scholarly journals On the evolution and physiology of cable bacteria

2019 ◽  
Vol 116 (38) ◽  
pp. 19116-19125 ◽  
Author(s):  
Kasper U. Kjeldsen ◽  
Lars Schreiber ◽  
Casper A. Thorup ◽  
Thomas Boesen ◽  
Jesper T. Bjerg ◽  
...  
Keyword(s):  
Electron Flow ◽  
Sulfide Oxidation ◽  
Gene Families ◽  
Last Common Ancestor ◽  
Long Distance ◽  
Microbial World ◽  
Single Filament ◽  
Oxic Zone ◽  
Pure Cultures ◽  
Unique Genes

Cable bacteria of the family Desulfobulbaceae form centimeter-long filaments comprising thousands of cells. They occur worldwide in the surface of aquatic sediments, where they connect sulfide oxidation with oxygen or nitrate reduction via long-distance electron transport. In the absence of pure cultures, we used single-filament genomics and metagenomics to retrieve draft genomes of 3 marine Candidatus Electrothrix and 1 freshwater Ca. Electronema species. These genomes contain >50% unknown genes but still share their core genomic makeup with sulfate-reducing and sulfur-disproportionating Desulfobulbaceae, with few core genes lost and 212 unique genes (from 197 gene families) conserved among cable bacteria. Last common ancestor analysis indicates gene divergence and lateral gene transfer as equally important origins of these unique genes. With support from metaproteomics of a Ca. Electronema enrichment, the genomes suggest that cable bacteria oxidize sulfide by reversing the canonical sulfate reduction pathway and fix CO2 using the Wood–Ljungdahl pathway. Cable bacteria show limited organotrophic potential, may assimilate smaller organic acids and alcohols, fix N2, and synthesize polyphosphates and polyglucose as storage compounds; several of these traits were confirmed by cell-level experimental analyses. We propose a model for electron flow from sulfide to oxygen that involves periplasmic cytochromes, yet-unidentified conductive periplasmic fibers, and periplasmic oxygen reduction. This model proposes that an active cable bacterium gains energy in the anodic, sulfide-oxidizing cells, whereas cells in the oxic zone flare off electrons through intense cathodic oxygen respiration without energy conservation; this peculiar form of multicellularity seems unparalleled in the microbial world.

scholarly journals Division of labor and growth during electrical cooperation in multicellular cable bacteria

2020 ◽  
Vol 117 (10) ◽  
pp. 5478-5485 ◽  
Author(s):  
Nicole M. J. Geerlings ◽  
Cheryl Karman ◽  
Stanislav Trashin ◽  
Karel S. As ◽  
Michiel V. M. Kienhuis ◽  
...  
Keyword(s):  
Energy Conservation ◽  
Oxygen Reduction ◽  
Division Of Labor ◽  
Resource Sharing ◽  
Secondary Ion Mass Spectrometry ◽  
Isotope Labeling ◽  
Sulfide Oxidation ◽  
Long Distance ◽  
Evolutionary Innovation ◽  
Oxic Zone

Multicellularity is a key evolutionary innovation, leading to coordinated activity and resource sharing among cells, which generally occurs via the physical exchange of chemical compounds. However, filamentous cable bacteria display a unique metabolism in which redox transformations in distant cells are coupled via long-distance electron transport rather than an exchange of chemicals. This challenges our understanding of organismal functioning, as the link among electron transfer, metabolism, energy conservation, and filament growth in cable bacteria remains enigmatic. Here, we show that cells within individual filaments of cable bacteria display a remarkable dichotomy in biosynthesis that coincides with redox zonation. Nanoscale secondary ion mass spectrometry combined with 13C (bicarbonate and propionate) and 15N-ammonia isotope labeling reveals that cells performing sulfide oxidation in deeper anoxic horizons have a high assimilation rate, whereas cells performing oxygen reduction in the oxic zone show very little or no label uptake. Accordingly, oxygen reduction appears to merely function as a mechanism to quickly dispense of electrons with little to no energy conservation, while biosynthesis and growth are restricted to sulfide-respiring cells. Still, cells can immediately switch roles when redox conditions change, and show no differentiation, which suggests that the “community service” performed by the cells in the oxic zone is only temporary. Overall, our data reveal a division of labor and electrical cooperation among cells that has not been seen previously in multicellular organisms.

