Redalyc.Shallow-Water Hydrothermal Vents in the Azores (Portugal)
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Albirhodobacter Marinus Gen. Nov., Sp. Nov., a Member of the Family Rhodobacteriaceae Isolated from Sea Shore Water of Visakhapatnam, India
Author version: Antonie van Leeuwenhoek, vol.103; 2013; 347-355 Albirhodobacter marinus gen. nov., sp. nov., a member of the family Rhodobacteriaceae isolated from sea shore water of Visakhapatnam, India Nupur1, Bhumika, Vidya1., Srinivas, T. N. R2,3, Anil Kumar, P1* 1Microbial Type Culture Collection and Gene bank, Institute of Microbial Technology (CSIR), Sector 39A, Chandigarh - 160 036, INDIA 2National Institute of Oceanography (CSIR), Regional centre, P B No. 1913, Dr. Salim Ali Road, Kochi - 682018 (Kerala), INDIA Present Address: 3National Institute of Oceanography (CSIR), Regional centre, 176, Lawsons Bay Colony, Visakhapatnam - 530 017 (Andhra Pradesh), INDIA Address for correspondence* Dr. P. Anil Kumar Microbial Type Culture Collection and Gene bank Institute of Microbial Technology, Sector 39A, Chandigarh - 160 036, INDIA Email: [email protected] Phone: +91-172-6665170 1 Abstract A novel marine, Gram-negative, rod-shaped bacterium, designated strain N9T, was isolated from a water sample of the sea shore at Visakhapatnam, Andhra Pradesh (India). Strain N9T was found to be positive for oxidase and catalase activities. The fatty acids were found to be dominated by C16:0, C18:1 ω7c and summed in feature 3 (C16:1 ω7c and/or C16:1 ω6c). Strain N9T was determined to contain Q-10 as the major respiratory quinone and phosphatidylethanolamine, phosphatidylglycerol, two aminophospholipids, two phospholipids and four unidentified lipids as polar lipids. The DNA G+C content of the strain N9T was found to be 63 mol%. 16S rRNA gene sequence analysis indicated that Rhodobacter sphaeroides, Rhodobacter johrii, Pseudorhodobacter ferrugineus, Rhodobacter azotoformans, Rhodobacter ovatus and Pseudorhodobacter aquimaris were the nearest phylogenetic neighbours, with pair-wise sequence similarities of 95.43, 95.36, 94.24, 95.31, 95.60 and 94.74 % respectively. -
Horizontal Operon Transfer, Plasmids, and the Evolution of Photosynthesis in Rhodobacteraceae
The ISME Journal (2018) 12:1994–2010 https://doi.org/10.1038/s41396-018-0150-9 ARTICLE Horizontal operon transfer, plasmids, and the evolution of photosynthesis in Rhodobacteraceae 1 2 3 4 1 Henner Brinkmann ● Markus Göker ● Michal Koblížek ● Irene Wagner-Döbler ● Jörn Petersen Received: 30 January 2018 / Revised: 23 April 2018 / Accepted: 26 April 2018 / Published online: 24 May 2018 © The Author(s) 2018. This article is published with open access Abstract The capacity for anoxygenic photosynthesis is scattered throughout the phylogeny of the Proteobacteria. Their photosynthesis genes are typically located in a so-called photosynthesis gene cluster (PGC). It is unclear (i) whether phototrophy is an ancestral trait that was frequently lost or (ii) whether it was acquired later by horizontal gene transfer. We investigated the evolution of phototrophy in 105 genome-sequenced Rhodobacteraceae and provide the first unequivocal evidence for the horizontal transfer of the PGC. The 33 concatenated core genes of the PGC formed a robust phylogenetic tree and the comparison with single-gene trees demonstrated the dominance of joint evolution. The PGC tree is, however, largely incongruent with the species tree and at least seven transfers of the PGC are required to reconcile both phylogenies. 1234567890();,: 1234567890();,: The origin of a derived branch containing the PGC of the model organism Rhodobacter capsulatus correlates with a diagnostic gene replacement of pufC by pufX. The PGC is located on plasmids in six of the analyzed genomes and its DnaA- like replication module was discovered at a conserved central position of the PGC. A scenario of plasmid-borne horizontal transfer of the PGC and its reintegration into the chromosome could explain the current distribution of phototrophy in Rhodobacteraceae. -
