scholarly journals Free-Living, Psychrotrophic Bacteria of the Genus Psychrobacter Are Descendants of Pathobionts

mSystems ◽  
2021 ◽  
Vol 6 (2) ◽  
Author(s):  
Daphne K. Welter ◽  
Albane Ruaud ◽  
Zachariah M. Henseler ◽  
Hannah N. De Jong ◽  
Peter van Coeverden de Groot ◽  
...  

ABSTRACT Host-adapted microorganisms are generally assumed to have evolved from free-living, environmental microorganisms, as examples of the reverse process are rare. In the phylum Gammaproteobacteria, family Moraxellaceae, the genus Psychrobacter includes strains from a broad ecological distribution including animal bodies as well as sea ice and other nonhost environments. To elucidate the relationship between these ecological niches and Psychrobacter’s evolutionary history, we performed tandem genomic analyses with phenotyping of 85 Psychrobacter accessions. Phylogenomic analysis of the family Moraxellaceae reveals that basal members of the Psychrobacter clade are Moraxella spp., a group of often-pathogenic organisms. Psychrobacter exhibited two broad growth patterns in our phenotypic screen: one group that we called the “flexible ecotype” (FE) had the ability to grow between 4 and 37°C, and the other, which we called the “restricted ecotype” (RE), could grow between 4 and 25°C. The FE group includes phylogenetically basal strains, and FE strains exhibit increased transposon copy numbers, smaller genomes, and a higher likelihood to be bile salt resistant. The RE group contains only phylogenetically derived strains and has increased proportions of lipid metabolism and biofilm formation genes, functions that are adaptive to cold stress. In a 16S rRNA gene survey of polar bear fecal samples, we detect both FE and RE strains, but in in vivo colonizations of gnotobiotic mice, only FE strains persist. Our results indicate the ability to grow at 37°C, seemingly necessary for mammalian gut colonization, is an ancestral trait for Psychrobacter, which likely evolved from a pathobiont. IMPORTANCE Host-associated microbes are generally assumed to have evolved from free-living ones. The evolutionary transition of microbes in the opposite direction, from host associated toward free living, has been predicted based on phylogenetic data but not studied in depth. Here, we provide evidence that the genus Psychrobacter, particularly well known for inhabiting low-temperature, high-salt environments such as sea ice, permafrost soils, and frozen foodstuffs, has evolved from a mammalian-associated ancestor. We show that some Psychrobacter strains retain seemingly ancestral genomic and phenotypic traits that correspond with host association while others have diverged to psychrotrophic or psychrophilic lifestyles.

