scholarly journals Genomic Variations Underlying Speciation and Niche Specialization of Shewanella baltica

mSystems ◽  
2019 ◽  
Vol 4 (5) ◽  
Author(s):  
Jie Deng ◽  
Jennifer M. Auchtung ◽  
Konstantinos T. Konstantinidis ◽  
Ingrid Brettar ◽  
Manfred G. Höfle ◽  
...  
Keyword(s):  
Baltic Sea ◽  
Water Column ◽  
Transition Zone ◽  
Anaerobic Respiration ◽  
Electron Acceptors ◽  
Gene Content ◽  
Content Type ◽  
Genomic Variations ◽  
Niche Specialization ◽  
Shewanella Baltica

ABSTRACT Shewanella baltica was the dominant culturable nitrate-reducing bacterium in the eutrophic and strongly stratified Baltic Sea in the 1980s, where it primarily inhabited the oxic-anoxic transition zone. The genomic structures of 46 of these isolates were investigated through comparative genomic hybridization (CGH), which revealed a gradient of genomic similarity, ranging from 65% to as high as 99%. The core genome of the S. baltica species was enriched in anaerobic respiration-associated genes. Auxiliary genes, most of which locate within a few genomic islands (GIs), were nonuniformly distributed among the isolates. Specifically, hypothetical and mobile genetic element (MGE)-associated genes dominated intraclade gene content differences, whereas gain/loss of functional genes drove gene content differences among less related strains. Among the major S. baltica clades, gene signatures related to specific redox-driven and spatial niches within the water column were identified. For instance, genes involved in anaerobic respiration of sulfur compounds may provide key adaptive advantages for clade A strains in anoxic waters where sulfur-containing electron acceptors are present. Genes involved in cell motility, in particular, a secondary flagellar biosynthesis system, may be associated with the free-living lifestyle by clade E strains. Collectively, this study revealed characteristics of genome variations present in the water column and active speciation of S. baltica strains, driven by niche partitioning and horizontal gene transfer (HGT). IMPORTANCE Speciation in nature is a fundamental process driving the formation of the vast microbial diversity on Earth. In the central Baltic Sea, the long-term stratification of water led to formation of a large-scale vertical redoxcline that provided a gradient of environmental niches with respect to the availability of electron acceptors and donors. The region was home to Shewanella baltica populations, which composed the dominant culturable nitrate-reducing bacteria, particularly in the oxic-anoxic transition zone. Using the collection of S. baltica isolates as a model system, genomic variations showed contrasting gene-sharing patterns within versus among S. baltica clades and revealed genomic signatures of S. baltica clades related to redox niche specialization as well as particle association. This study provides important insights into genomic mechanisms underlying bacterial speciation within this unique natural redoxcline.

scholarly journals Divergence in Gene Regulation Contributes to Sympatric Speciation of Shewanella baltica Strains

2017 ◽  
Vol 84 (4) ◽  
Author(s):  
Jie Deng ◽  
Jennifer M. Auchtung ◽  
Konstantinos T. Konstantinidis ◽  
Alejandro Caro-Quintero ◽  
Ingrid Brettar ◽  
...  
Keyword(s):  
Transition Zone ◽  
Sequence Divergence ◽  
Positive Association ◽  
Sulfur Compounds ◽  
Comparative Genomic ◽  
Sequence Evolution ◽  
Transcriptional Responses ◽  
Content Type ◽  
Redox Transition ◽  
Shewanella Baltica

