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1.
Elife ; 102021 05 10.
Article in English | MEDLINE | ID: mdl-33970104

ABSTRACT

Dimethylsulfoniopropionate (DMSP) is an abundant and ubiquitous organosulfur molecule in marine environments with important roles in global sulfur and nutrient cycling. Diverse DMSP lyases in some algae, bacteria, and fungi cleave DMSP to yield gaseous dimethyl sulfide (DMS), an infochemical with important roles in atmospheric chemistry. Here, we identified a novel ATP-dependent DMSP lyase, DddX. DddX belongs to the acyl-CoA synthetase superfamily and is distinct from the eight other known DMSP lyases. DddX catalyses the conversion of DMSP to DMS via a two-step reaction: the ligation of DMSP with CoA to form the intermediate DMSP-CoA, which is then cleaved to DMS and acryloyl-CoA. The novel catalytic mechanism was elucidated by structural and biochemical analyses. DddX is found in several Alphaproteobacteria, Gammaproteobacteria, and Firmicutes, suggesting that this new DMSP lyase may play an overlooked role in DMSP/DMS cycles.


The global sulfur cycle is a collection of geological and biological processes that circulate sulfur-containing compounds through the oceans, rocks and atmosphere. Sulfur itself is essential for life and important for plant growth, hence its widespread use in fertilizers. Marine organisms such as bacteria, algae and phytoplankton produce one particular sulfur compound, called dimethylsulfoniopropionate, or DMSP, in massive amounts. DMSP made in the oceans gets readily converted into a gas called dimethyl sulfide (DMS), which is the largest natural source of sulfur entering the atmosphere. In the air, DMS is converted to sulfate and other by-products that can act as cloud condensation nuclei, which, as the name suggests, are involved in cloud formation. In this way, DMS can influence weather and climate, so it is often referred to as 'climate-active' gas. At least eight enzymes are known to cleave DMSP into DMS gas with a few by-products. These enzymes are found in algae, bacteria and fungi, and are referred to as lyases, for the way they breakdown their target compounds (DMSP, in this case). Recently, researchers have identified some bacteria that produce DMS from DMSP without using known DMSP lyases. This suggests there are other, unidentified enzymes that act on DMSP in nature, and likely contribute to global sulfur cycling. Li, Wang et al. set out to uncover new enzymes responsible for converting the DMSP that marine bacteria produce into gaseous DMS. One new enzyme called DddX was identified and found to belong to a superfamily of enzymes quite separate to other known DMSP lyases. Li, Wang et al. also showed how DddX drives the conversion of DMSP to DMS in a two-step reaction, and that the enzyme is found across several classes of bacteria. Further experiments to characterise the protein structure of DddX also revealed the molecular mechanism for its catalytic action. This study offers important insights into how marine bacteria generate the climatically important gas DMS from DMSP, leading to a better understanding of the global sulfur cycle. It gives microbial ecologists a more comprehensive perspective of these environmental processes, and provides biochemists with data on a family of enzymes not previously known to act on sulfur-containing compounds.


Subject(s)
Carbon-Sulfur Lyases/chemistry , Psychrobacter/enzymology , Sulfonium Compounds/metabolism , Acyl Coenzyme A/metabolism , Adenosine Triphosphate , Bacteria/growth & development , Bacteria/isolation & purification , Bacterial Proteins/chemistry , Carbon-Sulfur Lyases/genetics , Psychrobacter/genetics , Psychrobacter/growth & development , Sulfides/metabolism
2.
Curr Microbiol ; 76(12): 1435-1442, 2019 Dec.
Article in English | MEDLINE | ID: mdl-31494741

