scholarly journals Cold-Active Shewanella glacialimarina TZS-4T nov. Features a Temperature-Dependent Fatty Acid Profile and Putative Sialic Acid Metabolism

2021 ◽  
Vol 12 ◽  
Author(s):  
Muhammad Suleman Qasim ◽  
Mirka Lampi ◽  
Minna-Maria K. Heinonen ◽  
Berta Garrido-Zabala ◽  
Dennis H. Bamford ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Sialic Acid ◽  
Sea Ice ◽  
Acid Metabolism ◽  
Elevated Temperatures ◽  
Consensus Sequence ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Wide Range ◽  
Cold Active

Species of genus Shewanella are among the most frequently identified psychrotrophic bacteria. Here, we have studied the cellular properties, growth dynamics, and stress conditions of cold-active Shewanella strain #4, which was previously isolated from Baltic Sea ice. The cells are rod-shaped of ~2μm in length and 0.5μm in diameter, and they grow between 0 and 25°C, with an optimum at 15°C. The bacterium grows at a wide range of conditions, including 0.5–5.5% w/v NaCl (optimum 0.5–2% w/v NaCl), pH 5.5–10 (optimum pH 7.0), and up to 1mM hydrogen peroxide. In keeping with its adaptation to cold habitats, some polyunsaturated fatty acids, such as stearidonic acid (18:4n-3), eicosatetraenoic acid (20:4n-3), and eicosapentaenoic acid (20:5n-3), are produced at a higher level at low temperature. The genome is 4,456kb in size and has a GC content of 41.12%. Uniquely, strain #4 possesses genes for sialic acid metabolism and utilizes N-acetyl neuraminic acid as a carbon source. Interestingly, it also encodes for cytochrome c3 genes, which are known to facilitate environmental adaptation, including elevated temperatures and exposure to UV radiation. Phylogenetic analysis based on a consensus sequence of the seven 16S rRNA genes indicated that strain #4 belongs to genus Shewanella, closely associated with Shewanella aestuarii with a ~97% similarity, but with a low DNA–DNA hybridization (DDH) level of ~21%. However, average nucleotide identity (ANI) analysis defines strain #4 as a separate Shewanella species (ANI score=76). Further phylogenetic analysis based on the 92 most conserved genes places Shewanella strain #4 into a distinct phylogenetic clade with other cold-active marine Shewanella species. Considering the phylogenetic, phenotypic, and molecular characterization, we conclude that Shewanella strain #4 is a novel species and name it Shewanella glacialimarina sp. nov. TZS-4T, where glacialimarina means sea ice. Consequently, S. glacialimarina TZS-4T constitutes a promising model for studying transcriptional and translational regulation of cold-active metabolism.

Amplification of 16S rRNA genes of Anaplasma species in China for phylogenetic analysis

2005 ◽  
Vol 107 (1-2) ◽  
pp. 145-148 ◽  
Author(s):  
Zhijie Liu ◽  
Jianxun Luo ◽  
Qi Bai ◽  
Miling Ma ◽  
Guiguan Guan ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Genes ◽  
Rrna Genes

scholarly journals Responses of Active Ammonia Oxidizers and Nitrification Activity in Eutrophic Lake Sediments to Nitrogen and Temperature

2019 ◽  
Vol 85 (18) ◽  
Author(s):  
Ling Wu ◽  
Cheng Han ◽  
Guangwei Zhu ◽  
Wenhui Zhong
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Ammonia Oxidizing Bacteria ◽  
Ammonia Oxidizers ◽  
Nitrogen Input ◽  
Nitrification Activity ◽  
Ammonia Oxidizing Archaea ◽  
Nitrogen Inputs