ABSTRACT Niche partitioning and sequence evolution drive genomic and phenotypic divergence, which ultimately leads to bacterial diversification. This study investigated the genomic composition of two Shewanella baltica clades previously identified through multilocus sequencing typing and recovered from the redox transition zone in the central Baltic Sea. Comparative genomic analysis revealed significantly higher interclade than intraclade genomic dissimilarity and that a subset of genes present in clade A were associated with potential adaptation to respiration of sulfur compounds present in the redox transition zone. The transcriptomic divergence between two representative strains of clades A and D, OS185 and OS195, was also characterized and revealed marked regulatory differences. We found that both the transcriptional divergence of shared genes and expression of strain-specific genes led to differences in regulatory patterns between strains that correlate with environmental redox niches. For instance, under anoxic conditions of respiratory nitrate ammonification, OS185—the strain isolated from a nitrate-rich environment—upregulated nearly twice the number of shared genes upregulated by OS195—the strain isolated from an H 2 S-containing anoxic environment. Conversely, OS195 showed stronger induction of strain-specific genes, especially those associated with sulfur compound respiration, under thiosulfate-reducing conditions. A positive association between the level of transcriptional divergence and the level of sequence divergence for shared genes was also noted. Our results provide further support for the hypothesis that genomic changes impacting transcriptional regulation play an important role in the diversification of ecologically distinct populations. IMPORTANCE This study examined potential mechanisms through which co-occurring Shewanella baltica strains diversified to form ecologically distinct populations. At the time of isolation, the strains studied composed the major fraction of culturable nitrate-reducing communities in the Baltica Sea. Analysis of genomic content of 13 S. baltica strains from two clades representing different ecotypes demonstrated that one clade specifically possesses a number of genes that could favor successful adaptation to respire sulfur compounds in the portion of the water column from which these strains were isolated. In addition, transcriptional profiling of fully sequenced strains representative of these two clades, OS185 and OS195, under oxygen-, nitrate-, and thiosulfate-respiring conditions demonstrated that the strains exhibit relatively similar transcriptional responses during aerobic growth but more-distinct transcriptional responses under nitrate- and thiosulfate-respiring conditions. Results from this study provide insights into how genomic and gene regulatory diversification together impacted the redox specialization of the S. baltica strains.

scholarly journals Genomes of Novel Microbial Lineages Assembled from the Sub-Ice Waters of Lake Baikal

2017 ◽  
Vol 84 (1) ◽  
Author(s):  
Pedro J. Cabello-Yeves ◽  
Tamara I. Zemskaya ◽  
Riccardo Rosselli ◽  
Felipe H. Coutinho ◽  
Alexandra S. Zakharenko ◽  
...  
Keyword(s):  
Baltic Sea ◽  
Snow Cover ◽  
Water Column ◽  
Lake Baikal ◽  
Light Penetration ◽  
Freshwater Lakes ◽  
The Baltic Sea ◽  
Content Type ◽  
Freshwater Bodies ◽  
The Baltic

ABSTRACT We present a metagenomic study of Lake Baikal (East Siberia). Two samples obtained from the water column under the ice cover (5 and 20 m deep) in March 2016 have been deep sequenced and the reads assembled to generate metagenome-assembled genomes (MAGs) that are representative of the microbes living in this special environment. Compared with freshwater bodies studied around the world, Lake Baikal had an unusually high fraction of Verrucomicrobia. Other groups, such as Actinobacteria and Proteobacteria, were in proportions similar to those found in other lakes. The genomes (and probably cells) tended to be small, presumably reflecting the extremely oligotrophic and cold prevalent conditions. Baikal microbes are novel lineages recruiting very little from other water bodies and are distantly related to other freshwater microbes. Despite their novelty, they showed the closest relationship to genomes discovered by similar approaches from other freshwater lakes and reservoirs. Some of them were particularly similar to MAGs from the Baltic Sea, which, although it is brackish, connected to the ocean, and much more eutrophic, has similar climatological conditions. Many of the microbes contained rhodopsin genes, indicating that, in spite of the decreased light penetration allowed by the thick ice/snow cover, photoheterotrophy could be widespread in the water column, either because enough light penetrates or because the microbes are already adapted to the summer ice-less conditions. We have found a freshwater SAR11 subtype I/II representative showing striking synteny with Pelagibacter ubique strains, as well as a phage infecting the widespread freshwater bacterium Polynucleobacter. IMPORTANCE Despite the increasing number of metagenomic studies on different freshwater bodies, there is still a missing component in oligotrophic cold lakes suffering from long seasonal frozen cycles. Here, we describe microbial genomes from metagenomic assemblies that appear in the upper water column of Lake Baikal, the largest and deepest freshwater body on Earth. This lake is frozen from January to May, which generates conditions that include an inverted temperature gradient (colder up), decrease in light penetration due to ice, and, especially, snow cover, and oligotrophic conditions more similar to the open-ocean and high-altitude lakes than to other freshwater or brackish systems. As could be expected, most reconstructed genomes are novel lineages distantly related to others in cold environments, like the Baltic Sea and other freshwater lakes. Among them, there was a broad set of streamlined microbes with small genomes/intergenic spacers, including a new nonmarine Pelagibacter-like (subtype I/II) genome.

