Home Journals Articles Updates About
CN
image
收藏切换
Phylogenetic diversity of dimethylsulfoniopropionate-dependent demethylase gene dmdA in distantly related bacteria isolated from Arctic and Antarctic marine environments
收藏切换
PDF
Yinxin ZENG1, *
Acta Oceanologica Sinica | 2019, 38(8) : 64 - 71
Less
收藏切换
Acta Oceanologica Sinica | 2019, 38(8): 64-71
• Marine Biology •
Phylogenetic diversity of dimethylsulfoniopropionate-dependent demethylase gene dmdA in distantly related bacteria isolated from Arctic and Antarctic marine environments
Full
Yinxin ZENG1, *
Affiliations
  • 1 Key Laboratory for Polar Science of State Oceanic Administration, Polar Research Institute of China, Shanghai 200136, China
Published: 2019-08-25 doi: 10.1007/s13131-019-1393-7
Outline
收藏切换

Dimethylsulfoniopropionate (DMSP) is mainly produced by marine phytoplankton as an osmolyte, antioxidant, predator deterrent, or cryoprotectant. DMSP is also an important carbon and sulfur source for marine bacteria. Bacteria may metabolize DMSP via the demethylation pathway involving the DMSP demethylase gene (dmdA) or the cleavage pathway involving several different DMSP lyase genes. Most DMSP released into seawater is degraded by bacteria via demethylation. To test a hypothesis that the high gene frequency of dmdA among major marine taxa results in part from horizontal gene transfer (HGT) events, a total of thirty-one bacterial strains were isolated from Arctic Kongsfjorden seawater in this study. Analysis of 16S rRNA gene sequences showed that, except for strains BSw22118, BSw22131 and BSw22132 belonging to the genera Colwellia, Pseudomonas and Glaciecola, respectively, all bacteria fell into the genus Pseudoalteromonas. DmdA genes were detected in five distantly related bacterial strains, including four Arctic strains (Pseudoalteromonas sp. BSw22112, Colwellia sp. BSw22118, Pseudomonas sp. BSw22131 and Glaciecola sp. BSw22132) and one Antarctic strain (Roseicitreum antarcticum ZS2–28). Their dmdA genes showed significant similarities (97.7%–98.3%) to that of Ruegeria pomeroyi DSS–3, which was originally isolated from temperate coastal seawater. In addition, the sequence of the gene transfer agent (GTA) capsid protein gene (g5) detected in Antarctic strain ZS2–28 exhibited a genetically closely related to that of Ruegeria pomeroyi DSS–3. Among the five tested strains, only Pseudomonas sp. BSw22131 could grow using DMSP as the sole carbon source. The results of this study support the hypothesis of HGT for dmdA among taxonomically heterogeneous bacterioplankton, and suggest a wide distribution of functional gene (i.e., dmdA) in global marine environments.

dimethylsulfoniopropionate-dependent demethylase gene (dmdA)  /  horizontal gene transfer  /  marine bacteria  /  Arctic  /  Antarctic
Yinxin ZENG. Phylogenetic diversity of dimethylsulfoniopropionate-dependent demethylase gene dmdA in distantly related bacteria isolated from Arctic and Antarctic marine environments[J]. Acta Oceanologica Sinica, 2019 , 38 (8) : 64 -71 . DOI: 10.1007/s13131-019-1393-7
Full Text
Less
1 Introduction
Less
Dimethylsulfoniopropionate (DMSP) is an organic sulfur compound produced in massive amounts worldwide (~109 t per annum; Johnston et al., 2008), mainly by marine phytoplankton (Keller, 1989; Bürgermeister et al., 1990; Turner et al., 1995). DMSP may function as an osmolyte, antioxidant, predator deterrent, and cryoprotectant (Kirst et al., 1990; Karsten et al., 1996; Wolfe et al., 1997; Sunda et al., 2002). DMSP is perhaps best known as the major precursor of gaseous dimethyl sulfide (DMS), which is the major sulfur compound emitted into the atmosphere from the ocean (Andreae, 1990). Dimethyl sulfide emissions have the potential to influence the Earth’s climatic system through formation of aerosols that scatter solar radiation and affect cloud radiative properties (Shaw, 1983; Charlson et al., 1987; Schwartz and Andreae, 1996).
