The ecology of diatoms inhabiting cryoconite holes in Antisana Glacier, Ecuador

Abstract In the ablation zone of glacier habitats, cryoconite holes are known to harbor diverse microbial communities, including unique diatom floras distinct from those of surrounding aquatic and terrestrial systems. Besides descriptive studies, little is known about the diversity of cryoconite diatoms and their response to environmental stressors, particularly in low-latitude glaciers. This paper documents an extremely diversified diatom community in Antisana Glacier (Ecuador), reporting 278 taxa found in 54 surface holes, although with low individual abundances. Contrary to our expectations, assemblage structure did not respond to water physical or chemical characteristics, nor to cryoconite hole morphology, but to elevation. We demonstrate that elevation is a driver of diatom assemblages. Both alpha diversity (measured as Fisher's index) and species richness (corrected for unequal sample sizes) correlated negatively with elevation, suggesting a replacement toward simplified, poorer communities along this gradient. The taxonomic composition also changed significantly, as revealed by multivariate statistics. In summary, cryoconite holes are sites of high taxonomic diversity composed of taxa that are allochthonous in origin.

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Metagenomics Study To Compare The Taxonomy And Metabolism of a Lignocellulolytic Microbial Consortium Cultured in Different Carbon Conditions

10.21203/rs.3.rs-1076547/v1 ◽

2021 ◽

Author(s):

Qinggeer BORJIGIN ◽

Bizhou ZHANG ◽

Xiaofang Yu ◽

Julin Gao ◽

Xin ZHANG ◽

...

Keyword(s):

Microbial Consortium ◽

Agricultural Waste ◽

Taxonomic Diversity ◽

Taxonomic Composition ◽

Microbial Consortia ◽

Rich Diversity ◽

Cazy Database ◽

Taxonomic Affiliation ◽

In Situ Biodegradation

Abstract A lignocellulolytic microbial consortium holds promise for the in situ biodegradation of crop straw and the comprehensive and effective utilization of agricultural waste. In this study, we applied metagenomics technology to comprehensively explore the metabolic functional potential and taxonomic diversity of the microbial consortia CS (cultured on corn stover) and FP (cultured on filter paper).Analyses of the metagenomics taxonomic affiliation data showed considerable differences in the taxonomic composition and functional profile of the microbial consortia CS and FP. The microbial consortia CS primarily contained members from the genera Pseudomonas, Stenotrophomonas, Achromobacter, Dysgonomonas, Flavobacterium and Sphingobacterium, as well as Cellvibrio, Azospirillum, Pseudomonas, Dysgonomonas and Cellulomonas in FP. The COG and KEGG annotation analyses revealed considerable levels of diversity. Further analysis determined that the CS consortium had an increase in the acid and ester metabolism pathways, while carbohydrate metabolism was enriched in the FP consortium. Furthermore, a comparison against the CAZy database showed that the microbial consortia CS and FP contain a rich diversity of lignocellulose degrading families, in which GH5, GH6, GH9, GH10, GH11, GH26, GH42, and GH43 were enriched in the FP consortium, and GH44, GH28, GH2, and GH29 increased in the CS consortium. The degradative mechanism of lignocellulose metabolism by the two microbial consortia is similar, but the annotation of quantity of genes indicated that they are diverse and vary greatly. The lignocellulolytic microbial consortia cultured under different carbon conditions (CS and FP) differed substantially in their composition of the microbial community at the genus level. The changes in functional diversity were accompanied with variation in the composition of microorganisms, many of which are related to the degradation of lignocellulolytic materials. The genera Pseudomonas, Dysgonomonas and Sphingobacterium in CS and the genera Cellvibrio and Pseudomonas in FP exhibited a much wider distribution of lignocellulose degradative ability.

