First Insights into the Microbiology of Three Antarctic Briny Systems of the Northern Victoria Land

Different polar environments (lakes and glaciers), also in Antarctica, encapsulate brine pools characterized by a unique combination of extreme conditions, mainly in terms of high salinity and low temperature. Since 2014, we have been focusing our attention on the microbiology of brine pockets from three lakes in the Northern Victoria Land (NVL), lying in the Tarn Flat (TF) and Boulder Clay (BC) areas. The microbial communities have been analyzed for community structure by next generation sequencing, extracellular enzyme activities, metabolic potentials, and microbial abundances. In this study, we aim at reconsidering all available data to analyze the influence exerted by environmental parameters on the community composition and activities. Additionally, the prediction of metabolic functions was attempted by the phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt2) tool, highlighting that prokaryotic communities were presumably involved in methane metabolism, aromatic compound biodegradation, and organic compound (proteins, polysaccharides, and phosphates) decomposition. The analyzed cryoenvironments were different in terms of prokaryotic diversity, abundance, and retrieved metabolic pathways. By the analysis of DNA sequences, common operational taxonomic units ranged from 2.2% to 22.0%. The bacterial community was dominated by Bacteroidetes. In both BC and TF brines, sequences of the most thermally tolerant and methanogenic Archaea were detected, some of them related to hyperthermophiles.

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Biogeography of terrestrial cyanobacteria from Antarctic ice-free areas

Annals of Glaciology ◽

10.3189/172756411795931930 ◽

2010 ◽

Vol 51 (56) ◽

pp. 171-177 ◽

Cited By ~ 37

Author(s):

Z. Namsaraev ◽

M.-J. Mano ◽

R. Fernandez ◽

Annick Wilmotte

Keyword(s):

Rrna Gene ◽

Distribution Analysis ◽

Operational Taxonomic Units ◽

Terrestrial Cyanobacteria ◽

Victoria Land ◽

Low Degree ◽

Range Transport ◽

Antarctic Continent ◽

The Antarctic ◽

Further Development

AbstractCyanobacteria inhabit the Antarctic continent and have even been observed in the most southerly ice-free areas of Antarctica (86–87° S). The highest molecular diversity of cyanobacterial communities was found in the areas located between 70° S and 80° S. Further south and further north from this zone, the diversity abruptly decreased. Seventy-nine per cent (33 of 42 operational taxonomic units) of Antarctic terrestrial cyanobacteria have a cosmopolitan distribution. Analysis of the sampling efforts shows that only three regions (southern Victoria Land, the Sør Rondane Mountains and Alexander Island) have been particularly well studied, while other areas did not receive enough attention. Although cyanobacteria possess a capacity for long-range transport, regional populations in Antarctic ice-free areas seem to exist. The cyanobacterial communities of the three most intensively studied regions, separated from each other by a distance of 3000–3400 km, had a low degree of similarity with each other. Further development of microbial biogeography demands a standardized approach. For this purpose, as a minimal standard, we suggest using the sequence of cyanobacterial 16S rRNA gene between Escherichia coli positions 405 and 780.

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Early Methanogenic Colonisation in the Faeces of Meishan and Yorkshire Piglets as Determined by Pyrosequencing Analysis

Archaea ◽

10.1155/2014/547908 ◽

2014 ◽

Vol 2014 ◽

pp. 1-10 ◽

Cited By ~ 21

Author(s):

Yong Su ◽

Gaorui Bian ◽

Zhigang Zhu ◽

Hauke Smidt ◽

Weiyun Zhu

Keyword(s):