ABSTRACTAmmonium concentrations and temperature drive the activities of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB), but their effects on these microbes in eutrophic freshwater sediments are unclear. In this study, surface sediments collected from areas of Taihu Lake (China) with different degrees of eutrophication were incubated under three levels of nitrogen input and temperature, and the autotrophic growth of ammonia oxidizers was assessed using13C-labeled DNA-based stable-isotope probing (SIP), while communities were characterized using MiSeq sequencing and phylogenetic analysis of 16S rRNA genes. Nitrification rates in sediment microcosms were positively correlated with nitrogen inputs, but there was no marked association with temperature. Incubation of SIP microcosms indicated that AOA and AOBamoAgenes were labeled by13C at 20°C and 30°C in the slightly eutrophic sediment, and AOBamoAgenes were labeled to a much greater extent than AOAamoAgenes in the moderately eutrophic sediment after 56 days. Phylogenetic analysis of13C-labeled 16S rRNA genes revealed that the active AOA were mainly affiliated with theNitrosopumiluscluster, with theNitrososphaeracluster dominating in the slightly eutrophic sediment at 30°C with low ammonium input (1 mM). Active AOB communities were more sensitive to nitrogen input and temperature than were AOA communities, and they were exclusively dominated by theNitrosomonascluster, which tended to be associated withNitrosomonadaceae-like lineages.Nitrosomonassp. strain Is79A3 tended to dominate the moderately eutrophic sediment at 10°C with greater ammonium input (2.86 mM). The relative abundance responses of the major active communities to nitrogen input and temperature gradients varied, indicating niche differentiation and differences in the physiological metabolism of ammonia oxidizers that are yet to be described.IMPORTANCEBoth archaea and bacteria contribute to ammonia oxidation, which plays a central role in the global cycling of nitrogen and is important for reducing eutrophication in freshwater environments. The abundance and activities of ammonia-oxidizing archaea and bacteria in eutrophic limnic sediments vary with different ammonium concentrations or with seasonal shifts, and how the two factors affect nitrification activity, microbial roles, and active groups in different eutrophic sediments is unclear. The significance of our research is in identifying the archaeal and bacterial responses to anthropogenic activity and climate change, which will greatly enhance our understanding of the physiological metabolic differences of ammonia oxidizers.

scholarly journals Census of the Viral Metagenome within an Activated Sludge Microbial Assemblage

2010 ◽  
Vol 76 (8) ◽  
pp. 2673-2677 ◽  
Author(s):  
Larissa C. Parsley ◽  
Erin J. Consuegra ◽  
Stephen J. Thomas ◽  
Jaysheel Bhavsar ◽  
Andrew M. Land ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
Activated Sludge ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Bacterial Isolates ◽  
Microbial Assemblage ◽  
Culture Independent ◽  
Culture Dependent

ABSTRACT The viral metagenome within an activated sludge microbial assemblage was sampled using culture-dependent and culture-independent methods and compared to the diversity of activated sludge bacterial taxa. A total of 70 unique cultured bacterial isolates, 24 cultured bacteriophages, 829 bacterial metagenomic clones of 16S rRNA genes, and 1,161 viral metagenomic clones were subjected to a phylogenetic analysis.

Phylogenetic analysis of several Thermus strains from Rehai of Tengchong, Yunnan, China

2005 ◽  
Vol 51 (10) ◽  
pp. 881-886 ◽  
Author(s):  
Lianbing Lin ◽  
Jie Zhang ◽  
Yunlin Wei ◽  
Chaoyin Chen ◽  
Qian Peng
Keyword(s):  
Phylogenetic Analysis ◽  
Secondary Structure ◽  
16S Rrna ◽  
Hot Springs ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Structure Comparison ◽  
Rdna Sequences ◽  
16S Rdna Sequences ◽  
Rehai Geothermal Area

Several Thermus strains were isolated from 10 hot springs of the Rehai geothermal area in Tengchong, Yunnan province. The diversity of Thermus strains was examined by sequencing the 16S rRNA genes and comparing their sequences. Phylogenetic analysis showed that the 16S rDNA sequences from the Rehai geothermal isolates form four branches in the phylogenetic tree and had greater than 95.9% similarity in the phylogroup. Secondary structure comparison also indicated that the 16S rRNA from the Rehai geothermal isolates have unique secondary structure characteristics in helix 6, helix 9, and helix 10 (reference to Escherichia coli). This research is the first attempt to reveal the diversity of Thermus strains that are distributed in the Rehai geothermal area.Key words: Thermus, diversity, phylogenetic analysis, RNA secondary structure.

scholarly journals Survey of bacteria associated with western corn rootworm life stages reveals no difference between insects reared in different soils

