scholarly journals Using Captain Scott's Discovery specimens to unlock the past: has Antarctic cyanobacterial diversity changed over the last 100 years?

2017 ◽  
Vol 284 (1857) ◽  
pp. 20170833 ◽  
Author(s):  
Anne D. Jungblut ◽  
Ian Hawes
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Environmental Change ◽  
Microbial Mats ◽  
Freshwater Ecosystems ◽  
Rrna Gene ◽  
Biological Communities ◽  
Freshwater Organisms ◽  
Molecular Comparison ◽  
Cyanobacterial Diversity

Evidence of climate-driven environmental change is increasing in Antarctica, and with it comes concern that this will propagate to impacts on biological communities. Recognition and prediction of change needs to incorporate the extent and timescales over which communities vary under extant conditions. However, few observations of Antarctic microbial communities, which dominate inland habitats, allow this. We therefore carried out the first molecular comparison of Cyanobacteria in historic herbarium microbial mats from freshwater ecosystems on Ross Island and the McMurdo Ice Shelf, collected by Captain R.F. Scott's ‘Discovery’ Expedition (1902–1903), with modern samples from those areas. Using 16S rRNA gene surveys, we found that modern and historic cyanobacteria assemblages showed some variation in community structure but were dominated by the same genotypes. Modern communities had a higher richness, including genotypes not found in historic samples, but they had the highest similarity to other cyanobacteria sequences from Antarctica. The results imply slow cyanobacterial 16S rRNA gene genotype turnover and considerable community stability within Antarctic microbial mats. We suggest that this relates to Antarctic freshwater 'organisms requiring a capacity to withstand diverse stresses, and that this could also provide a degree of resistance and resilience to future climatic-driven environmental change in Antarctica.

scholarly journals Biogeochemistry and Community Composition of Iron- and Sulfur-Precipitating Microbial Mats at the Chefren Mud Volcano (Nile Deep Sea Fan, Eastern Mediterranean)

2008 ◽  
Vol 74 (10) ◽  
pp. 3198-3215 ◽  
Author(s):  
Enoma O. Omoregie ◽  
Vincent Mastalerz ◽  
Gert de Lange ◽  
Kristina L. Straub ◽  
Andreas Kappler ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Mats ◽  
Eastern Mediterranean ◽  
Sulfide Oxidation ◽  
Mud Volcano ◽  
Rrna Gene ◽  
Anaerobic Oxidation Of Methane ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences

ABSTRACT In this study we determined the composition and biogeochemistry of novel, brightly colored, white and orange microbial mats at the surface of a brine seep at the outer rim of the Chefren mud volcano. These mats were interspersed with one another, but their underlying sediment biogeochemistries differed considerably. Microscopy revealed that the white mats were granules composed of elemental S filaments, similar to those produced by the sulfide-oxidizing epsilonproteobacterium “Candidatus Arcobacter sulfidicus.” Fluorescence in situ hybridization indicated that microorganisms targeted by a “Ca. Arcobacter sulfidicus”-specific oligonucleotide probe constituted up to 24% of the total the cells within these mats. Several 16S rRNA gene sequences from organisms closely related to “Ca. Arcobacter sulfidicus” were identified. In contrast, the orange mat consisted mostly of bright orange flakes composed of empty Fe(III) (hydr)oxide-coated microbial sheaths, similar to those produced by the neutrophilic Fe(II)-oxidizing betaproteobacterium Leptothrix ochracea. None of the 16S rRNA gene sequences obtained from these samples were closely related to sequences of known neutrophilic aerobic Fe(II)-oxidizing bacteria. The sediments below both types of mats showed relatively high sulfate reduction rates (300 nmol·cm−3·day−1) partially fueled by the anaerobic oxidation of methane (10 to 20 nmol·cm−3·day−1). Free sulfide produced below the white mat was depleted by sulfide oxidation within the mat itself. Below the orange mat free Fe(II) reached the surface layer and was depleted in part by microbial Fe(II) oxidation. Both mats and the sediments underneath them hosted very diverse microbial communities and contained mineral precipitates, most likely due to differences in fluid flow patterns.

scholarly journals Isolation and Distribution of a Novel Iron-Oxidizing Crenarchaeon from Acidic Geothermal Springs in Yellowstone National Park