DMSP in marine algae can be released into seawater due to algal senescence, viral lysis and zooplankton grazing, and forms a dissolved pool (DMSPd) for marine bacteria (Kiene, 1990; Visscher et al., 1992). DMSP can be utilized by marine bacteria via the cleavage or the demethylation pathway (Kiene et al., 2000). The cleavage pathway is mediated by various DMSP lyases and results in the formation of DMS. To date, seven DMSP lyase genes (dddD, dddK, dddL, dddP, dddQ, dddY and dddW) have been identified from bacterial isolates (Curson et al., 2011; Sun et al., 2016). DmdA, the only gene found to encode the first step in the DMSP demethylation pathway (Johnston et al., 2016), is the most widely distributed DMSP degradation genes in the oceans. Approximately 60% of marine bacteria in the open ocean and coastal waters contain the dmdA gene (Howard et al., 2008; Cui et al., 2015). Compared with that only a minor proportion (2%–21%) of DMSPd in the marine water column is cleaved into DMS (Kiene et al., 2000; Kiene and Linn, 2000), the demethylation pathway converts a large fraction (50%–90%) of DMSPd to 3-methylmercaptopropionate (MMPA), which can serve as a reduced carbon and sulfur source for microbial cells (Kiene et al., 1999; Howard et al., 2008; Reisch et al., 2011; Sun et al., 2016).
DmdA genes have been detected in members of the Alphaproteobacteria, including SAR11 (e.g., Pelagibacter ubique), SAR116 (e.g., Candidatus Puniceispirillum marium), the Rhodospirillales and Roseobacter clade, and Gammaproteobacteria (e.g., the OM60 clade; Curson et al., 2011; Howard et al., 2011; Johnston et al., 2016), with most being found in the Roseobacter and SAR11 clades (Howard et al., 2006, 2008). These genes are also detected in members of Actinobacteria and Planctomycetes and even in the animal Amphimedon queenslandica (https://www.ncbi.nlm.nih.gov/nuccore). This distribution may reflect at least one horizontal gene transfer (HGT) event, contributing to the homogenization of biogeochemical roles of dmdA among heterotrophic marine bacterioplankton (Howard et al., 2008).
HGT through transformation, transduction, and conjugation is important in prokaryotic evolution. Recently, a novel genetic exchange process mediated by phage-like gene transfer agents (GTAs) has been reported to be active in marine environments and to have the potential to catalyze high levels of gene transfer (McDaniel et al., 2010). GTAs are found in phylogenetically diverse prokaryotes (Lang et al., 2012). A capsid protein-encoding gene (g5) from the GTA gene cluster has been used as a marker to characterize the Rhodobacterales community structure because GTA genes are well conserved in the Rhodobacterales (Zhao et al., 2008; Fu et al., 2010).
To test the hypothesis that the high gene frequency of dmdA among major marine taxa results in part from HGT events (Howard et al., 2008), marine bacteria belonging to different genera were isolated from Arctic seawater and Antarctic intertidal sediment and then analyzed for the dmdA gene using a PCR method. Phylogenetic analyses of the dmdA gene sequences and DmdA amino acid sequences were then conducted. In addition, GTA capsid protein gene (g5) was examined and analyzed in the investigated isolates.
2 Materials and methods
Less
2.1 Sample collection and bacterial isolation
Arctic seawater samples K3, K4 and K5 were collected from Kongsfjorden, Spitsbergen, in July of 2016. Bacteria were isolated by direct plating serial dilutions of seawater onto three different agar plates. These included low-nutrient seawater medium agar plate as described by González et al. (2003), 1.5% agar plate supplemented with f/2 media (Guillard and Ryther, 1962) and 1 mmol/L DMSP, and seawater medium agar plate as described by Fuhrman et al. (1994). After 30 d of incubation in the dark at 8°C, colonies were selected for further testing after purification. Strain Roseicitreum antarcticum ZS2-28 was isolated from intertidal sediment on the coast of the Larsemann Hills of Princess Elizabeth Land, East Antarctica (Yu et al., 2011). The reference strain Ruegeria pomeroyi DSS-3 was obtained from the German Collection of Microorganisms and Cell Cultures (DSMZ).
2.2 DNA extraction and PCR amplification of 16S rRNA, dmdA and g5 genes
Bacterial DNA preparation and PCR amplification and sequencing of 16S rRNA gene were performed as described by Zeng et al. (2007). One of bacterial strains within the same genus was randomly selected as a representative of distantly related bacteria for further analysis. Using primer pair dmdA282F (5′-TGCTSTSAACGAYCCSGT-3′) and dmdA591R (5′-ACRTAGAYYTCRAAVCCBCCYT-3′), bacterial dmdA genes were cloned and sequenced as described earlier (Zeng et al., 2016). PCR amplification and sequencing of gene transfer agent g5 gene were performed as described by Zhao et al. (2008). The PCR reaction mixture for the g5 gene consisted of 1 μL of template DNA, 12.5 μL of DreamTaq Green PCR Master Mix (2×; Thermo Scientific, Germany), 2 μg bovine serum albumin (BSA), and 0.4 μmol/L of each primer. Genomic DNA from one reference strain Ruegeria pomeroyi DSS-3, which possesses a dmdA gene of 1 095 bp and a g5 gene of 1 179 bp (CP000031), was used as a template for standards. Both distilled water and genomic DNA from Escherichia coli DH5α were used as a template for negative controls.