Energy Metabolism ◽

Methanogenic Archaea ◽

Rrna Gene ◽

Methanogenic Community ◽

Neonatal Piglets ◽

Operational Taxonomic Units ◽

Faecal Samples ◽

16S Rrna Gene Pyrosequencing ◽

Pyrosequencing Analysis ◽

Early Establishment

Gut methanogenic archaea of monogastric animals are considered to be related to energy metabolism and adipose deposition of the host; however, information on their development in young piglets is limited. Thus, to investigate early methanogenic colonisation in the faeces of Meishan and Yorkshire piglets, faecal samples were collected from piglets at 1, 3, 7, and 14 days after birth and used to analyse the methanogenic community with 16S rRNA gene pyrosequencing. Results showed that the diversity of the methanogenic community in the faeces of neonatal piglets decreased from one to 14 days of age, as the total methanogen populations increased. The age of piglets, but not the breed, significantly affected the diversity of the methanogenic community which was dominated by the genusMethanobrevibacter. From the ages of one to 14 days, the abundance ofM. smithii-related operational taxonomic units (OTUs) increased significantly, while the abundances ofM. thaueri- andM. millerae-related OTUs decreased significantly. The substitution ofM. smithiiforM. thaueri/M. milleraewas faster in Yorkshire piglets than in Meishan piglets. These results suggest that the early establishment of microbiota in neonatal piglets is accompanied by dramatic changes in the methanogenic community, and that the changes vary among pigs of different genotypes.

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Photosynthetic responses of three common mosses from continental Antarctica

Antarctic Science ◽

10.1017/s0954102005002774 ◽

2005 ◽

Vol 17 (3) ◽

pp. 341-352 ◽

Cited By ~ 36

Author(s):

STEFAN PANNEWITZ ◽

T.G. ALLAN GREEN ◽

KADMIEL MAYSEK ◽

MARK SCHLENSOG ◽

ROD SEPPELT ◽

...

Keyword(s):

Climate Change ◽

Water Content ◽

Dark Respiration ◽

Temperature Response ◽

Environmental Parameters ◽

Net Photosynthesis ◽

Photon Flux ◽

Terrestrial Vegetation ◽

Moss Species ◽

Victoria Land

Predicting the effects of climate change on Antarctic terrestrial vegetation requires a better knowledge of the ecophysiology of common moss species. In this paper we provide a comprehensive matrix for photosynthesis and major environmental parameters for three dominant Antarctic moss species (Bryum subrotundifolium, B. pseudotriquetrum and Ceratodon purpureus). Using locations in southern Victoria Land, (Granite Harbour, 77°S) and northern Victoria Land (Cape Hallett, 72°S) we determined the responses of net photosynthesis and dark respiration to thallus water content, thallus temperature, photosynthetic photon flux densities and CO2 concentration over several summer seasons. The studies also included microclimate recordings at all sites where the research was carried out in field laboratories. Plant temperature was influenced predominantly by the water regime at the site with dry mosses being warmer. Optimal temperatures for net photosynthesis were 13.7°C, 12.0°C and 6.6°C for B. subrotundifolium, B. pseudotriquetrum and C. purpureus, respectively and fall within the known range for Antarctic mosses. Maximal net photosynthesis at 10°C ranked as B. subrotundifolium > B. pseudotriquetrum > C. purpureus. Net photosynthesis was strongly depressed at subzero temperatures but was substantial at 0°C. Net photosynthesis of the mosses was not saturated by light at optimal water content and thallus temperature. Response of net photosynthesis to increase in water content was as expected for mosses although B. subrotundifolium showed a large depression (60%) at the highest hydrations. Net photosynthesis of both B. subrotundifolium and B. pseudotriquetrum showed a large response to increase in CO2 concentration and this rose with increase in temperature; saturation was not reached for B. pseudotriquetrum at 20°C. There was a high level of variability for species at the same sites in different years and between different locations. This was substantial enough to make prediction of the effects of climate change very difficult at the moment.

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RECRUITMENT OF GROUPER BROODSTOCK ON THE BASIS OF SINGLE LOCUS DNA MARKERS

10.1101/067231 ◽

2016 ◽

Author(s):

Kenneth F. Rodrigues ◽

Ahmad Z. Tani ◽

Syarul N. Baharum

Keyword(s):