Copper Recovery by Bioleaching of Chalcopyrite: A Microcalorimetric Approach for the Fast Determination of Bioleaching Activity

2013 ◽  
Vol 825 ◽  
pp. 322-325
Author(s):  
Beate Krok ◽  
Axel Schippers ◽  
Wolfgang Sand
Keyword(s):  
Enrichment Culture ◽  
Sulfide Oxidation ◽  
Exothermic Reaction ◽  
Metal Sulfide ◽  
Copper Recovery ◽  
Heat Output ◽  
Low Grade ◽  
Non Invasive ◽  
Pure Cultures ◽  
Invasive Method

Low grade copper ores containing chalcopyrite are increasingly used for copper recovery via biomining. Since metal sulfide oxidation is an exothememic process, bioleaching activity can be measured due to the heat output by microcalorimetry, which is a non-destructive and non-invasive method. The bioleaching activity of pure cultures ofSulfolobus metallicus,Metallosphaera hakonensisand a moderate thermophilic enrichment culture on high grade chalcopyrite was evaluated. Chalcopyrite leaching by microorganisms showed a higher copper recovery than sterile controls. Chemical chalcopyrite leaching by acid produced heat due to the exothermic reaction, the heat output was increased while metal sulfide oxidation by microorganisms.

scholarly journals Disguised as a Sulfate Reducer: Growth of the Deltaproteobacterium Desulfurivibrio alkaliphilus by Sulfide Oxidation with Nitrate

mBio ◽  
2017 ◽  
Vol 8 (4) ◽  
Author(s):  
Casper Thorup ◽  
Andreas Schramm ◽  
Alyssa J. Findlay ◽  
Kai W. Finster ◽  
Lars Schreiber
Keyword(s):  
Sulfate Reduction ◽  
Elemental Sulfur ◽  
Sulfide Oxidation ◽  
Model Organism ◽  
Sulfur Cycle ◽  
High Expression ◽  
Sulfate Reducer ◽  
Expression Of Genes ◽  
Complex Picture ◽  
Pure Cultures

ABSTRACT This study demonstrates that the deltaproteobacterium Desulfurivibrio alkaliphilus can grow chemolithotrophically by coupling sulfide oxidation to the dissimilatory reduction of nitrate and nitrite to ammonium. Key genes of known sulfide oxidation pathways are absent from the genome of D. alkaliphilus. Instead, the genome contains all of the genes necessary for sulfate reduction, including a gene for a reductive-type dissimilatory bisulfite reductase (DSR). Despite this, growth by sulfate reduction was not observed. Transcriptomic analysis revealed a very high expression level of sulfate-reduction genes during growth by sulfide oxidation, while inhibition experiments with molybdate pointed to elemental sulfur/polysulfides as intermediates. Consequently, we propose that D. alkaliphilus initially oxidizes sulfide to elemental sulfur, which is then either disproportionated, or oxidized by a reversal of the sulfate reduction pathway. This is the first study providing evidence that a reductive-type DSR is involved in a sulfide oxidation pathway. Transcriptome sequencing further suggests that nitrate reduction to ammonium is performed by a novel type of periplasmic nitrate reductase and an unusual membrane-anchored nitrite reductase. IMPORTANCE Sulfide oxidation and sulfate reduction, the two major branches of the sulfur cycle, are usually ascribed to distinct sets of microbes with distinct diagnostic genes. Here we show a more complex picture, as D. alkaliphilus, with the genomic setup of a sulfate reducer, grows by sulfide oxidation. The high expression of genes typically involved in the sulfate reduction pathway suggests that these genes, including the reductive-type dissimilatory bisulfite reductases, are also involved in as-yet-unresolved sulfide oxidation pathways. Finally, D. alkaliphilus is closely related to cable bacteria, which grow by electrogenic sulfide oxidation. Since there are no pure cultures of cable bacteria, D. alkaliphilus may represent an exciting model organism in which to study the physiology of this process. IMPORTANCE Sulfide oxidation and sulfate reduction, the two major branches of the sulfur cycle, are usually ascribed to distinct sets of microbes with distinct diagnostic genes. Here we show a more complex picture, as D. alkaliphilus, with the genomic setup of a sulfate reducer, grows by sulfide oxidation. The high expression of genes typically involved in the sulfate reduction pathway suggests that these genes, including the reductive-type dissimilatory bisulfite reductases, are also involved in as-yet-unresolved sulfide oxidation pathways. Finally, D. alkaliphilus is closely related to cable bacteria, which grow by electrogenic sulfide oxidation. Since there are no pure cultures of cable bacteria, D. alkaliphilus may represent an exciting model organism in which to study the physiology of this process.

