scholarly journals A Systems biology approach to energy flow in H2 producing microbial communities: Microbial mats

2018 ◽  
Author(s):  
Brad Bebout
Keyword(s):  
Systems Biology ◽  
Microbial Communities ◽  
Energy Flow ◽  
Microbial Mats

scholarly journals Energetic and Environmental Constraints on the Community Structure of Benthic Microbial Mats in Lake Fryxell, Antarctica

2019 ◽  
Author(s):  
Megan L. Dillon ◽  
Ian Hawes ◽  
Anne D. Jungblut ◽  
Tyler J. Mackey ◽  
Jonathan A. Eisen ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Communities ◽  
Energy Flow ◽  
Energy Use ◽  
Microbial Mats ◽  
Environmental Gradients ◽  
Dependent Manner ◽  
Ecological Communities ◽  
Overlying Water ◽  
Lake Fryxell

AbstractEcological communities are commonly thought to be controlled by the dynamics of energy flow through environments. Two of the most important energetic constraints on all communities are photosynthetically active radiation (PAR) and oxygen concentration ([O2]). Microbial mats growing on the bottom of Lake Fryxell, Antarctica, span environmental gradients in PAR and [O2], which we used to test the extent to which each controls community structure. Metagenomic analyses showed variation in the diversity and relative abundances of Archaea, Bacteria, and Eukaryotes across three [O2] and PAR conditions. Where [O2] saturated the mats or was absent from the overlying water, PAR structured the community. Where [O2] varied within mats, microbial communities changed across covarying PAR and [O2] gradients. Diversity negatively correlated with [O2] and PAR through mat layers in each habitat suggesting that, on the millimeter-scale, communities are structured by the optimization of energy use. In contrast, [O2] positively correlated with diversity and affected the distribution of dominant populations across the three habitats, suggesting that meter-scale diversity is structured by energy availability. The benthic microbial communities in Lake Fryxell are thus structured by energy flow in a scale-dependent manner.

scholarly journals Energetic and Environmental Constraints on the Community Structure of Benthic Microbial Mats in Lake Fryxell, Antarctica

2020 ◽  
Vol 96 (2) ◽  
Author(s):  
Megan L Dillon ◽  
Ian Hawes ◽  
Anne D Jungblut ◽  
Tyler J Mackey ◽  
Jonathan A Eisen ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Communities ◽  
Energy Flow ◽  
Energy Use ◽  
Microbial Mats ◽  
Environmental Gradients ◽  
Ecological Communities ◽  
Lake Fryxell ◽  
High O2 ◽  
Lower Maximum

ABSTRACT Ecological communities are regulated by the flow of energy through environments. Energy flow is typically limited by access to photosynthetically active radiation (PAR) and oxygen concentration (O2). The microbial mats growing on the bottom of Lake Fryxell, Antarctica, have well-defined environmental gradients in PAR and (O2). We analyzed the metagenomes of layers from these microbial mats to test the extent to which access to oxygen and light controls community structure. We found variation in the diversity and relative abundances of Archaea, Bacteria and Eukaryotes across three (O2) and PAR conditions: high (O2) and maximum PAR, variable (O2) with lower maximum PAR, and low (O2) and maximum PAR. We found distinct communities structured by the optimization of energy use on a millimeter-scale across these conditions. In mat layers where (O2) was saturated, PAR structured the community. In contrast, (O2) positively correlated with diversity and affected the distribution of dominant populations across the three habitats, suggesting that meter-scale diversity is structured by energy availability. Microbial communities changed across covarying gradients of PAR and (O2). The comprehensive metagenomic analysis suggests that the benthic microbial communities in Lake Fryxell are structured by energy flow across both meter- and millimeter-scales.

scholarly journals Cyanobacterial Mats in Calcite-Precipitating Serpentinite-Hosted Alkaline Springs of the Voltri Massif, Italy

2020 ◽  
Vol 9 (1) ◽  
pp. 62
Author(s):  
Aysha Kamran ◽  
Kathrin Sauter ◽  
Andreas Reimer ◽  
Theresa Wacker ◽  
Joachim Reitner ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Microbial Mats ◽  
Environmental Dna ◽  
Cyanobacterial Mats ◽  
Cyanobacterial Community ◽  
Mineral Precipitation ◽  
Community Based ◽  
Specific Adaptation ◽  
Carbonate Buildups ◽  
Generation Sequencing

