Fig 2 - uploaded by Francesco Smedile
Content may be subject to copyright.
Phylogenetic tree of Photobacterium including the four bioluminescent strains isolated in this study. The tree was rooted and out-grouped with 16S rRNA genes of Cycloclasticus pugetii (U57920) and Vibrio fischeri ATCC T (X74702), respectively. Numbers at nodes are bootstrap support values based on 5000 resampling replicates. The scale bar represents 2% nucleotide sequence divergence.
Source publication
The present study is focused on the development of a cultivation-independent molecular approach for specific detection of bioluminescent bacteria within microbial communities by direct amplification of luxA gene from environmental DNA. A new set of primers, specifically targeting free-living bioluminescent bacteria, was designed on the base of luxA...
Context in source publication
Context 1
... bioluminescent isolates retrieved from Station 6 (500 m depth) were unambiguously affiliated to the Photobacterium phosphoreum clade, while the isolates obtained from deeper water masses of Station 4 were distantly related to the clade of Photobacterium kishitanii, a new luminous marine bacterium symbiotic with deep-sea fishes (Ast et al., 2007) (Fig. ...
Similar publications
Lysis of marine bacteria by viruses releases a range of organic compounds into the environment, including d- and l-amino acids, but the uptake of these compounds by other bacteria is not well characterized. This study determined that Photobacterium sp. strain SKA34 (Gammaproteobacteria) increased in abundance following uptake of d- and l-amino acid...
En este artículo os contamos cómo gracias al trabajo con
un patógeno humano Acinetobacter baumannii hemos
conseguido descubrir varios aspectos novedosos de la
biología del patógeno de peces Gram negativo Photobacterium
damselae subsp. piscicida (Pdsp), antiguamente conocido
como Pasteurella piscicida. Queremos hacer énfasis
en varios conceptos: la...
Photobacterium profundum SS9 is a Gram-negative bacterium, originally collected from the Sulu Sea. Its genome consists of two chromosomes and a 80 kb plasmid. Although it can grow under a wide range of pressures, P. profundum grows optimally at 28 MPa and 15°C. Its ability to grow at atmospheric pressure allows for both easy genetic manipulation an...
A total of 23 strains of halophilic histamine-producing bacteria previously isolated from marine fish and seawater were studied phenotypically, genotypically, and phylogenetically. These organisms are facultatively anaerobic, gram-negative, short rods that are motile by means of one to three unsheathed polar flagella. They are mesophilic and nonlum...
Tetrabromobisphenol A (TBBPA) is one of the most widely used brominated flame retar-dants and has attracted more and more attention. In this work, the parent TBBPA with an initial concentration of 100 mg/L was completely removed after 6 min of ozonation at pH 8.0, and alkaline conditions favored a more rapid removal than acidic and neutral conditio...
Citations
... The LuxAB gene was searched for all bacterial isolates. The gene was amplified by using the specific Primers Lux AB-66F (3 -CAAATGTGRAAAGGTCGTTTTAATTTTGG-5 ) and 611R (3 -AACRAAATCWYKCCATTGRCCTTTAT-5 ) [54]. The reaction mixtures were carried out as described above, and the PCR program was as follows: an initial polymerase activation at 95 • C for 1 min, 30 cycles of 15 s at 95 • C for denaturation, 15 s at 37 • C for an annealing phase, 10 s at 72 • C for elongation, and a final elongation for 5 min at 72 • C. The PCR products were confirmed by visualization on agarose gel electrophoresis (1.5%, w/v) in TAE buffer (0.04 M Tris-acetate, 0.02 M acetic acid, and 0.001 M EDTA). ...
