Distinct processes structure bacterioplankton and protist communities across an oceanic front

2020 ◽  
Vol 85 ◽  
pp. 19-34
Author(s):  
R Allen ◽  
TC Summerfield ◽  
K Currie ◽  
PW Dillingham ◽  
LJ Hoffmann
Keyword(s):  
High Throughput Sequencing ◽  
Null Model ◽  
Rrna Genes ◽  
Water Type ◽  
System A ◽  
Deterministic Processes ◽  
Seawater Samples ◽  
18S Rrna Genes ◽  
Abundance And Distribution

Bacterioplankton and protists fulfil key roles in marine ecosystems. Understanding the abundance and distribution of these organisms through space and time is a central focus of biological oceanographers. The role of oceanographic features, in addition to environmental conditions, in structuring bacterioplankton and protist communities has been increasingly recognised. We investigated patterns in bacterioplankton and protist diversity and community structure across the Southland Front system, a compaction of the subtropical front zone, to the east of New Zealand’s South Island. We collected 24 seawater samples across a ~65 km transect and characterised bacterioplankton and protist community composition using high-throughput sequencing of the 16S and 18S rRNA genes, respectively. We identified frontal waters as a bacterioplankton diversity hotspot relative to neighbouring subtropical and subantarctic waters, but did not find evidence of this effect in protists. Bacterioplankton showed pronounced spatial structuring across the front, with communities closely tracking water type through the region. Protist communities also tracked water type through the region, though this effect was substantially less pronounced. We used an ecological null model approach to demonstrate that protist communities are primarily assembled through stochastic processes, whilst bacterioplankton are primarily assembled through deterministic processes across the Southland Front system. We suggest that this divergence emerges from fundamental differences in the characteristics of bacterioplankton and protist communities. Our findings add to a growing body of literature highlighting the importance of oceanographic features in shaping bacterioplankton and protist communities, promoting the necessity for such features to be considered more explicitly in the future.

scholarly journals Microbial Diversity of Pinnacle and Conical Microbial Mats in the Perennially Ice-Covered Lake Untersee, East Antarctica

2020 ◽  
Vol 11 ◽  
Author(s):  
Carla Greco ◽  
Dale T. Andersen ◽  
Ian Hawes ◽  
Alexander M. C. Bowles ◽  
Marian L. Yallop ◽  
...  
Keyword(s):  
Community Structure ◽  
18S Rrna ◽  
High Throughput Sequencing ◽  
Microbial Mats ◽  
East Antarctica ◽  
Rrna Genes ◽  
Microbial Composition ◽  
Small Spatial Scale ◽  
Lake Floor ◽  
18S Rrna Genes

Antarctic perennially ice-covered lakes provide a stable low-disturbance environment where complex microbially mediated structures can grow. Lake Untersee, an ultra-oligotrophic lake in East Antarctica, has the lake floor covered in benthic microbial mat communities, where laminated organo-sedimentary structures form with three distinct, sympatric morphologies: small, elongated cuspate pinnacles, large complex cones and flat mats. We examined the diversity of prokaryotes and eukaryotes in pinnacles, cones and flat microbial mats using high-throughput sequencing of 16S and 18S rRNA genes and assessed how microbial composition may underpin the formation of these distinct macroscopic mat morphologies under the same environmental conditions. Our analysis identified distinct clustering of microbial communities according to mat morphology. The prokaryotic communities were dominated by Cyanobacteria, Proteobacteria, Verrucomicrobia, Planctomycetes, and Actinobacteria. While filamentous Tychonema cyanobacteria were common in all mat types, Leptolyngbya showed an increased relative abundance in the pinnacle structures only. Our study provides the first report of the eukaryotic community structure of Lake Untersee benthic mats, which was dominated by Ciliophora, Chlorophyta, Fungi, Cercozoa, and Discicristata. The eukaryote richness was lower than for prokaryote assemblages and no distinct clustering was observed between mat morphologies. These findings suggest that cyanobacterial assemblages and potentially other bacteria and eukaryotes may influence structure morphogenesis, allowing distinct structures to form across a small spatial scale.

scholarly journals The Biodiversity and Geochemistry of Cryoconite Holes in Queen Maud Land, East Antarctica