2.3 Phylogenetic analysis
The obtained 16S rRNA gene, dmdA gene, and g5 gene sequences were checked for chimeras using the Bellerophon program (Huber et al., 2004), then subjected to a BLAST sequence similarity search in GenBank (http://blast.ncbi.nlm.nih.gov/Blast.cgi). Bacterial 16S rRNA gene sequence was subsequently aligned against those of type strains within the same genus or family obtained from the GenBank database via Clustal W (Thompson et al., 1994), while the dmdA gene and g5 gene sequences of the bacterial isolates were aligned against those reported for organisms belonging to different taxa in GenBank, respectively. The DNA sequences of dmdA gene were subsequently translated into amino acid sequences. The resulting DmdA sequences were aligned and compared with reference sequences from different taxa in the GenBank database. Maximum-likelihood phylogenetic trees were constructed using the MEGA5.1 software (Tamura et al., 2011). For DNA sequences of the 16S rRNA gene, the dmdA gene and the g5 gene, the evolutionary distances were calculated under the Kimura two-parameter model. For DmdA amino-acid sequences, the evolution distances were calculated under the Jones-Taylor-Thornton model. Neighbor-joining bootstrap tests of phylogeny were performed using 1000 replicates.
2.4 Bacterial growth
To check the ability to use DMSP as the sole carbon source for cell growth, five selected isolates, BSw22112, BSw22118, BSw22131, BSw22132 and Roseicitreum antarcticum ZS2-28, were cultured in two media: basal carbon utilization medium (0.5 g (NH4)2HPO4, 1.3 g KH2PO4, 3.2 g Na2HPO4, 0.8 g Na2SO4, 1.0 g NaNO3, 2.0 g DMSP, 30.0 g Sigma sea salts per liter distilled water) and modified M9 medium (3.0 g KH2PO4, 12.8 g Na2HPO4, 0.5 g NaCl, 1.0 g NH4Cl, 240 mg MgSO4, 111 mg CaCl2, 1.7 g DMSP, 24.0 g Sigma sea salts per liter distilled water; Sambrook and Russell, 2001). Bacterial growth was observed after incubation at 15°C in dark for 8 d.
2.5 Nucleotide sequence accession numbers
Sequences have been deposited in the GenBank database under accession numbers MF630588–630618 (16S rRNA genes), MF621769–621772 (dmdA genes), MG569947 (dmdA gene), and MG569950 (g5 gene).
3 Results
Less
3.1 Diversity of bacterial isolates from Arctic Kongsfjorden
A total of thirty-one bacterial strains were isolated from seawaters in Kongsfjorden. Among them, thirteen strains were isolated from low-nutrient seawater medium plates containing DMSP. Moreover, these all fell into the genus Pseudoalteromonas except for strains BSw22131 and BSw22132, which belonged to the Pseudomonas and Glaciecola, respectively. Eight strains isolated on seawater medium plate were members of the genus Pseudoalteromonas. The rest of the bacterial strains were isolated on 1.5% agar plate supplemented with f/2 media and DMSP. All of these were also in the genus Pseudoalteromonas, except for strain BSw22118 which belonged to the genus Colwellia. Among the twenty-eight Pseudoalteromonas isolates, strain BSw22112 was randomly selected as a representative of the genus Pseudoalteromonas for further analysis.
The 16S rRNA gene phylogenetic tree (Fig. 1) revealed that strains BSw22112, 22118, 22131 and 22132 fell into the cluster composed of Pseudoalteromonas species, Colwellia species, Pseudomonas species and Glaciecola species, respectively. In addition, the four gammaproteobacterial strains formed a large cluster separate from the cluster consisting of the Alphaproteobacteria (e.g., Roseicitreum and Ruegeria).
Four Arctic isolates, Pseudoalteromonas sp. BSw22112, Colwellia sp. BSw22118, Pseudomonas sp. BSw22131 and Glaciecola sp. BSw22132 belonging to different genera within the Gammaproteobacteria, were selected for further study. In addition, since dmdA genes appeared to be most prevalent among members of the Alphaproteobacteria (Moran et al., 2012; Reisch et al., 2008), one Antarctic marine bacterium Roseicitreum antarcticum ZS2-28 isolated from sediment was also used for further study.
3.2 Phylogenetic relationships of dmdA genes between bacterial isolates and reported organisms
Using primer pair dmdA282F and dmdA591R, a major PCR product band of approximately 308 bp was obtained from each of the investigated isolates (BSw22112, BSw22118, BSw22131, BSw22132 and ZS2-28), showing significant similarity (97.7%–98.3%) to the dmdA gene of Ruegeria pomeroyi DSS-3. A maximum-likelihood tree (Fig. 2) revealed that the dmdA genes of the five isolates formed a coherent cluster with each other as well as Ruegeria pomeroyi DSS-3 and Leisingera methylohalidivorans DSM 14336, but distinctly separate from those of other organisms. Both Ruegeria pomeroyi DSS-3 and Leisingera methylohalidivorans DSM 14336 are within the family Rhodobacteraceae, and were isolated from seawater in the United States (data from GenBank).