2007 ◽  
Vol 74 (4) ◽  
pp. 942-949 ◽  
Author(s):  
M. Kozubal ◽  
R. E. Macur ◽  
S. Korf ◽  
W. P. Taylor ◽  
G. G. Ackerman ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Yellowstone National Park ◽  
National Park ◽  
Microbial Mats ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Geothermal Springs

ABSTRACT Novel thermophilic crenarchaea have been observed in Fe(III) oxide microbial mats of Yellowstone National Park (YNP); however, no definitive work has identified specific microorganisms responsible for the oxidation of Fe(II). The objectives of the current study were to isolate and characterize an Fe(II)-oxidizing member of the Sulfolobales observed in previous 16S rRNA gene surveys and to determine the abundance and distribution of close relatives of this organism in acidic geothermal springs containing high concentrations of dissolved Fe(II). Here we report the isolation and characterization of the novel, Fe(II)-oxidizing, thermophilic, acidophilic organism Metallosphaera sp. strain MK1 obtained from a well-characterized acid-sulfate-chloride geothermal spring in Norris Geyser Basin, YNP. Full-length 16S rRNA gene sequence analysis revealed that strain MK1 exhibits only 94.9 to 96.1% sequence similarity to other known Metallosphaera spp. and less than 89.1% similarity to known Sulfolobus spp. Strain MK1 is a facultative chemolithoautotroph with an optimum pH range of 2.0 to 3.0 and an optimum temperature range of 65 to 75°C. Strain MK1 grows optimally on pyrite or Fe(II) sorbed onto ferrihydrite, exhibiting doubling times between 10 and 11 h under aerobic conditions (65°C). The distribution and relative abundance of MK1-like 16S rRNA gene sequences in 14 acidic geothermal springs containing Fe(III) oxide microbial mats were evaluated. Highly related MK1-like 16S rRNA gene sequences (>99% sequence similarity) were consistently observed in Fe(III) oxide mats at temperatures ranging from 55 to 80°C. Quantitative PCR using Metallosphaera-specific primers confirmed that organisms highly similar to strain MK1 comprised up to 40% of the total archaeal community at selected sites. The broad distribution of highly related MK1-like 16S rRNA gene sequences in acidic Fe(III) oxide microbial mats is consistent with the observed characteristics and growth optima of Metallosphaera-like strain MK1 and emphasizes the importance of this newly described taxon in Fe(II) chemolithotrophy in acidic high-temperature environments of YNP.

scholarly journals Re-evaluating the salty divide: phylogenetic specificity of transitions between marine and freshwater systems

2018 ◽  
Author(s):  
Sara F. Paver ◽  
Daniel J. Muratore ◽  
Ryan J. Newton ◽  
Maureen L. Coleman
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Communities ◽  
Relative Abundance ◽  
Environmental Changes ◽  
Habitat Type ◽  
Freshwater Ecosystems ◽  
Rrna Gene ◽  
Minimum Entropy ◽  
Habitat Types

AbstractMarine and freshwater microbial communities are phylogenetically distinct and transitions between habitat types are thought to be infrequent. We compared the phylogenetic diversity of marine and freshwater microorganisms and identified specific lineages exhibiting notably high or low similarity between marine and freshwater ecosystems using a meta-analysis of 16S rRNA gene tag-sequencing datasets. As expected, marine and freshwater microbial communities differed in the relative abundance of major phyla and contained habitat-specific lineages; at the same time, however, many shared taxa were observed in both environments. Betaproteobacteria and Alphaproteobacteria sequences had the highest similarity between marine and freshwater sample pairs. Gammaproteobacteria and Alphaproteobacteria contained the highest number of Minimum Entropy Decomposition nodes shared by marine and freshwater samples. Shared nodes included lineages of the abundant alphaproteobacterial group SAR11 that have not previously been reported in 16S rRNA gene surveys of freshwater lakes. Our results suggest that shared taxa are numerous, but tend to occur sporadically and at low relative abundance in one habitat type, leading to an underestimation of transition frequency between marine and freshwater habitats. Lineages with a high degree of shared taxa or habitat-specific diversification represent targets for genome-scale investigations into microbial adaptations and evolutionary innovations. Rare taxa with abundances near or below detection, including lineages that appear to have crossed the salty divide relatively recently, may have novel adaptations enabling them to exploit opportunities for niche expansion when environments are disturbed or conditions change.ImportanceThe distribution of microbial diversity across environments yields insight into processes that create and maintain this diversity as well as potential to infer how communities will respond to future environmental changes. We integrated datasets from dozens of freshwater lake and marine samples to compare diversity across open water habitats differing in salinity. Our novel combination of sequence-based approaches revealed phyla and proteobacterial classes inferred to include more or less recent transitions across habitat types as well as specific lineages that are shared by marine and freshwater environments at the level of 16S rRNA sequence types. Our findings contribute to understanding the ecological and evolutionary controls on microbial distributions, and open up new questions regarding the plasticity and adaptability of particular lineages.