Luminescent bacteria are a fascinating component of marine microbial communities, often related to the light emissions in deep sea marine organisms. They are mainly affiliated with specific phylogenetic groups, such as Photobacterium, Vibrio, and Photorhabdus, and are sometimes involved in symbiotic relationships. However, the luminescence of some marine organisms remains a poorly understood process, and it is not always certain whether their luminescence is attributable to associated luminescent bacteria. In this study, for the first time, luminescent bacteria were isolated from two deep sea organisms, namely, the cephalopod Neorossia caroli and the teleost Chlorophthalmus agassizi. The isolation was carried out on glycerol-supplemented medium, and the search for the luxAB gene was performed on all isolates as a complementary tool to the culture-dependent techniques to detect bioluminescence by molecular approach. The optimum of salinity, temperature, and pH was evaluated by physiological tests for all isolates. The production of extracellular polymeric substances was also preliminarily screened. A total of 24 luminescent isolates were obtained, with an abundance from C. agassizi specimens. All the isolates were taxonomically characterized and were related to different species of Photobacterium, with the exception of Vibrio sp. CLD11 that was from C. agassizi. The luxAB gene was detected in about the 90% of the analysed strains.
... Out of these, Vibrio and Photobacterium are mostly found in marine ecosystems, whereas Xenorhabdus inhabits terrestrial habitats [14]. New strains of bioluminescent bacteria are still being discovered [15]. A remarkable fact about bacterial bioluminescence is that all bacterial bioluminescent systems are exactly alike in terms of biochemistry, i.e., they all rely on flavin mononucleotide (FMN), myristic aldehyde and NADH, and also oxygen [16]. ...
Bioluminescence, or the ability to emit light biologically, has evolved multiple times across various taxa. As fascinating as the phenomenon is, various studies have been undertaken to harness this phenomenon for human use. However, the origins, distribution and ecology of bioluminescence still remain obscure. The capability to produce biological light is found in various species, ranging from tiny bacteria to huge fishes like lantern sharks. Many organisms that do not possess this ability partake in symbiotic relationships, resulting in a variety of anatomical and behavioral modifications. The ecological interactions resulting from bioluminescence are even more interesting and diverse, but many of them are still shrouded in mystery because of a lack of in-situ study. As agreed by many, bioluminescence conferred certain evolutionary advantages which still remain unclear. In spite of the lack of understanding, many spectacular ecological interactions like offence, defense, courtship or intra-specific synchrony have been observed, studied and documented, and their significance understood. As far as humans are concerned, efforts are being made to channel this capability to the best of our use, though some of these are still in their infancy. This chapter explores the origins, ecology and future prospects of bioluminescence in detail.
... Recent literature shows that lux genes have the ability to transfer to other nonluminous Vibrio and Photobacterium, resulting non-luminous bacteria to luminous (Urbanczyk et al., 2008;Dunlap and Urbanczyk, 2013). LuxA gene has been used as a potential molecular marker to identify luminous bacteria species and to test the species novelty (Gentile et al., 2009). Luminous bacteria are primarily found in Vibrionaceae family that consists of four luminous genera Aliivibrio, Photobacterium, and Vibrio. ...
The diversity, distribution, and mechanisms of bacterial speciation of Vibrio species belonging to Harveyi clade are an important global research interests due to their pathogenic activity in coastal environments. Luminous bacteria are also known to act as environmental indicators in coastal waters. This study demonstrates that luminous bacteria belonging to harveyi clade are predominant in seawater, sediment, surfaces of marine animals and plants, and light organs of leiognathid fishes. Molecular phylogenies for eighteen morphologically distinct and potentially luminous strains chosen out of 57 isolated luminous bacteria. Sequence analysis of luxA gene as a molecular marker identified luminous bacteria belonging to Harveyi clade, Photobacterium clade, and Anguillarum clade distinctly. Rich biodiversity and distribution of luminous bacterial species (30% to 40%) was found in association with coral reef samples of south Andaman. This study confirms and reveals the evidence on predominant association of Harveyi clade luminous vibrio's in coastal waters of south Andaman.
... Seasonal variations have been identified, in both abundance and predominant species (O'Brien and Sizemore, 1979;Ruby and Nealson, 1978;Yetinson and Shilo, 1979). A wide variability has been observed in species repartition over depth and between geographic areas (DeLuca, 2006;Gentile et al., 2009;Nealson and Hastings, 1979;Ramaiah and Chandramohan, 1992;Ruby et al., 1980). Horizontal, vertical and seasonal variations were presumed to reflect physiological preferences most of the time, and particularly temperature or salinity sensitivity (Orndorff and Colwell, 1980;Ramesh et al., 1990;Ruby and Nealson, 1978;Shilo and Yetinson, 1979;Yetinson and Shilo, 1979). ...