The dmdA gene sequences of the five isolates were subsequently translated into amino acid sequences. Phylogenetic analysis of dmdA amino-acid sequences placed the five isolates in a cluster consisting of Ruegeria pomeroyi DSS-3 and Leisingera methylohalidivorans DSM 14336 (Fig. 3), showing an essentially similar topology with that of the maximum-likelihood dmdA gene tree. The results revealed close phylogenetic relationships of dmdA genes among the five bacteria isolated from polar regions and Ruegeria pomeroyi DSS-3, which is a well-known roseobacterium possessing both pathways for metabolism of DMSP (González et al., 1999).
3.3 Phylogenetic relationships of g5 genes between bacterial isolates and reported organisms
Using primer pair MCP-109F and MCP-368R, no PCR product band was obtained from bacterial isolates BSw22112, BSw22118, or BSw22132 within the Gammaproteobacteria. Although three PCR product bands were detected in strain Pseudomonas sp. BSw22131, sequence analysis based on BLASTX revealed that none of these PCR bands were related to the gene transfer agent. A single PCR product band of 782 bp was obtained from strain ZS2-28 within the Rhodobacterales, showing significant similarity (99.6%) to the gene transfer agent major capsid protein gene (g5) of Ruegeria pomeroyi DSS-3. A maximum-likelihood tree (Fig. 4) showed that the g5 gene of strain ZS2-28 formed a coherent cluster with Ruegeria pomeroyi DSS-3 that was distinctly separate from those of other organisms.
3.4 Bacterial growth with DMSP as the sole carbon source
No cell growth was observed for strains BSw22112, BSw22118, BSw22132 or ZS2-28 in either basal carbon utilization medium or M9 medium when DMSP was used as the sole carbon source. However, strain Pseudomonas sp. BSw22131 was found to be able to grow in M9 medium supplemented with DMSP, but unable to grow in basal carbon utilization medium supplemented with DMSP.
4 Discussion
Less
The DMSP demethylase, DmdA, is primarily found in the Roseobacter and SAR11 clades of marine Alphaproteobacteria (Howard et al., 2006, 2008), both of which are very populous in oceans. However, besides Antarctic Roseicitreum antarcticum ZS2-28 within the Roseobacter, Arctic strains Pseudoalteromonas sp. BSw22112, Colwellia sp. BSw22118, Pseudomonas sp. BSw22131 and Glaciecola sp. BSw22132 belonging to the Gammaproteobacteria were all found to harbor dmdA genes in the present study. In addition, significant relationships were observed between the dmdA genes from the five bacterial isolates and Ruegeria pomeroyi DSS-3, a model microorganism for DMSP degradation studies (Salgado et al., 2014), suggesting that horizontal gene transfer (HGT) is likely responsible for the wide distribution of dmdA among diverse bacterial taxa (Howard et al., 2008). HGT activity in the ocean is thought to contribute to the homogenization of biogeochemical roles among planktonic heterotrophic bacteria (Howard et al., 2008).
It has been suggested that high gene frequency results in part from horizontal transfer events of the dmdA gene among major marine taxa (Howard et al., 2008). One genetic exchange process of HGT is mediated by phage-like gene transfer agents (GTAs; Zhao et al., 2008) that contain a random piece of the genome of the producing cell (Solioz and Marrs, 1977). GTA activity may facilitate gene homogenization among diverse bacteria (Biers et al., 2008), since GTA particles contain only host genomes (Marrs, 1974; Yen et al., 1979). To date, four genetically unrelated GTAs have been identified in proteobacteria, archaea and virus (Lang et al., 2012). Among them, RcGTA (Rhodobacter capsulatus GTA) are usually observed in the Rhodobacterales and some other Alphaproteobacteria (e.g., marine Parvularculales, Rhizobiales and Sphingomonadales; Lang and Beatty, 2007; Biers et al., 2008). In the present study, the five bacterial isolates were in the Proteobacteria and harbored dmdA genes showing close relationships with Ruegeria pomeroyi DSS-3. Therefore, a highly conserved RcGTA major capsid protein gene (g5; Lang and Beatty, 2007) was examined in those isolates. The results revealed the existence of the g5 gene in strain Roseicitreum antarcticum ZS2-28, which agrees with the ubiquitous presence of RcGTA genes in members of the Rhodobacterales (Lang et al., 2012). However, GTA-like genes are not harbored by the Pelagibacterales (Biers et al., 2008), which is known as the ecologically dominant marine alphaproteobacterial SAR11 clade (Herlemann et al., 2014). GTA transduction is likely to be most efficient for marine roseobacters associated with particle surfaces, biofilms, and other high-cell-density habitats (Ripp and Miller, 1995; Vettori et al., 1999; Weinbauer, 2004; Biers et al., 2008). Expression of GTA genes and extracellular release of GTA particles has been reported for Ruegeria pomeroyi DSS-3, and intraspecific gene transfer has been documented (Biers et al., 2008). It has also been suggested that the gene transfer agent (GTA) evolved from a prophage that was present before the divergence of Proteobacteria (Lang and Beatty, 2007); however, the g5 gene was not found in four gammaproteobacterial strains in this study. Therefore, considering that both dmdA and g5 gene sequences of Antarctic Roseicitreum antarcticum ZS2-28 exhibited a closely related genetically to those of Ruegeria pomeroyi DSS-3 from coastal Georgia seawater, the results of this study indicate in part that GTA can serve as one of the HGT mechanisms leading to the dmdA gene distribution among the Rhodobacterales bacteria. For the gammaproteobacterial strains, the genetic exchange process of HGT of dmdA genes remains unclear, and further study is required to clarify the mechanism of HGT between marine Alpha- and Gammaproteobacteria.