Dna Sequences ◽

Dna Markers ◽

Single Locus ◽

Representative Specimen ◽

Genomic Libraries ◽

Operational Taxonomic Units ◽

Breeding Populations ◽

Epinephelus Fuscoguttatus ◽

Species Specific ◽

Dna Profiles

AbstractScientific breeding programs are founded on the screening and recruitment of genetically diverse broodstock, with the ultimate aim of developing heterogeneous breeding populations that host a collection of desirable traits. Single locus DNA markers can be applied to facilitate the process of selection as they are species specific, reliable, reproducible and easy to use. This study set forth to develop a library of single locus DNA markers for two commercially cultured species of groupers, Epinephelus fuscoguttatus and E. corallicola. DNA was isolated from one representative specimen of each species and utilized to construct shotgun genomic libraries. DNA sequences derived from the library were selected for the development of 42 and 41 single locus DNA markers for E. fuscoguttatus and E. corallicola respectively. The markers were then tested against randomly selected specimens obtained from the wild. Genotyping results revealed that the species specific primers demonstrated the ability to distinguish between individuals from the same species into distinct operational taxonomic units (OTUs) on the basis of their differential DNA profiles, thus establishing a basis for selection based on genetic heterogeneity. The findings of this study present a strong case for the application of single locus DNA markers as molecular tools for the selection of broodstock on the basis of genotyping.

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Increases in the abundance of microbial genes encoding halotolerance and photosynthesis along a sediment salinity gradient

Biogeosciences ◽

10.5194/bg-9-815-2012 ◽

2012 ◽

Vol 9 (2) ◽

pp. 815-825 ◽

Cited By ~ 18

Author(s):

T. C. Jeffries ◽

J. R. Seymour ◽

K. Newton ◽

R. J. Smith ◽

L. Seuront ◽

...

Keyword(s):

Microbial Community ◽

Dna Sequences ◽

Salinity Gradient ◽

Compatible Solutes ◽

Environmental Parameters ◽

Sediment Samples ◽

Genetic Potential ◽

Genes Encoding ◽

Physical And Chemical ◽

Photosynthesis Gene

Abstract. Biogeochemical cycles are driven by the metabolic activity of microbial communities, yet the environmental parameters that underpin shifts in the functional potential coded within microbial community genomes are still poorly understood. Salinity is one of the primary determinants of microbial community structure and can vary strongly along gradients within a variety of habitats. To test the hypothesis that shifts in salinity will also alter the bulk biogeochemical potential of aquatic microbial assemblages, we generated four metagenomic DNA sequence libraries from sediment samples taken along a continuous, natural salinity gradient in the Coorong lagoon, Australia, and compared them to physical and chemical parameters. A total of 392483 DNA sequences obtained from four sediment samples were generated and used to compare genomic characteristics along the gradient. The most significant shifts along the salinity gradient were in the genetic potential for halotolerance and photosynthesis, which were more highly represented in hypersaline samples. At these sites, halotolerance was achieved by an increase in genes responsible for the acquisition of compatible solutes – organic chemicals which influence the carbon, nitrogen and methane cycles of sediment. Photosynthesis gene increases were coupled to an increase in genes matching Cyanobacteria, which are responsible for mediating CO2 and nitrogen cycles. These salinity driven shifts in gene abundance will influence nutrient cycles along the gradient, controlling the ecology and biogeochemistry of the entire ecosystem.

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Defining DNA-Based Operational Taxonomic Units for Microbial-Eukaryote Ecology

Applied and Environmental Microbiology ◽

10.1128/aem.00298-09 ◽

2009 ◽

Vol 75 (18) ◽

pp. 5797-5808 ◽

Cited By ~ 139

Author(s):

David A. Caron ◽

Peter D. Countway ◽

Pratik Savai ◽

Rebecca J. Gast ◽

Astrid Schnetzer ◽

...

Keyword(s):

