Comparative genomics of the marine bacterial genus <scp><i>G</i></scp><i>laciecola</i> reveals the high degree of genomic diversity and genomic characteristic for cold adaptation

Qin, Qi‐Long; Xie, Bin-Bin; Yu, Yong; Shu, Yan-Li; Rong, Jin-Cheng; Zhang, Yan-Jiao; Zhao, Dian‐Li; Chen, Xiu-Lan; Zhang, Xiying; Chen, Bo; Zhou, Biao; Zhang, Yuzhong

doi:10.1111/1462-2920.12318

Cited by 67 publications

(56 citation statements)

References 60 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…An OTU related to Psychroflexus torques, which is known to associate with ice algae (Bowman et al, 1998) and may oxidize dimethylsulfoniopropionate, was also exclusive to the core MYI group. One of the OTUs was closely related to Glacicola nitratireducens (Supplementary Table S3), which is involved in the nitrogen cycle through denitrification (Qin et al, 2014). The fact that these Glacicola sequences are found in high abundance in all MYI samples may explain a previous observation that denitrification occurs much more strongly in MYI than in FYI (Rysgaard et al, 2008).…”

Section: Myi and Fyi Have Distinct Membership But Not Compositionmentioning

confidence: 83%

“…Both of these genera are known to have a role in the degradation of dimethylsulfoniopropionate originating from marine algae (Gonzalez et al, 1999;Moran et al, 2007). Other OTUs were members of the genus Glacicola (Supplementary Table S3) known for their role in hydrolyzing complex organic carbon molecules such as cellulose and chitin originating from algae (Qin et al, 2014). An OTU related to Psychroflexus torques, which is known to associate with ice algae (Bowman et al, 1998) and may oxidize dimethylsulfoniopropionate, was also exclusive to the core MYI group.…”

Section: Myi and Fyi Have Distinct Membership But Not Compositionmentioning

confidence: 99%

See 1 more Smart Citation

Bacterial communities from Arctic seasonal sea ice are more compositionally variable than those from multi-year sea ice

et al. 2016

View full text Add to dashboard Cite

Arctic sea ice can be classified into two types: seasonal ice (first-year ice, FYI) and multi-year ice (MYI). Despite striking differences in the physical and chemical characteristics of FYI and MYI, and the key role sea ice bacteria play in biogeochemical cycles of the Arctic Ocean, there are a limited number of studies comparing the bacterial communities from these two ice types. Here, we compare the membership and composition of bacterial communities from FYI and MYI sampled north of Ellesmere Island, Canada. Our results show that communities from both ice types were dominated by similar class-level phylogenetic groups. However, at the operational taxonomic unit (OTU) level, communities from MYI and FYI differed in both membership and composition. Communities from MYI sites had consistent structure, with similar membership (presence/absence) and composition (OTU abundance) independent of location and year of sample. By contrast, communities from FYI were more variable. Although FYI bacterial communities from different locations and different years shared similar membership, they varied significantly in composition. Should these findings apply to sea ice across the Arctic, we predict increased compositional variability in sea ice bacterial communities resulting from the ongoing transition from predominantly MYI to FYI, which may impact nutrient dynamics in the Arctic Ocean.

show abstract

Section: Myi and Fyi Have Distinct Membership But Not Compositionmentioning

confidence: 83%

Section: Myi and Fyi Have Distinct Membership But Not Compositionmentioning

confidence: 99%

Bacterial communities from Arctic seasonal sea ice are more compositionally variable than those from multi-year sea ice

et al. 2016

View full text Add to dashboard Cite

show abstract

“…As a reference, in the comparison of 7 species of the genus Pseudomonas which genome has a similar genome size to the genus Alteromonas , were found ca .1500 genes making up the core [63]. In the same way, 11 species of the genus Glaciecola that belong to the same family had 1257 genes [64]. Actually, from the ANI values A. macleodii could be in really composed of at least 3 species, the strains defined as the deep ecotype, the yellow sea isolate and the global surface ecotype with ANIs ranging from 73.7 to 80.6%.…”

Section: Discussionmentioning

confidence: 99%

“…The flexible part of the genome thus far would add up to ca . 13000 genes, also a typical value if is compared with the marine bacteria of the related genus Glaciecola (17276 gene families) [64] or the more than 17000 of the Vibrio pangenome [65]. …”

Section: Discussionmentioning

confidence: 99%

Genomes of Alteromonas australica,a world apart

et al. 2014

View full text Add to dashboard Cite

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.

show abstract

“…Adaptation by the genus Glaciecola to low temperatures and cold environments is suggested by a number of studies. A recent metagenomic analysis of the genus Glaciecola identified several cold-adapted mechanisms in the pan-genome that would allow the survival and growth of this genus at low temperatures (Qin et al, 2014). Although cold environments (e.g., in polar regions) seem to be the favored habitat of Glaciecola (Bowman et al, 1998; Nichols et al, 1999; van Trappen et al, 2004; Zhang et al, 2006; Prabagaran et al, 2007), its members have also been found in Mediterranean coastal waters (Alonso-Sáez et al, 2007) and during a phytoplankton spring bloom in the North Sea (Teeling et al, 2012).…”

Section: Discussionmentioning

confidence: 99%

Tight Coupling of Glaciecola spp. and Diatoms during Cold-Water Phytoplankton Spring Blooms

2017

View full text Add to dashboard Cite

Early spring phytoplankton blooms can occur at very low water temperatures but they are often decoupled from bacterial growth, which is assumed to be often temperature controlled. In a previous mesocosm study with Baltic Sea plankton communities, an early diatom bloom was associated with a high relative abundance of Glaciecola sequences (Gammaproteobacteria), at both low (2°C) and elevated (8°C) temperatures, suggesting an important role for this genus in phytoplankton-bacteria coupling. In this study, the temperature-dependent dynamics of free-living Glaciecola spp. during the bloom were analyzed by catalyzed reporter deposition fluorescence in situ hybridization using a newly developed probe. The analysis revealed the appearance of Glaciecola spp. in this and in previous spring mesocosm experiments as the dominating bacterial clade during diatom blooms, with a close coupling between the population dynamics of Glaciecola and phytoplankton development. Although elevated temperature resulted in a higher abundance and a higher net growth rate of Glaciecola spp. (Q10 ∼ 2.2), their growth was, in contrast to that of the bulk bacterial assemblages, not suppressed at 2°C and showed a similar pattern at 8°C. Independent of temperature, the highest abundance of Glaciecola spp. (24.0 ± 10.0% of total cell number) occurred during the peak of the phytoplankton bloom. Together with the slightly larger cell size of Glaciecola, this resulted in a ∼30% contribution of Glaciecola to total bacterial biomass. Overall, the results of this and previous studies suggest that Glaciecola has an ecological niche during early diatom blooms at low temperatures, when it becomes a dominant consumer of phytoplankton-derived dissolved organic matter.

show abstract

Comparative genomics of the marine bacterial genus Glaciecola reveals the high degree of genomic diversity and genomic characteristic for cold adaptation

Cited by 67 publications

References 60 publications

Bacterial communities from Arctic seasonal sea ice are more compositionally variable than those from multi-year sea ice

Bacterial communities from Arctic seasonal sea ice are more compositionally variable than those from multi-year sea ice

Genomes of Alteromonas australica,a world apart

Tight Coupling of Glaciecola spp. and Diatoms during Cold-Water Phytoplankton Spring Blooms

Contact Info

Product

Resources

About