scholarly journals A shared core microbiome in soda lakes separated by large distances

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Jackie K. Zorz ◽  
Christine Sharp ◽  
Manuel Kleiner ◽  
Paul M. K. Gordon ◽  
Richard T. Pon ◽  
...  
Keyword(s):  
Microbial Mats ◽  
Carbon Fixation ◽  
Soda Lakes ◽  
Soda Lake ◽  
Sequencing Data ◽  
Core Microbiome ◽  
Lake Ecology ◽  
Selection Principles ◽  
Globally Distributed ◽  
Insight Into

Abstract In alkaline soda lakes, concentrated dissolved carbonates establish productive phototrophic microbial mats. Here we show how microbial phototrophs and autotrophs contribute to this exceptional productivity. Amplicon and shotgun DNA sequencing data of microbial mats from four Canadian soda lakes indicate the presence of > 2,000 species of Bacteria and Eukaryotes. We recover metagenome-assembled-genomes for a core microbiome of < 100 abundant bacteria, present in all four lakes. Most of these are related to microbes previously detected in sediments of Asian alkaline lakes, showing that common selection principles drive community assembly from a globally distributed reservoir of alkaliphile biodiversity. Detection of > 7,000 proteins show how phototrophic populations allocate resources to specific processes and occupy complementary niches. Carbon fixation proceeds by the Calvin-Benson-Bassham cycle, in Cyanobacteria, Gammaproteobacteria, and, surprisingly, Gemmatimonadetes. Our study provides insight into soda lake ecology, as well as a template to guide efforts to engineer biotechnology for carbon dioxide conversion.

scholarly journals A shared core microbiome in soda lakes separated by large distances

2019 ◽  
Author(s):  
Jackie K. Zorz ◽  
Christine Sharp ◽  
Manuel Kleiner ◽  
Paul M.K. Gordon ◽  
Richard T. Pon ◽  
...  
Keyword(s):  
Carbon Dioxide ◽  
Microbial Mats ◽  
Carbon Fixation ◽  
Global Climate ◽  
Soda Lakes ◽  
Soda Lake ◽  
Sequencing Data ◽  
Carbon Dioxide Conversion ◽  
Core Microbiome ◽  
Central Asian

AbstractIn alkaline soda lakes, high concentrations of dissolved carbonates establish an environment favouring productive phototrophic microbial mat communities. Here we show how different species of microbial phototrophs and autotrophs contribute to this exceptional productivity. Four years of amplicon and shotgun DNA sequencing data from microbial mats from four different lakes indicated the presence of over 2,000 different species of Bacteria and Eukaryotes. Metagenome-assembled-genomes were obtained for a core microbiome of <100 abundant bacteria, which was shared among lakes and accounted for half of the extracted DNA throughout the four year sampling period. Most of the associated species were related to similar microbes previously detected in sediments of Central Asian alkaline soda lakes, showing that common selection principles drive community assembly from a globally distributed reservoir of alkaliphile biodiversity. Dispersal events between the two distant lake systems were shown to be extremely rare, with dispersal rates a function of abundance in microbial mats, but not sediments. Detection of more than 7,000 expressed proteins showed how phototrophic populations allocated resources to specific processes and occupied complementary niches. Carbon fixation only proceeded by the Calvin-Benson-Bassham cycle, detected in Cyanobacteria, Alphaproteobacteria, and, suprisingly, Gemmatomonadetes. Our study not only provides new fundamental insight into soda lake ecology, but also provides a template, guiding future efforts to engineer robust and productive biotechnology for carbon dioxide conversion.ImportanceAlkaline soda lakes are among the most productive ecosystems worldwide, despite their high pH. This high productivity leads to growth of thick “mats” of filamentous cyanobacteria. Here, we show that such mats have very high biodiversity, but at the same time contain a core, shared set of only approximately 100 different bacteria that perform key functions, such as photosynthesis. This “core microbiome” occurs both in Canadian and Central Asian soda lakes, >8,000 km apart. We present evidence for (very rare) dispersion of some core microbiome members from Canadian mats to Central Asian soda lake sediments. The close similarity between distant microbial communities indicates that these communities share common design principles, that reproducibly lead to a high and robust productivity. We unravel a few examples of such principles and speculate that these might be applied to create robust biotechnology for carbon dioxide conversion, to mitigate of global climate change.

scholarly journals Aerobic carboxydotrophy under extremely haloalkaline conditions in Alkalispirillum/Alkalilimnicola strains isolated from soda lakes

