scholarly journals A Novel Microbialite-Associated Phototrophic Chloroflexi Lineage Exhibiting a Quasi-Clonal Pattern along Depth

2020 ◽  
Vol 12 (7) ◽  
pp. 1207-1216
Author(s):  
Aurélien Saghaï ◽  
Yvan Zivanovic ◽  
David Moreira ◽  
Rosaluz Tavera ◽  
Purificación López-García
Keyword(s):  
Microbial Mats ◽  
Hot Springs ◽  
Phylogenetic Analyses ◽  
Central Carbon Metabolism ◽  
Depth Gradient ◽  
Community Members ◽  
Diel Cycles ◽  
Its Gene ◽  
Lake Alchichica ◽  
Different Depths

Abstract Chloroflexales (Chloroflexi) are typical members of the anoxygenic photosynthesizing component of microbial mats and have mostly been characterized from communities associated to hot springs. Here, we report the assembly of five metagenome-assembled genomes (MAGs) of a novel lineage of Chloroflexales found in mesophilic lithifying microbial mats (microbialites) in Lake Alchichica (Mexico). Genomic and phylogenetic analyses revealed that the bins shared 92% of their genes, and these genes were nearly identical despite being assembled from samples collected along a depth gradient (1–15 m depth). We tentatively name this lineage Candidatus Lithoflexus mexicanus. Metabolic predictions based on the MAGs suggest that these chlorosome-lacking mixotrophs share features in central carbon metabolism, electron transport, and adaptations to life under oxic and anoxic conditions, with members of two related lineages, Chloroflexineae and Roseiflexineae. Contrasting with the other diverse microbialite community members, which display much lower genomic conservation along the depth gradient, Ca. L. mexicanus MAGs exhibit remarkable similarity. This might reflect a particular flexibility to acclimate to varying light conditions with depth or the capacity to occupy a very specific spatial ecological niche in microbialites from different depths. Alternatively, Ca. L. mexicanus may also have the ability to modulate its gene expression as a function of the local environmental conditions during diel cycles in microbialites along the depth gradient.

scholarly journals In-Situ Metatranscriptomic Analyses Reveal the Metabolic Flexibility of the Thermophilic Anoxygenic Photosynthetic Bacterium Chloroflexusaggregans in a Hot Spring Cyanobacteria-Dominated Microbial Mat

2021 ◽  
Vol 9 (3) ◽  
pp. 652
Author(s):  
Shigeru Kawai ◽  
Joval N. Martinez ◽  
Mads Lichtenberg ◽  
Erik Trampe ◽  
Michael Kühl ◽  
...  
Keyword(s):  
Energy Metabolism ◽  
Environmental Conditions ◽  
Microbial Mats ◽  
Carbon Fixation ◽  
Hot Springs ◽  
Hot Spring ◽  
Photosynthetic Bacterium ◽  
Early Morning ◽  
Metabolic Flexibility

Chloroflexus aggregans is a metabolically versatile, thermophilic, anoxygenic phototrophic member of the phylum Chloroflexota (formerly Chloroflexi), which can grow photoheterotrophically, photoautotrophically, chemoheterotrophically, and chemoautotrophically. In hot spring-associated microbial mats, C. aggregans co-exists with oxygenic cyanobacteria under dynamic micro-environmental conditions. To elucidate the predominant growth modes of C. aggregans, relative transcription levels of energy metabolism- and CO2 fixation-related genes were studied in Nakabusa Hot Springs microbial mats over a diel cycle and correlated with microscale in situ measurements of O2 and light. Metatranscriptomic analyses indicated two periods with different modes of energy metabolism of C. aggregans: (1) phototrophy around midday and (2) chemotrophy in the early morning hours. During midday, C. aggregans mainly employed photoheterotrophy when the microbial mats were hyperoxic (400–800 µmol L−1 O2). In the early morning hours, relative transcription peaks of genes encoding uptake hydrogenase, key enzymes for carbon fixation, respiratory complexes as well as enzymes for TCA cycle and acetate uptake suggest an aerobic chemomixotrophic lifestyle. This is the first in situ study of the versatile energy metabolism of C. aggregans based on gene transcription patterns. The results provide novel insights into the metabolic flexibility of these filamentous anoxygenic phototrophs that thrive under dynamic environmental conditions.