2019 ◽  
Vol 7 (6) ◽  
pp. 160 ◽  
Author(s):  
Stefanie Lutz ◽  
Lori A. Ziolkowski ◽  
Liane G. Benning
Keyword(s):  
High Throughput Sequencing ◽  
Geographic Location ◽  
Carbon Accumulation ◽  
The Arctic ◽  
Rrna Genes ◽  
Geochemical Data ◽  
Eukaryotic Community ◽  
Continental Antarctica ◽  
18S Rrna Genes ◽  
First Time

Cryoconite holes are oases of microbial diversity on ice surfaces. In contrast to the Arctic, where during the summer most cryoconite holes are ‘open’, in Continental Antarctica they are most often ‘lidded’ or completely frozen year-round. Thus, they represent ideal systems for the study of microbial community assemblies as well as carbon accumulation, since individual cryoconite holes can be isolated from external inputs for years. Here, we use high-throughput sequencing of the 16S and 18S rRNA genes to describe the bacterial and eukaryotic community compositions in cryoconite holes and surrounding lake, snow, soil and rock samples in Queen Maud Land. We cross correlate our findings with a broad range of geochemical data including for the first time 13C and 14C analyses of Antarctic cryoconites. We show that the geographic location has a larger effect on the distribution of the bacterial community compared to the eukaryotic community. Cryoconite holes are distinct from the local soils in both 13C and 14C and their isotopic composition is different from similar samples from the Arctic. Carbon contents were generally low (≤0.2%) and older (6–10 ky) than the surrounding soils, suggesting that the cryoconite holes are much more isolated from the atmosphere than the soils.

scholarly journals Diversity, spatial distribution and activity of fungi in freshwater ecosystems

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6247 ◽  
Author(s):  
Cécile Lepère ◽  
Isabelle Domaizon ◽  
Jean-Francois Humbert ◽  
Ludwig Jardillier ◽  
Mylène Hugoni ◽  
...  
Keyword(s):  
18S Rrna ◽  
High Throughput Sequencing ◽  
Taxonomic Composition ◽  
Freshwater Ecosystems ◽  
Rrna Genes ◽  
Active Fraction ◽  
Catchment Areas ◽  
Freshwater Habitats ◽  
Taxonomic Affiliation ◽  
18S Rrna Genes

High-throughput sequencing has given new insights into aquatic fungal community ecology over the last 10 years. Based on 18S ribosomal RNA gene sequences publicly available, we investigated fungal richness and taxonomic composition among 25 lakes and four rivers. We used a single pipeline to process the reads from raw data to the taxonomic affiliation. In addition, we studied, for a subset of lakes, the active fraction of fungi through the 18S rRNA transcripts level. These results revealed a high diversity of fungi that can be captured by 18S rRNA primers. The most OTU-rich groups were Dikarya (47%), represented by putative filamentous fungi more diverse and abundant in freshwater habitats than previous studies have suggested, followed by Cryptomycota (17.6%) and Chytridiomycota (15.4%). The active fraction of the community showed the same dominant groups as those observed at the 18S rRNA genes level. On average 13.25% of the fungal OTUs were active. The small number of OTUs shared among aquatic ecosystems may result from the low abundances of those microorganisms and/or they constitute allochthonous fungi coming from other habitats (e.g., sediment or catchment areas). The richness estimates suggest that fungi have been overlooked and undersampled in freshwater ecosystems, especially rivers, though they play key roles in ecosystem functioning as saprophytes and parasites.

scholarly journals Constructing graphs from genetic encodings

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Dániel L. Barabási ◽  
Dániel Czégel
Keyword(s):  
Brain Connectivity ◽  
Null Model ◽  
Hierarchical Networks ◽  
Targeted Attacks ◽  
Wide Range ◽  
Network Topologies ◽  
Deterministic Processes ◽  
Representational Power ◽  
Structured Graphs

AbstractOur understanding of real-world connected systems has benefited from studying their evolution, from random wirings and rewirings to growth-dependent topologies. Long overlooked in this search has been the role of the innate: networks that connect based on identity-dependent compatibility rules. Inspired by the genetic principles that guide brain connectivity, we derive a network encoding process that can utilize wiring rules to reproducibly generate specific topologies. To illustrate the representational power of this approach, we propose stochastic and deterministic processes for generating a wide range of network topologies. Specifically, we detail network heuristics that generate structured graphs, such as feed-forward and hierarchical networks. In addition, we characterize a Random Genetic (RG) family of networks, which, like Erdős–Rényi graphs, display critical phase transitions, however their modular underpinnings lead to markedly different behaviors under targeted attacks. The proposed framework provides a relevant null-model for social and biological systems, where diverse metrics of identity underpin a node’s preferred connectivity.