scholarly journals Dissimilatory Reduction of Extracellular Electron Acceptors in Anaerobic Respiration

2011 ◽  
Vol 78 (4) ◽  
pp. 913-921 ◽  
Author(s):  
Katrin Richter ◽  
Marcus Schicklberger ◽  
Johannes Gescher
Keyword(s):  
Outer Membrane ◽  
Manganese Oxides ◽  
Current Knowledge ◽  
Anaerobic Respiration ◽  
Electron Acceptors ◽  
Transfer Reactions ◽  
Model Organisms ◽  
Content Type ◽  
The Past ◽  
Respiratory Chains

ABSTRACTAn extension of the respiratory chain to the cell surface is necessary to reduce extracellular electron acceptors like ferric iron or manganese oxides. In the past few years, more and more compounds were revealed to be reduced at the surface of the outer membrane of Gram-negative bacteria, and the list does not seem to have an end so far.Shewanellaas well asGeobacterstrains are model organisms to discover the biochemistry that enables the dissimilatory reduction of extracellular electron acceptors. In both cases,c-type cytochromes are essential electron-transferring proteins. They make the journey of respiratory electrons from the cytoplasmic membrane through periplasm and over the outer membrane possible. Outer membrane cytochromes have the ability to catalyze the last step of the respiratory chains. Still, recent discoveries provided evidence that they are accompanied by further factors that allow or at least facilitate extracellular reduction. This review gives a condensed overview of our current knowledge of extracellular respiration, highlights recent discoveries, and discusses critically the influence of different strategies for terminal electron transfer reactions.

The influence of potassium dichromate on dissimilatory reduction of sulfate and nitrate ions by bacteria Desulfovibrio sp.

2017 ◽  
Vol 28 (1-2) ◽  
pp. 84-95
Author(s):  
O. M. Moroz ◽  
S. O. Hnatush ◽  
Ch. I. Bohoslavets ◽  
T. M. Hrytsun’ ◽  
B. M. Borsukevych
Keyword(s):  
Electron Acceptor ◽  
Potassium Dichromate ◽  
Anaerobic Respiration ◽  
Sulfate Reducing Bacteria ◽  
Negative Influence ◽  
Electron Acceptors ◽  
Metal Compounds ◽  
Nitrate Ions ◽  
Sulfate Reducing ◽  
Reducing Bacteria