Microbiology ◽  
2010 ◽  
Vol 156 (3) ◽  
pp. 819-827 ◽  
Author(s):  
Dimitry Yu. Sorokin ◽  
Tatjana P. Tourova ◽  
Olga L. Kovaleva ◽  
J. Gijs Kuenen ◽  
Gerard Muyzer
Keyword(s):  
Carbon Fixation ◽  
Soda Lakes ◽  
Large Subunit ◽  
Calvin Cycle ◽  
Soda Lake ◽  
Protein Profiling ◽  
Bacterial Strains ◽  
Gene Encoding ◽  
Respiration Activity ◽  
Ph Range

Aerobic enrichments from soda lake sediments with CO as the only substrate resulted in the isolation of five bacterial strains capable of autotrophic growth with CO at extremely high pH and salinity. The strains belonged to the Alkalispirillum/Alkalilimnicola cluster in the Gammaproteobacteria, where the ability to oxidize CO, but not growth with CO, has been demonstrated previously. The growth with CO was possible only at an oxygen concentration below 5 % and CO concentration below 20 % in the gas phase. The isolates were also capable of growth with formate but not with H2. The carboxydotrophic growth occurred within a narrow pH range from 8 to 10.5 (optimum at 9.5) and a broad salt concentration from0.3 to 3.5 M total Na+ (optimum at 1.0 M). Cells grown on CO had high respiration activity with CO and formate, while the cells grown on formate actively oxidized formate alone. In CO-grown cells, CO-dehydrogenase (CODH) activity was detectable both in soluble and membrane fractions, while the NAD-independent formate dehydrogenase (FDH) resided solely in membranes. The results of total protein profiling and the failure to detect CODH with conventional primers for the coxL gene indicated that the CO-oxidizing enzyme in haloalkaliphilic isolates might differ from the classical aerobic CODH complex. A single cbbL gene encoding the RuBisCO large subunit was detected in all strains, suggesting the presence of the Calvin cycle of inorganic carbon fixation. Overall, these results demonstrated the possibility of aerobic carboxydotrophy under extremely haloalkaline conditions.

Microbially induced pseudotraces from a Pantanal soda lake, Brazil: Alternative interpretations for Ediacaran simple trails and their limits

Geology ◽  
2020 ◽  
Vol 48 (9) ◽  
pp. 857-861
Author(s):  
L.V. Warren ◽  
L.A. Buatois ◽  
M.G. Mángano ◽  
M.G. Simões ◽  
M.G.M. Santos ◽  
...  
Keyword(s):  
Cross Section ◽  
Microbial Mats ◽  
Soda Lakes ◽  
Sedimentary Environment ◽  
Extreme Environments ◽  
Soda Lake ◽  
Trace Fossils ◽  
Wave Direction ◽  
Section Type ◽  
Size And Morphology

Abstract Despite the absence of metazoans, structures resembling animal traces are common in a soda lake from the western Brazil Pantanal wetland. Pantanal soda lakes are ecologically extreme environments that preclude complex life, allowing extremophiles to flourish. Direct observation indicates that these structures are pseudotraces, representing groove marks that result from the interaction of wave-transported floating rafts of epibenthic microbial mat fragments with the substrate. Variations in wind/wave direction and intensity result in marks of different size and morphology. The most common pseudotraces are simple and slightly curved, narrow grooves (type 1), whereas others are straight and present raised lateral ridges (type 2). Both are V-shaped in cross section. Type 3 comprises long, sinuous, shallow grooves, displaying internal crescentic laminated infill and U-shaped cross section. The similarity of these pseudotraces to Ediacaran structures usually interpreted as animal trace fossils suggests that care should be exercised in their analysis. A set of criteria is proposed to differentiate microbially induced pseudotraces from trace fossils. Analysis of Ediacaran structures needs to be performed on a case-by-case basis, taking into account morphology, orientation, and preservation style of the structure, sedimentary environment, and presence or absence of microbial mats.

scholarly journals Nucleus-specific expression in the multinuclear mushroom-forming fungusAgaricus bisporusreveals different nuclear regulatory programs

2018 ◽  
Vol 115 (17) ◽  
pp. 4429-4434 ◽  
Author(s):  
Thies Gehrmann ◽  
Jordi F. Pelkmans ◽  
Robin A. Ohm ◽  
Aurin M. Vos ◽  
Anton S. M. Sonnenberg ◽  
...  
Keyword(s):  
Agaricus Bisporus ◽  
Sequencing Data ◽  
Carbohydrate Active Enzymes ◽  
Nuclear Level ◽  
Specific Expression ◽  
Phenotypic Differences ◽  
Gene Level ◽  
Nuclear Separation ◽  
Insight Into ◽  
Specific Mrna