The close phylogenetic relationships of dmdA genes among the bacteria BSw22112, BSw22118, BSw22131, BSw22132 and ZS2-28 isolated from cold marine environments in the Antarctic or Arctic, and strain Ruegeria pomeroyi DSS-3 from temperate coastal Georgia (USA) seawater (González et al., 1999), indicate the adaptability of DmdA and its wide distribution in global marine environments. In addition, a significant relationship between g5 genes from the Antarctic bacterium Roseicitreum antarcticum ZS2-28 and bacterium Ruegeria pomeroyi DSS-3 from the Northern hemisphere was observed. The results of the present study indicate a cosmopolitan distribution of some functional genes (e.g., dmdA genes and GTA major capsid protein g5 genes) in marine environments, which is in agreement with previous findings pertaining to bipolar gene flow in deep-sea benthic foraminifera (Pawlowski et al., 2007) and marine bacterioplankton (Hollibaugh et al., 2002; Pommier et al., 2005).
Except for strain Pseudomonas sp. BSw22131, four bacterial strains harboring dmdA genes in this study could not grow when DMSP was used as the sole carbon source. These suggest that marine bacteria containing only dmdA gene cannot utilize DMSP as the sole carbon source for cell growth. In addition, no dddP gene (the most widely distributed DMSP lyase gene in marine environments; Bullock et al., 2017) was detected in the five investigated strains using a PCR method (data not shown). Therefore, strain Pseudomonas sp. BSw22131 may have other DMSP lyase(s) so that it can utilize DMSP as a carbon source for cell growth.
In conclusion, the results of the present study revealed the existence of dmdA genes showing significant relationships with each other in various bacteria isolated from bipolar and temperate marine environments, supporting the hypothesis that the same DmdA proteins may be harbored by taxonomically heterogeneous marine bacteria due to HGT of dmdA (Howard et al., 2008). Moreover, bipolar, or even global, distribution of functional gene (i.e., dmdA) was observed in this study. However, partial dmdA gene sequences with only approximately 308 bp were investigated in this study; therefore, complete dmdA gene sequences of the five bacterial isolates are required for further analysis to ensure their phylogenetic relationship to the model organism Ruegeria pomeroyi DSS-3.
Acknowledgements
Less
I appreciate the assistance of the Chinese Arctic and Antarctic Administration (CAA) who organized the Chinese Arctic Yellow River Station Expedition in 2016.
Funding
Less
  • The National Natural Science Foundation of China under contract No. 41476171; the Chinese Polar Environment Comprehensive Investigation and Assessment Program under contract No. CHINARE04-01.
References
Less
Andreae M O. 1990. Ocean-atmosphere interactions in the global biogeochemical sulfur cycle. Marine Chemistry, 30: 1–29, doi: 10.1016/0304-4203(90)90059-L
Bürgermeister S, Georgii H W, Zimmermann R L, et al. 1990. On the biogenic origin of dimethylsulfide: relation between chlorophyll, ATP, organismic DMSP, phytoplankton species, and DMS distribution in Atlantic surface water and atmosphere. Journal of Geophysical Research: Atmosphere, 95(D12): 20607–20615, doi: 10.1029/JD095iD12p20607
Biers E J, Wang Kui, Pennington C, et al. 2008. Occurrence and expression of gene transfer agent genes in marine bacterioplankton. Applied and Environmental Microbiology, 74(10): 2933–2939, doi: 10.1128/AEM.02129-07
Bullock H A, Luo Haiwei, Whitman W B. 2017. Evolution of dimethylsulfoniopropionate metabolism in marine phytoplankton and bacteria. Frontiers in Microbiology, 8: 637, doi: 10.3389/fmicb.2017.00637
Charlson R J, Lovelock J E, Andreae M O, et al. 1987. Oceanic phytoplankton, atmospheric sulphur, cloud albedo and climate. Nature, 326(6114): 655–661, doi: 10.1038/326655a0
Cui Yingshun, Suzuki S, Omori Y, et al. 2015. Abundance and distribution of dimethylsulfoniopropionate degradation genes and the corresponding bacterial community structure at dimethyl sulfide hot spots in the tropical and subtropical Pacific Ocean. Applied and Environmental Microbiology, 81(12): 4184–4194, doi: 10.1128/AEM.03873-14