scholarly journals Shewanella loihica sp. nov., isolated from iron-rich microbial mats in the Pacific Ocean

2006 ◽  
Vol 56 (8) ◽  
pp. 1911-1916 ◽  
Author(s):  
Haichun Gao ◽  
Anna Obraztova ◽  
Nathan Stewart ◽  
Radu Popa ◽  
James K. Fredrickson ◽  
...  
Keyword(s):  
Pacific Ocean ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Mats ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Major Fatty Acid ◽  
Rrna Gene ◽  
The Pacific ◽  
The Pacific Ocean

A novel marine bacterial strain, PV-4T, isolated from a microbial mat located at a hydrothermal vent of Loihi Seamount in the Pacific Ocean, has been characterized. This micro-organism is orangey in colour, Gram-negative, polarly flagellated, facultatively anaerobic and psychrotolerant (temperature range, 0–42 °C). No growth was observed with nitrate, nitrite, DMSO or thiosulfate as the electron acceptor and lactate as the electron donor. The major fatty acid detected in strain PV-4T was iso-C15 : 0. Strain PV-4T had ubiquinones consisting mainly of Q-7 and Q-8, and possessed menaquinone MK-7. The DNA G+C content of the strain was 53.8 mol% and the genome size was about 4.5 Mbp. Phylogenetic analyses based on 16S rRNA gene sequences placed PV-4T within the genus Shewanella. PV-4T exhibited 16S rRNA gene sequence similarity levels of 99.6 and 97.5 %, respectively, with respect to the type strains of Shewanella aquimarina and Shewanella marisflavi. DNA from strain PV-4T showed low mean levels of relatedness to the DNAs of S. aquimarina (50.5 %) and S. marisflavi (8.5 %). On the basis of phylogenetic and phenotypic characteristics, the bacterium was classified in the genus Shewanella within a distinct novel species, for which the name Shewanella loihica sp. nov. is proposed. The type strain is PV-4T (=ATCC BAA-1088T=DSM 17748T).

scholarly journals Depthwise microbiome and isotopic profiling of a moderately saline microbial mat in a solar saltern

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Varun Paul ◽  
Yogaraj Banerjee ◽  
Prosenjit Ghosh ◽  
Susheel Bhanu Busi
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Mats ◽  
Salinity Gradient ◽  
Microbial Mat ◽  
Rrna Gene ◽  
16S Rrna Gene Analysis ◽  
Eukaryotic Algae ◽  
Culture Independent ◽  
Isotopic Characterization

AbstractThe solar salterns in Tuticorin, India, are man-made, saline to hypersaline systems hosting some uniquely adapted populations of microorganisms and eukaryotic algae that have not been fully characterized. Two visually different microbial mats (termed ‘white’ and ‘green’) developing on the reservoir ponds (53 PSU) were isolated from the salterns. Firstly, archaeal and bacterial diversity in different vertical layers of the mats were analyzed. Culture-independent 16S rRNA gene analysis revealed that both bacteria and archaea were rich in their diversity. The top layers had a higher representation of halophilic archaea Halobacteriaceae, phylum Chloroflexi, and classes Anaerolineae, Delta- and Gamma- Proteobacteria than the deeper sections, indicating that a salinity gradient exists within the mats. Limited presence of Cyanobacteria and detection of algae-associated bacteria, such as Phycisphaerae, Phaeodactylibacter and Oceanicaulis likely implied that eukaryotic algae and other phototrophs could be the primary producers within the mat ecosystem. Secondly, predictive metabolic pathway analysis using the 16S rRNA gene data revealed that in addition to the regulatory microbial functions, methane and nitrogen metabolisms were prevalent. Finally, stable carbon and nitrogen isotopic compositions determined from both mat samples showed that the δ13Corg and δ15Norg values increased slightly with depth, ranging from − 16.42 to − 14.73‰, and 11.17 to 13.55‰, respectively. The isotopic signature along the microbial mat profile followed a pattern that is distinctive to the community composition and net metabolic activities, and comparable to saline mats in other salterns. The results and discussions presented here by merging culture-independent studies, predictive metabolic analyses and isotopic characterization, provide a collective strategy to understand the compositional and functional characteristics of microbial mats in saline environments.