Sulfate reducing bacteria, capable to reductive transformation of different nature pollutants, used in biotechnologies of purification of sewage, contaminated by carbon, sulfur, nitrogen and metal compounds. H2S formed by them sediment metals to form of insoluble sulfides. Number of metals can be used by these microorganisms as electron acceptors during anaerobic respiration. Because under the influence of metal compounds observed slowing of bacteria metabolism, selection isolated from technologically modified ecotops resistant to pollutions strains is important task to create a new biotechnologies of purification. That’s why the purpose of this work was to study the influence of potassium dichromate, present in medium, on reduction of sulfate and nitrate ions by sulfate reducing bacteria Desulfovibrio desulfuricans IMV K-6, Desulfovibrio sp. Yav-6 and Desulfovibrio sp. Yav-8, isolated from Yavorivske Lake, to estimate the efficiency of possible usage of these bacteria in technologies of complex purification of environment from dangerous pollutants. Bacteria were cultivated in modified Kravtsov-Sorokin medium without SO42- and FeCl2×4H2O for 10 days. To study the influence of K2Cr2O7 on usage by bacteria SO42- or NO3- cells were seeded to media with Na2SO4×10H2O or NaNO3 and K2Cr2O7 at concentrations of 1.74 mM for total content of electron acceptors in medium 3.47 mM (concentration of SO42- in medium of standard composition). Cells were also seeded to media with 3.47 mM Na2SO4×10H2O, NaNO3 or K2Cr2O7 to investigate their growth in media with SO42-, NO3- or Cr2O72- as sole electron acceptor (control). Biomass was determined by turbidymetric method, content of sulfate, nitrate, dichromate, chromium (III) ions, hydrogen sulfide or ammonia ions in cultural liquid – by spectrophotometric method. It was found that K2Cr2O7 inhibits growth (2.2 and 1.3 times) and level of reduction by bacteria sulfate or nitrate ions (4.2 and 3.0 times, respectively) at simultaneous addition into cultivation medium of 1.74 mM SO42- or NO3- and 1.74 mM Cr2O72-, compared with growth and level of reduction of sulfate or nitrate ions in medium only with SO42- or NO3- as sole electron acceptor. Revealed that during cultivation of bacteria in presence of equimolar amount of SO42- or NO3- and Cr2O72-, last used by bacteria faster, content of Cr3+ during whole period of bacteria cultivation exceeded content H2S or NH4+. K2Cr2O7 in medium has most negative influence on dissimilatory reduction by bacteria SO42- than NO3-, since level of nitrate ions reduction by cells in medium with NO3- and Cr2O72- was a half times higher than level of sulfate ions reduction by it in medium with SO42- and Cr2O72-. The ability of bacteria Desulfovibrio sp. to priority reduction of Cr2O72- and after their exhaustion − NO3- and SO42- in the processes of anaerobic respiration can be used in technologies of complex purification of environment from toxic compounds.

scholarly journals Denitrification in the water column of the central Baltic Sea

2013 ◽  
Vol 106 ◽  
pp. 247-260 ◽  
Author(s):  
Tage Dalsgaard ◽  
Loreto De Brabandere ◽  
Per O.J. Hall
Keyword(s):  
Baltic Sea ◽  
Water Column

scholarly journals Identification of a Second Two-Component Signal Transduction System That Controls Fosfomycin Tolerance and Glycerol-3-Phosphate Uptake

2014 ◽  
Vol 197 (5) ◽  
pp. 861-871 ◽  
Author(s):  
Kumiko Kurabayashi ◽  
Yuko Hirakawa ◽  
Koichi Tanimoto ◽  
Haruyoshi Tomita ◽  
Hidetada Hirakawa
Keyword(s):  
Phosphate Uptake ◽  
Response Regulator ◽  
Anaerobic Respiration ◽  
Regulatory System ◽  
Carbon Substrate ◽  
Two Component System ◽  
Component System ◽  
Content Type ◽  
Two Component ◽  
Biological Cost