(1) Background: Microbial communities in terrestrial, calcifying high-alkaline springs are not well understood. In this study, we investigate the structure and composition of microbial mats in ultrabasic (pH 10–12) serpentinite springs of the Voltri Massif (Italy). (2) Methods: Along with analysis of chemical and mineralogical parameters, environmental DNA was extracted and subjected to analysis of microbial communities based upon next-generation sequencing. (3) Results: Mineral precipitation and microbialite formation occurred, along with mat formation. Analysis of the serpentinite spring microbial community, based on Illumina sequencing of 16S rRNA amplicons, point to the relevance of alkaliphilic cyanobacteria, colonizing carbonate buildups. Cyanobacterial groups accounted for up to 45% of all retrieved sequences; 3–4 taxa were dominant, belonging to the filamentous groups of Leptolyngbyaceae, Oscillatoriales, and Pseudanabaenaceae. The cyanobacterial community found at these sites is clearly distinct from creek water sediment, highlighting their specific adaptation to these environments.

scholarly journals Systems biology approach to elucidation of contaminant biodegradation in complex samples – integration of high-resolution analytical and molecular tools

2019 ◽  
Vol 218 ◽  
pp. 481-504 ◽  
Author(s):  
Caroline Gauchotte-Lindsay ◽  
Thomas J. Aspray ◽  
Mara Knapp ◽  
Umer Z. Ijaz
Keyword(s):  
Systems Biology ◽  
High Resolution ◽  
Microbial Communities ◽  
Contaminated Soils ◽  
Rational Design ◽  
Data Driven ◽  
Molecular Tools ◽  
Complex Samples ◽  
Driven Systems

We present here a data-driven systems biology framework for the rational design of biotechnological solutions for contaminated environments with the aim of understanding the interactions and mechanisms underpinning the role of microbial communities in the biodegradation of contaminated soils.

Sea-level variation and the zonation of microbialites in Hamelin Pool, Shark Bay, Western Australia

2012 ◽  
Vol 63 (11) ◽  
pp. 994 ◽  
Author(s):  
Robert V. Burne ◽  
Ken Johnson
Keyword(s):  
Microbial Communities ◽  
Sea Level ◽  
Seasonal Cycle ◽  
Microbial Mats ◽  
Level Variation ◽  
Short Term ◽  
Shark Bay ◽  
Astronomical Tide ◽  
Sea Level Variation ◽  
Modern Methods

The application of modern methods of time-series analysis to a record of sea-level variation at Flint Cliff, Hamelin Pool, between October 1983 and April 1985, shows that astronomical tides account for only one of the following five key components of the record: a seasonal oceanic cycle; a short-term irregular cycle; the complex astronomical tidal system in the Pool; isolated major events; and less marked variations probably reflecting wind stress, still able to defeat the astronomical tide in the short-term. We have compared the inundation record with precisely surveyed elevation ranges of various microbial communities. The dominance of a seasonal cycle is the fundamental determinant of variation in the duration of immersion and exposure determining the littoral zonation of microbial mats in Hamelin Pool. The astronomical tide is not the major cause of this variation. The microbial communities fall into three zones. In Zone 3, the microbialite-forming colloform mat is virtually never exposed. In Zone 2, smooth, reticulate and mamillate mats colonise the lower littoral environment. Here, many of the exposed microbialites have been stranded by the falling sea level, and are colonised by intermittently submerged microbial communities that modify the stranded lithified microbialites. Zone 1 is inundated only under exceptional circumstances and microbial communities are ephemeral.

scholarly journals The influence of microbial mats on travertine precipitation in active hydrothermal systems (Central Italy)

2020 ◽  
Author(s):  
Giovanna Della Porta ◽  
Joachim Reitner
Keyword(s):  
Microbial Communities ◽  
Extracellular Polymeric Substances ◽  
Microbial Mats ◽  
Central Italy ◽  
Hydrothermal Systems ◽  
Crystal Nucleation ◽  
Anoxygenic Phototrophic Bacteria ◽  
Physico Chemical ◽  
Slope System ◽  
Aluminium Silicates

ABSTRACTThe study of hydrothermal travertines contributes to the understanding of the interaction between physico-chemical processes and the role played by microbial mats and biofilms in influencing carbonate precipitation. Three active travertine sites were investigated in Central Italy to identify the types of carbonate precipitates and the associated microbial mats at varying physico-chemical parameters. Carbonate precipitated fabrics at the decimetre- to millimetre-scale and microbial mats vary with decreasing water temperature: a) at high temperature (55-44°C) calcite or aragonite crystals precipitate on microbial mats of sulphide oxidizing, sulphate reducing and anoxygenic phototrophic bacteria forming filamentous streamer fabrics, b) at intermediate temperature (44-40°C), rafts, coated gas bubbles and dendrites are associated with Spirulina cyanobacteria and other filamentous and rod-shaped cyanobacteria, c) low temperature (34-33°C) laminated crusts and oncoids in a terraced slope system are associated with diverse Oscillatoriales and Nostocales filamentous cyanobacteria, sparse Spirulina and diatoms. At the microscale, carbonate precipitates are similar in the three sites consisting of prismatic calcite (40-100 μm long, 20-40 μm wide) or acicular aragonite crystals organized in radial spherulites, overlying or embedded within biofilm EPS (Extracellular Polymeric Substances). Microsparite and sparite crystal size decreases with decreasing temperature and clotted peloidal micrite dominates at temperatures < 40°C, also encrusting filamentous microbes. Carbonates are associated with gypsum and Ca-phosphate crystals; EPS elemental composition is enriched in Si, Al, Mg, Ca, P, S and authigenic aluminium-silicates form aggregates on EPS.This study confirms that microbial communities in hydrothermal travertine settings vary as a function of temperature. Carbonate precipitate types at the microscale do not vary considerably, despite different microbial communities suggesting that travertine precipitation, driven by CO2 degassing, is influenced by biofilm EPS acting as template for crystal nucleation (EPS-mediated mineralization) and affecting the fabric types, independently from specific microbial metabolism.