2021 ◽  
Author(s):  
◽  
David Joll Burr

<p>Although homogenous in appearance, Antarctic sea ice forms a complex habitat that is characterised by steep vertical gradients of temperature, irradiance and salinity. Despite these harsh and variable environmental conditions, numerous microbial organisms prosper within Antarctic sea ice. In 2010, bacteria bearing the proteorhodopsin (PR) gene were found within Antarctic sea ice. PR is a photoactive membrane protein that functions as a light-driven proton pump. The hydrogen ion membrane gradient that PR establishes has the potential to drive ATP synthesis, thus allowing PR-bearing bacteria to obtain energy from solar radiation. Although this gene is present in up to 80% of marine bacteria, the active contribution of PR in vivo is debatable. Light induced growth or enhanced survival is generally observed only when PR-bearing bacteria are grown under sub-optimum conditions, such as limited nutrients or carbon, or variations in salinity. This has lead to the general hypothesis that PR has multiple functions, becoming most influential under conditions of stress. In this way, Antarctic sea-ice bacteria may utilise PR to promote survival and enhance energy inputs, when exposed to the harsh conditions of this environment.  To explore this hypothesis, potential PR-bearing isolates were cultured from samples of Antarctic sea-ice bacteria. Using 16S rRNA gene sequencing as well as a comparison of phenotypic and environmental characteristics, the isolates were identified as; Psychrobacter nivimaris, Polaribacter dokdonensis, Paracoccus marcusii and Micrococcus sp. These species, along with Psychroflexus torquis (an Antarctic sea-ice bacterium known to possess PR) were examined for the presence of the PR gene. This gene was identified in P. torquis, Ps. nivimaris and Po. dokdonensis. To my knowledge, this is the first time PR has been found in Ps. nivimaris.  To assess the influence of irradiance on these species, a series of culture based experiments were undertaken. In 2012, a preliminary field experiment was conducted in which a mixed culture of PR-bearing and non PR-bearing bacteria; Ps. nivimaris, Po. dokdonensis, Pa. marcusii and Micrococcus sp., was incubated in situ in the annual sea ice surrounding Ross Island, Antarctica. The method developed for these experiments is unique, in that cultures of sea-ice bacteria have not before been incubated within their natural environment. No major differences in growth patterns were observed when bacteria were incubated under different wavelengths and light intensities, however, valuable insight into methodological improvement was obtained. Using these refinements, a second in situ incubation experiment was conducted at the same field site, in 2013. Over this 2 week incubation, monocultures of P. torquis grown in full strength media grew most readily under 50%- and blue-light treatments, with red- and green-light yielding lower biomasses, and no growth occurring in the dark. Ambient sea-ice irradiance resulted in highly variable growth, attributed to high irradiance growth-inhibition. These results indicate that P. torquis utilises low levels of light in order to increase its growth in Antarctic sea ice.  The influence of light on the growth of P. torquis, Ps. nivimaris and Po. dokdonensis was examined in a laboratory-based experiment, in which media strength and temperature were varied. When cultured at 12°C, Ps. nivimaris grown under constant irradiance reached a higher biomass than in darkness. This trend was most pronounced when this species was cultured in a 10% media concentration. A trend of decreased exponential-growth was observed in light-incubated cultures of Ps. nivimaris, grown at 4°C or -1°C. Elevated maximum growth of Po. dokdonensis was observed under irradiated conditions in the 10% media treatment. This species however, only grew at 12°C; an unexpected result for an Antarctic microbe. P. torquis was not affected by irradiance under any culture conditions and did not grow at -1°C. This last result contrasts the results of the in situ incubations and may have been affected by factors such as culture age.  This research demonstrates multiple examples of light-enhanced growth occurring in PR-bearing Antarctic sea-ice bacteria, with the most prominent trends occurring in reduced concentration media. Therefore, this work agrees with the overarching hypothesis that PR is most influential under conditions of stress. The varying effect of temperature on the influence of PR suggests that some species are able to use this protein at low temperatures, whilst others cannot. Therefore, PR likely provides a selective advantage to some species, depending on a variety of physicochemical factors, including nutrient and carbon availability, salinity and temperature.</p>


2021 ◽  
Author(s):  
◽  
David Joll Burr

<p>Although homogenous in appearance, Antarctic sea ice forms a complex habitat that is characterised by steep vertical gradients of temperature, irradiance and salinity. Despite these harsh and variable environmental conditions, numerous microbial organisms prosper within Antarctic sea ice. In 2010, bacteria bearing the proteorhodopsin (PR) gene were found within Antarctic sea ice. PR is a photoactive membrane protein that functions as a light-driven proton pump. The hydrogen ion membrane gradient that PR establishes has the potential to drive ATP synthesis, thus allowing PR-bearing bacteria to obtain energy from solar radiation. Although this gene is present in up to 80% of marine bacteria, the active contribution of PR in vivo is debatable. Light induced growth or enhanced survival is generally observed only when PR-bearing bacteria are grown under sub-optimum conditions, such as limited nutrients or carbon, or variations in salinity. This has lead to the general hypothesis that PR has multiple functions, becoming most influential under conditions of stress. In this way, Antarctic sea-ice bacteria may utilise PR to promote survival and enhance energy inputs, when exposed to the harsh conditions of this environment.  To explore this hypothesis, potential PR-bearing isolates were cultured from samples of Antarctic sea-ice bacteria. Using 16S rRNA gene sequencing as well as a comparison of phenotypic and environmental characteristics, the isolates were identified as; Psychrobacter nivimaris, Polaribacter dokdonensis, Paracoccus marcusii and Micrococcus sp. These species, along with Psychroflexus torquis (an Antarctic sea-ice bacterium known to possess PR) were examined for the presence of the PR gene. This gene was identified in P. torquis, Ps. nivimaris and Po. dokdonensis. To my knowledge, this is the first time PR has been found in Ps. nivimaris.  To assess the influence of irradiance on these species, a series of culture based experiments were undertaken. In 2012, a preliminary field experiment was conducted in which a mixed culture of PR-bearing and non PR-bearing bacteria; Ps. nivimaris, Po. dokdonensis, Pa. marcusii and Micrococcus sp., was incubated in situ in the annual sea ice surrounding Ross Island, Antarctica. The method developed for these experiments is unique, in that cultures of sea-ice bacteria have not before been incubated within their natural environment. No major differences in growth patterns were observed when bacteria were incubated under different wavelengths and light intensities, however, valuable insight into methodological improvement was obtained. Using these refinements, a second in situ incubation experiment was conducted at the same field site, in 2013. Over this 2 week incubation, monocultures of P. torquis grown in full strength media grew most readily under 50%- and blue-light treatments, with red- and green-light yielding lower biomasses, and no growth occurring in the dark. Ambient sea-ice irradiance resulted in highly variable growth, attributed to high irradiance growth-inhibition. These results indicate that P. torquis utilises low levels of light in order to increase its growth in Antarctic sea ice.  The influence of light on the growth of P. torquis, Ps. nivimaris and Po. dokdonensis was examined in a laboratory-based experiment, in which media strength and temperature were varied. When cultured at 12°C, Ps. nivimaris grown under constant irradiance reached a higher biomass than in darkness. This trend was most pronounced when this species was cultured in a 10% media concentration. A trend of decreased exponential-growth was observed in light-incubated cultures of Ps. nivimaris, grown at 4°C or -1°C. Elevated maximum growth of Po. dokdonensis was observed under irradiated conditions in the 10% media treatment. This species however, only grew at 12°C; an unexpected result for an Antarctic microbe. P. torquis was not affected by irradiance under any culture conditions and did not grow at -1°C. This last result contrasts the results of the in situ incubations and may have been affected by factors such as culture age.  This research demonstrates multiple examples of light-enhanced growth occurring in PR-bearing Antarctic sea-ice bacteria, with the most prominent trends occurring in reduced concentration media. Therefore, this work agrees with the overarching hypothesis that PR is most influential under conditions of stress. The varying effect of temperature on the influence of PR suggests that some species are able to use this protein at low temperatures, whilst others cannot. Therefore, PR likely provides a selective advantage to some species, depending on a variety of physicochemical factors, including nutrient and carbon availability, salinity and temperature.</p>