2018 ◽  
Author(s):  
Dalton C. Ludwick ◽  
Aaron C. Ericsson ◽  
Lisa N. Meihls ◽  
Michelle L.J. Gregory ◽  
Deborah L. Finke ◽  
...  
Keyword(s):  
Pest Management ◽  
Life Stage ◽  
Diabrotica Virgifera Virgifera ◽  
Western Corn Rootworm ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Corn Rootworm ◽  
Life Stages ◽  
Wide Range ◽  
Different Soils

AbstractWestern corn rootworm (Diabrotica virgifera virgifera LeConte) is a serious pest of maize (Zea mays L.) in North America and parts of Europe. With most of its life cycle spent in the soil feeding on maize root tissues, this insect is likely to encounter and interact with a wide range of soil and rhizosphere microbes. Our knowledge of the role of microbes in pest management and plant health remains incomplete. An important component of an effective pest management strategy is to know which microorganisms are present that could play a role in life history or management. For this study, insects were reared in soils from different locations. Insects were sampled at each life stage to determine the possible core bacteriome. Additionally, soil was sampled at each life stage and resulting bacteria were identified to determine the contribution of soil to the rootworm bacteriome, if any. We analyzed the V4 hypervariable region of bacterial 16S rRNA genes with Illumina MiSeq to survey the different species of bacteria associated with the insects and the soils. The bacterial community associated with insects was significantly different from that in the soil. Some differences appear to exist between insects from non-diapausing and diapausing colonies while no significant differences in community composition existed between the insects reared on different soils. Despite differences in the bacteria present in immature stages and in male and female adults, there is a possible core bacteriome of approximately 16 operational taxonomic units (i.e., present across all life stages). This research may give insights into how resistance to Bt develops, improved nutrition in artificial rearing systems, and new management strategies.

scholarly journals A Comparative Study: Taxonomic Grouping of Alkaline Protease Producing Bacilli

2017 ◽  
Vol 66 (1) ◽  
pp. 39-56
Author(s):  
Nilgun Tekin ◽  
Arzu Coleri Cihan ◽  
Basar Karaca ◽  
Cumhur Cokmus
Keyword(s):  
16S Rrna ◽  
Alkaline Protease ◽  
Phylogenetic Analyses ◽  
Molecular Techniques ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Protease Production ◽  
Rrna Gene ◽  
Wide Range ◽  
Its Pcr

Alkaline proteases have biotechnological importance due to their activity and stability at alkaline pH. 56 bacteria, capable of growing under alkaline conditions were isolated and their alkaline protease activities were carried out at different parameters to determine their optimum alkaline protease production conditions. Seven isolates were showed higher alkaline protease production capacity than the reference strains. The highest alkaline protease producing isolates (103125 U/g), E114 and C265, were identified as Bacillus licheniformis with 99.4% and Bacillus mojavensis 99.8% based on 16S rRNA gene sequence similarities, respectively. Interestingly, the isolates identified as Bacillus safensis were also found to be high alkaline protease producing strains. Genotypic characterizations of the isolates were also determined by using a wide range of molecular techniques (ARDRA, ITS-PCR, (GTG)5-PCR, BOX-PCR). These different techniques allowed us to differentiate the alkaliphilic isolates and the results were in concurrence with phylogenetic analyses of the 16S rRNA genes. While ITS-PCR provided the highest correlation with 16S rRNA groups, (GTG)5-PCR showed the highest differentiation at species and intra-species level. In this study, each of the biotechnologically valuable alkaline protease producing isolates was grouped into their taxonomic positions with multi-genotypic analyses.

Polyphasic analysis for elucidating the taxonomic position of selected unicellular marine cyanobacteria from Indian and Hong Kong coast

Phytotaxa ◽  
2017 ◽  
Vol 307 (4) ◽  
pp. 263
Author(s):  
T. BHUVANESHWARI ◽  
M. SHYLAJANACIYAR ◽  
P. ARUL PRAKASAM ◽  
K. EZHILMARAN ◽  
L. KARTHICK ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
Evolutionary Relationship ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Valuable Insight ◽  
Internal Transcribed Spacer Region ◽  
Ultrastructural Studies ◽  
Marine Habitats