... where bacteria are present or on organisms with associated bacteria. First, vertical samplings in the water column were performed using sterile-bag samplers (Ruby et al., 1980), or later using Niskin bottles (mounted on rosette profilers, Fig. 1c) (Al Ali et al., 2010;Gentile et al., 2009;Martini et al., 2016;Yetinson and Shilo, 1979). This approach is commonly set up in oceanography but relies on relatively small volumes of water (up to 20 L). ...
Around 30 species of marine bacteria can emit light, a
critical characteristic in the oceanic environment is mostly
deprived of sunlight. In this article, we first review current knowledge on
bioluminescent bacteria symbiosis in light organs. Then, focusing on
gut-associated bacteria, we highlight that recent works, based on omics
methods, confirm previous claims about the prominence of bioluminescent
bacterial species in fish guts. Such host–symbiont relationships are
relatively well-established and represent important knowledge in the
bioluminescence field. However, the consequences of bioluminescent bacteria
continuously released from light organs and through the digestive tracts to
the seawater have been barely taken into account at the ecological and
biogeochemical level. For too long neglected, we propose considering the
role of bioluminescent bacteria and reconsidering the biological carbon
pump, taking into account the bioluminescence effect (“bioluminescence shunt
hypothesis”). Indeed, it has been shown that marine snow and fecal pellets
are often luminous due to microbial colonization, which makes them a visual
target. These luminous particles seem preferentially consumed by organisms
of higher trophic levels in comparison to nonluminous ones. As a
consequence, the sinking rate of consumed particles could be either
increased (due to repackaging) or reduced (due to sloppy feeding or
coprophagy/coprorhexy), which can imply a major impact on global biological
carbon fluxes. Finally, we propose a strategy, at a worldwide scale, relying
on recently developed instrumentation and methodological tools to quantify
the impact of bioluminescent bacteria in the biological carbon pump.
... Recent literature shows that lux genes have the ability to transfer to other nonluminous Vibrio and Photobacterium, resulting non-luminous bacteria to luminous (Urbanczyk et al., 2008;Dunlap and Urbanczyk, 2013). LuxA gene has been used as a potential molecular marker to identify luminous bacteria species and to test the species novelty (Gentile et al., 2009). Luminous bacteria are primarily found in Vibrionaceae family that consists of four luminous genera Aliivibrio, Photobacterium, and Vibrio. ...
The diversity, distribution, and mechanisms of bacterial speciation of Vibrio species belonging to Harveyi clade are an important global research interests due to their pathogenic activity in coastal environments. Luminous bacteria are also known to act as environmental indicators in coastal waters. This study demonstrates that luminous bacteria belonging to harveyi clade are predominant in seawater, sediment, surfaces of marine animals and plants, and light organs of leiognathid fishes. Molecular phylogenies for eighteen morphologically distinct and potentially luminous strains chosen out of 57 isolated luminous bacteria. Sequence analysis of luxA gene as a molecular marker identified luminous bacteria belonging to Harveyi clade, Photobacterium clade, and Anguillarum clade distinctly. Rich biodiversity and distribution of luminous bacterial species (30% to 40%) was found in association with coral reef samples of south Andaman. This study confirms and reveals the evidence on predominant association of Harveyi clade luminous vibrio's in coastal waters of south Andaman.
... As a matter of fact, P. phosphoreum ANT-2200 was found free in the deep waters of the Mediterranean Sea during a high level of bioluminescence (in relationship with a strong convection event) detected by the underwater neutrino telescope ANTARES (Tamburini et al., 2013). This result is coherent with the description of this species as the dominant bioluminescent microorganism in the Mediterranean Sea (Gentile et al., 2009). Moreover, the genus of Photobacterium has also been found as active even during a stable hydrological period suggesting an ecological benefit of bioluminescence (Martini et al., 2016). ...