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Antarctic notothenioid fishes as subjects for research in evolutionary biology

Antarctic Science ◽

10.1017/s0954102000000341 ◽

2000 ◽

Vol 12 (3) ◽

pp. 276-287 ◽

Cited By ~ 72

Author(s):

Joseph T. Eastman

Keyword(s):

Evolutionary Biology ◽

Fish Fauna ◽

Taxonomic Diversity ◽

Late Eocene ◽

Taxonomic Composition ◽

Species Flock ◽

Subzero Temperatures ◽

Key Innovation ◽

The Antarctic ◽

Upper Slope

Antarctica is a continental island and the waters of its shelf and upper slope are an insular evolutionary site. The shelf waters resemble a closed basin in the Southern Ocean, separated from other continents by distance, current patterns and subzero temperatures. The benthic fish fauna of the shelf and upper slope of the Antarctic Region includes 213 species with higher taxonomic diversity confined to 18 families. Ninety-six notothenioids, 67 liparids and 23 zoarcids comprise 45%, 32% and 11% of the fauna, a combined total of 88%. In high latitude (71–78°S) shelf areas notothenioids dominate abundance and biomass at levels of 90–95%. Notothenioids are also morphologically and ecologically diverse. Although they lack a swim bladder, the hallmark of the notothenioid radiation has been repeated diversification into water column habitats. There are pelagic, semipelagic, cryopelagic and epibenthic species. Notothenioids exhibit the disproportionate speciosity and high endemism characteristic of fish species flock. Antifreeze glycopeptides originating from a transformed trypsinogen gene are a key innovation. It is not known when the modern Antarctic shelf fauna assumed its current taxonomic composition. A late Eocene fossil fauna was taxonomically diverse and cosmopolitan. There was a subsequent faunal replacement with little carryover of families into the modern fauna. Basal notothenioid clades probably diverged in Gondwanan shelf locations during the early Tertiary. Dates inferred from molecular sequences suggest that phyletically derived Antarctic clades arose 15–5 m.y.a.

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Sputum Microbiome Composition in Patients With Squamous Cell Lung Carcinoma

10.21203/rs.3.rs-902707/v1 ◽

2021 ◽

Author(s):

E. D. Baranova ◽

V. G. Druzhinin ◽

L. V. Matskova ◽

P. S. Demenkov ◽

V. P . Volobaev ◽

...

Keyword(s):

Squamous Cell ◽

Inflammatory Responses ◽

Alpha Diversity ◽

Taxonomic Composition ◽

16S Rrna Genes ◽

Rrna Genes ◽

Cell Lung Carcinoma ◽

Microbiome Composition ◽

Β Diversity ◽

Genome Damage

Abstract Recent findings indicate that the microbiome can have a significant impact on the development of lung cancer by inducing inflammatory responses, causing dysbiosis and generating genome damage. The aim of this study was to search for bacterial markers of squamous cell carcinoma (LUSC). In the study, the taxonomic composition of the sputum microbiome of 40 men with untreated LUSC was compared with 40 healthy controls. Next Generation sequencing of bacterial 16S rRNA genes was used to determine the taxonomic composition of the respiratory microbiome. There was no differences in alpha diversity between the LUSC and control groups. Meanwhile, differences in the structure of bacterial communities (β diversity) among patients and controls differed significantly in sputum samples (pseudo-F = 1.65; p = 0.026). Only Streptococcus, Bacillus, Gemella and Haemophilus were found to be significantly increased in patients with LUSC compared to the control subjects, while 19 bacterial genera were significantly reduced, indicating a decrease in beta diversity in the microbiome of patients with LUSC. From our study, Streptococcus (Streptococcus agalactiae) emerges as the most likely LUSC biomarker, but more research is needed to confirm this assumption.