scholarly journals Reference transcriptomes and comparative analyses of six species in the threatened rosewood genus Dalbergia

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Tin Hang Hung ◽  
Thea So ◽  
Syneath Sreng ◽  
Bansa Thammavong ◽  
Chaloun Boounithiphonh ◽  
...  
Keyword(s):  
Population Genomics ◽  
Association Studies ◽  
Divergence Time ◽  
Gene Families ◽  
Resistance Proteins ◽  
Gene Environment ◽  
International Attention ◽  
Phylogenomic Analyses ◽  
Unique Genes ◽  
Future Population

Abstract Dalbergia is a pantropical genus with more than 250 species, many of which are highly threatened due to overexploitation for their rosewood timber, along with general deforestation. Many Dalbergia species have received international attention for conservation, but the lack of genomic resources for Dalbergia hinders evolutionary studies and conservation applications, which are important for adaptive management. This study produced the first reference transcriptomes for 6 Dalbergia species with different geographical origins and predicted ~ 32 to 49 K unique genes. We showed the utility of these transcriptomes by phylogenomic analyses with other Fabaceae species, estimating the divergence time of extant Dalbergia species to ~ 14.78 MYA. We detected over-representation in 13 Pfam terms including HSP, ALDH and ubiquitin families in Dalbergia. We also compared the gene families of geographically co-occurring D. cochinchinensis and D. oliveri and observed that more genes underwent positive selection and there were more diverged disease resistance proteins in the more widely distributed D. oliveri, consistent with reports that it occupies a wider ecological niche and has higher genetic diversity. We anticipate that the reference transcriptomes will facilitate future population genomics and gene-environment association studies on Dalbergia, as well as contributing to the genomic database where plants, particularly threatened ones, are currently underrepresented.

scholarly journals Development and Evaluation of Functional Gene Arrays for Detection of Selected Genes in the Environment

2001 ◽  
Vol 67 (12) ◽  
pp. 5780-5790 ◽  
Author(s):  
Liyou Wu ◽  
Dorothea K. Thompson ◽  
Guangshan Li ◽  
Richard A. Hurt ◽  
James M. Tiedje ◽  
...  
Keyword(s):  
Signal Intensity ◽  
Genomic Dna ◽  
Gene Diversity ◽  
Gene Array ◽  
Sequence Divergence ◽  
Quantitative Relationship ◽  
Gene Families ◽  
Functional Gene ◽  
Sequence Identity ◽  
Pure Cultures

ABSTRACT To determine the potential of DNA array technology for assessing functional gene diversity and distribution, a prototype microarray was constructed with genes involved in nitrogen cycling: nitrite reductase (nirS and nirK) genes, ammonia mono-oxygenase (amoA) genes, and methane mono-oxygenase (pmoA) genes from pure cultures and those cloned from marine sediments. In experiments using glass slide microarrays, genes possessing less than 80 to 85% sequence identity were differentiated under hybridization conditions of high stringency (65°C). The detection limit fornirS genes was approximately 1 ng of pure genomic DNA and 25 ng of soil community DNA using our optimized protocol. A linear quantitative relationship (r 2 = 0.89 to 0.94) was observed between signal intensity and target DNA concentration over a range of 1 to 100 ng for genomic DNA (or genomic DNA equivalent) from both pure cultures and mixed communities. However, the quantitative capacity of microarrays for measuring the relative abundance of targeted genes in complex environmental samples is less clear due to divergent target sequences. Sequence divergence and probe length affected hybridization signal intensity within a certain range of sequence identity and size, respectively. This prototype functional gene array did reveal differences in the apparent distribution ofnir and amoA and pmoA gene families in sediment and soil samples. Our results indicate that glass-based microarray hybridization has potential as a tool for revealing functional gene composition in natural microbial communities; however, more work is needed to improve sensitivity and quantitation and to understand the associated issue of specificity.