scholarly journals Changes in Quinone Profiles of Hot Spring Microbial Mats with a Thermal Gradient

1999 ◽  
Vol 65 (1) ◽  
pp. 198-205 ◽  
Author(s):  
Akira Hiraishi ◽  
Taichi Umezawa ◽  
Hiroyuki Yamamoto ◽  
Kenji Kato ◽  
Yonosuke Maki
Keyword(s):  
Thermal Gradient ◽  
Microbial Mats ◽  
Hot Springs ◽  
Hot Spring ◽  
Thermal Gradients ◽  
Cyanobacterial Mats ◽  
Dissimilarity Index ◽  
Quinone Profile ◽  
Bacterial Mats ◽  
Different Temperatures

ABSTRACT The respiratory and photosynthetic quinones of microbial mats which occurred in Japanese sulfide-containing neutral-pH hot springs at different temperatures were analyzed by spectrochromatography and mass spectrometry. All of the microbial mats that developed at high temperatures (temperatures above 68°C) were so-called sulfur-turf bacterial mats and produced methionaquinones (MTKs) as the major quinones. A 78°C hot spring sediment had a similar quinone profile.Chloroflexus-mixed mats occurred at temperatures of 61 to 65°C and contained menaquinone 10 (MK-10) as the major component together with significant amounts of either MTKs or plastoquinone 9 (PQ-9). The sunlight-exposed biomats growing at temperatures of 45 to 56°C were all cyanobacterial mats, in which the photosynthetic quinones (PQ-9 and phylloquinone) predominated and MK-10 was the next most abundant component in most cases. Ubiquinones (UQs) were not found or were detected in only small amounts in the biomats growing at temperatures of 50°C and above, whereas the majority of the quinones of a purple photosynthetic mat growing at 34°C were UQs. A numerical analysis of the quinone profiles was performed by using the following three parameters: dissimilarity index (D), microbial divergence index (MDq ), and bioenergetic divergence index (BDq ). A D matrix tree analysis showed that the hot spring mats consisting of the sulfur-turf bacteria, Chloroflexus spp., cyanobacteria, and purple phototrophic bacteria formed distinct clusters. Analyses ofMDq and BDq values indicated that the microbial diversity of hot spring mats decreased as the temperature of the environment increased. The changes in quinone profiles and physiological types of microbial mats in hot springs with thermal gradients are discussed from evolutionary viewpoints.

scholarly journals Short-Term Stable Isotope Probing of Proteins Reveals Taxa Incorporating Inorganic Carbon in a Hot Spring Microbial Mat

2020 ◽  
Vol 86 (7) ◽  
Author(s):  
Laurey Steinke ◽  
Gordon W. Slysz ◽  
Mary S. Lipton ◽  
Christian Klatt ◽  
James J. Moran ◽  
...  
Keyword(s):  
Stable Isotope ◽  
Inorganic Carbon ◽  
Microbial Mats ◽  
Carbon Fixation ◽  
Hot Springs ◽  
Hot Spring ◽  
Stable Isotope Probing ◽  
Short Term ◽  
Low Light ◽  
Assembly Sequences