Limibaculum Halophilum Gen. Nov., Sp. Nov., a New Member of the Family Rhodobacteraceae
TAXONOMIC DESCRIPTION Shin et al., Int J Syst Evol Microbiol 2017;67:3812–3818 DOI 10.1099/ijsem.0.002200 Limibaculum halophilum gen. nov., sp. nov., a new member of the family Rhodobacteraceae Yong Ho Shin,1 Jong-Hwa Kim,1 Ampaitip Suckhoom,2 Duangporn Kantachote2 and Wonyong Kim1,* Abstract A Gram-stain-negative, cream-pigmented, aerobic, non-motile, non-spore-forming and short-rod-shaped bacterial strain, designated CAU 1123T, was isolated from mud from reclaimed land. The strain’s taxonomic position was investigated by using a polyphasic approach. Strain CAU 1123T grew optimally at 37 C and at pH 7.5 in the presence of 2 % (w/v) NaCl. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain CAU 1123T formed a monophyletic lineage within the family Rhodobacteraceae with 93.8 % or lower sequence similarity to representatives of the genera Rubrimonas, Oceanicella, Pleomorphobacterium, Rhodovulum and Albimonas. The major fatty acids were C18 : 1 !7c and 11-methyl C18 : 1 !7c and the predominant respiratory quinone was Q-10. The polar lipids were phosphatidylethanolamine, phosphatidylglycerol, two unidentified phospholipids, one unidentified aminolipid and one unidentified lipid. The DNA G+C content was 71.1 mol%. Based on the data from phenotypic, chemotaxonomic and phylogenetic studies, it is proposed that strain CAU 1123T represents a novel genus and novel species of the family Rhodobacteraceae, for which the name Limibaculumhalophilum gen. nov., sp. nov. The type strain is CAU 1123T (=KCTC 52187T, =NBRC 112522T). The family Rhodobacteraceae was first established by Garr- chemotaxonomic properties along with a detailed phyloge- ity et al. -
Phylogenetic Diversity of Culturable Bacteria in Chaetoceros Gracilis Mass Culture System of a Marine Finfish Hatchery
Available online at: www.mbai.org.in doi: 10.6024/jmbai.2017.59.2.2017-02 Phylogenetic diversity of culturable bacteria in Chaetoceros gracilis mass culture system of a marine finfish hatchery S. V. Sandhya, K. Preetha1, K. K. Vijayan2* ICAR-Central Marine Fisheries Research Institute, Ernakulam North P.O, PB No: 1603, Cochin, 682 018, Kerala, India. 1]School of Marine Sciences, Cochin University of Science and Technology, Cochin, 682 016, Kerala, India. 2Central Institute of Brackishwater Aquaculture, #75, Santhome High Road, Raja Annamalai Puram, Chennai, Tamil Nadu, 600 028, India. *Correspondence e-mail: [email protected] Received: 12 Oct 2017 Accepted: 30 Dec 2017 Published: 10 Jan 2018 Original Article Abstract Keywords : Algal-bacterial association, live feed, culturable bacteria, Microalgae, a major live feed in aquaculture always coexist with aquaculture, molecular phylogeny associated bacteria. Hence a better understanding of algal-bacterial interaction is essential for maintaining a stable environment in intensive larval rearing tanks. Therefore, herein we attempted to determine the phylogenetic diversity of culturable bacteria associated with microalgal production system of a marine finfish hatchery with special Introduction reference to Chaetoceros gracilis mass culture. The sequencing of 16S rDNA of representative from each phylotypes revealed that the Aquaculture is the fastest growing food-producing sector in the associated microflora belong to the classesGammaproteo bacteria, world and it is estimated that 44.14 % of fish produced globally Alphaproteo bacteria, and Bacilli. In particular, members of Marinobacter is contributed by aquaculture (Dauda et al., 2018). Microalgae genus showed higher degree of association followed by Leisingera, are ideal candidates as major live feeds in aquaculture, especially Alteromonas, Nautella, Halomonas and Ruegeria. -