ABSTRACT

Bacteria under stress increase the proportion of dormant cells to ensure their survival. Cold and osmotic stress are similar, because in both the availability of water is reduced. Glycine betaine (GB) is one of the most common osmoprotectants in bacteria and possesses cryoprotectant properties. Our aim was to determine whether GB modifies the proportion of dormant Deinococcus sp. UDEC-P1 and Psychrobacter sp. UDEC-A5 cells exposed to osmotic stress. Both bacterial strains were incubated in the presence of up to 1 M NaCl with or without GB. Active and dormant cells were evaluated by both spectrophotometric and flow cytometry analysis. Without GB, Deinococcus sp. UDEC-P1 grew in the presence of 0.05 M NaCl, but with 5 mM GB grew at 0.1 M NaCl. Psychrobacter sp. UDEC-A5 grew in the presence of up to 0.25 M NaCl, but with 5 mM GB grew at 0.5 M NaCl. Under osmotic stress, the proportion of dormant cells of Deinococcus sp. UDEC-P1 and Psychrobacter sp. UDEC-A5 increased significantly (about eightfold and fivefold, respectively). The addition of GB (5 mM) exerted a different effect on the two strains, since it avoided the entrance into the dormancy of Psychrobacter sp. UDEC-A5 cells, but not of Deinococcus sp. UDEC-P1 cells. Our results suggest that the effect of GB on bacterial metabolism is strain dependent. For bacteria in which GB avoids dormancy, such as Psychrobacter sp. UDEC-A5, it could be a "double-edged sword" by reducing the "seed bank" available to recover the active population when favorable conditions return.


Subject(s)
Betaine/metabolism , Deinococcus/growth & development , Psychrobacter/growth & development , Bacterial Proteins/metabolism , Deinococcus/physiology , Osmotic Pressure , Psychrobacter/physiology , Sodium Chloride/metabolism , Stress, Physiological
3.
FEMS Microbiol Ecol ; 94(7)2018 07 01.
Article in English | MEDLINE | ID: mdl-29868789

ABSTRACT

While cold-adapted bacteria isolated from marine or terrestrial low temperature environments share many similarities, cold-adapted bacteria from terrestrial environments usually grow over a broader range of temperatures suggesting different constraints of these two low temperature environments. The diversity of habitats from which Psychrobacter have been isolated (e.g. cold marine environments, frozen soils, permafrost and humans) provides a unique opportunity to examine habitat specific adaptations while reducing phylogenetic effects. Here, comparative genomic analyses of 26 strains of Psychrobacter revealed several clusters with characteristics that correlated with habitat. Marine and terrestrial Psychrobacter have amino acid composition typical of psychrophiles (e.g. fewer proline and lysine, more acidic) when compared to Psychrobacter strains associated with warm hosts, and have many potentially cold-adapted core genes (e.g. ClpX, DsbC, GroEL/GroES and MutS2). Marine and terrestrial Psychrobacter share many genes (e.g. FadB) not found in warm host Psychrobacter, which had their own distinct gene content (e.g. collagenase-like protease). Furthermore, terrestrial Psychrobacter were differentiated from marine Psychrobacter by the use of different cold adaptations and more hydrophobic and aliphatic proteins. These data suggest that terrestrial and marine Psychrobacter evolved from a mesophilic ancestor and are accumulating adaptations for low temperatures as well as for their respective habitats.


Subject(s)
Acclimatization/genetics , Psychrobacter/genetics , Psychrobacter/physiology , Antarctic Regions , Arctic Regions , Cold Temperature , Ecosystem , Freezing , Genomics , Humans , Permafrost , Phylogeny , Psychrobacter/growth & development
4.
Appl Environ Microbiol ; 79(13): 3967-73, 2013 Jul.
Article in English | MEDLINE | ID: mdl-23603675

ABSTRACT

Psychrobacter arcticus strain 273-4, an isolate from a Siberian permafrost core, is capable of forming biofilms when grown in minimal medium under laboratory conditions. Biofilms form at 4 to 22°C when acetate is supplied as the lone carbon source and with 1 to 7% sea salt. P. arcticus is also capable of colonizing quartz sand. Transposon mutagenesis identified a gene important for biofilm formation by P. arcticus. Four transposon mutants were mapped to a 20.1-kbp gene, which is predicted to encode a protein of 6,715 amino acids (Psyc_1601). We refer to this open reading frame as cat1, for cold attachment gene 1. The cat1 mutants are unable to form biofilms at levels equivalent to that of the wild type, and there is no impact on the planktonic growth characteristics of the strains, indicating a specific role in biofilm formation. Through time course studies of the static microtiter plate assay, we determined that cat1 mutants are unable to form biofilms equivalent to that of the wild type under all conditions tested. In flow cell experiments, cat1 mutants initially are unable to attach to the surface. Over time, however, they form microcolonies, an architecture very different from that produced by wild-type biofilms. Our results demonstrate that Cat1 is involved in the initial stages of bacterial attachment to surfaces.