Many fungi are polykaryotic, containing multiple nuclei per cell. In the case of heterokaryons, there are different nuclear types within a single cell. It is unknown what the different nuclear types contribute in terms of mRNA expression levels in fungal heterokaryons. Each cell of the mushroomAgaricus bisporuscontains two to 25 nuclei of two nuclear types originating from two parental strains. Using RNA-sequencing data, we assess the differential mRNA contribution of individual nuclear types and its functional impact. We studied differential expression between genes of the two nuclear types, P1 and P2, throughout mushroom development in various tissue types. P1 and P2 produced specific mRNA profiles that changed through mushroom development. Differential regulation occurred at the gene level, rather than at the locus, chromosomal, or nuclear level. P1 dominated mRNA production throughout development, and P2 showed more differentially up-regulated genes in important functional groups. In the vegetative mycelium, P2 up-regulated almost threefold more metabolism genes and carbohydrate active enzymes (cazymes) than P1, suggesting phenotypic differences in growth. We identified widespread transcriptomic variation between the nuclear types ofA. bisporus. Our method enables studying nucleus-specific expression, which likely influences the phenotype of a fungus in a polykaryotic stage. Our findings have a wider impact to better understand gene regulation in fungi in a heterokaryotic state. This work provides insight into the transcriptomic variation introduced by genomic nuclear separation.

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 Determination of important enzymes and antimicrobial resistances of gram-positive haloalkaliphilic bacteria isolated from Salda Lake

2021 ◽  
Vol 38 (3) ◽  
pp. 375-382
Author(s):  
Pınar Çağlayan
Keyword(s):  
Bacillus Subtilis ◽  
Soda Lakes ◽  
Soda Lake ◽  
16S Rrna Gene Sequencing ◽  
Extreme Environment ◽  
Rrna Gene ◽  
Sequencing Analysis ◽  
Haloalkaliphilic Bacteria ◽  
Rrna Gene Sequencing

As an extreme environment, soda lakes harbor various haloalkaliphilic microorganisms. Salda Lake is one of the natural soda lake (pH˃9) in Turkey. Haloalkaliphiles are unique microorganisms in their ability to live in high alkaline and high saline conditions, and play an important role in biodegradation and bioremediation of hydrocarbons. Hence, the aims of this study were to isolate haloalkaliphilic bacteria from water sample of Salda Lake, to identify these isolates by both conventional and molecular methods, to screen their industrially important enzymes, and to investigate their antimicrobial resistance profiles. Six isolates were identified as Bacillus horneckiae, Bacillus subtilis, Bacillus paramycoides, Bacillus pumilus, Staphylococcus epidermidis, Bacillus haynesii according to 16S rRNA gene sequencing analysis. The industrially important enzymes (amylase, cellulase, pullulanase, lipase, urease, protease, caseinase, oxidase, catalase) were produced by haloalkaliphilic isolates. These enzymes maybe used in alkaline and saline industrial processes. Although Bacillus subtilis was susceptible to all antibiotics, other isolates showed resistance to at least one antibiotic. The resistance against antibiotics were found as ampicillin/sulbactam 83%, amoxycillin/clavulanic acid 83%, ampicillin 67%, mupirocin 67%, chloramphenicol 50%, tetracycline 50%, imipenem 50%, meropenem 50%, cefadroxil 17%. These bacteria may have develope resistance to antibiotics that entering their natural environment in different ways.

scholarly journals Skin and Gut Microbiome in Psoriasis: Gaining Insight Into the Pathophysiology of It and Finding Novel Therapeutic Strategies

2020 ◽  
Vol 11 ◽  
Author(s):  
Lihui Chen ◽  
Jie Li ◽  
Wu Zhu ◽  
Yehong Kuang ◽  
Tao Liu ◽  
...  
Keyword(s):  
Therapeutic Strategy ◽  
Therapeutic Strategies ◽  
Intestinal Microbiome ◽  
Core Microbiome ◽  
The Core ◽  
The World ◽  
Novel Therapeutic Strategies ◽  
Insight Into ◽  
Gaining Insight

Psoriasis affects the health of myriad populations around the world. The pathogenesis is multifactorial, and the exact driving factor remains unclear. This condition arises from the interaction between hyperproliferative keratinocytes and infiltrating immune cells, with poor prognosis and high recurrence. Better clinical treatments remain to be explored. There is much evidence that alterations in the skin and intestinal microbiome play an important role in the pathogenesis of psoriasis, and restoration of the microbiome is a promising preventive and therapeutic strategy for psoriasis. Herein, we have reviewed recent studies on the psoriasis-related microbiome in an attempt to confidently identify the “core” microbiome of psoriasis patients, understand the role of microbiome in the pathogenesis of psoriasis, and explore new therapeutic strategies for psoriasis through microbial intervention.