scholarly journals The Composition and Assembly of Bacterial Communities across the Rhizosphere and Phyllosphere Compartments of Phragmites Australis

Diversity ◽  
2019 ◽  
Vol 11 (6) ◽  
pp. 98 ◽  
Author(s):  
Qi Zhou ◽  
Xiaomin Zhang ◽  
Rujia He ◽  
Shuren Wang ◽  
Congcong Jiao ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Phragmites Australis ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Null Model ◽  
Rrna Gene ◽  
Rare Taxa ◽  
Alpha And Beta Diversity ◽  
Deterministic Processes ◽  
The Difference

The rhizosphere and the phyllosphere represent two different epiphytic compartments of host plant, which are closely related to plant growth, health, and productivity. However, the understanding of the diversity, composition, and assembly of the bacterial communities in different epiphytic microenvironments of large emerged macrophytes has remained elusive, especially the abundant and rare taxa across rhizosphere and phyllosphere communities. In this study, we collected samples of two different epiphytic compartments (rhizosphere and phyllosphere) of Phragmites australis. Both 16S rRNA gene-based high-throughput sequencing and null-model analysis were employed to determine the difference in the composition and assembly of above-mentioned epiphytic bacterial communities. Our results indicated that bacterial communities of rhizosphere exhibited higher diversity and richness than those of phyllosphere. Deterministic processes dominated the assembly of bacterial community in both compartments, and stochastic processes contributed a certain proportion (30.30%) in the assembly of phyllosphere bacterial community. We also found that rare taxa contributed more significantly to the alpha- and beta-diversity of bacterial community than those of abundant taxa. The obtained data are useful for better understanding the bacterial community of different epiphytic compartments of P. australis.

scholarly journals Geographical Distribution of Iron Redox Cycling Bacterial Community in Peatlands: Distinct Assemble Mechanism Across Environmental Gradient

2021 ◽  
Vol 12 ◽  
Author(s):  
Liang Yang ◽  
Ming Jiang ◽  
Yuanchun Zou ◽  
Lei Qin ◽  
Yingyi Chen
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Geographic Distance ◽  
Null Model ◽  
Redox Cycling ◽  
Biogeographic Patterns ◽  
Deterministic Processes ◽  
Iron Redox ◽  
Soil And Water

Microbial-mediated iron (Fe) oxidation and reduction greatly contribute to the biogeochemistry and mineralogy of ecosystems. However, knowledge regarding the composition and distribution patterns of iron redox cycling bacteria in peatlands remains limited. Here, using high-throughput sequencing, we compared biogeographic patterns and assemblies of the iron redox cycling bacterial community between soil and water samples obtained from different types of peatland across four regions in Northeast China. A total of 48 phylotypes were identified as potential iron redox bacteria, which had greater than 97% similarity with Fe(II)-oxidizing bacteria (FeOB) and Fe(III)-reducing bacteria (FeRB). Among them, Rhodoferax, Clostridium, Geothrix, Sideroxydans, Geobacter, Desulfovibrio, and Leptothrix could be used as bioindicators in peatlands for characterizing different hydrological conditions and nutrient demands. Across all samples, bacterial communities associated with iron redox cycling were mainly affected by pH, dissolved organic carbon (DOC), and Fe2+. Distance–decay relationship (DDR) analysis indicated that iron redox cycling bacterial communities in soil, but not in water, were highly correlated with geographic distance. Additionally, null model analysis revealed that stochastic processes substituted deterministic processes from minerotrophic fens to ombrotrophic bogs in soils, whereas deterministic processes were dominant in water. Overall, these observations suggest that bacteria involved in iron redox cycling are widespread in diverse habitats and exhibit distinct patterns of distribution and community assembly mechanisms between soil and water in peatlands.

scholarly journals Constructing Graphs from Genetic Encodings

2020 ◽  
Author(s):  
Dániel L. Barabási ◽  
Dániel Czégel
Keyword(s):  
Brain Connectivity ◽  
Null Model ◽  
Hierarchical Networks ◽  
Targeted Attacks ◽  
Wide Range ◽  
Network Topologies ◽  
Deterministic Processes ◽  
Representational Power ◽  
Structured Graphs