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StrainPro – a highly accurate Metagenomic strain-level profiling tool

10.1101/807149 ◽

2019 ◽

Author(s):

Hsin-Nan Lin ◽

Yaw-Ling Lin ◽

Wen-Lian Hsu

Keyword(s):

Microbial Community ◽

Relative Abundance ◽

Taxonomic Diversity ◽

Evaluation Study ◽

Taxonomic Composition ◽

Strain Level ◽

Metagenomic Analysis ◽

Reference Database ◽

Analysis Tool ◽

Analysis Tools

ABSTRACTCharacterizing the taxonomic diversity of a microbial community is very important to understand the roles of microorganisms. Next generation sequencing (NGS) provides great potential for investigation of a microbial community and leads to Metagenomic studies. NGS generates DNA fragment sequences directly from microorganism samples, and it requires analysis tools to identify microbial species (or taxonomic composition) and estimate their relative abundance in the studied community. However, only a few tools could achieve strain-level identification and most tools estimate the microbial abundances simply according to the read counts. An evaluation study on metagenomic analysis tools concludes that the predicted abundance differed significantly from the true abundance. In this study, we present StrainPro, a novel metagenomic analysis tool which is highly accurate both at characterizing microorganisms at strain-level and estimating their relative abundances. A unique feature of StrainPro is it identifies representative sequence segments from reference genomes. We generate three simulated datasets using known strain sequences and another three simulated datasets using unknown strain sequences. We compare the performance of StrainPro with seven existing tools. The results show that StrainPro not only identifies metagenomes with high precision and recall, but it is also highly robust even when the metagenomes are not included in the reference database. Moreover, StrainPro estimates the relative abundance with high accuracy. We demonstrate that there is a strong positive linear relationship between observed and predicted abundances.

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Abundance and Taxonomic Diversity of Bacteria Inhabiting the Sediment-Water Interface in a Marine Harbor Channel

Ocean Science Journal ◽

10.1007/s12601-019-0023-9 ◽

2019 ◽

Vol 54 (3) ◽

pp. 407-418

Author(s):

Piotr Perliński ◽

Zbigniew J. Mudryk ◽

Marta Zdanowicz

Keyword(s):

Seasonal Fluctuation ◽

Taxonomic Diversity ◽

Taxonomic Composition ◽

Bacterial Number ◽

Water Interface ◽

Phylogenetic Groups ◽

Cell Counts ◽

Study Sites ◽

Taxonomic Groups

Abstract The abundance of bacteria inhabiting the sediment-water interface and their taxonomic composition were determined with the fluorescence in situ hybridization (FISH) method in a marine harbor channel in Ustka. Among bacteria inhabiting the studied layer Gammaproteobacteria (1.4 cells 108·dm−3) and Cytophaga-Flavobacterium (1.1 cells 108·dm−3) dominated. Vibrio and Pseudomonas represented only a small fraction of the total cell counts. All taxonomic groups of studied bacteria show significant positive correlation between their abundance. The total bacterial number varied from 3.3 to 23.5 cells 108·dm−3 and their biomass oscillated from 39.4 to 282.4 μg C·dm−3. This parameter differed along horizontal profiles, while there were no significant differences in the abundance of the studied taxonomic groups among the study sites of the channel in Ustka. The total number of bacteria as well as the abundance of bacterial phylogenetic groups were subject to seasonal fluctuation in the studied water basin.

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Current Velocity in Streams and the Composition of Benthic Algal Mats

Canadian Journal of Fisheries and Aquatic Sciences ◽

10.1139/f86-144 ◽

1986 ◽

Vol 43 (6) ◽

pp. 1156-1162 ◽

Cited By ~ 34

Author(s):

Michael A. Reiter ◽

Robert E. Carlson

Keyword(s):

Current Velocity ◽

Free Water ◽

Open Water ◽

Dry Weight ◽

Taxonomic Diversity ◽

Taxonomic Composition ◽

Water Velocity ◽

Algal Mats ◽

Laboratory Flume ◽

Algal Mat

Water velocity is commonly accepted as a factor in the development of benthic algal mats in streams. Within a stream, two different zones of velocity are observed: the free-water velocity of the open water and the local velocity near the stream substrate. A closed laboratory flume system was used to observe the taxonomic composition of benthic algal mats and corresponding changes in the local velocities under different free-water velocities. As the algal mat developed under each experimental velocity, local velocities diminished and eventually became equal in all sections, while free-water velocities remained different. After a period of maximum taxonomic diversity during the first 2 wk of mat development, taxonomic composition, relative abundance of the taxa, and dry weight biomass became increasingly similar in the three velocity regimes, although the mats appeared different upon casual observation. Differences in composition and morphology in natural algal mats may not result from differences in current velocity, and the idea of a "closed monolayer" algal mat may not be appropriate in all situations.