Curson A R J, Todd J D, Sullivan M J, et al. 2011. Catabolism of dimethylsulphoniopropionate: microorganisms, enzymes and genes. Nature Reviews Microbiology, 9(12): 849–859, doi: 10.1038/nrmicro2653
Fu Yunyun, MacLeod D M, Rivkin R B, et al. 2010. High diversity of Rhodobacterales in the subarctic North Atlantic Ocean and gene transfer agent protein expression in isolated strains. Aquatic Microbial Ecology, 59(3): 283–293, doi: 10.3354/ame01398
Fuhrman J A, Lee S H, Masuchi Y, et al. 1994. Characterization of marine prokaryotic communities via DNA and RNA. Microbial Ecology, 28(2): 133–145, doi: 10.1007/BF00166801
González J M, Covert J S, Whitman W B, et al. 2003. Silicibacter pomeroyi sp. nov. and Roseovarius nubinhibens sp. nov., dimethylsulfoniopropionate-demethylating bacteria from marine environments. International Journal of Systematic and Evolutionary Microbiology, 53(5): 1261–1269, doi: 10.1099/ijs.0.02491-0
González J M, Kiene R P, Moran M A. 1999. Transformation of sulfur compounds by an abundant lineage of marine bacteria in the α-subclass of the class Proteobacteria. Applied and Environmental Microbiology, 65(9): 3810–3819
Guillard R R L, Ryther J H. 1962. Studies of marine planktonic diatoms: I. Cyclotella nana Hustedt, and Detonula confervacea (Cleve) Gran. Canadian Journal of Microbiology, 8(2): 229–239, doi: 10.1139/m62-029
Herlemann D P R, Woelk J, Labrenz M, et al. 2014. Diversity and abundance of “Pelagibacterales” (SAR11) in the Baltic Sea salinity gradient. Systematic and Applied Microbiology, 37(8): 601–604, doi: 10.1016/j.syapm.2014.09.002
Hollibaugh J T, Bano N, Ducklow H W. 2002. Widespread distribution in polar oceans of a 16S rRNA gene sequence with affinity to Nitrosospira-like ammonia-oxidizing bacteria. Applied and Environmental Microbiology, 68(3): 1478–1484, doi: 10.1128/AEM.68.3.1478-1484.2002
Howard E C, Henriksen J R, Buchan A, et al. 2006. Bacterial taxa that limit sulfur flux from the ocean. Science, 314(5799): 649–652, doi: 10.1126/science.1130657
Howard E C, Sun Shulei, Biers E J, et al. 2008. Abundant and diverse bacteria involved in DMSP degradation in marine surface waters. Environmental Microbiology, 10(9): 2397–2410, doi: 10.1111/j.1462-2920.2008.01665.x
Howard E C, Sun Shulei, Reisch C R, et al. 2011. Changes in dimethylsulfoniopropionate demethylase gene assemblages in response to an induced phytoplankton bloom. Applied and Environmental Microbiology, 77(2): 524–531, doi: 10.1128/AEM.01457-10
Huber T, Faulkner G, Hugenholtz P. 2004. Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics, 20(14): 2317–2319, doi: 10.1093/bioinformatics/bth226
Johnston A W B, Green R T, Todd J D. 2016. Enzymatic breakage of dimethylsulfoniopropionate—a signature molecule for life at sea. Current Opinion in Chemical Biology, 31: 58–65, doi: 10.1016/j.cbpa.2016.01.011
Johnston A W B, Todd J D, Sun Lei, et al. 2008. Molecular diversity of bacterial production of the climate-changing gas, dimethyl sulphide, a molecule that impinges on local and global symbioses. Journal of Experimental Botany, 59(5): 1059–1067, doi: 10.1093/jxb/erm264
Karsten U, Kück K, Vogt C, et al. 1996. Dimethylsulfoniopropionate production in phototrophic organisms and its physiological functions as a cryoprotectant. In: Kiene R P, Visscher P T, Keller M D, et al., eds. Biological and Environmental Chemistry of DMSP and Related Sulfonium Compounds. New York: Plenum Press, 143–153
Keller M D. 1989. Dimethyl sulfide production and marine phytoplankton: the importance of species composition and cell size. Biological Oceanography, 6(5–6): 375–382, doi: 10.1080/01965581.1988.10749540
Kiene R P. 1990. Dimethyl sulfide production from dimethylsulfoniopropionate in coastal seawater samples and bacterial cultures. Applied and Environmental Microbiology, 56(11): 3292–3297
Kiene R P, Linn L J. 2000. Distribution and turnover of dissolved DMSP and its relationship with bacterial production and dimethylsulfide in the Gulf of Mexico. Limnology and Oceanography, 45(4): 849–861, doi: 10.4319/lo.2000.45.4.0849