Particular interest in fosfomycin has resurfaced because it is a highly beneficial antibiotic for the treatment of refractory infectious diseases caused by pathogens that are resistant to other commonly used antibiotics. The biological cost to cells of resistance to fosfomycin because of chromosomal mutation is high. We previously found that a bacterial two-component system, CpxAR, induces fosfomycin tolerance in enterohemorrhagicEscherichia coli(EHEC) O157:H7. This mechanism does not rely on irreversible genetic modification and allows EHEC to relieve the fitness burden that results from fosfomycin resistance in the absence of fosfomycin. Here we show that another two-component system, TorSRT, which was originally characterized as a regulatory system for anaerobic respiration utilizing trimethylamine-N-oxide (TMAO), also induces fosfomycin tolerance. Activation of the Tor regulatory pathway by overexpression oftorR, which encodes the response regulator, or addition of TMAO increased fosfomycin tolerance in EHEC. We also show that phosphorylated TorR directly represses the expression ofglpT, a gene that encodes a symporter of fosfomycin and glycerol-3-phosphate, and activation of the TorR protein results in the reduced uptake of fosfomycin by cells. However, cells in which the Tor pathway was activated had an impaired growth phenotype when cultured with glycerol-3-phosphate as a carbon substrate. These observations suggest that the TorSRT pathway is the second two-component system to reversibly control fosfomycin tolerance and glycerol-3-phosphate uptake in EHEC, and this may be beneficial for bacteria by alleviating the biological cost. We expect that this mechanism could be a potential target to enhance the utility of fosfomycin as chemotherapy against multidrug-resistant pathogens.

Sulfonates: novel electron acceptors in anaerobic respiration

1996 ◽  
Vol 166 (3) ◽  
pp. 204-210 ◽  
Author(s):  
Thomas J. Lie ◽  
Thomas Pitta ◽  
E. R. Leadbetter ◽  
Walter Godchaux III. ◽  
Jared R. Leadbetter
Keyword(s):  
Anaerobic Respiration ◽  
Electron Acceptors

scholarly journals Bacteriohopanepolyols record stratification, nitrogen fixation and other biogeochemical perturbations in Holocene sediments of the central Baltic Sea

2013 ◽  
Vol 10 (4) ◽  
pp. 2725-2735 ◽  
Author(s):  
M. Blumenberg ◽  
C. Berndmeyer ◽  
M. Moros ◽  
M. Muschalla ◽  
O. Schmale ◽  
...  
Keyword(s):  
Baltic Sea ◽  
Water Column ◽  
Stable Stratification ◽  
The Baltic Sea ◽  
Allochthonous Input ◽  
The North ◽  
Water Column Stratification ◽  
Gotland Deep ◽  
History Of ◽  
The Baltic

Abstract. The Baltic Sea, one of the world's largest brackish-marine basins, established after deglaciation of Scandinavia about 17 000 to 15 000 yr ago. In the changeable history of the Baltic Sea, the initial freshwater system was connected to the North Sea about 8000 yr ago and the modern brackish-marine setting (Littorina Sea) was established. Today, a relatively stable stratification has developed in the water column of the deep basins due to salinity differences. Stratification is only occasionally interrupted by mixing events, and it controls nutrient availability and growth of specifically adapted microorganisms and algae. We studied bacteriohopanepolyols (BHPs), lipids of specific bacterial groups, in a sediment core from the central Baltic Sea (Gotland Deep) and found considerable differences between the distinct stages of the Baltic Sea's history. Some individual BHP structures indicate contributions from as yet unknown redoxcline-specific bacteria (bacteriohopanetetrol isomer), methanotrophic bacteria (35-aminobacteriohopanetetrol), cyanobacteria (bacteriohopanetetrol cyclitol ether isomer) and from soil bacteria (adenosylhopane) through allochthonous input after the Littorina transgression, whereas the origin of other BHPs in the core has still to be identified. Notably high BHP abundances were observed in the deposits of the brackish-marine Littorina phase, particularly in laminated sediment layers. Because these sediments record periods of stable water column stratification, bacteria specifically adapted to these conditions may account for the high portions of BHPs. An additional and/or accompanying source may be nitrogen-fixing (cyano)bacteria, which is indicated by a positive correlation of BHP abundances with Corg and δ15N.

Sign in / Sign up

Export Citation Format

Share Document