Bacterial-bioluminescence regulation is often associated with quorum sensing. Indeed, many studies have been made on this subject and indicate that the expression of the light-emission-involved genes is density-dependent. However, most of these studies have concerned two model species, A. fischeri and V.campbellii. Very few works have been done on bioluminescence regulation for the other bacterial genera. Yet, according to the large variety of habitats of luminous marine bacteria, it would not be surprising to find different light-regulation systems. In this study, we used Photobacterium phosphoreum ANT-2200, a piezophilic bioluminescent strain isolated from Mediterranean deep-sea waters (2200-m depth). To answer the question of whether or not the bioluminescence of P. phosphoreum ANT-2200 is under quorum-sensing control, we focused on the correlation between growth and light emission through physiological, genomic and, transcriptomic approaches. Unlike A. fischeri and V.campbellii, the light of P. phosphoreum ANT-2200 immediately increases from its initial level. Interestingly, the emitted light increases at much higher rate at the low cell density than it does for higher cell-density values. The expression level of the light-emission-involved genes stays constant all along the exponential growth phase. We also showed that, even when more light is produced, when the strain is cultivated at high hydrostatic pressure, no change in the transcription level of these genes can be detected. Through different experiments and approaches, our results clearly indicate that, under the tested conditions, the genes, directly involved in the bioluminescence in P. phosphoreum ANT-2200, are not controlled at a transcriptomic level. Quite obviously, these results demonstrate that the light emission of the strain is not density-dependent, which means not under quorum-sensing control. Through this study, we point out that bacterial-bioluminescence regulation should not, from now on, be always linked with the quorum-sensing control.
... The DNA extraction was further proceeded to amplify the Lux-AB gene with 2x power taq PCR Master Mix (Bioteke, Beijing) and universal primers with PCR conditions using the following for 20 cycles: 94°C for 30 seconds, 50°C for 30 seconds, and 72°C for 60 seconds. The Lux-AB gene with 611R reverse primer (3'-AACRAAATCWYKCCATTGRCCTTTAT-5) and 66F forward primer (3'-CAAATGTGRAAAGGTCGTTTTAATTTTGG-5') (Gabriela et al., 2009) used for five different temperature at 37°C, 39°C, 41°C, 43°C, and 45°C to produce PCR band performed in 2% agarose gel electrophoresis at 75 V for 40 minutes. 100bp and 1kb of DNA ladder (Bioteke, Beijing) used as a gel view marker. ...
Luminescent bacteria had been broadly studied for its ability to convert chemical energy into light energy source by bioluminescent reaction. There are three main classifications of luminescent glowing bacteria which are mostly distinguished as Photobacterium, Vibrio, and Photorhabdus. Luminescent bacteria such as Photobacterium spp. and Vibrio spp. exist as symbionts within marine organisms such as squids, lantern fish, jelly fish, the angler fish, clams and the eel. Whereas, Photorhabdus spp. were found in earthbound insects like caterpillar and nematode as the intermediate host for the bacterial growth. The objective of this study is to isolate and to amplify the Lux-AB gene for confirmation of producing luminescent light bacteria from marine squid, Loligo spp. In this study conducted, the marine squids were brought from fisherman at Remis Beach, Kuala Selangor and the ink samples were obtained from its internal part containing ink sac. The ink sample was collected and was diluted from 10-1 to 10-5 and then was spread plate onto Luminescent agar (LA) medium. The LA plates were incubated at room temperature (~27°C) for 24 hours and every 6 hours the appearance of luminescent colonies was observed for the luminescene light in the dark room. The distinct 10 single colonies that were produced the most glow in the dark were randomly picked and further re-streaked to get pure culture onto LA plate and incubated again at room temperature (~27°C) for 24 hours. Gram stain test were done for the morphological study of luminescent bacteria. As result, 10 isolates showed as gram negative bacteria, pinkish color and it's a short rod shape morphology when view under 100x magnificent with immersion oil. Then, the isolates were sub-culture into Luminescent broth (LB) for overnight and the genomic extraction were done (Bioteke, Beijing) to amplify the Lux-AB gene cassette by using primer 611R (reverse) and 66F (forward). The Lux-AB gene present a PCR product band at 561-567bp using different temperature at 39°C, 41°C, 43°C, and 45°C respectively for gene producing the luminescent light. All the isolates were successful produced expected band with different optimum temperature. These luminescent bacteria which contained Lux-AB gene proven to be transmitted the light when it's catalysed by the enzyme called luciferase. These luminescent bacteria obtained will be further studied for its potential bio-light application as biosensor, reporter gene and biolight source.
