Genomes of surface isolates of Alteromonas macleodii: the life of a widespread marine opportunistic copiotroph

López‐Pérez, Mario; Gonzaga, Aitor; Martín-Cuadrado, Ana-Belén; Onyshchenko, Olga; Ghavidel, Akbar; Ghai, Rohit; Rodrı́guez-Valera, Francisco

doi:10.1038/srep00696

Cited by 120 publications

(146 citation statements)

References 74 publications

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“…DNA attachment sites attL and attR could be identified confirming this region as a prophage [53]. Interestingly, a highly related prophage (Figure 5) was previously described in the strain A. macleodii 673 (related only by a 74.1% ANI with DE170) [18]. This strain comes from the Western English Channel, showing the remarkably wide distribution of this phage.…”

Section: Resultssupporting

confidence: 59%

Genomes of Alteromonas australica,a world apart

et al. 2014

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BackgroundAlteromonas is a genus of marine bacteria that is very easy to isolate and grow in the laboratory. There are genomes available of the species Alteromonas macleodii from different locations around the world and an Alteromonas sp. isolated from a sediment in Korea. We have analyzed the genomes of two strains classified by 16S rRNA (>99% similarity) as the recently described species Alteromonas australica, and isolated from opposite ends of the world; A. australica DE170 was isolated in the South Adriatic (Mediterranean) at 1000 m depth while A. australica H17T was isolated from a sea water sample collected in St Kilda Beach, Tasman Sea.ResultsAlthough these two strains belong to a clearly different species from A. macleodii, the overall synteny is well preserved and the flexible genomic islands seem to code for equivalent functions and be located at similar positions. Actually the genomes of all the Alteromonas species known to date seem to preserve synteny quite well with the only exception of the sediment isolate SN2. Among the specific metabolic features found for the A. australica isolates there is the degradation of xylan and production of cellulose as extracellular polymeric substance by DE170 or the potential ethanol/methanol degradation by H17T.ConclusionsThe genomes of the two A. australica isolates are not more different than those of strains of A. macleodii isolated from the same sample. Actually the recruitment from metagenomes indicates that all the available genomes are found in most tropical-temperate marine samples analyzed and that they live in consortia of several species and multiple clones within each. Overall the hydrolytic activities of the Alteromonas genus as a whole are impressive and fit with its known capabilities to exploit sudden inputs of organic matter in their environment.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-483) contains supplementary material, which is available to authorized users.

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Section: Resultssupporting

confidence: 59%

Genomes of Alteromonas australica,a world apart

et al. 2014

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“…For example, isolates belonging to Vibrionaceae doubled in as little as 12 min (Ulitzur 1974) while Alteromonas macleodii isolates doubled in 2.4 h (López-Pérez et al 2012). Some have argued that organisms with short division times are more important in biogeochemical cycles, and that organisms with long division times succeed by being 'defense specialists' (Suttle 2007).…”

Section: Discussionmentioning

confidence: 99%

Spatiotemporal distributions of rare bacterioplankton populations indicate adaptive strategies in the oligotrophic ocean

Vergin¹,

Done²,

Carlson³

et al. 2013

Aquat. Microb. Ecol.

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Spatiotemporal distributions of rare microbial taxa were examined in 384 samples from the Bermuda Atlantic Time-series Study (BATS) site, in the northwestern Sargasso Sea. Sequences were partitioned into 6 mutually exclusive sets based on abundance (abundant, rare, and very rare) and frequency of detection (frequent and infrequent). Analyses of variance for taxa that were frequently present, across all levels of abundance, demonstrated environmental filtering, indicating that gradients in environmental factors, such as season and depth, drive community assembly for rare taxa, as they do for abundant taxa. All abundant nodal taxonomic units (NTUs) had spatiotemporal periods of rarity, providing a clear demonstration of the role of fluctuating reproductive success in population dynamics, and the role of rare populations as seed banks. An inverse relationship between the number of rare taxa and physical stratification indicates that transport by mixing drives increased community diversity throughout most of the year. Populations of selected copiotrophic taxa varied in episodic patterns that were not tightly entrained to season and depth, indicating that these populations are not governed by the same rules of community assembly that apply to most other taxa and may be adapted to exploit infrequent, unknown disturbances. Overall, the findings support the perspective that the success of most rare populations was driven by the same fundamental patterns of spatiotemporal variation that drove the success of dominant populations, but also indicate potentially important roles for transport by mixing and atypical life histories in determination of community composition.

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“…To get a better insight into the mechanisms behind these interactions, we selected one heterotrophic strain belonging to the Alteromonas clade for in-depth analysis. Alteromonas are typically not very common in the oceans (Eilers et al, 2000) yet are often identified in rRNA-based analyses of microbial communities in open water, and thus naturally co-occur with Prochlorococcus (García- Martínez et al, 2002;Ivars-Martinez et al, 2008;Lopez-Perez et al, 2012). They are metabolically-versatile copiotrophs (Pedler et al, 2014), rapidly responding to increases in dissolved organic matter and often dominating mesocosm experiments (McCarren et al, 2010).…”

Section: Introductionmentioning

confidence: 99%

Transcriptional response of Prochlorococcus to co-culture with a marine Alteromonas: differences between strains and the involvement of putative infochemicals

Aharonovich

Sher

2016

The ISME Journal

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Interactions between marine microorganisms may determine the dynamics of microbial communities. Here, we show that two strains of the globally abundant marine cyanobacterium Prochlorococcus, MED4 and MIT9313, which belong to two different ecotypes, differ markedly in their response to coculture with a marine heterotrophic bacterium, Alteromonas macleodii strain HOT1A3. HOT1A3 enhanced the growth of MIT9313 at low cell densities, yet inhibited it at a higher concentration, whereas it had no effect on MED4 growth. The early transcriptomic responses of Prochlorococcus cells after 20 h in co-culture showed no evidence of nutrient starvation, whereas the expression of genes involved in photosynthesis, protein synthesis and stress responses typically decreased in MED4 and increased in MIT313. Differential expression of genes involved in outer membrane modification, efflux transporters and, in MIT9313, lanthipeptides (prochlorosins) suggests that Prochlorococcus mount a specific response to the presence of the heterotroph in the cultures. Intriguingly, many of the differentially-expressed genes encoded short proteins, including two new families of co-culture responsive genes: CCRG-1, which is found across the Prochlorococcus lineage and CCRG-2, which contains a sequence motif involved in the export of prochlorosins and other bacteriocin-like peptides, and are indeed released from the cells into the media.

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Genomes of surface isolates of Alteromonas macleodii: the life of a widespread marine opportunistic copiotroph

Cited by 120 publications

References 74 publications

Genomes of Alteromonas australica,a world apart

Genomes of Alteromonas australica,a world apart

Spatiotemporal distributions of rare bacterioplankton populations indicate adaptive strategies in the oligotrophic ocean

Transcriptional response of Prochlorococcus to co-culture with a marine Alteromonas: differences between strains and the involvement of putative infochemicals

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