scholarly journals Motility of Marichromatium gracilein Response to Light, Oxygen, and Sulfide

2001 ◽  
Vol 67 (12) ◽  
pp. 5410-5419 ◽  
Author(s):  
Roland Thar ◽  
Michael Kühl
Keyword(s):  
Cell Tracking ◽  
Tracking System ◽  
Sulfide Oxidation ◽  
Purple Sulfur Bacterium ◽  
Light Regimes ◽  
Chemical Gradients ◽  
Protection Strategies ◽  
Oxic Zone ◽  
Sulfur Globules ◽  
Oxygen Concentrations

ABSTRACT The motility of the purple sulfur bacterium Marichromatium gracile was investigated under different light regimes in a gradient capillary setup with opposing oxygen and sulfide gradients. The gradients were quantified with microsensors, while the behavior of swimming cells was studied by video microscopy in combination with a computerized cell tracking system. M. gracile exhibited photokinesis, photophobic responses, and phobic responses toward oxygen and sulfide. The observed migration patterns could be explained solely by the various phobic responses. In the dark, M. gracileformed an ∼500-μm-thick band at the oxic-anoxic interface, with a sharp border toward the oxic zone always positioned at ∼10 μM O2. Flux calculations yielded a molar conversion ratio Stot/O2 of 2.03:1 (Stot = [H2S] + [HS−] + [S2−]) for the sulfide oxidation within the band, indicating that in darkness the bacteria oxidized sulfide incompletely to sulfur stored in intracellular sulfur globules. In the light, M. gracilespread into the anoxic zone while still avoiding regions with >10 μM O2. The cells also preferred low sulfide concentrations if the oxygen was replaced by nitrogen. A light-dark transition experiment demonstrated a dynamic interaction between the chemical gradients and the cell's metabolism. In darkness and anoxia, M. gracile lost its motility after ca. 1 h. In contrast, at oxygen concentrations of >100 μM with no sulfide present the cells remained viable and motile for ca. 3 days both in light and darkness. Oxygen was respired also in the light, but respiration rates were lower than in the dark. Observed aggregation patterns are interpreted as effective protection strategies against high oxygen concentrations and might represent first stages of biofilm formation.

scholarly journals Phylogenetic diversification of sirtuin genes with a description of a new family member

2020 ◽  
Author(s):  
Juan C. Opazo ◽  
Kattina Zavala ◽  
Michael W. Vandewege ◽  
Federico G. Hoffmann
Keyword(s):  
Gene Family ◽  
Family Member ◽  
Gene Families ◽  
Last Common Ancestor ◽  
Gene Repertoire ◽  
Origin And Evolution ◽  
New Family ◽  
Wide Range ◽  
Evolutionary Context ◽  
History Of

AbstractStudying the evolutionary history of gene families is a challenging and exciting task with a wide range of implications. In addition to exploring fundamental questions about the origin and evolution of genes, disentangling their evolution is also critical to those who do functional/structural work, as the correct interpretation of their results needs to be done in a robust evolutionary context. The sirtuin gene family is a group of genes that are involved in a variety of biological functions mostly related to aging. Their duplicative history is an open question, as well as the definition of the repertoire of sirtuin genes among vertebrates. Our goal is to take advantage of the genomic data available in public databases to advance our understanding of how sirtuin genes are related to each other, and to characterize the gene repertoire in species representative of all the main groups of vertebrates. Our results show a well-resolved phylogeny that represents a significant improvement in our understanding of the duplicative history of the sirtuin gene family. We identified a new sirtuin family member (SIRT3-like) that was apparently lost in amniotes, but retained in all other groups of jawed vertebrates. Our results indicate that there are at least eight sirtuin paralogs among vertebrates and that all of them can be traced back to the last common ancestor of the group that existed between 676 and 615 millions of years ago.

scholarly journals Protist.Guru: A Comparative Transcriptomics Database for the Protist Kingdom