Dna Sequences ◽

18S Rrna ◽

Species Level ◽

Rrna Gene ◽

Sequence Information ◽

Ecological Studies ◽

Gene Sequences ◽

Operational Taxonomic Units ◽

Microbial Eukaryotes ◽

Protistan Species

ABSTRACT DNA sequence information has increasingly been used in ecological research on microbial eukaryotes. Sequence-based approaches have included studies of the total diversity of selected ecosystems, studies of the autecology of ecologically relevant species, and identification and enumeration of species of interest for human health. It is still uncommon, however, to delineate protistan species based on their genetic signatures. The reluctance to assign species-level designations based on DNA sequences is in part a consequence of the limited amount of sequence information presently available for many free-living microbial eukaryotes and in part a consequence of the problematic nature of and debate surrounding the microbial species concept. Despite the difficulties inherent in assigning species names to DNA sequences, there is a growing need to attach meaning to the burgeoning amount of sequence information entering the literature, and there is a growing desire to apply this information in ecological studies. We describe a computer-based tool that assigns DNA sequences from environmental databases to operational taxonomic units at approximately species-level distinctions. This approach provides a practical method for ecological studies of microbial eukaryotes (primarily protists) by enabling semiautomated analysis of large numbers of samples spanning great taxonomic breadth. Derivation of the algorithm was based on an analysis of complete small-subunit (18S) rRNA gene sequences and partial gene sequences obtained from the GenBank database for morphologically described protistan species. The program was tested using environmental 18S rRNA data sets for two oceanic ecosystems. A total of 388 operational taxonomic units were observed for 2,207 sequences obtained from samples collected in the western North Atlantic and eastern North Pacific oceans.

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Characteristics and Metabolic Patterns of Soil Methanogenic Archaea Communities in the High Latitude Natural Wetlands of China

10.21203/rs.3.rs-54821/v1 ◽

2020 ◽

Author(s):

Di Wu ◽

Caihong Zhao ◽

Hui Bai ◽

Fujuan Feng ◽

Xin Sui ◽

...

Keyword(s):

Community Structure ◽

Vegetation Type ◽

Methanogenic Archaea ◽

Mountain Region ◽

Methanogenic Community ◽

Operational Taxonomic Units ◽

Hydrogenotrophic Methanogenesis ◽

Different Seasons ◽

Natural Wetlands ◽

And Cluster Analysis

Abstract Background: Soil methanogenic microorganisms are one of the primary methane-producing microbes in wetlands. However, we still poorly understand the community characteristic and metabolic patterns of these microorganisms according to vegetation type and seasonal changes. Therefore, to better elucidate the effects of the vegetation type and seasonal factors on the methanogenic community structure and metabolic patterns, we detected the characteristics of the soil methanogenic mcrA gene from three types of natural wetlands in different seasons in the Xiaoxing'an Mountain region, China. Result: The results indicated that the distribution of Methanobacteriaceae (hydrogenotrophic methanogens) was higher in winter, while Methanosarcinaceae and Methanosaetaceae accounted for a higher proportion in summer. Hydrogenotrophic methanogenesis was the dominant trophic pattern in each wetland. The results of principal coordinate analysis and cluster analysis showed that the vegetation type considerably influenced the methanogenic community composition. The methanogenic community structure in the Betula platyphylla – Larix gmelinii wetland was relatively different from the structure of the other two wetland types. Indicator species analysis further demonstrated that the corresponding species of indicator operational taxonomic units from the Alnus sibirica wetland and the Betula ovalifolia wetland were closer. Network analysis showed that cooperative and competitive relationships exist both within and between the same or different trophic methanogens. The core methanogens with higher abundance in each wetland were conducive to adaptation to environmental disturbances. Conclusions: This information is crucial for the assessment of metabolic patterns of soil methanogenic archaea and future fluxes in the wetlands of the Xiaoxing'an Mountain region given their vulnerability.

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An Analysis of the Temperature Profiles of Some Antarctic Lakes

10.26686/wgtn.16945933.v1 ◽

2021 ◽

Author(s):

◽

T. G. L. Shirtcliffe

Keyword(s):

Heat Source ◽

Temperature Profile ◽

Fresh Water ◽

Solute Concentration ◽

Temperature Profiles ◽

Antarctic Lakes ◽

Taylor Valley ◽

Victoria Land ◽

Brine Pools

<p>The temperature profiles of certain lakes in Taylor Valley, Victoria Land, Antarctica, are shown to be consistent with the hypothesis that these lakes were formerly cold brine pools; that their levels were raised by the addition of fresh water; and that they have since been heated principally by the absorption of sunlight. The temperature profile of a lake in Wright Valley, Victoria Land, is shown to be consistent with the hypothesis that this lake was formerly warm and stable, as are those Taylor Valley lakes which were analysed; that the addition of a further large quantity of fresh water caused instability and limited convection; and that the heat source is again absorbed sunlight. The study of this lake requires an understanding of convection in the presence of a gradient of solute concentration. A survey of existing knowledge of this type of convection shows that it is inadequate for the task. Experiments which provide the necessary information are described.</p>