Subject(s)
Adhesins, Bacterial/physiology , Biofilms/growth & development , Psychrobacter/growth & development , Soil Microbiology , Cloning, Molecular , DNA Primers/genetics , DNA Transposable Elements/genetics , Microscopy, Fluorescence , Microscopy, Phase-Contrast , Mutagenesis , Open Reading Frames/genetics , Psychrobacter/genetics , Real-Time Polymerase Chain Reaction , Siberia , Silicon Dioxide/chemistry , Surface Properties
5.
Appl Environ Microbiol ; 78(14): 4995-8, 2012 Jul.
Article in English | MEDLINE | ID: mdl-22582053

ABSTRACT

A haloalkane dehalogenase, DpcA, from Psychrobacter cryohalolentis K5, representing a novel psychrophilic member of the haloalkane dehalogenase family, was identified and biochemically characterized. DpcA exhibited a unique temperature profile with exceptionally high activities at low temperatures. The psychrophilic properties of DpcA make this enzyme promising for various environmental applications.


Subject(s)
Adaptation, Physiological , Cold Temperature , Hydrolases/metabolism , Psychrobacter/enzymology , Bacterial Proteins/chemistry , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Hydrogen-Ion Concentration , Hydrolases/chemistry , Hydrolases/genetics , Kinetics , Psychrobacter/genetics , Psychrobacter/growth & development , Psychrobacter/physiology , Substrate Specificity
6.
Biol Bull ; 222(1): 56-62, 2012 Feb.
Article in English | MEDLINE | ID: mdl-22426632

ABSTRACT

We examined the possibility that decreased environmental oxygen can elevate the levels of indigenous bacteria in the hemolymph of Cancer magister. Crabs were exposed to air-saturated and hypoxic (50% air-saturation) water for 3 days and levels of culturable bacteria in hemolymph were measured every 24 h as the total number of colony-forming units (CFU) per milliliter of hemolymph. Bacteremia increased after 24 h of exposure to hypoxia and persisted for 72 h, whereas crabs exposed to normoxia had no measurable change in number of culturable bacteria. The predominant persistent bacteria in the hemolymph was isolated and identified by DNA sequence-based methods as Psychrobacter cibarus. Crabs were injected with P. cibarus or with buffered saline as a control after 3 h of hypoxia. Levels of culturable bacteria were significantly higher in hypoxic crabs than in normoxic ones (about 2500 versus 1000 CFU ml(-1) 80 min post-injection, respectively), and circulating levels of oxygen were significantly reduced in infected animals compared to uninfected ones after 48 h in hypoxia and after 72 h in air-saturated water post-injection. These data demonstrate that P. cibarius is present in Dungeness crabs, that environmental hypoxia can dramatically elevate levels of persistent bacteria, and that hypoxia in the presence of hemolymph bacteria may ultimately reduce immune and respiratory ability.


Subject(s)
Bacteremia/microbiology , Brachyura/microbiology , Oxygen/metabolism , Psychrobacter/pathogenicity , Anaerobiosis , Animals , Bacteremia/metabolism , Bacterial Load , Bacteriological Techniques , Brachyura/metabolism , Hemolymph/metabolism , Hemolymph/microbiology , Male , Psychrobacter/growth & development , Psychrobacter/metabolism , Time Factors
7.
Int J Food Microbiol ; 153(3): 332-8, 2012 Feb 15.
Article in English | MEDLINE | ID: mdl-22177851

ABSTRACT

The impact of the growth of two Gram-negative bacteria, Psychrobacter celer and Hafnia alvei, inoculated at 10(2) and 10(6) cfu/g, on the dynamics of a multispecies community as well as on volatile aroma compound production during cheese ripening was investigated. Results showed that P. celer was able to successfully implant itself in cheese, regardless of its inoculation level. However, when it was inoculated at a high level, the bacterial biodiversity was drastically lowered from day 25 to the end of ripening. Overall, the presence of P. celer led to the higher production of volatile aroma compounds such as aldehydes, ketones and sulfur compounds. Regardless of its inoculation level, H. alvei barely affected the growth of the bacterial community and was subdominant at the end of ripening. It influenced total volatile aroma compound production with volatile sulfur compounds being the most abundant. Overall, these two bacteria were able to implant themselves in a cheese community and significantly contributed to the aromatic properties of the cheese. Their role in flavoring and their interactions with the technological microorganisms must be considered during cheese ripening and should be further investigated.