scholarly journals Freshwater Chlorobia Exhibit Metabolic Specialization among Cosmopolitan and Endemic Populations

mSystems ◽  
2021 ◽  
Vol 6 (3) ◽  
Author(s):  
Sarahi L. Garcia ◽  
Maliheh Mehrshad ◽  
Moritz Buck ◽  
Jackson M. Tsuji ◽  
Josh D. Neufeld ◽  
...  
Keyword(s):  
Carbon Fixation ◽  
Carbon Sources ◽  
Natural Populations ◽  
Freshwater Ecosystems ◽  
Electron Donors ◽  
Functional Ecology ◽  
Lake Ecosystems ◽  
Tropical Regions ◽  
Metabolic Versatility ◽  
Globally Distributed

ABSTRACT Photosynthetic bacteria from the class Chlorobia (formerly phylum Chlorobi) sustain carbon fixation in anoxic water columns. They harvest light at extremely low intensities and use various inorganic electron donors to fix carbon dioxide into biomass. Until now, most information on the functional ecology and local adaptations of Chlorobia members came from isolates and merely 26 sequenced genomes that may not adequately represent natural populations. To address these limitations, we analyzed global metagenomes to profile planktonic Chlorobia cells from the oxyclines of 42 freshwater bodies, spanning subarctic to tropical regions and encompassing all four seasons. We assembled and compiled over 500 genomes, including metagenome-assembled genomes (MAGs), single-amplified genomes (SAGs), and reference genomes from cultures, clustering them into 71 metagenomic operational taxonomic units (mOTUs or “species”). Of the 71 mOTUs, 57 were classified within the genus Chlorobium, and these mOTUs represented up to ∼60% of the microbial communities in the sampled anoxic waters. Several Chlorobium-associated mOTUs were globally distributed, whereas others were endemic to individual lakes. Although most clades encoded the ability to oxidize hydrogen, many lacked genes for the oxidation of specific sulfur and iron substrates. Surprisingly, one globally distributed Scandinavian clade encoded the ability to oxidize hydrogen, sulfur, and iron, suggesting that metabolic versatility facilitated such widespread colonization. Overall, these findings provide new insight into the biogeography of the Chlorobia and the metabolic traits that facilitate niche specialization within lake ecosystems. IMPORTANCE The reconstruction of genomes from metagenomes has helped explore the ecology and evolution of environmental microbiota. We applied this approach to 274 metagenomes collected from diverse freshwater habitats that spanned oxic and anoxic zones, sampling seasons, and latitudes. We demonstrate widespread and abundant distributions of planktonic Chlorobia-associated bacteria in hypolimnetic waters of stratified freshwater ecosystems and show they vary in their capacities to use different electron donors. Having photoautotrophic potential, these Chlorobia members could serve as carbon sources that support metalimnetic and hypolimnetic food webs.

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 Morphological and Transcriptomic Analysis of the Inhibitory Effects of Lactobacillus plantarum on Aspergillus flavus Growth and Aflatoxin Production

Toxins ◽  
2019 ◽  
Vol 11 (11) ◽  
pp. 636 ◽  
Author(s):  
Zhao ◽  
Zhang ◽  
Folly ◽  
Chang ◽  
Wang ◽  
...  
Keyword(s):  
Lactobacillus Plantarum ◽  
Aspergillus Flavus ◽  
Aflatoxin Production ◽  
Inhibitory Effect ◽  
Transcriptional Level ◽  
Sequencing Data ◽  
Inhibitory Effects ◽  
Cell Wall Polysaccharides ◽  
Colony Forming Units ◽  
Insight Into

Lactobacillus plantarum, as a natural bio-preservative, has attracted a great deal of attention in recent years. In this study, 22 L. plantarum strains were tested against the aflatoxin-producing fungus, Aspergillus flavus; strain IAMU80070 showed the highest antifungal activity. At a concentration of 5 × 105 colony-forming units (CFU) mL−1, it completely inhibited A. flavus growth and decreased aflatoxin production by 93%. Furthermore, ultrastructural examination showed that IAMU80070 destroyed the cellular structure of hyphae and spores. To explore the inhibitory effect of IAMU80070 on A. flavus at the transcriptional level, transcriptome data were obtained and subjected to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. The aflatoxin biosynthetic process was the most significantly downregulated functional category, while genes implicated in the synthesis and organization of cell wall polysaccharides were upregulated. Quantitative real-time PCR results verified the credibility and reliability of the RNA sequencing data. These results provided insight into the transcriptome of A. flavus in response to the antagonistic effects of L. plantarum IAMU80070.

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