Identification of Microbiological Activities in Wet Flue Gas Desulfurization Systems
fmicb-12-675628 June 23, 2021 Time: 17:59 # 1 ORIGINAL RESEARCH published: 28 June 2021 doi: 10.3389/fmicb.2021.675628 Identification of Microbiological Activities in Wet Flue Gas Desulfurization Systems Gregory Martin1†, Shagun Sharma1,2, William Ryan1, Nanda K. Srinivasan3 and John M. Senko1,2,4* 1 Department of Biology, The University of Akron, Akron, OH, United States, 2 Integrated Bioscience Program, The University of Akron, Akron, OH, United States, 3 Electric Power Research Institute, Palo Alto, CA, United States, 4 Department of Geosciences, The University of Akron, Akron, OH, United States Thermoelectric power generation from coal requires large amounts of water, much of Edited by: which is used for wet flue gas desulfurization (wFGD) systems that minimize sulfur Anna-Louise Reysenbach, emissions, and consequently, acid rain. The microbial communities in wFGDs and Portland State University, throughout thermoelectric power plants can influence system performance, waste United States processing, and the long term stewardship of residual wastes. Any microorganisms Reviewed by: Nils-Kaare Birkeland, that survive in wFGD slurries must tolerate high total dissolved solids concentrations University of Bergen, Norway (TDS) and temperatures (50–60◦C), but the inocula for wFGDs are typically from Hannah Schweitzer, UiT The Arctic University of Norway, fresh surface waters (e.g., lakes or rivers) of low TDS and temperatures, and whose Norway activity might be limited under the physicochemically extreme conditions of the wFGD. *Correspondence: To determine the extents of microbiological activities in wFGDs, we examined the John M. Senko microbial activities and communities associated with three wFGDs. O consumption [email protected] 2 ◦ † Present address: rates of three wFGD slurries were optimal at 55 C, and living cells could be detected Gregory Martin, microscopically, indicating that living and active communities of organisms were present Division of Plant and Soil Sciences, in the wFGD and could metabolize at the high temperature of the wFGD. -
Albidovulum Xiamenense Sp. Nov., a Moderately Thermophilic Bacterium from a Terrestrial Hot Spring
International Journal of Systematic and Evolutionary Microbiology (2012), 62, 1609–1612 DOI 10.1099/ijs.0.034454-0 Albidovulum xiamenense sp. nov., a moderately thermophilic bacterium from a terrestrial hot spring Decui Yin,1,2 Jing Xiao,2 Jingqun Ao,2 Chunxiang Ai1 and Xinhua Chen2 Correspondence 1School of Oceanography and Environmental Science, Xiamen University, Xiamen 361005, Fujian, Xinhua Chen PR China [email protected] 2Laboratory of Marine Biogenetic Resources of State Oceanic Administration, Chunxiang Ai Third Institute of Oceanography, Xiamen 361005, Fujian, PR China [email protected] An aerobic, motile, moderately thermophilic, rod-shaped bacterium, strain YBY-7T, was isolated from a terrestrial hot spring of a garden exhibition located in Xiamen City, Fujian Province, People’s Republic of China. Cells of strain YBY-7T were Gram-negative, irregular rods, 2–6 mm long and 0.4–0.6 mm wide, with polar flagella, and the organism formed beige colonies. The temperature and pH ranges for growth of strain YBY-7T were 28–65 6C (optimum 50–58 6C) and pH 6.5–9.5 (optimum pH 7.5–8.5). Growth occurred in the presence of 5.5 % NaCl (optimum 3.0 %). Phylogenetic analysis based on the 16S rRNA gene sequence revealed that Albidovulum inexpectatum FRR-10T was its closest neighbour (95.9 % similarity). Ubiquinone (Q-10) was the sole respiratory quinone and the DNA G+C content of strain YBY-7T was 70.6 mol%. The predominant polar lipids were phosphatidylcholine, phosphatidylglycerol and phosphatidylethanolamine. The major fatty acids were C18 : 1v7c (29.3 %), C19 : 0 cyclo v8c (25.6 %), C18 : 0 (23.6 %) and C16 : 0 (9.6 %). -