Subject(s)
Cheese/microbiology , Hafnia alvei/growth & development , Psychrobacter/growth & development , Aldehydes/analysis , Bacteria/growth & development , Ecology , Food Microbiology , Gram-Negative Bacteria , Hafnia alvei/metabolism , Ketones/analysis , Psychrobacter/metabolism , Smell , Sulfur Compounds/analysis , Volatilization
8.
Int J Phytoremediation ; 13(2): 126-39, 2011 Feb.
Article in English | MEDLINE | ID: mdl-21598781

ABSTRACT

This study was conducted to elucidate effects of inoculating plant growth-promoting bacterium Psychrobacter sp. SRS8 on the growth and phytoextraction potential of energy crops Ricinus communis and Helianthus annuus in artificially Ni contaminated soils. The toxicity symptom in plants under Ni stress expressed as chlorophyll, protein content, growth inhibition, and Fe, P concentrations were studied, and the possible relationship among them were also discussed. The PGPB SRS8 was found capable of stimulating plant growth and Ni accumulation in both plant species. Further, the stimulation effect on plant biomass, chlorophyll, and protein content was concomitant with increased Fe and P assimilation from soil to plants. Further, the induction of catalase and peroxidase activities was also involved in the ability of SRS8 to increase the tolerance in both plant species under Ni stress. The findings suggest that strain SRS8 play an important role in promoting the growth and phytoextraction efficiency of R. communis and H. annuus, which may be used for remediation of metal contaminated sites.


Subject(s)
Helianthus/metabolism , Nickel/metabolism , Psychrobacter/metabolism , Ricinus/metabolism , Soil Pollutants/metabolism , Biodegradation, Environmental , Biomass , Catalase/metabolism , Chlorophyll/analysis , Helianthus/drug effects , Helianthus/growth & development , Helianthus/microbiology , Iron/metabolism , Nickel/pharmacology , Peroxidase/metabolism , Phosphorus/metabolism , Plant Proteins/analysis , Psychrobacter/drug effects , Psychrobacter/growth & development , Ricinus/drug effects , Ricinus/growth & development , Ricinus/microbiology , Soil/analysis , Soil Pollutants/analysis
9.
J Food Sci ; 74(6): M258-67, 2009 Aug.
Article in English | MEDLINE | ID: mdl-19723210

ABSTRACT

The aim of these experiments was to evaluate the effect of brining, modified atmosphere packaging (MAP), and superchilling on the quality changes of cod loins as measured by microbial, sensory, and chemical analysis. Unbrined and brined (2.5 +/- 1.0% NaCl) cod loins were kept in styrofoam boxes (air) and under modified atmosphere (MA, CO(2)/O(2)/N(2): 50/5/45) at 0, -2, and -3.6 degrees C. Samples were examined over a 4-wk period. Total viable psychrotrophic counts and counts of H(2)S-producing bacteria reached higher numbers in the air-packed brined fish at -2 and -3.6 degrees C than in comparable unbrined groups, being significantly different (P < 0.05) at the lower temperature. However, lower counts of these bacteria were obtained in the brined MAP fish than in comparable unbrined fish. Counts of Photobacterium phosphoreum increased most rapidly in air- and MA-packed loins kept at 0 degrees C. Lower counts were found at superchilled temperatures. According to sensory analysis the shelf life of unbrined air-packed loins was about 11 d at 0 degrees C and 14 to 15 d at -2 degrees C. The shelf life of MA-packed unbrined loins was about 14 to 15 d at 0 degrees C but 21 d at -2 degrees C. Thus, synergism of combined superchilling (-2 degrees C) and MA led to a considerable shelf life increase for unbrined loins despite the fact that processing and packaging took place 4 to 5 d post-catch. The shelf life of air-packed brined loins at -2 degrees C was 12 to 15 d but only 13 d under MA. The same synergistic effect did therefore not apply to brined loins as with unbrined ones.