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Seasonal changes of ice surface characteristics and productivity in the ablation zone of the Greenland Ice Sheet

The Cryosphere ◽

10.5194/tc-9-487-2015 ◽

2015 ◽

Vol 9 (2) ◽

pp. 487-504 ◽

Cited By ~ 27

Author(s):

D. M. Chandler ◽

J. D. Alcock ◽

J. L. Wadham ◽

S. L. Mackie ◽

J. Telling

Keyword(s):

Remote Sensing ◽

Surface Albedo ◽

Ice Sheet ◽

Greenland Ice Sheet ◽

Surface Characteristics ◽

Biological Processes ◽

Ablation Zone ◽

Ice Surface ◽

Surface Productivity ◽

Cryoconite Hole

Abstract. Field and remote sensing observations in the ablation zone of the Greenland Ice Sheet have revealed a diverse range of ice surface characteristics, primarily reflecting the variable distribution of fine debris (cryoconite). This debris reduces the surface albedo and is therefore an important control on melt rates and ice sheet mass balance. Meanwhile, studies of ice sheet surface biological processes have found active microbial communities associated with the cryoconite debris, which may themselves modify the cryoconite distribution. Due to the considerable difficulties involved with collecting ground-based observations of the ice surface, our knowledge of the physical and biological surface processes, and their links, remains very limited. Here we present data collected at a field camp established in the ice sheet ablation zone at 67° N, occupied for almost the entire melt season (26 May–10 August 2012), with the aim of gaining a much more detailed understanding of the physical and biological processes occurring on the ice surface. These data sets include quadrat surveys of surface type, measurements of ice surface ablation, and in situ biological oxygen demand incubations to quantify microbial activity. In addition, albedo at the site was retrieved from AVHRR (Advanced Very High Resolution Radiometer) remote sensing data. Observations of the areal coverage of different surface types revealed a rapid change from complete snow cover to the "summer" (summer study period) ice surface of patchy debris ("dirty ice") and cryoconite holes. There was significant correlation between surface albedo, cryoconite hole coverage and surface productivity during the melt season, but microbial activity in "dirty ice" was not correlated with albedo and varied widely throughout the season. While this link suggests the potential for a remote-sensing approach to monitoring cryoconite hole biological processes, very wide seasonal and spatial variability in net surface productivity demonstrates the need for caution when extrapolating point measurements of biological processes to larger temporal or spatial scales.

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Reduced diversity and productivity of diatoms and other protists during the Early Holocene in the subarctic North Pacific

10.5194/egusphere-egu2020-11144 ◽

2020 ◽

Author(s):

Heike H. Zimmermann ◽

Stefan Kruse ◽

Kathleen R. Stoof-Leichsenring ◽

Luise Schulte ◽

Dirk Nürnberg ◽

...

Keyword(s):