ABSTRACT The upper green layer of the chlorophototrophic microbial mats associated with the alkaline siliceous hot springs of Yellowstone National Park consists of oxygenic cyanobacteria (Synechococcus spp.), anoxygenic Roseiflexus spp., and several other anoxygenic chlorophototrophs. Synechococcus spp. are believed to be the main fixers of inorganic carbon (Ci), but some evidence suggests that Roseiflexus spp. also contribute to inorganic carbon fixation during low-light, anoxic morning periods. Contributions of other phototrophic taxa have not been investigated. In order to follow the pathway of Ci incorporation into different taxa, mat samples were incubated with [13C]bicarbonate for 3 h during the early-morning, low-light anoxic period. Extracted proteins were treated with trypsin and analyzed by mass spectrometry, leading to peptide identifications and peptide isotopic profile signatures containing evidence of 13C label incorporation. A total of 25,483 peptides, corresponding to 7,221 proteins, were identified from spectral features and associated with mat taxa by comparison to metagenomic assembly sequences. A total of 1,417 peptides, derived from 720 proteins, were detectably labeled with 13C. Most 13C-labeled peptides were derived from proteins of Synechococcus spp. and Roseiflexus spp. Chaperones and proteins of carbohydrate metabolism were most abundantly labeled. Proteins involved in photosynthesis, Ci fixation, and N2 fixation were also labeled in Synechococcus spp. Importantly, most proteins of the 3-hydroxypropionate bi-cycle for Ci fixation in Roseiflexus spp. were labeled, establishing that members of this taxocene contribute to Ci fixation. Other taxa showed much lower [13C]bicarbonate incorporation. IMPORTANCE Yellowstone hot spring mats have been studied as natural models for understanding microbial community ecology and as modern analogs of stromatolites, the earliest community fossils on Earth. Stable-isotope probing of proteins (Pro-SIP) permitted short-term interrogation of the taxa that are involved in the important process of light-driven Ci fixation in this highly active community and will be useful in linking other metabolic processes to mat taxa. Here, evidence is presented that Roseiflexus spp., which use the 3-hydroxypropionate bi-cycle, are active in Ci fixation. Because this pathway imparts a lower degree of selection of isotopically heavy Ci than does the Calvin-Benson-Bassham cycle, the results suggest a mechanism to explain why the natural abundance of 13C in mat biomass is greater than expected if only the latter pathway were involved. Understanding how mat community members influence the 13C/12C ratios of mat biomass will help geochemists interpret the 13C/12C ratios of organic carbon in the fossil record.

scholarly journals Limnology of Lake Bogakain, Bandarban, Bangladesh

1970 ◽  
Vol 39 (2) ◽  
pp. 153-159 ◽  
Author(s):  
Moniruzzaman Khondker ◽  
Md Almujaddade Alfasane ◽  
Md Shafiqul Islam ◽  
M Azmal Hossain Bhuiyan ◽  
Md Ataul Gani
Keyword(s):  
Water Temperature ◽  
Negative Correlation ◽  
Phytoplankton Biomass ◽  
Thermal Spring ◽  
Turbid Water ◽  
Depth Gradient ◽  
Chl A ◽  
Different Depths ◽  
First Time ◽  
Depth Water

Bogakain, a natural high altitude (372 m) lake of Bangladesh has been limnologically investigated for the first time. At mid-point, the depth of the lake was measured 46.54 m and the Secchi visibility was 2.37 m. Water temperature from 1-10 m depth gradient showed slight stratification in the lake which varied from 27.0 - 22.4° C at 1.00 pm. pH at the different depths ranged from 7.8 - 9.1, conductivity from 75 - 80 μS/cm and TDS from 39 - 42 mg/l. Alkalinity ranged from 0.8 - 1.24 meq/l and DO from 0.61 - 11.39 mg/l. A total of 40 species of phytoplank-ton were recorded from the lake of which 21 belonged to Chlorophyceae followed by Cynaophyceae (5), Bacillariophyceae (4), Cryptophyceae (4), Euglenophyceae (3), Dinophyceae (2) and Chrysophyceae (1). Bloom by Synnechocystis salina Wisl was observed at 10 m depth. Water temperature correlated negatively and significantly with depth. Phytoplankton biomass as chl a correlated positively with phytoplankton density and water depth. The former variable showed negative correlation with pH and water temperature. Lake Bogakain is the deepest natural lake of Bangladesh and many of the previous concepts regarding the lake i.e., fishless, highly turbid water and it has got a thermal spring at the bottom was found invalid. Key words: Bogakain; Limnology; Macrophyte; Phytoplankton; Bangladesh DOI: 10.3329/bjb.v39i2.7301 Bangladesh J. Bot. 39(2): 153-159, 2010 (December)  