Subject(s)
Food Packaging/methods , Food Preservation/methods , Food Preservatives/chemistry , Gadus morhua , Seafood , Animals , Bacterial Physiological Phenomena , Carbon Dioxide , Cold Temperature , Colony Count, Microbial , Food Microbiology , Humans , Odorants , Photobacterium/growth & development , Pigmentation , Pseudomonas/growth & development , Psychrobacter/growth & development , Quality Control , Salts , Seafood/analysis , Seafood/microbiology , Sulfur-Reducing Bacteria/growth & development , Taste , Time Factors , Volatile Organic Compounds/analysis
10.
Astrobiology ; 9(2): 221-8, 2009 Mar.
Article in English | MEDLINE | ID: mdl-19371162

ABSTRACT

Spacecraft launched to Mars can retain viable terrestrial microorganisms on board that may survive the interplanetary transit. Such biota might compromise the search for life beyond Earth if capable of propagating on Mars. The current study explored the survivability of Psychrobacter cryohalolentis K5, a psychrotolerant microorganism obtained from a Siberian permafrost cryopeg, under simulated martian surface conditions of high ultraviolet irradiation, high desiccation, low temperature, and low atmospheric pressure. First, a desiccation experiment compared the survival of P. cryohalolentis cells embedded, or not embedded, within a medium/salt matrix (MSM) maintained at 25 degrees C for 24 h within a laminar flow hood. Results indicate that the presence of the MSM enhanced survival of the bacterial cells by 1 to 3 orders of magnitude. Second, tests were conducted in a Mars Simulation Chamber to determine the UV tolerance of the microorganism. No viable vegetative cells of P. cryohalolentis were detected after 8 h of exposure to Mars-normal conditions of 4.55 W/m(2) UVC irradiation (200-280 nm), -12.5 degrees C, 7.1 mbar, and a Mars gas mix composed of CO(2) (95.3%), N(2) (2.7%), Ar (1.6%), O(2) (0.2%), and H(2)O (0.03%). Third, an experiment was conducted within the Mars chamber in which total atmospheric opacities were simulated at tau = 0.1 (dust-free CO(2) atmosphere at 7.1 mbar), 0.5 (normal clear sky with 0.4 = dust opacity and 0.1 = CO(2)-only opacity), and 3.5 (global dust storm) to determine the survivability of P. cryohalolentis to partially shielded UVC radiation. The survivability of the bacterium increased with the level of UVC attenuation, though population levels still declined several orders of magnitude compared to UVC-absent controls over an 8 h exposure period.


Subject(s)
Extraterrestrial Environment , Mars , Psychrobacter/radiation effects , Space Simulation , Ultraviolet Rays , Aluminum , Atmospheric Pressure , Desiccation , Dose-Response Relationship, Radiation , Dust , Environmental Microbiology , Exobiology , Microbial Viability/radiation effects , Psychrobacter/growth & development , Psychrobacter/physiology , Spacecraft , Time Factors
11.
J Bacteriol ; 191(7): 2340-52, 2009 Apr.
Article in English | MEDLINE | ID: mdl-19168616

ABSTRACT

Permafrost soils are extreme environments that exert low-temperature, desiccation, and starvation stress on bacteria over thousands to millions of years. To understand how Psychrobacter arcticus 273-4 survived for >20,000 years in permafrost, transcriptome analysis was performed during growth at 22 degrees C, 17 degrees C, 0 degrees C, and -6 degrees C using a mixed-effects analysis of variance model. Genes for transcription, translation, energy production, and most biosynthetic pathways were downregulated at low temperatures. Evidence of isozyme exchange was detected over temperature for D-alanyl-D-alanine carboxypeptidases (dac1 and dac2), DEAD-box RNA helicases (csdA and Psyc_0943), and energy-efficient substrate incorporation pathways for ammonium and acetate. Specific functions were compensated by upregulation of genes at low temperature, including genes for the biosynthesis of proline, tryptophan, and methionine. RNases and peptidases were generally upregulated at low temperatures. Changes in energy metabolism, amino acid metabolism, and RNase gene expression were consistent with induction of a resource efficiency response. In contrast to results observed for other psychrophiles and mesophiles, only clpB and hsp33 were upregulated at low temperature, and there was no upregulation of other chaperones and peptidyl-prolyl isomerases. relA, csdA, and dac2 knockout mutants grew more slowly at low temperature, but a dac1 mutant grew more slowly at 17 degrees C. The combined data suggest that the basal biological machinery, including translation, transcription, and energy metabolism, is well adapted to function across the growth range of P. arcticus from -6 degrees C to 22 degrees C, and temperature compensation by gene expression was employed to address specific challenges to low-temperature growth.