Green Algae ◽

Taxonomic Diversity ◽

Taxonomic Composition ◽

Shotgun Sequencing ◽

Early Holocene ◽

The Past ◽

Subarctic North Pacific ◽

Morphological Differences ◽

Marine Protists

Marine protists are a phylogenetically diverse group of single-celled eukaryotes that respond sensitively to changes in environmental conditions. Yet, our understanding how long-term climate variability has shaped the taxonomic composition is mostly unknown, especially of non-biomineralizing groups, such as green algae, since traditional micropaleontological studies are limited to the analysis of microfossil remains with often hardly discernable morphological differences between species (e.g. diatoms). Here we present a sedimentary ancient DNA (sedaDNA) record of the marine sediment core SO201-2-12KL, which was retrieved from the eastern continental slope of Kamchatka at 2173 m water depth (N 53.992660&#176;, E 162.375830&#176;) and covers the past 19.9 thousand years. We applied sedaDNA metabarcoding to 63 samples using a diatom-specific, short plastid marker that is part of the rbcL gene. Additionally, we used metagenomic shotgun sequencing on a subset of 26 samples to investigate the overall taxonomic composition of protists. Metagenomic shotgun sequencing revealed a variety of unicellular plankton groups mostly from green algae (especially Bathycoccus) and diatoms. At 11.1 cal kyr BP only single sequences assigned to green algae, diatoms and coccolithophorids could be detected. Metabarcoding showed strong variability in the richness of diatom sequence variants, which was highest during Heinrich Stadial 1 and the Younger Dryas. From about 11.4 cal kyr BP diatom taxonomic diversity strongly decreased until about 10.7 cal kyr BP. This was associated with highest taxonomic and phylogenetic turnover recorded over the past 19.9 cal kyr. Concomitant with this we recorded sequences assigned to Skeletonema subsalsum, a coastal diatom associated with low salinities or freshwater. Tentatively, as we wait for the confirmation by further sequencing, we suggest that the reduced protist diversity during the Early Holocene resulted from sea surface freshening, which led to a strengthened vertical stratification which could have reduced past productivity due to limited nutrient supply from deeper waters to the photic zone.

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Ichthyofauna of Sungai Merbok Mangrove Forest Reserve, northwest Peninsular Malaysia, and its adjacent marine waters

Check List ◽

10.15560/17.2.601 ◽

2021 ◽

Vol 17 (2) ◽

pp. 601-631

Author(s):

Danial Hariz Zainal Abidin ◽

Sébastien Lavoué ◽

Norli Fauzani Mohd Abu Hassan Alshari ◽

Siti Azizah Mohd. Nor ◽

Masazurah A. Rahim ◽

...

Keyword(s):

Mangrove Forest ◽

River Estuary ◽

Alpha Diversity ◽

Taxonomic Diversity ◽

Peninsular Malaysia ◽

Fish Diversity ◽

Marine Waters ◽

Forest Patch ◽

Forest Reserve ◽

Aquatic Biodiversity

Sungai Merbok Mangrove Forest Reserve, encompassing the Merbok river estuary, was established as a permanent forest reserve in 1951 and is the second-largest intact mangrove forest patch in Peninsular Malaysia. Despite its importance, few studies have been conducted to assess its aquatic biodiversity. In this study, we surveyed the fish diversity of the Merbok river estuary, and its adjacent marine waters. We recorded 138 fish species belonging to two classes, 18 orders, 47 families, and 94 genera. The richest order is Perciformes, with 32 recorded species, represents 23% of the alpha diversity, followed by Carangiformes with 21 recorded species or 14% of the diversity. Low taxonomic diversity overlaps with previous inventories and indicates that the inventory is still incomplete. All specimens examined are catalogued and deposited in a local museum collection. The fish checklist presented here represents a step forward in the conservation of fish diversity in the Merbok river estuary.

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INTERANNUAL DYNAMICS OF PLANKTON COMMUNITIES IN THE CHANNEL SECTIONS OF THE KUIBYSHEV RESERVOIR

Regional Problems ◽

10.31433/2618-9593-2021-24-2-3-112-115 ◽

2021 ◽

Vol 24 (2-3) ◽

pp. 112-115

Author(s):

M.A. Gvozdareva ◽

O.S. Lyubina ◽

A.V. Melnikova ◽

L.G. Grechukhina

Keyword(s):

Taxonomic Diversity ◽

Taxonomic Composition ◽

Kuibyshev Reservoir ◽

Biological Studies ◽

Interannual Dynamics ◽

Quantitative Indicators ◽

Plankton Communities

Based on the materials of hydro-biological studies in the Volga part of the Kuibyshev reservoir in 2018 and 2019, the authors evaluated changes in the quantitative indicators and taxonomic composition of phytoplankton and zooplankton. According to the results of the study, it was revealed that in 2019 the taxonomic diversity increased, but the abundance and biomass indices of phytoplankton decreased, while zooplankton decreased only in its abundance.

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