Kiene R P, Linn L J, Bruton J A. 2000. New and important roles for DMSP in marine microbial communities. Journal of Sea Research, 43(3–4): 209–224, doi: 10.1016/S1385-1101(00)00023-X
Kiene R P, Linn L J, González J, et al. 1999. Dimethylsulfoniopropionate and methanethiol are important precursors of methionine and protein-sulfur in marine bacterioplankton. Applied and Environmental Microbiology, 65(10): 4549–4558
Kirst G O, Thiel C, Wolff H, et al. 1990. Dimethylsulfoniopropionate (DMSP) in icealgae and its possible biological role. Marine Chemistry, 35(1–4): 381–388, doi: 10.1016/S0304-4203(09)90030-5
Lang A S, Beatty J T. 2007. Importance of widespread gene transfer agent genes in α-proteobacteria. Trends in Microbiology, 15(2): 54–62, doi: 10.1016/j.tim.2006.12.001
Lang A S, Zhaxybayeva O, Beatty J T. 2012. Gene transfer agents: phage-like elements of genetic exchange. Nature Reviews Microbiology, 10(7): 472–482, doi: 10.1038/nrmicro2802
Marrs B. 1974. Genetic recombination in Rhodopseudomonas capsulata. Proceedings of the National Academy of Sciences of the United States of America, 71(3): 971–973, doi: 10.1073/pnas.71.3.971
McDaniel L D, Young E, Delaney J, et al. 2010. High frequency of horizontal gene transfer in the oceans. Science, 330(6000): 50, doi: 10.1126/science.1192243
Moran M A, Reisch C R, Kiene R P, et al. 2012. Genomic insights into bacterial DMSP transformations. Annual Review of Marine Science, 4: 523–542, doi: 10.1146/annurev-marine-120710-100827
Pawlowski J, Fahrni J, Lecroq B, et al. 2007. Bipolar gene flow in deep-sea benthic foraminifera. Molecular Ecology, 16(19): 4089–4096, doi: 10.1111/j.1365-294X.2007.03465.x
Pommier T, Pinhassi J, Hagström A. 2005. Biogeographic analysis of ribosomal RNA clusters from marine bacterioplankton. Aquatic Microbial Ecology, 41(1): 79–89, doi: 10.3354/ame041079
Reisch C R, Moran M A, Whitman W B. 2008. Dimethylsulfoniopropionate-dependent demethylase (DmdA) from Pelagibacter ubique and Silicibacter pomeroyi. Journal of Bacteriology, 190(24): 8018–8024, doi: 10.1128/JB.00770-08
Reisch C R, Stoudemayer M J, Varaljay V A, et al. 2011. Novel pathway for assimilation of dimethylsulphoniopropionate widespread in marine bacteria. Nature, 473(7346): 208–211, doi: 10.1038/nature10078
Ripp S, Miller R V. 1995. Effects of suspended particulates on the frequency of transduction among Pseudomonas aeruginosa in a freshwater environment. Applied and Environmental Microbiology, 61(4): 1214–1219
Salgado P, Kiene R, Wiebe W, et al. 2014. Salinity as a regulator of DMSP degradation in Ruegeria pomeroyi DSS-3. Journal of Microbiology, 52(11): 948–954, doi: 10.1007/s12275-014-4409-1
Sambrook J, Russell D W. 2001. Molecular Cloning: A Laboratory Manual. New York: Cold Spring Harbor Laboratory Press
Schwartz S E, Andreae M O. 1996. Uncertainty in climate change caused by aerosols. Science, 272(5265): 1121, doi: 10.1126/science.272.5265.1121
Shaw G E. 1983. Bio-controlled thermostasis involving the sulfur cycle. Climatic Change, 5(3): 297–303, doi: 10.1007/BF02423524
Solioz M, Marrs B. 1977. The gene transfer agent of Rhodopseudomonas capsulata: purification and characterization of its nucleic acid. Archives of Biochemistry and Biophysics, 181(1): 300–307, doi: 10.1016/0003-9861(77)90508-2
Sun Jing, Todd J D, Thrash J C, et al. 2016. The abundant marine bacterium Pelagibacter simultaneously catabolizes dimethylsulfoniopropionate to the gases dimethyl sulfide and methanethiol. Nature Microbiology, 1(8): 16065, doi: 10.1038/nmicrobiol.2016.65
Sunda W, Kieber D J, Kiene R P, et al. 2002. An antioxidant function for DMSP and DMS in marine algae. Nature, 418(6895): 317–320, doi: 10.1038/nature00851
Tamura K, Peterson D, Peterson N, et al. 2011. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution, 28(10): 2731–2739, doi: 10.1093/molbev/msr121
Thompson J D, Higgins D G, Gibson T J. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research, 22(22): 4673–4680, doi: 10.1093/nar/22.22.4673