2012 ◽  
Vol 62 (2) ◽  
pp. 376-383 ◽  
Author(s):  
Martin W. Hahn ◽  
Arevik Minasyan ◽  
Elke Lang ◽  
Ulrike Koll ◽  
Catrin Spröer

Strain AM-8B5T, isolated from Lake Sevan in Armenia, was characterized phenotypically, chemotaxonomically and phylogenetically. This chemo-organoheterotrophic, aerobic, facultatively anaerobic, catalase- and oxidase-positive, non-motile strain grew on NSY medium at NaCl concentrations of 0.0–0.2 % (w/v) and at 4–30 °C. Whole-cell fatty acids were dominated by summed feature 3 (including C16 : 1ω7c and iso-C15 : 0 2-OH), C16 : 0 and C18 : 1ω7c. C12 : 0 2-OH and C16 : 1 2-OH were the only hydroxylated fatty acids detected. Phylogenetic analysis as well as phenotypic and chemotaxonomic similarities indicated that the novel isolate was affiliated with the genus Polynucleobacter. 16S rRNA gene similarity values with the four previously described Polynucleobacter species ranged from 96.2 to 98.7 %. DNA–DNA hybridization experiments showed that the isolate did not belong to any of the previously described Polynucleobacter species. The isolate could be distinguished from all previously established Polynucleobacter species based on chemotaxonomic and phenotypic traits. The bacterium possessed a free-living lifestyle and represents a group of bacteria inhabiting the water column of many freshwater lakes. Based on the revealed phylogeny, and chemotaxonomic and phenotypic differences to previously described Polynucleobacter species, it is proposed that the isolate represents a novel species, Polynucleobacter difficilis sp. nov.; the type strain is AM-8B5T ( = DSM 22349T = CIP 110078T).