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Molecular evidence for sweeping discontinuity between peracarid (Crustacea) fauna of Macaronesian islands and nearby continental coasts: over fifty candidate endemic species

10.1101/2021.06.22.449383 ◽

2021 ◽

Author(s):

Pedro E Vieira ◽

Andrea Desiderato ◽

Carla L Azevedo ◽

Patricia Esquete ◽

Filipe O Costa ◽

...

Keyword(s):

Dna Sequences ◽

Marine Invertebrates ◽

Genetic Distances ◽

Oceanic Islands ◽

Marine Conservation ◽

Molecular Evidence ◽

Network Analyses ◽

Operational Taxonomic Units ◽

La Palma ◽

Macaronesian Islands

Oceanic islands are recognized evolutionary hotspots for terrestrial organisms, but little is known about their impact on marine organisms' evolution and biogeography. The volcanic archipelagos of Macaronesia occupy a vast and complex region which is particularly suitable to investigate marine island biogeography. In this study, we used mitochondrial DNA sequences to investigate the genetic diferentiation between the populations from Webbnesia (i.e. Madeira, Selvagens and Canaries) and adjacent coasts, of 23 intertidal peracarid species. All species had unexpectedly high intraspecific genetic distances, reaching more than 20% in some cases. Between 79 and 95 Molecular Operational Taxonomic Units (MOTUs) were found in these species. Webbnesia populations displayed an impressive genetic diversity and high endemicity, with 83% of the MOTUs being private to these islands, particularly La Palma and Madeira. Network analyses suggested higher similarity between Webbnesia and Azores than with adjacent continental coasts. These results reveal an unanticipated and sweeping biogeographic discontinuity of peracaridean fauna between Webbnesia and the Iberian Peninsula, raising suspicion about the possible occurrence of identical patterns in other groups of marine invertebrates in the region. We emphasize the unique genetic heritage hosted by these islands, underlining the need to consider the fine scale endemicity in marine conservation efforts.

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Quantitative Genetic Analysis of the Maize Leaf Microbiome

10.1101/268532 ◽

2018 ◽

Cited By ~ 2

Author(s):

Jason G. Wallace ◽

Karl A. Kremling ◽

Edward S. Buckler

Keyword(s):

Community Diversity ◽

Exact Nature ◽

Common Environment ◽

Operational Taxonomic Units ◽

Metabolic Functions ◽

Genome Wide ◽

Significant Enrichment ◽

Heritability Analysis ◽

Founder Events ◽

Diversity Metrics

AbstractThe degree to which an organism can affect its associated microbial communities (“microbiome”) varies by organism and habitat, and in many cases is unknown. We address this question by analyzing the metabolically active bacteria of the maize phyllosphere across 300 diverse maize lines growing in a common environment. We performed comprehensive heritability analysis for 49 community diversity metrics, 380 bacterial clades (individual operational taxonomic units and higher-level groupings), and 9042 predicted metagenomic functions. We find that only a few few bacterial clades (5) and diversity metrics (2) are significantly heritable, while a much larger number of metabolic functions (200) are. Many of these associations appear to be driven by the amount of Methylobacteria present in each sample, and we find significant enrichment for traits relating to short-chain carbon metabolism, secretion, and nitrotoluene degradation. Genome-wide association analysis identifies a small number of associated loci for these heritable traits, including two loci (on maize chromosomes 7 and 10) that affect a large number of traits even after correcting for correlations among traits. This work is among the most comprehensive analyses of the maize phyllosphere to date. Our results indicate that while most of the maize phyllosphere composition is driven by environmental factors and/or stochastic founder events, a subset of bacterial taxa and metabolic functions is nonetheless significantly impacted by host plant genetics. Additional work will be needed to identify the exact nature of these interactions and what effects they may have on the phenotype of host plants.

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