Amplicons’ from Whole-Metagenome Datasets
Kelpie: generating full-length `amplicons' from whole-metagenome datasets Paul Greenfield1,2,3, Nai Tran-Dinh1 and David Midgley1 1 Commonwealth Scientific and Industrial Research Organisation, North Ryde, NSW, Australia 2 School of Biological Sciences, Macquarie University, Australia 3 School of Information Technologies, University of Sydney, Australia ABSTRACT Introduction. Whole-metagenome sequencing can be a rich source of information about the structure and function of entire metagenomic communities, but getting accurate and reliable results from these datasets can be challenging. Analysis of these datasets is founded on the mapping of sequencing reads onto known genomic regions from known organisms, but short reads will often map equally well to multiple regions, and to multiple reference organisms. Assembling metagenomic datasets prior to mapping can generate much longer and more precisely mappable sequences but the presence of closely related organisms and highly conserved regions makes metagenomic assembly challenging, and some regions of particular interest can assemble poorly. One solution to these problems is to use specialised tools, such as Kelpie, that can accurately extract and assemble full-length sequences for defined genomic regions from whole- metagenome datasets. Methods. Kelpie is a kMer-based tool that generates full-length amplicon-like se- quences from whole-metagenome datasets. It takes a pair of primer sequences and a set of metagenomic reads, and uses a combination of kMer filtering, error correction and assembly techniques to construct sets of full-length inter-primer sequences. Results. The effectiveness of Kelpie is demonstrated here through the extraction and assembly of full-length ribosomal marker gene regions, as this allows comparisons with conventional amplicon sequencing and published metagenomic benchmarks. -
Novel Nitrite Reductase Domain Structure Suggests a Chimeric
Novel nitrite reductase domain structure suggests a chimeric denitrification repertoire in Phylum Chloroflexi Sarah Schwartz1, Lily Momper1, L. Thiberio Rangel1, Cara Magnabosco2, Jan Amend3, and Gregory Fournier1 1Massachusetts Institute of Technology 2ETH Zurich 3University of Southern California June 11, 2021 Abstract Denitrification plays a central role in the global nitrogen cycle, reducing and removing nitrogen from marine and terrestrial ecosystems. The flux of nitrogen species through this pathway has a widespread impact, affecting ecological carrying capacity, agriculture, and climate. Nitrite reductase (Nir) and nitric oxide reductase (NOR) are the two central enzymes in this pathway. Here we present a previously unreported Nir domain architecture in members of Phylum Chloroflexi. Phylogenetic analyses of protein domains within Nir indicate that an ancestral horizontal transfer and fusion event produced this chimeric domain architecture. We also identify an expanded genomic diversity of a rarely reported nitric oxide reductase subtype, eNOR. Together, these results suggest a greater diversity of denitrification enzyme arrangements exist than have been previously reported. RESEARCH PAPER TITLE: Novel nitrite reductase domain structure suggests a chimeric denitrification repertoire in Phylum Chloroflexi SHORT TITLE: Novel Denitrification Architecture in Chloroflexi Sarah L. Schwartz1,2*, Lily M. Momper2,3, L. Thiberio Rangel2, Cara Magnabosco4, Jan P. Amend5,6, and Gregory P. Fournier2 1. Microbiology Graduate Program, Massachusetts Institute of Technology 2. Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology 3. Exponent, Inc., Pasadena, CA 4. Department of Earth Sciences, ETH Zurich 5. Department of Earth Sciences, University of Southern California 6. Department of Biological Sciences, University of Southern California *Correspondence: [email protected], +1 (415) 497-1747 SUMMARY Denitrification plays a central role in the global nitrogen cycle, reducing and removing nitrogen from ma- rine and terrestrial ecosystems. -