2011 ◽  
Vol 61 (4) ◽  
pp. 788-794 ◽  
Author(s):  
Martin W. Hahn ◽  
Elke Lang ◽  
Ulrike Brandt ◽  
Cathrin Spröer

The heterotrophic, aerobic, facultatively anaerobic, catalase- and oxidase-positive, non-motile strain MWH-PoolGreenA3T, isolated from a rock pool filled with freshwater, was characterized. The strain grew on NSY medium over a NaCl range of 0.0–0.3 % (w/v). Whole-cell fatty acids were dominated by C16 : 1ω7c (feature 3), C18 : 1ω7c and straight-chain C16 : 0; furthermore, the components C12 : 0 and C14 : 0 2-OH were present. The DNA G+C content was 48.3 mol%. Phylogenetic analysis as well as strong similarities in phenotypic and chemotaxonomic traits indicated the affiliation with the genus Polynucleobacter. 16S rRNA gene similarity values with the three described species of the genus Polynucleobacter ranged from 96.7 to 97.8 %. DNA–DNA hybridization experiments did not reveal that the strain belongs to a previously described species of the genus Polynucleobacter. The strain can be discriminated from previously established species of the genus Polynucleobacter by chemotaxonomic and phenotypic traits. The bacterium possesses a free-living lifestyle and represents a group of planktonic freshwater bacteria occurring with high cell numbers in many freshwater lakes. Based on the phylogeny revealed and the chemotaxonomic and phenotypic differences from previously described species of the genus Polynucleobacter, we propose to establish the novel species Polynucleobacter acidiphobus sp. nov. with the type strain MWH-PoolGreenA3T ( = DSM 21994T  = CIP 110079T).


2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Toshinori Tanaka ◽  
Yoshio Yahata ◽  
Keisuke Handa ◽  
Suresh V. Venkataiah ◽  
Mary M. Njuguna ◽  
...  

Abstract Background We established an in vivo intraradicular biofilm model of apical periodontitis in pigs in which we compared the efficacy of different irrigant activation techniques for biofilm removal. Methods Twenty roots from the deciduous mandibular second premolar of 5 male pigs were used. After pulpectomy, canals were left open for 2 weeks and then sealed for 4 weeks to enable the development of an intracanal biofilm. The intraradicular biofilms was evaluated using SEM and bacterial 16S rRNA gene-sequencing. To investigate the efficacy of biofilm removal, root canal irrigations were performed using conventional needle, passive ultrasonic, subsonic, or laser-activated irrigation. Real-time PCR was conducted to quantitate the remaining biofilm components. Statistical analysis was performed using ANOVA followed by a Tukey kramer post-hoc test with α = 0.05. Results The pulp exposure model was effective in inducing apical periodontitis and SEM analysis revealed a multi-layer biofilm formation inside the root canal. 16S rRNA sequence analysis identified Firmicutes, Bacteroidetes, and Fusobacteria as the predominant bacterial phyla components, which is similar to the microbiome profile seen in humans. None of the tested irrigation techniques completely eradicated the biofilm components from the root canal, but the subsonic and laser-activated irrigation methods produced the lowest bacterial counts (p < 0.05). Conclusions An experimental intraradicular biofilm model has been successfully established in pigs. Within the limitations of the study, subsonic or laser-activated irrigation demonstrated the best biofilm removal results in the pig system.


Nutrients ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 1673
Author(s):  
Inmaculada Acuña ◽  
Tomás Cerdó ◽  
Alicia Ruiz ◽  
Francisco J. Torres-Espínola ◽  
Ana López-Moreno ◽  
...  

BACKGROUND: During early life, dynamic gut colonization and brain development co-occur with potential cross-talk mechanisms affecting behaviour. METHODS: We used 16S rRNA gene sequencing to examine the associations between gut microbiota and neurodevelopmental outcomes assessed by the Bayley Scales of Infant Development III in 71 full-term healthy infants at 18 months of age. We hypothesized that children would differ in gut microbial diversity, enterotypes obtained by Dirichlet multinomial mixture analysis and specific taxa based on their behavioural characteristics. RESULTS: In children dichotomized by behavioural trait performance in above- and below-median groups, weighted Unifrac b-diversity exhibited significant differences in fine motor (FM) activity. Dirichlet multinomial mixture modelling identified two enterotypes strongly associated with FM outcomes. When controlling for maternal pre-gestational BMI and breastfeeding for up to 3 months, the examination of signature taxa in FM groups showed that Turicibacter and Parabacteroides were highly abundant in the below-median FM group, while Collinsella, Coprococcus, Enterococcus, Fusobacterium, Holdemanella, Propionibacterium, Roseburia, Veillonella, an unassigned genus within Veillonellaceae and, interestingly, probiotic Bifidobacterium and Lactobacillus were more abundant in the above-median FM group. CONCLUSIONS: Our results suggest an association between enterotypes and specific genera with FM activity and may represent an opportunity for probiotic interventions relevant to treatment for motor disorders.