... The best-studied symbiotic bacteria are in the genus Vibrio including the predominantly free-living species V. harveyi (sometimes called Beneckea harveyi), although the genus Shewanella also includes a bioluminescent species [59]. A study recently showed that many new strains of luminous bacteria, that has traditionally been called Photobacterium phosphoreum, are present in the deep sea [60], and many of them actually represent diverse assemblages [61]. Although there are many exceptions, Vibrio fischeri, often called Photobacterium (Figure 2a and b) is part of the species-complex typically involved in symbiosis with sepiolid and loliginid squid and monocentrid fishes, while Photobacterium leiognathi and relatives are primarily symbionts for leiognathid, apogonid, and morid fishes [62]. ...
... For bacteria, bioluminescence activity is driven by the products of the lux ICDAB(F)EG genes, organized into a single operon, with expression regulated by the product of the luxR gene. Based on the luxA gene amplification, Gentile et al. (2009) detected bioluminescent bacteria in the deep Mediterranean Sea (Thyrrenian Sea). These authors found an unexpected high number of luxA lineages, mainly belonging to the Photobacterium cluster, in this zone. ...
... As expected, sequences of the lux RT-qPCR fragment obtained in May (34 sequences) and October (34 sequences) were related to the luxF cluster of Photobacterium including P. phosphoreum, kishitanii and leiognathi (Supplement material S3). This observation is similar to the data reported in Gentile et al. (2009) from the Tyrrhenian Sea at 2750 m depth, where numerous luxA genes fell into the Photobacterium cluster. Furthermore, a Photobacterium strain was also isolated at the ANTARES station (Al Ali et al., 2010) revealing the presence of such bioluminescent bacteria at this station. ...
... It is therefore unlikely that complex bioluminescent signatures can be used to reveal the distribution of bioluminescent dinoflagellates in diverse oceanic plankton communities. Conversely, gene specific primers designed for the amplification of the luciferase gene (lcf) from bacteria [28] and dinoflagellates [23] have detected diverse assemblages of each in natural environments. While the detection of lcf only reveals the potential for a cell to produce bioluminescence, we assume that this potential is realized because cells are known to invest considerable resources in bioluminescence, even in long-term culture, and there are no known environmental conditions that suppress the expression of bioluminescence [14,29]. ...
We investigated the distribution of bioluminescent dinoflagellates in the Patagonian Shelf region using "universal" PCR primers for the dinoflagellate luciferase gene. Luciferase gene sequences and single cell PCR tests, in conjunction with taxonomic identification by microscopy, allowed us to identify and quantify bioluminescent dinoflagellates. We compared these data to coincidental discrete optical measurements of stimulable bioluminescence intensity. Molecular detection of the luciferase gene showed that bioluminescent dinoflagellates were widespread across the majority of the Patagonian Shelf region. Their presence was comparatively underestimated by optical bioluminescence measurements, whose magnitude was affected by interspecific differences in bioluminescence intensity and by the presence of other bioluminescent organisms. Molecular and microscopy data showed that the complex hydrography of the area played an important role in determining the distribution and composition of dinoflagellate populations. Dinoflagellates were absent south of the Falkland Islands where the cold, nutrient-rich, and well-mixed waters of the Falklands Current favoured diatoms instead. Diverse populations of dinoflagellates were present in the warmer, more stratified waters of the Patagonian Shelf and Falklands Current as it warmed northwards. Here, the dinoflagellate population composition could be related to distinct water masses. Our results provide new insight into the prevalence of bioluminescent dinoflagellates in Patagonian Shelf waters and demonstrate that a molecular approach to the detection of bioluminescent dinoflagellates in natural waters is a promising tool for ecological studies of these organisms.