Subject(s)
Psychrobacter/physiology , Adaptation, Physiological , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Cold Temperature , Gene Expression Profiling , Gene Expression Regulation, Bacterial , Psychrobacter/enzymology , Psychrobacter/genetics , Psychrobacter/growth & development
12.
Extremophiles ; 13(1): 21-30, 2009 Jan.
Article in English | MEDLINE | ID: mdl-18818866

ABSTRACT

We describe the development of genetic tools (electroporation, conjugation, vector for targeted gene replacement) for use in the psychrophile Psychrobacter arcticus 273-4 to test hypotheses about cold adaptation. Successful electroporation only occurred with nonstandard parameters, such as: electrocompetent cells freshly prepared from stationary-phase cultures, high field strengths (25 kV cm(-1)), long recovery times (16-24 h), and selection with low concentrations of antibiotics. Transformation frequencies were greatly affected by a methylation-dependent restriction barrier homologous to DpnI. The vector pJK100 (which was self-transmissible and contained a Pir-dependent R6K origin of replication) proved effective as a suicide plasmid that could be used to recombine mutations into the P. arcticus 273-4 genome. We used this vector for targeted replacement of dctT, the substrate-binding periplasmic subunit of a TRAP (tripartite ATP-independent periplasmic) transporter (which we have named dctTUF), as it was more highly expressed at cold temperatures. The replacement of dctT (with kan) decreased the rate of growth at low temperatures in mineral medium with glutamate, acetate, butyrate, and fumarate, but not with pyruvate suggesting that DctTUF participates in the transport of glutamate, acetate, butyrate, and fumarate at cold temperatures. This is the first report to demonstrate the creation of site-specific mutants in the genus Psychrobacter, their affect on low-temperature growth, and a substrate range for TAXI proteins of TRAP transporters.


Subject(s)
Cold Temperature , Genes, Bacterial , Psychrobacter/growth & development , Adaptation, Physiological , Electroporation , Genetic Vectors , Membrane Fluidity , Plasmids , Psychrobacter/genetics , Psychrobacter/physiology , Reverse Transcriptase Polymerase Chain Reaction
13.
Appl Microbiol Biotechnol ; 82(1): 169-77, 2009 Feb.
Article in English | MEDLINE | ID: mdl-19083231

ABSTRACT

The growth and aroma contribution of Microbacterium foliorum, Proteus vulgaris and Psychrobacter sp., some common but rarely mentioned cheese bacteria, were investigated in a cheese model deacidified by Debaryomyces hansenii during the ripening process. Our results show that these bacteria had distinct growth and cheese flavour production patterns during the ripening process. P. vulgaris had the greatest capacity to produce not only the widest variety but also the highest quantities of volatile compounds with low olfactive thresholds, e.g. volatile sulphur compounds and branched-chain alcohols. Such compounds produced by P. vulgaris increased after 21 days of ripening and reached a maximum at 41 days. The three bacteria studied exhibited various degrees of caseinolytic, aminopeptidase and deaminase activities. Moreover, P. vulgaris had a greater capacity for hydrolysing casein and higher deaminase activity. Our results show that P. vulgaris, a Gram-negative bacterium naturally present on the surface of ripened cheeses, could produce high concentrations of flavour compounds from amino acid degradation during the ripening process. Its flavouring role in cheese cannot be neglected. Moreover, it could be a useful organism for producing natural flavours as dairy ingredients.


Subject(s)
Actinomycetales/growth & development , Cheese/microbiology , Food Microbiology , Models, Biological , Proteus/growth & development , Psychrobacter/growth & development , Actinomycetales/metabolism , Ammonia/metabolism , Cheese/analysis , Fermentation , Proteus/metabolism , Psychrobacter/metabolism , Volatilization
14.
Appl Environ Microbiol ; 74(15): 4889-97, 2008 Aug.
Article in English | MEDLINE | ID: mdl-18515474

ABSTRACT

Microorganisms comprise the bulk of biodiversity, but only a small fraction of this diversity grows on artificial media. This phenomenon was noticed almost a century ago, repeatedly confirmed, and termed the "great plate count anomaly." Advances in microbial cultivation improved microbial recovery but failed to explain why most microbial species do not grow in vitro. Here we show that at least some of such species can form domesticated variants capable of growth on artificial media. We also present evidence that small signaling molecules, such as short peptides, may be essential factors in initiating growth of nongrowing cells. We identified one 5-amino-acid peptide, LQPEV, that at 3.5 nM induces the otherwise "uncultivable" strain Psychrobacter sp. strain MSC33 to grow on standard media. This demonstrates that the restriction preventing microbial in vitro growth may be different from those offered to date to explain the "great plate count anomaly," such as deficiencies in nutrient composition and concentrations in standard media, medium toxicity, and inappropriate incubation time. Growth induction of MSC33 illustrates that some microorganisms do not grow in vitro because they are removed from their native communities and the signals produced therein. "Uncultivable" species represent the largest source of unexplored biodiversity, and provide remarkable opportunities for both basic and applied research. Access to cultures of some of these species should be possible through identification of the signaling compounds necessary for growth, their addition to standard medium formulations, and eventual domestication.