Turner S M, Nightingale P D, Broadgate W, et al. 1995. The distribution of dimethyl sulphide and dimethylsulphoniopropionate in Antarctic waters and sea ice. Deep Sea Research Part II: Topical Studies in Oceanography, 42(4–5): 1059–1080, doi: 10.1016/0967-0645(95)00066-y
Vettori C, Stotzky G, Yoder M, et al. 1999. Interaction between bacteriophage PBS1 and clay minerals and transduction of Bacillus subtilis by clay-phage complexes. Environmental Microbiology, 1(4): 347–355, doi: 10.1046/j.1462-2920.1999.00044.x
Visscher P T, Diaz M R, Taylor B F. 1992. Enumeration of bacteria which cleave or demethylate dimethylsulfoniopropionate in the Caribbean Sea. Marine Ecology Progress Series, 89: 293–296, doi: 10.3354/meps089293
Weinbauer M G. 2004. Ecology of prokaryotic viruses. FEMS Microbiology Reviews, 28(2): 127–181, doi: 10.1016/j.femsre.2003.08.001
Wolfe G V, Steinke M, Kirst G O. 1997. Grazing-activated chemical defence in a unicellular marine alga. Nature, 387(6636): 894–897, doi: 10.1038/43168
Yen H C, Hu N T, Marrs B L. 1979. Characterization of the gene transfer agent made by an overproducer mutant of Rhodopseudomonas capsulata. Journal of Molecular Biology, 131(2): 157–168, doi: 10.1016/0022-2836(79)90071-8
Yu Yong, Yan Shulin, Li Huirong, et al. 2011. Roseicitreum antarcticum gen. nov., sp. nov., an aerobic bacteriochlorophyll a-containing alphaproteobacterium isolated from Antarctic sandy intertidal sediment. International Journal of Systematic and Evolutionary Microbiology, 61(9): 2173–2179, doi: 10.1099/ijs.0.024885-0
Zeng Yinxin, Liu Wenqi, Li Huirong, et al. 2007. Effect of restriction endonucleases on assessment of biodiversity of cultivable polar marine planktonic bacteria by amplified ribosomal DNA restriction analysis. Extremophiles, 11(5): 685–692, doi: 10.1007/s00792-007-0086-x
Zeng Yinxin, Qiao Zongyun, Yu Yong, et al. 2016. Diversity of bacterial dimethylsulfoniopropionate degradation genes in surface seawater of Arctic Kongsfjorden. Scientific Reports, 6: 33031, doi: 10.1038/srep33031
Zhao Yanlin, Wang Kui, Budinoff C, et al. 2008. Gene transfer agent (GTA) genes reveal diverse and dynamic Roseobacter and Rhodobacter populations in the Chesapeake bay. The ISME Journal, 3(3): 364–373, doi: 10.1038/ismej.2008.115
Appendix
Less
Year 2019 volume 38 Issue 8
PDF
32
17
Cite this Article
BibTeX
Article Info
doi: 10.1007/s13131-019-1393-7
  • Receive Date：2018-02-23
  • Online Date：2026-04-01
  • Published：2019-08-25
Article Data
Affiliations
History
  • Received：2018-02-23
  • Accepted：2018-09-29
Funding
The National Natural Science Foundation of China under contract No. 41476171; the Chinese Polar Environment Comprehensive Investigation and Assessment Program under contract No. CHINARE04-01.
Affiliations
    1 Key Laboratory for Polar Science of State Oceanic Administration, Polar Research Institute of China, Shanghai 200136, China

Corresponding:

References
Share
https://castjournals.cast.org.cn/joweb/aos/EN/10.1007/s13131-019-1393-7
Share to
QR

Scan QR to access full text

Cite this article
BibTeX
Citations
表12种不同金属材料的力学参数
科
Family		 属数
Number of
genus		 种数
Number of
species		 占总种数比例
Percentage of
total species (%)		 属
Genus		 种数
Number of
species		 占总种数比例
Percentage of total
species (%)
鹅膏菌科Amanitaceae 2 11 5.26 鹅膏菌属 Amanita 10 4.78
小菇科 Mycenaceae 2 12 5.74 丝盖伞属 Inocybe 5 2.39
多孔菌科 Polyporaceae 8 14 6.70 蜡蘑属 Laccaria 5 2.39
红菇科 Russulaceae 3 23 11.00 小皮伞属 Marasmius 6 2.87
小菇属 Mycena 11 5.26
光柄菇属 Pluteus 5 2.39
红菇属 Russula 17 8.13
栓菌属 Trametes 5 2.39
关闭全屏
  • BibTeX
  • EndNote
  • RefWorks
  • TxT
Links
Articles
Latest Articles
Most Read
Collections
Updates
Events
News
Multimedia
About
About Us
Contact
No. 86 Xueyuan South Road, Haidian District, Beijing
100081
010-62199257
qkjq@cast.org.cn

Copyright © 2025 China Association for Science and Technology. All rights reserved. For all open access content, the relevant licensing terms apply.
Sponsored by the Office of the Leading Group for Cybersecurity and Informatization of CAST, and supported by Science and Technology Review Publishing House