Gene Finding in Distinct Metagenomic Data Complexities Raíssa Silva, Kleber Padovani, Fabiana Góes and Ronnie Alves
geneRFinder: gene finding in distinct metagenomic data complexities Raíssa Silva, Kleber Padovani, Fabiana Góes and Ronnie Alves 1. Additional information about GeneRFinder-Benchmark The ORFs extracted from CAMI genome assemblies have similar size distribution, with a predominance of sequences smaller than 200bp (Figure1). This is due to the fact that ORF extraction considered as ORF all sequences started with start codon and ended with some stop codon, regardless of its position. In this way, ORFs that were inside ORFs were also extracted. Thus, even though an ORF is part of the coding sequence, does not represent the entire gene, but only a fraction of it. ORFs from the 12 annotated genomes of the first set of tests, named Test in Figure1, have a more balanced size distribution, however, ORFs under 200bp are also greater in this dataset. It is worth noting that the amount of ORFs less than 200bp is inversely proportional to the complexity of these samples. This is probably due to the fact that low complexity samples have, by definition, fewer genomes [1], that can reduce the complexity of the assembly process and thus obtaining larger and more reliable sequences, which will be used for the process of ORF extraction. This scenario may justify the increase in ORFs as complexity decreases. Figure 1. ORFs length distribution in the benchmark dataset. 2. Additional information about simulated genomes from CAMI In order to increase strain level diversity, CAMI used 12 strain genomes that were simulated to produce the low complexity dataset. All information about related organisms and simulation process can be found at CAMI paper [2]. -
The Microbiome of the Egyptian Red Sea Proper and Gulf of Aqaba
American University in Cairo AUC Knowledge Fountain Theses and Dissertations 2-1-2016 The microbiome of The Egyptian Red Sea proper and Gulf of Aqaba Ghada Alaa El-Din Mustafa Follow this and additional works at: https://fount.aucegypt.edu/etds Recommended Citation APA Citation Mustafa, G. (2016).The microbiome of The Egyptian Red Sea proper and Gulf of Aqaba [Master’s thesis, the American University in Cairo]. AUC Knowledge Fountain. https://fount.aucegypt.edu/etds/33 MLA Citation Mustafa, Ghada Alaa El-Din. The microbiome of The Egyptian Red Sea proper and Gulf of Aqaba. 2016. American University in Cairo, Master's thesis. AUC Knowledge Fountain. https://fount.aucegypt.edu/etds/33 This Dissertation is brought to you for free and open access by AUC Knowledge Fountain. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of AUC Knowledge Fountain. For more information, please contact [email protected]. The American University in Cairo School of Sciences and Engineering THE MICROBIOME OF THE EGYPTIAN RED SEA PROPER AND GULF OF AQABA A Thesis Submitted to The Applied Sciences Graduate Program in partial fulfillment of the requirements for the degree of Doctorate in Applied Sciences (Biotechnology) By Ghada Alaa El-Din Kamal Mustafa Masters of Science- American University in Cairo Bachelor of Science - Ain Shams University Under the supervision of Professor Rania Siam Chair of the Biology Department Fall 2015 I The American University in Cairo The Microbiome of the Egyptian Red Sea Proper and Gulf of Aqaba A Thesis Submitted by Ghada Alaa El-Din Kamal Mustafa To the Biotechnology Graduate Program, Fall 2015 in partial fulfillment of the requirements for the degree of Doctorate of Applied Sciences in Biotechnology has been approved by Dr. -