Subject(s)
Growth Substances/pharmacology , Oligopeptides/pharmacology , Pantoea/growth & development , Pseudoalteromonas/growth & development , Psychrobacter/growth & development , Diffusion , Pantoea/drug effects , Pantoea/isolation & purification , Pseudoalteromonas/drug effects , Pseudoalteromonas/isolation & purification , Psychrobacter/drug effects , Psychrobacter/isolation & purification , Seawater/microbiology
15.
Appl Microbiol Biotechnol ; 76(5): 1161-71, 2007 Oct.
Article in English | MEDLINE | ID: mdl-17701035

ABSTRACT

Twelve bacterial strains belonging to eight taxonomic groups: Brevibacterium linens, Microbacterium foliorum, Arthrobacter arilaitensis, Staphylococcus cohnii, Staphylococcus equorum, Brachybacterium sp., Proteus vulgaris and Psychrobacter sp., isolated from different surface-ripened French cheeses, were investigated for their abilities to generate volatile aroma compounds. Out of 104 volatile compounds, 54 volatile compounds (identified using dynamic headspace technique coupled with gas chromatography-mass spectrometry [GC-MS]) appeared to be produced by the different bacteria on a casamino acid medium. Four out of eight species used in this study: B. linens, M. foliorum, P. vulgaris and Psychrobacter sp. showed a high flavouring potential. Among these four bacterial species, P. vulgaris had the greatest capacity to produce not only the widest varieties but also the highest quantities of volatile compounds having low olfactive thresholds such as sulphur compounds. Branched aldehydes, alcohols and esters were produced in large amounts by P. vulgaris and Psychrobacter sp. showing their capacity to breakdown the branched amino acids. This investigation shows that some common but rarely mentioned bacteria present on the surface of ripened cheeses could play a major role in cheese flavour formation and could be used to produce cheese flavours.


Subject(s)
Bacteria/classification , Bacteria/metabolism , Cheese/microbiology , Aldehydes/metabolism , Amino Acids/metabolism , Bacteria/growth & development , Bacteria/isolation & purification , Cheese/analysis , Culture Media , Esters/metabolism , Gas Chromatography-Mass Spectrometry , Industrial Microbiology , Ketones/metabolism , Proteus vulgaris/classification , Proteus vulgaris/growth & development , Proteus vulgaris/isolation & purification , Proteus vulgaris/metabolism , Psychrobacter/classification , Psychrobacter/growth & development , Psychrobacter/isolation & purification , Psychrobacter/metabolism , Sulfur Compounds/metabolism , Transaminases/metabolism , Volatilization
16.
Extremophiles ; 11(2): 343-54, 2007 Mar.
Article in English | MEDLINE | ID: mdl-17123128

ABSTRACT

It is crucial to examine the physiological processes of psychrophiles at temperatures below 4 degrees C, particularly to facilitate extrapolation of laboratory results to in situ activity. Using two dimensional electrophoresis, we examined patterns of protein abundance during growth at 16, 4, and -4 degrees C of the eurypsychrophile Psychrobacter cryohalolentis K5 and report the first identification of cold inducible proteins (CIPs) present during growth at subzero temperatures. Growth temperature substantially reprogrammed the proteome; the relative abundance of 303 of the 618 protein spots detected (approximately 31% of the proteins at each growth temperature) varied significantly with temperature. Five CIPs were detected specifically at -4 degrees C; their identities (AtpF, EF-Ts, TolC, Pcryo_1988, and FecA) suggested specific stress on energy production, protein synthesis, and transport during growth at subzero temperatures. The need for continual relief of low-temperature stress on these cellular processes was confirmed via identification of 22 additional CIPs whose abundance increased during growth at -4 degrees C (relative to higher temperatures). Our data suggested that iron may be limiting during growth at subzero temperatures and that a cold-adapted allele was employed at -4 degrees C for transport of iron. In summary, these data suggest that low-temperature stresses continue to intensify as growth temperatures decrease to -4 degrees C.