1985 ◽  
Vol 5 (3) ◽  
pp. 554-562 ◽  
Author(s):  
K G Miller ◽  
J Tower ◽  
B Sollner-Webb

To determine the size and location of the mouse rDNA promoter, we constructed systematic series of deletion mutants approaching the initiation site from the 5' and 3' directions. These templates were transcribed in vitro under various conditions with S-100 and whole-cell extracts. Surprisingly, the size of the rDNA region that determines the level of transcription differed markedly, depending on the reaction conditions. In both kinds of cell extracts, the apparent 5' border of the promoter was at residue ca. -27 under optimal transcription conditions, but as reaction conditions became less favorable, the 5' border moved progressively out to residues -35, -39, and -45. The complete promoter, however, extends considerably further, for under other nonoptimal conditions, we observed major effects of promoter domains extending in the 5' direction to positions ca. -100 and -140. In contrast, the apparent 3' border of the mouse rDNA promoter was at residue ca. +9 under all conditions examined. We also show that the subcloned rDNA region from -39 to +9 contains sufficient information to initiate accurately and that the region between +2 and +9 can influence the specificity of initiation. These data indicate that, although the polymerase I transcription factors recognize and accurately initiate with only the sequences downstream of residue -40, sequences extending out to residue -140 greatly favor the initiation reaction; presumably, this entire region is involved in rRNA transcription in vivo.


Parasitology ◽  
2014 ◽  
Vol 141 (9) ◽  
pp. 1203-1215 ◽  
Author(s):  
VICTORIA GILLAN ◽  
EILEEN DEVANEY

SUMMARYNematodes are amongst the most successful and abundant organisms on the planet with approximately 30 000 species described, although the actual number of species is estimated to be one million or more. Despite sharing a relatively simple and invariant body plan, there is considerable diversity within the phylum. Nematodes have evolved to colonize most ecological niches, and can be free-living or can parasitize plants or animals to the detriment of the host organism. In this review we consider the role of heat shock protein 90 (Hsp90) in the nematode life cycle. We describe studies on Hsp90 in the free-living nematode Caenorhabditis elegans and comparative work on the parasitic species Brugia pahangi, and consider whether a dependence upon Hsp90 can be exploited for the control of parasitic species.


2010 ◽  
Vol 76 (21) ◽  
pp. 7144-7153 ◽  
Author(s):  
Rinske M. Valster ◽  
Bart A. Wullings ◽  
Dick van der Kooij

ABSTRACT Legionella pneumophila proliferates in aquatic habitats within free-living protozoa, 17 species of which have been identified as hosts by using in vitro experiments. The present study aimed at identifying protozoan hosts for L. pneumophila by using a biofilm batch test (BBT). Samples (600 ml) collected from 21 engineered freshwater systems, with added polyethylene cylinders to promote biofilm formation, were inoculated with L. pneumophila and subsequently incubated at 37°C for 20 days. Growth of L. pneumophila was observed in 16 of 18 water types when the host protozoan Hartmannella vermiformis was added. Twelve of the tested water types supported growth of L. pneumophila or indigenous Legionella anisa without added H. vermiformis. In 12 of 19 BBT flasks H. vermiformis was indicated as a host, based on the ratio between maximum concentrations of L. pneumophila and H. vermiformis, determined with quantitative PCR (Q-PCR), and the composition of clone libraries of partial 18S rRNA gene fragments. Analyses of 609 eukaryotic clones from the BBTs revealed that 68 operational taxonomic units (OTUs) showed the highest similarity to free-living protozoa. Forty percent of the sequences clustering with protozoa showed ≥99.5% similarity to H. vermiformis. None of the other protozoa serving as hosts in in vitro studies were detected in the BBTs. In several tests with growth of L. pneumophila, the protozoa Diphylleia rotans, Echinamoeba thermarum, and Neoparamoeba sp. were identified as candidate hosts. In vitro studies are needed to confirm their role as hosts for L. pneumophila. Unidentified protozoa were implicated as hosts for uncultured Legionella spp. grown in BBT flasks at 15°C.


Development ◽  
1992 ◽  
Vol 114 (2) ◽  
pp. 317-330 ◽  
Author(s):  
O. Bossinger ◽  
E. Schierenberg

The pattern of autofluorescence in the two free-living namatodes Rhabditis dolichura and Caenorhabditis compared. In C. elegans, during later embryogenesis cells develop a typical bluish autofluorescence as illumination, while in Rh. dolichura a strong already present in the unfertilized egg. Using a new,


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