scholarly journals Late Ediacaran organic microfossils from Finland

2021 ◽  
pp. 1-14
Author(s):  
Sebastian Willman ◽  
Ben J. Slater
Keyword(s):  
Microbial Communities ◽  
Microbial Mats ◽  
Trace Fossils ◽  
Impact Structure ◽  
Meteorite Impact ◽  
Fine Grained ◽  
Body Fossil ◽  
New Evidence ◽  
Insight Into ◽  
Direct Body

Abstract Here we present a detailed accounting of organic microfossils from late Ediacaran sediments of Finland, from the island of Hailuoto (northwest Finnish coast), and the Saarijärvi meteorite impact structure (~170 km northeast of Hailuoto, mainland Finland). Fossils were recovered from fine-grained thermally immature mudstones and siltstones and are preserved in exquisite detail. The majority of recovered forms are sourced from filamentous prokaryotic and protistan-grade organisms forming interwoven microbial mats. Flattened Nostoc-ball-like masses of bundled Siphonophycus filaments are abundant, alongside Rugosoopsis and Palaeolyngbya of probable cyanobacterial origin. Acritarchs include Chuaria, Leiosphaeridia, Symplassosphaeridium and Synsphaeridium. Significantly, rare spine-shaped sclerites of bilaterian origin were recovered, providing new evidence for a nascent bilaterian fauna in the terminal Ediacaran. These findings offer a direct body-fossil insight into Ediacaran mat-forming microbial communities, and demonstrate that alongside trace fossils, detection of a bilaterian fauna prior to the Cambrian might also be sought among the emerging record of small carbonaceous fossils (SCFs).

scholarly journals Multivariate statistical techniques for metagenomic analysis of microbial community recovered from environmental samples

2018 ◽  
Vol 24 ◽  
pp. 45-53 ◽  
Author(s):  
Z Akond ◽  
M Alam ◽  
MS Ahmed ◽  
MNH Mollah
Keyword(s):  
Microbial Communities ◽  
Microbial Mats ◽  
Statistical Techniques ◽  
Multivariate Statistical ◽  
Linear Discriminant ◽  
Metabolic Functions ◽  
Metabolic Variables ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing ◽  
Shed Light

High-throughput big dataset generated through next generation sequencing (NGS) of DNA samples helps identify key differences in the function and taxonomy between microbial communities as well as shed light on the diversity of microbes, cooperation and evolution in any particular ecosystem. During this study, three statistical techniques namely, Random Forest (RF), Multidimensional Scaling (MDS) and Linear Discriminant Analysis (LDA) approaches were employed for functional analysis of 212 publicly available metagenomic datasets within and between 10 environments against 27 metabolic functions. RF generates the 8 most important metabolic variables along with MDS and LDA among which Photosynthesis has the highest score (70.20); Phages, prophages has the second highest score (61.31) and Membrane Transport was found to have the eighth highest score (45.29). The MDS plot was found useful to visualize the separation of the microbes from human or animal hosts from other samples along the first dimension and the separation of the aquatic and mat communities along the second dimension. LDA analyses compared the extent of the microbial samples into three broad groups: the human and animal associated samples, the microbial mats, and the aquatic samples. RF showed that phage activity is a major difference between host-associated microbial communities and free-living. The MDS and LDA techniques suggest that mat communities were unique from both the animal associated metagenomes and the aquatic samples with differences in the vitamin and cofactor metabolism.J. bio-sci. 24: 45-53, 2016

Development of versicolored microbial mats: Succession of microbial communities

1994 ◽  
pp. 415-420 ◽  
Author(s):  
Isabel Esteve ◽  
Dolores Ceballos ◽  
Maira Martínez-Alonso ◽  
Núria Gaju ◽  
Ricardo Guerrero
Keyword(s):  
Microbial Communities ◽  
Microbial Mats
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