Calcite lilypads and ledges at Lorusio Hot Springs, Kenya Rift Valley: travertine precipitation at the air-water interface

1999 ◽  
Vol 36 (4) ◽  
pp. 649-666 ◽  
Author(s):  
Robin W Renaut ◽  
Brian Jones ◽  
Caroline Le Turdu
Keyword(s):  
Water Surface ◽  
Microbial Mats ◽  
Hot Springs ◽  
Water Interface ◽  
Kenya Rift ◽  
Similar Morphology ◽  
Northern Kenya ◽  
Air Water Interface ◽  
Capillary Evaporation ◽  
Outflow Channel

Travertine forming at Lorusio Hot Springs in the northern Kenya Rift is constructed mainly by lilypads and ledges. The lilypads are flat, accretionary structures rooted to the substrate that are composed mostly of platy calcite crystals. They grow outward from a nucleus, subparallel to the water surface, at or just below the air-water interface. Precipitation results from rapid degassing of CO2. Ledges, which have a similar morphology and internal structure, are attached to the margin of a spring pool or outflow channel. As they grow laterally, lilypads and ledges may coalesce with their neighbours to produce thin (1-3 cm) beds of travertine, examples of which are exposed in subfossil deposits at the site. Once established, lilypads and ledges modify the outflow and can act as substrates for precipitation of other minerals and colonization by microbes on their cooler subaerial surfaces. Pore fluids are drawn upward through the lilypads by capillary evaporation. Amorphous silica then precipitates as surficial crusts upon microbial mats or forms spicular microstromatolites, some of which also contain calcite laminae. Efflorescent Na-CO3 salts commonly encrust the drier central platforms of the exposed lilypad. The unusual abundance of lilypads and ledges at Lorusio reflects (i) the low-relief setting and the hydrostatic head, which limit terrace development, and (ii) the high temperature (>75°C) of the waters, which inhibits colonization by microbial mats at crystal growth sites. Similar structures form in cave pools, evaporating brines, and freezing water at sites where precipitation is induced by several processes active at the air-water interface.

A new species of Coccomyces from Guizhou Province of China

Phytotaxa ◽  
2020 ◽  
Vol 446 (1) ◽  
pp. 23-32
Author(s):  
WEI ZANG ◽  
TU LV ◽  
JIANQIU SUN ◽  
CHENGLIN HOU
Keyword(s):  
New Species ◽  
Life Science ◽  
Nature Reserve ◽  
Phylogenetic Analyses ◽  
Guizhou Province ◽  
New Taxon ◽  
Its Gene ◽  
Close Relationship ◽  
Beijing China ◽  
A New Species

Specimens of Coccomyces collected from Fanjingshan National Nature Reserve in Guizhou Province of China were identified as a new species and named as Coccomyces fanjingshanensis. Phylogenetic analyses of the ITS gene and combined LSU and mtSSU genes indicate that this new taxon has a close relationship with Coccomyces huangshanensis, Coccomyces cupressinus and Coccomyces radiatus.The type collection was deposited in the Herbarium of the College of Life Science, Capital Normal University, Beijing, China (BJTC).

scholarly journals A New Niche for Anoxygenic Phototrophs as Endoliths

2017 ◽  
Vol 84 (4) ◽  
Author(s):  
Daniel Roush ◽  
Estelle Couradeau ◽  
Brandon Guida ◽  
Susanne Neuer ◽  
Ferran Garcia-Pichel
Keyword(s):  
High Throughput Sequencing ◽  
Microbial Mats ◽  
Hot Springs ◽  
Significant Proportion ◽  
Anoxygenic Phototrophic Bacteria ◽  
Major Type ◽  
Carbonate Platforms ◽  
Content Type ◽  
Wide Range ◽  
Isla De Mona

