecular chaperone, preventing aggregation of unfolded proteins. It is essentially a prokaryotic protein which is absent in eukaryotes, but found extensively in bacteria and earlier thought to be widely present in archaea...
September 18, 2017: Critical Reviews in Microbiology
https://www.readbyqxmd.com/read/28918153/linseed-oil-and-dgat1-k232a-polymorphism-effects-on-methane-emission-energy-and-nitrogen-metabolism-lactation-performance-ruminal-fermentation-and-rumen-microbial-composition-of-holstein-friesian-cows
#19
S van Gastelen, M H P W Visker, J E Edwards, E C Antunes-Fernandes, K A Hettinga, S J J Alferink, W H Hendriks, H Bovenhuis, H Smidt, J Dijkstra
Complex interactions between rumen microbiota, cow genetics, and diet composition may exist. Therefore, the effect of linseed oil, DGAT1 K232A polymorphism (DGAT1), and the interaction between linseed oil and DGAT1 on CH4 and H2 emission, energy and N metabolism, lactation performance, ruminal fermentation, and rumen bacterial and archaeal composition was investigated. Twenty-four lactating Holstein-Friesian cows (i.e., 12 with DGAT1 KK genotype and 12 with DGAT1 AA genotype) were fed 2 diets in a crossover design: a control diet and a linseed oil diet (LSO) with a difference of 22 g/kg of dry matter (DM) in fat content between the 2 diets...
September 13, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/28917104/bacteria-and-archaea-communities-in-full-scale-thermophilic-and-mesophilic-anaerobic-digesters-treating-food-wastewater-key-process-parameters-and-microbial-indicators-of-process-instability
#20
Joonyeob Lee, Seung Gu Shin, Gyuseong Han, Taewoan Koo, Seokhwan Hwang
In this study, four different mesophilic and thermophilic full-scale anaerobic digesters treating food wastewater (FWW) were monitored for 1-2years in order to investigate: 1) microbial communities underpinning anaerobic digestion of FWW, 2) significant factors shaping microbial community structures, and 3) potential microbial indicators of process instability. Twenty-seven bacterial genera were identified as abundant bacteria underpinning the anaerobic digestion of FWW. Methanosaeta harundinacea, M. concilii, Methanoculleus bourgensis, M...
September 5, 2017: Bioresource Technology
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