Cyanobacteria, the primordial oxygenic photosynthetic prokaryotes encompass a wide spectrum of morphologies and ecologies. The diversity of twelve marine unicellular cyanobacteria isolated from different marine habitats was analyzed morphologically. The evolutionary relationship among the investigated strains was examined by phylogenetic analysis of nearly complete 16S rRNA gene and 16-23S internal transcribed spacer region. Phylogenetic analysis of both 16S rRNA genes and internal spacer regions exhibited coherent clustering patterns. The genetic relatedness of the investigated strains was largely congruent with morphology-based taxonomic groupings. All the investigated strains possess both the types of tRNA (tRNAIle and tRNAAla) in their 16-23S internal spacer regions and significantly varied GC contents and spacer sequence lengths. Further, ultrastructural studies provide a more valuable insight into the cyanobacterial taxa studied. Our study helps to apply the polyphasic approach (use of morphology, ultra-structure, ecology, and molecular analysis of complete 16S rRNA genes and 16-23S internal spacer regions) to resolve taxonomic ambiguities and provide a fairly robust cyanobacterial classification system among the unicellular forms studied.

scholarly journals Computer-simulated RFLP analysis of 16S rRNA genes: identification of ten new phytoplasma groups

2007 ◽  
Vol 57 (8) ◽  
pp. 1855-1867 ◽  
Author(s):  
Wei Wei ◽  
Robert E. Davis ◽  
Ing-Ming Lee ◽  
Yan Zhao
Keyword(s):  
16S Rrna ◽  
Classification Scheme ◽  
Rflp Analysis ◽  
Plant Diseases ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Similarity Coefficients ◽  
Wide Range

Phytoplasmas are cell wall-less bacteria that cause numerous plant diseases. As no phytoplasma has been cultured in cell-free medium, phytoplasmas cannot be differentiated and classified by the traditional methods which are applied to culturable prokaryotes. Over the past decade, the establishment of a phytoplasma classification scheme based on 16S rRNA restriction fragment length polymorphism (RFLP) patterns has enabled the accurate and reliable identification and classification of a wide range of phytoplasmas. In the present study, we expanded this classification scheme through the use of computer-simulated RFLP analysis, achieving rapid differentiation and classification of phytoplasmas. Over 800 publicly available phytoplasma 16S rRNA gene sequences were aligned using the clustal_x program and the aligned 1.25 kb fragments were exported to pDRAW32 software for in silico restriction digestion and virtual gel plotting. Based on distinctive virtual RFLP patterns and calculated similarity coefficients, phytoplasma strains were classified into 28 groups. The results included the classification of hundreds of previously unclassified phytoplasmas and the delineation of 10 new phytoplasma groups representing three recently described and seven novel putative ‘Candidatus Phytoplasma’ taxa.

scholarly journals Relationship of Vibrio Species Infection and Elevated Temperatures to Yellow Blotch/Band Disease in Caribbean Corals

2004 ◽  
Vol 70 (11) ◽  
pp. 6855-6864 ◽  
Author(s):  
James M. Cervino ◽  
Raymond L. Hayes ◽  
Shawn W. Polson ◽  
Sara C. Polson ◽  
Thomas J. Goreau ◽  
...  
Keyword(s):  
Elevated Temperatures ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Coral Tissue ◽  
Symbiotic Algae ◽  
Rate Of Spread ◽  
Lower Division ◽  
Elevated Water ◽  
Relationship Of ◽  
Temperature Factors

ABSTRACT The bacterial and temperature factors leading to yellow blotch/band disease (YBD), which affects the major reef-building Caribbean corals Montastrea spp., have been investigated. Groups of bacteria isolated from affected corals and inoculated onto healthy corals caused disease signs similar to those of YBD. The 16S rRNA genes from these bacteria were sequenced and found to correspond to four Vibrio spp. Elevating the water temperature notably increased the rate of spread of YBD on inoculated corals and induced greater coral mortality. YBD-infected corals held at elevated water temperatures had 50% lower zooxanthella densities, 80% lower division rates, and a 75% decrease in chlorophyll a and c 2 pigments compared with controls. Histological sections indicated that the algal pyrenoid was fragmented into separate segments, along with a reconfiguration and swelling of the zooxanthellae, as well as vacuolization. YBD does not appear to produce the same physiological response formerly observed in corals undergoing temperature-related bleaching. Evidence indicates that YBD affects primarily the symbiotic algae rather than coral tissue.

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