ABSTRACTAnoxygenic phototrophic bacteria (APBs) occur in a wide range of aquatic habitats, from hot springs to freshwater lakes and intertidal microbial mats. Here, we report the discovery of a novel niche for APBs: endoliths within marine littoral carbonates. In a study of 40 locations around Isla de Mona, Puerto Rico, and Menorca, Spain, 16S rRNA high-throughput sequencing of endolithic community DNA revealed the presence of abundant phylotypes potentially belonging to well-known APB clades. Anad hocphylogenetic classification of these sequences enabled us to refine the assignments more stringently. Even then, all locations contained such putative APBs, often reaching a significant proportion of all phototrophic sequences. In fact, in some 20% of samples, their contribution exceeded that of oxygenic phototrophs, previously regarded as the major type of endolithic microbe in carbonates. The communities contained representatives of APBs in theChloroflexales, various proteobacterial groups, andChlorobi. The most abundant phylotypes varied with geography: on Isla de Mona,RoseiflexusandChlorothrix-related phylotypes dominated, whereas those related toErythrobacterwere the most common in Menorca. The presence of active populations of APBs was corroborated through an analysis of photopigments: bacteriochlorophylls were detected in all samples, bacteriochlorophyllcandabeing most abundant. We discuss the potential metabolism and geomicrobial roles of endolithic APBs. Phylogenetic inference suggests that APBs may be playing a role as photoheterotrophs, adding biogeochemical complexity to our understanding of such communities. Given the global extent of coastal carbonate platforms, they likely represent a very large and unexplored habitat for APBs.IMPORTANCEEndolithic microbial communities from carbonates, which have been explored for over 2 centuries in predominantly naturalistic studies, were thought to be primarily composed of eukaryotic algae and cyanobacteria. Our report represents a paradigm shift in this regard, at least for the marine environment, demonstrating the presence of ubiquitous and abundant populations of APBs in this habitat. It raises questions about the role of these organisms in the geological dynamics of coastal carbonates, including coral reefs.

scholarly journals 16S rRNA Phylogenetic Investigation of the Candidate Division “Korarchaeota”

2006 ◽  
Vol 72 (7) ◽  
pp. 5077-5082 ◽  
Author(s):  
Thomas A. Auchtung ◽  
Cristina D. Takacs-Vesbach ◽  
Colleen M. Cavanaugh
Keyword(s):  
16S Rrna ◽  
Hot Springs ◽  
Phylogenetic Analyses ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Environmental Distribution ◽  
Candidate Division ◽  
High Level ◽  
The 16S Rrna Gene

ABSTRACT The environmental distribution and phylogeny of “Korarchaeota,” a proposed ancient archaeal division, was investigated by using the 16S rRNA gene framework. Korarchaeota-specific primers were designed based on previously published sequences and used to screen a variety of environments. Korarchaeota 16S rRNA genes were amplified exclusively from high temperature Yellowstone National Park hot springs and a 9°N East Pacific Rise deep-sea hydrothermal vent. Phylogenetic analyses of these and all available sequences suggest that Korarchaeota exhibit a high level of endemicity.

Diversity of phototrophic bacteria in microbial mats from Arctic hot springs (Greenland)

2007 ◽  
Vol 9 (1) ◽  
pp. 26-38 ◽  
Author(s):  
Guus Roeselers ◽  
Tracy B. Norris ◽  
Richard W. Castenholz ◽  
Søren Rysgaard ◽  
Ronnie N. Glud ◽  
...  
Keyword(s):  
Microbial Mats ◽  
Hot Springs ◽  
Phototrophic Bacteria
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