Subject(s)
Adaptation, Physiological/physiology , Bacterial Proteins/metabolism , Proteome/metabolism , Psychrobacter/metabolism , Bacterial Proteins/analysis , Cold Temperature , Proteome/analysis , Psychrobacter/growth & development
17.
Int J Syst Evol Microbiol ; 55(Pt 2): 577-582, 2005 Mar.
Article in English | MEDLINE | ID: mdl-15774627

ABSTRACT

Two novel Psychrobacter-like bacterial strains, JG-219(T) and JG-220, were isolated from jeotgal, a traditional Korean fermented seafood. Cells of strains JG-219(T) and JG-220 were Gram-negative, non-motile coccobacilli. Growth of the two strains was observed at 4-32 degrees C. They grew optimally in the presence of 2-5 % (w/v) NaCl. Strains JG-219(T) and JG-220 contained C(18 : 1)omega9c and C(17 : 1)omega8c as the major fatty acids and Q-8 as the predominant ubiquinone. The DNA G+C contents of strains JG-219(T) and JG-220 were 43.5 and 43.0 mol%, respectively. The two strains showed no difference in their 16S rRNA gene sequences but exhibited minor differences in their phenotypic properties. Strains JG-219(T) and JG-220 exhibited levels of 16S rRNA gene sequence similarity of 95.2-98.7 % to the type strains of recognized Psychrobacter species. The mean level of DNA-DNA relatedness between strains JG-219(T) and JG-220 was 84.4 %. The two strains exhibited levels of DNA-DNA relatedness of 1.5-32.9 % to the type strains of eight phylogenetically related Psychrobacter species. On the basis of phenotypic data and phylogenetic and genetic distinctiveness, the two strains were classified as representing a novel species within the genus Psychrobacter, Psychrobacter cibarius sp. nov. The type strain is JG-219(T) (=KCTC 12256(T)=DSM 16327(T)).


Subject(s)
Psychrobacter/classification , Psychrobacter/genetics , Seafood/microbiology , Bacterial Typing Techniques , Base Composition , DNA, Bacterial/analysis , DNA, Ribosomal/analysis , Fermentation , Genes, rRNA , Korea , Molecular Sequence Data , Nucleic Acid Hybridization , Phenotype , Phylogeny , Psychrobacter/growth & development , Psychrobacter/isolation & purification , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA
18.
J Bacteriol ; 186(8): 2340-5, 2004 Apr.
Article in English | MEDLINE | ID: mdl-15060036

ABSTRACT

Most microorganisms isolated from low-temperature environments (below 4 degrees C) are eury-, not steno-, psychrophiles. While psychrophiles maximize or maintain growth yield at low temperatures to compensate for low growth rate, the mechanisms involved remain unknown, as does the strategy used by eurypsychrophiles to survive wide ranges of temperatures that include subzero temperatures. Our studies involve the eurypsychrophilic bacterium Psychrobacter cryopegella, which was isolated from a briny water lens within Siberian permafrost, where the temperature is -12 degrees C. P. cryopegella is capable of reproducing from -10 to 28 degrees C, with its maximum growth rate at 22 degrees C. We examined the temperature dependence of growth rate, growth yield, and macromolecular (DNA, RNA, and protein) synthesis rates for P. cryopegella. Below 22 degrees C, the growth of P. cryopegella was separated into two domains at the critical temperature (T(critical) = 4 degrees C). RNA, protein, and DNA synthesis rates decreased exponentially with decreasing temperatures. Only the temperature dependence of the DNA synthesis rate changed at T(critical). When normalized to growth rate, RNA and protein synthesis reached a minimum at T(critical), while DNA synthesis remained constant over the entire temperature range. Growth yield peaked at about T(critical) and declined rapidly as temperature decreased further. Similar to some stenopsychrophiles, P. cryopegella maximized growth yield at low temperatures and did so by streamlining growth processes at T(critical). Identifying the specific processes which result in T(critical) will be vital to understanding both low-temperature growth and growth over a wide range of temperatures.


Subject(s)
Psychrobacter/growth & development , Psychrobacter/metabolism , Temperature , Bacterial Proteins/biosynthesis , DNA, Bacterial/biosynthesis , RNA, Bacterial/biosynthesis
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