AbstractOur understanding of real-world connected systems has benefited from studying their evolution, from random wirings and rewirings to growth-dependent topologies. Long overlooked in this search has been the role of the innate: networks that connect based on identity-dependent compatibility rules. Inspired by the genetic principles that guide brain connectivity, we derive a network encoding process that can utilize wiring rules to reproducibly generate specific topologies. To illustrate the representational power of this approach, we propose stochastic and deterministic processes for generating a wide range of network topologies. Specifically, we detail network heuristics that generate structured graphs, such as feed-forward and hierarchical networks. In addition, we characterize a Random Genetic (RG) family of networks, which, like Erdős-Rényi graphs, display critical phase transitions, however their modular underpinnings lead to markedly different behaviors under targeted attacks. The proposed framework provides a relevant null-model for social and biological systems, where diverse metrics of identity underpin a node’s preferred connectivity.

Bioinformatics Analysis and Validation of Differentially Expressed MicroRNAs with Their Target Genes Involved in GLP-1RA Facilitated Osteogenesis

2020 ◽  
Vol 15 ◽  
Author(s):  
Na Wang ◽  
Yukun Li ◽  
Sijing Liu ◽  
Liu Gao ◽  
Chang Liu ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Target Genes ◽  
Bioinformatics Analysis ◽  
Differentially Expressed ◽  
Functional Study ◽  
Regulation Network ◽  
Glucagon Like Peptide 1 ◽  
G Protein Coupled ◽  
Lower Expression

Background: Recent studies revealed that the hypoglycemic hormone, glucagon-like peptide-1 (GLP-1), acted as an important modulator in osteogenesis of bone marrow derived mesenchymal stem cells (BMSCs). Objectives: The aim of this study was to identify the specific microRNA (miRNA) using bioinformatics analysis and validate the presence of differentially expressed microRNAs with their target genes after GLP-1 receptor agonist (GLP-1RA) administration involved in ostogenesis of BMSCs. Methods: MiRNAs were extracted from BMSCs after 5 days’ treatment and sent for high-throughput sequencing for differentially expressed (DE) miRNAs analyses. Then the expression of the DE miRNAs verified by the real-time RT-PCR analyses. Target genes were predicted, and highly enriched GOs and KEGG pathway analysis were conducted using bioinformatics analysis. For the functional study, two of the target genes, SRY (sex determining region Y)-box 5 (SOX5) and G protein-coupled receptor 84 (GPR84), were identified. Results: A total of 5 miRNAs (miRNA-509-5p, miRNA-547-3p, miRNA-201-3p, miRNA-201-5p, and miRNA-novel-272-mature) were identified differentially expressed among groups. The expression of miRNA-novel-272-mature were decreased during the osteogenic differentiation of BMSCs, and GLP-1RA further decreased its expression. MiRNA-novel-272-mature might interact with its target mRNAs to enhance osteogenesis. The lower expression of miRNA-novel-272-mature led to an increase in SOX5 and a decrease in GPR84 mRNA expression, respectively. Conclusions: Taken together, these results provide further insights to the pharmacological properties of GLP-1RA and expand our knowledge on the role of miRNAs-mRNAs regulation network in BMSCs’ differentiation.

The SORS Decision-Making Support System: A statistical tool for better policy making in the Republic of Serbia

2021 ◽  
pp. 1-11
Author(s):  
Miladin Kovačević ◽  
Katarina Stančić
Keyword(s):  
Policy Making ◽  
Modern Society ◽  
Monitoring And Evaluation ◽  
Public Debate ◽  
Statistical Tool ◽  
The Public ◽  
System A ◽  
The Republic ◽  
Trusted Data

Modern society is witnessing a data revolution which necessarily entails changes to the overall behavior of citizens, governments and companies. This is a big challenge and an opportunity for National Statistics Offices (NSOs). Especially after the outbreak of COVID-19, when the public debate about the number of mortalities and tested and infected persons escalated, trusted data is required more than ever. Which data can modern society trust? Are modern societies being subjected to opinion rather than fact? This paper introduces a new statistical tool to facilitate policy-making based on trusted statistics. Using economic indicators to illustrate implementation, the new statistical tool is shown to be a flexible instrument for analysis, monitoring and evaluation of the economic situation in the Republic of Serbia. By taking a role in public policy management, the tool can be used to transform the NSO’s role in the statistical system into an active participant in public debate in contrast to the previous traditional, usually passive role of collecting, processing and publishing data. The tool supports the integration of statistics into public policies and connects the knowledge and expertise of official statisticians on one side with political decision makers on the other.

Sign in / Sign up

Export Citation Format

Share Document