A Report of 42 Unrecorded Bacterial Species Belonging to the Alphaproteobacteria in Korea
Journal206 of Species Research 5(2):206-219, 2016JOURNAL OF SPECIES RESEARCH Vol. 5, No. 2 A report of 42 unrecorded bacterial species belonging to the Alphaproteobacteria in Korea Hyun Mi Jin1,2, Jung-Hoon Yoon3, Seung-Bum Kim4, Kwang-Yeop Jahng5, Jang-Cheon Cho6, Ki-seong Joh7, Chang-Jun Cha8, Chi-Nam Seong9, Jin-Woo Bae10, Wan-Taek Im11 and Che-Ok Jeon1,* 1Department of Life Science, Chung-Ang University, Seoul 06974, Korea 2Freshwater Bioresources Utilization Division, Nakdonggang National Institute of Biological Resources, Gyeongsangbuk-do 37242, Korea 3Department of Food Science and Biotechnology, Sungkyunkwan University, Suwon 16419, Korea 4Department of Microbiology, Chungnam National University, Daejeon 34134, Korea 5Department of Life Sciences, Chonbuk National University, Jeonju-si 54899, Korea 6Department of Biological Sciences, Inha University, Incheon 22212, Korea 7Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies, Geonggi 02450, Korea 8Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Korea 9Department of Biology, Sunchon National University, Suncheon 57922, Korea 10Department of Biology, Kyung Hee University, Seoul 02453, Korea 11Department of Biotechnology, Hankyong National University, Anseong 17546, Korea *Correspondent: [email protected] As a subset study to discover indigenous prokaryotic species in Korea, a total of 42 bacterial strains assigned to the class Alphaproteobacteria were isolated from diverse environmental habitats including plant roots, ginseng soil, -
Isolation and Partial Characterization of a New Moderate Thermophilic Albidovulum Sp. SLM16 with Transaminase Activity from Deception Island, Antarctica Sebastián L
Márquez and Blamey Biol Res (2019) 52:5 https://doi.org/10.1186/s40659-018-0210-7 Biological Research RESEARCH ARTICLE Open Access Isolation and partial characterization of a new moderate thermophilic Albidovulum sp. SLM16 with transaminase activity from Deception Island, Antarctica Sebastián L. Márquez1,2 and Jenny M. Blamey1,2* Abstract Background: A moderately thermophilic, slightly halophilic, aerobic, Gram-stain negative, bacterial strain, SLM16, was isolated from a mixed of seawater–sand-sediment sample collected from a coastal fumarole located in Whalers Bay, Deception Island, Antarctica. The aim was to screen for thermophilic microorganisms able to degrade primary amines and search for amine transaminase activity for potential industrial application. Results: Identifcation and partial characterization of the microorganism SLM16 were carried out by means of mor- phological, physiological and biochemical tests along with molecular methods. Cells of strain SLM16 were non-motile irregular rods of 1.5–2.5 μm long and 0.3–0.45 μm wide. Growth occurred in the presence of 0.5–5.5% NaCl within temperature range of 35–55 °C and pH range of 5.5–9.5, respectively. The DNA G C composition, estimated from ftsY gene, was 66% mol. Phylogenetic analysis using de 16S rRNA gene sequence showed+ that strain SLM16 belongs to the marine bacterial genus Albidovulum. Conclusion: Strain SLM16 is a moderate thermophilic Gram negative microorganisms which belongs to the marine bacterial genus Albidovulum and is closely related to Albidovulum inexpectatum species based on phylogenetic analy- sis. Additionally, amine-transaminase activity towards the arylaliphatic amine α-methylbenzylamine was detected. Keywords: Antarctica, Albiduvulum, Moderate thermophile, Amine-transaminase Introduction have been described so far [1], mainly endospore-form- Deception Island (62°57′S, 60°38′W) in Antarctica is ing bacteria belonging to the genus Bacillus have been the caldera of a currently active volcano located in the reported.