scholarly journals Cyanobacterial Diversity in Natural and Artificial Microbial Mats of Lake Fryxell (McMurdo Dry Valleys, Antarctica): a Morphological and Molecular Approach

2003 ◽  
Vol 69 (9) ◽  
pp. 5157-5169 ◽  
Author(s):  
Arnaud Taton ◽  
Stana Grubisic ◽  
Evelyne Brambilla ◽  
Rutger De Wit ◽  
Annick Wilmotte
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Geographic Distribution ◽  
Rrna Gene ◽  
Molecular Tools ◽  
Its Sequence Analysis ◽  
Two Samples ◽  
Lake Fryxell ◽  
Cyanobacterial Diversity ◽  
The 16S Rrna Gene

ABSTRACT Currently, there is no consensus concerning the geographic distribution and extent of endemism in Antarctic cyanobacteria. In this paper we describe the phenotypic and genotypic diversity of cyanobacteria in a field microbial mat sample from Lake Fryxell and in an artificial cold-adapted sample cultured in a benthic gradient chamber (BGC) by using an inoculum from the same mat. Light microscopy and molecular tools, including 16S rRNA gene clone libraries, denaturing gradient gel electrophoresis, and sequencing, were used. For the first time in the study of cyanobacterial diversity of environmental samples, internal transcribed spacer (ITS) sequences were retrieved and analyzed to complement the information obtained from the 16S rRNA gene. Microscopy allowed eight morphotypes to be identified, only one of which is likely to be an Antarctic endemic morphotype. Molecular analysis, however, revealed an entirely different pattern. A much higher number of phylotypes (15 phylotypes) was found, but no sequences from Nodularia and Hydrocoryne, as observed by microscopy, were retrieved. The 16S rRNA gene sequences determined in this study were distributed in 11 phylogenetic lineages, 3 of which were exclusively Antarctic and 2 of which were novel. Collectively, these Antarctic sequences together with all the other polar sequences were distributed in 22 lineages, 9 of which were exclusively Antarctic, including the 2 novel lineages observed in this study. The cultured BGC mat had lower diversity than the field mat. However, the two samples shared three morphotypes and three phylotypes. Moreover, the BGC mat allowed enrichment of one additional phylotype. ITS sequence analysis revealed a complex signal that was difficult to interpret. Finally, this study provided evidence of molecular diversity of cyanobacteria in Antarctica that is much greater than the diversity currently known based on traditional microscopic analysis. Furthermore, Antarctic endemic species were more abundant than was estimated on the basis of morphological features. Decisive arguments concerning the global geographic distribution of cyanobacteria should therefore incorporate data obtained with the molecular tools described here.

scholarly journals Filamentous “Epsilonproteobacteria” Dominate Microbial Mats from Sulfidic Cave Springs

2003 ◽  
Vol 69 (9) ◽  
pp. 5503-5511 ◽  
Author(s):  
Annette Summers Engel ◽  
Natuschka Lee ◽  
Megan L. Porter ◽  
Libby A. Stern ◽  
Philip C. Bennett ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Mats ◽  
Class Group ◽  
Sequence Similarity ◽  
Extreme Environments ◽  
Rrna Gene ◽  
Group I ◽  
Group Ii