2021 ◽  
Author(s):  
Erielle Marie Fajardo Villanueva ◽  
Peng Ken Lim ◽  
Jolyn Jia Jia Lim ◽  
ShanChun Lim ◽  
Pei Yi Lau ◽  
...  
Keyword(s):  
Gene Families ◽  
Gene Clusters ◽  
Biological Processes ◽  
Expression Data ◽  
Online Database ◽  
Microbial World ◽  
Microbial Eukaryotes ◽  
Haematococcus Lacustris ◽  
Secondary Carotenoids ◽  
Protist Species

Abstract Summary: During the last few decades, the study of microbial ecology has been enabled by molecular and genomic data. DNA sequencing has revealed the surprising extent of microbial diversity and how microbial processes run global ecosystems. However, significant gaps in our understanding of the microbial world remain, and one example is that microbial eukaryotes, or protists, are still neglected. To address this gap, we used gene expression data from 15 distinct protist species to create protist.guru: an online database equipped with tools for identifying functional co-expression networks, gene families, and enriched gene clusters. Here, we show how our database can be used to reveal genes involved in essential pathways, such as the synthesis of secondary carotenoids in Haematococcus lacustris. We expect protist.guru to serve as a valuable resource for protistologists, as well as a catalyst for discoveries and new insights into the biological processes of microbial eukaryotes. Availability: The database and co-expression networks are freely available from http://protist.guru/. The expression matrices and sample annotations are found in the supplementary data.

scholarly journals Raman Spectroscopy of Microbial Pigments

2014 ◽  
Vol 80 (11) ◽  
pp. 3286-3295 ◽  
Author(s):  
Jan Jehlička ◽  
Howell G. M. Edwards ◽  
Aharon Oren
Keyword(s):  
Raman Spectroscopy ◽  
Environmental Samples ◽  
Structural Information ◽  
High Sensitivity ◽  
Nondestructive Technique ◽  
Microbial World ◽  
Different Types ◽  
Pure Cultures ◽  
Molecular Compounds

ABSTRACTRaman spectroscopy is a rapid nondestructive technique providing spectroscopic and structural information on both organic and inorganic molecular compounds. Extensive applications for the method in the characterization of pigments have been found. Due to the high sensitivity of Raman spectroscopy for the detection of chlorophylls, carotenoids, scytonemin, and a range of other pigments found in the microbial world, it is an excellent technique to monitor the presence of such pigments, both in pure cultures and in environmental samples. Miniaturized portable handheld instruments are available; these instruments can be used to detect pigments in microbiological samples of different types and origins under field conditions.

scholarly journals The Evolutionary History of New Zealand Deschampsia Is Marked by Long-Distance Dispersal, Endemism, and Hybridization

Biology ◽  
2021 ◽  
Vol 10 (10) ◽  
pp. 1001
Author(s):  
Zhiqing Xue ◽  
Josef Greimler ◽  
Ovidiu Paun ◽  
Kerry Ford ◽  
Michael H. J. Barfuss ◽  
...  
Keyword(s):  
New Zealand ◽  
Evolutionary History ◽  
Dna Analysis ◽  
Common Ancestor ◽  
Plastid Dna ◽  
Last Common Ancestor ◽  
Long Distance Dispersal ◽  
Long Distance ◽  
Test Species ◽  
History Of

The contrasting evolutionary histories of endemic versus related cosmopolitan species provide avenues to understand the spatial drivers and limitations of biodiversity. Here, we investigated the evolutionary history of three New Zealand endemic Deschampsia species, and how they are related to cosmopolitan D. cespitosa. We used RADseq to test species delimitations, infer a dated species tree, and investigate gene flow patterns between the New Zealand endemics and the D. cespitosa populations of New Zealand, Australia and Korea. Whole plastid DNA analysis was performed on a larger worldwide sampling. Morphometrics of selected characters were applied to New Zealand sampling. Our RADseq review of over 55 Mbp showed the endemics as genetically well-defined from each other. Their last common ancestor with D. cespitosa lived during the last ten MY. The New Zealand D. cespitosa appears in a clade with Australian and Korean samples. Whole plastid DNA analysis revealed the endemics as members of a southern hemisphere clade, excluding the extant D. cespitosa of New Zealand. Both data provided strong evidence for hybridization between D. cespitosa and D. chapmanii. Our findings provide evidence for at least two migration events of the genus Deschampsia to New Zealand and hybridization between D. cespitosa and endemic taxa.

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