ABSTRACT Hydrogen sulfide-rich groundwater discharges from springs into Lower Kane Cave, Wyoming, where microbial mats dominated by filamentous morphotypes are found. The full-cycle rRNA approach, including 16S rRNA gene retrieval and fluorescence in situ hybridization (FISH), was used to identify these filaments. The majority of the obtained 16S rRNA gene clones from the mats were affiliated with the “Epsilonproteobacteria” and formed two distinct clusters, designated LKC group I and LKC group II, within this class. Group I was closely related to uncultured environmental clones from petroleum-contaminated groundwater, sulfidic springs, and sulfidic caves (97 to 99% sequence similarity), while group II formed a novel clade moderately related to deep-sea hydrothermal vent symbionts (90 to 94% sequence similarity). FISH with newly designed probes for both groups specifically stained filamentous bacteria within the mats. FISH-based quantification of the two filament groups in six different microbial mat samples from Lower Kane Cave showed that LKC group II dominated five of the six mat communities. This study further expands our perceptions of the diversity and geographic distribution of “Epsilonproteobacteria” in extreme environments and demonstrates their biogeochemical importance in subterranean ecosystems.

Differentiation Of Clarias Batrachus, C. Gariepinus And Heteropneustes Fossilis By Pcr-Sequencing Of Mitochondrial 16s Rrna Gene

2015 ◽  
Vol 41 (1) ◽  
pp. 51-58
Author(s):  
Mohammad Shamimul Alam ◽  
Hawa Jahan ◽  
Rowshan Ara Begum ◽  
Reza M Shahjahan
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Fish Larva ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Valuable Insight ◽  
Multiple Sequence ◽  
Pcr Rflp ◽  
Alternative Means

Heteropneustesfossilis, Clariasbatrachus and C. gariepinus are three major catfishes ofecological and economic importance. Identification of these fish species becomes aproblem when the usual external morphological features of the fish are lost or removed,such as in canned fish. Also, newly hatched fish larva is often difficult to identify. PCRsequencingprovides accurate alternative means of identification of individuals at specieslevel. So, 16S rRNA genes of three locally collected catfishes were sequenced after PCRamplification and compared with the same gene sequences available from othergeographical regions. Multiple sequence alignment of the 16S rRNA gene fragments ofthe catfish species has revealed polymorphic sites which can be used to differentiate thesethree species from one another and will provide valuable insight in choosing appropriaterestriction enzymes for PCR-RFLP based identification in future. Asiat. Soc. Bangladesh, Sci. 41(1): 51-58, June 2015

Marine mammals are natural hosts of Oceanivirga salmonicida, a bacterial pathogen of Atlantic salmon

2020 ◽  
Vol 139 ◽  
pp. 161-174
Author(s):  
R Palmer ◽  
GTA Fleming ◽  
S Glaeser ◽  
T Semmler ◽  
A Flamm ◽  
...  
Keyword(s):  
16S Rrna ◽  
Atlantic Salmon ◽  
16S Rrna Gene ◽  
Marine Mammals ◽  
Rrna Gene ◽  
Bacterial Disease ◽  
Common Dolphin ◽  
Stenella Coeruleoalba ◽  
Striped Dolphin ◽  
Natural Hosts

During 1992 and 1993, a bacterial disease occurred in a seawater Atlantic salmon Salmo salar farm, causing serious mortalities. The causative agent was subsequently named as Oceanivirga salmonicida, a member of the Leptotrichiaceae. Searches of 16S rRNA gene sequence databases have shown sequence similarities between O. salmonicida and uncultured bacterial clones from the digestive tracts of marine mammals. In the current study, oral samples were taken from stranded dolphins (common dolphin Delphinus delphis, striped dolphin Stenella coeruleoalba) and healthy harbour seals Phoca vitulina. A bacterium with growth characteristics consistent with O. salmonicida was isolated from a common dolphin. The isolate was confirmed as O. salmonicida, by comparisons to the type strain, using 16S rRNA gene, gyrB, groEL, and recA sequence analyses, average nucleotide identity analysis, and MALDI-TOF mass spectrometry. Metagenomic analysis indicated that the genus Oceanivirga represented a significant component of the oral bacterial microbiomes of the dolphins and seals. However, sequences consistent with O. salmonicida were only found in the dolphin samples. Analyses of marine mammal microbiome studies in the NCBI databases showed sequences consistent with O. salmonicida from the common dolphin, striped dolphin, bottlenose dolphin Tursiops truncatus, humpback whale Megaptera novaeangliae, and harbour seal. Sequences from marine environmental studies in the NCBI databases showed no sequences consistent with O. salmonicida. The findings suggest that several species of marine mammals are natural hosts of O. salmonicida.

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