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Community structures of actively growing bacteria shift along a north-south transect in the western North Pacific.

Taniguchi A, Hamasaki K - Environ. Microbiol. (2007)

Bottom Line: Change of BrdU-incorporated community structures reflected the change of water masses along a north-south transect from subarctic to subtropical gyres in the North Pacific.Our result revealed phylogenetic affiliation of AGB and their dynamic change along with north-south environmental gradients in open oceans.Different species of AGB utilize different amount and kinds of substrates, which can affect the change of organic matter fluxes along transect.

View Article: PubMed Central - PubMed

Affiliation: Graduate School of Biosphere Science, Hiroshima University, 1-4-4 Kagamiyama, Higashi-Hiroshima, Hiroshima, Japan. htrakito@hiroshima-u.ac.jp

ABSTRACT
Bacterial community structures and their activities in the ocean are tightly coupled with organic matter fluxes and thus control ocean biogeochemical cycles. Bromodeoxyuridine (BrdU), halogenated nucleoside and thymidine analogue, has been recently used to monitor actively growing bacteria (AGB) in natural environments. We labelled DNA of proliferating cells in seawater bacterial assemblages with BrdU and determined community structures of the bacteria that were possible key species in mediating biochemical reactions in the ocean. Surface seawater samples were collected along a north-south transect in the North Pacific in October 2003 and subjected to BrdU magnetic beads immunocapture and PCR-DGGE (BUMP-DGGE) analysis. Change of BrdU-incorporated community structures reflected the change of water masses along a north-south transect from subarctic to subtropical gyres in the North Pacific. We identified 25 bands referred to AGB as BrdU-incorporated phylotypes, belonging to Alphaproteobacteria (5 bands), Betaproteobacteria (1 band), Gammaproteobacteria (4 bands), Cytophaga-Flavobacterium-Bacteroides (CFB) group bacteria (5 bands), Gram-positive bacteria (6 bands), and Cyanobacteria (4 bands). BrdU-incorporated phylotypes belonging to Vibrionales, Alteromonadales and Gram-positive bacteria appeared only at sampling stations in a subtropical gyre, while those belonging to Roseobacter-related bacteria and CFB group bacteria appeared at the stations in both subarctic and subtropical gyres. Our result revealed phylogenetic affiliation of AGB and their dynamic change along with north-south environmental gradients in open oceans. Different species of AGB utilize different amount and kinds of substrates, which can affect the change of organic matter fluxes along transect.

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A neighbour-joining tree of 16S rRNA gene sequences of actively growing bacteria from members of the Alphaproteobacteria, Betaproteobacteria and Gammaproteobacteria retrieved from the coastal (Inland Sea of Japan; Hamasaki et al., 2007) and the oceanic (western North Pacific) sites. The band names of green and blue letters represent phylotypes retrieved from coastal and oceanic environments respectively. Bootstrap values > 50% are indicated. The scale bar represents 2% estimated sequence divergence.
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fig03: A neighbour-joining tree of 16S rRNA gene sequences of actively growing bacteria from members of the Alphaproteobacteria, Betaproteobacteria and Gammaproteobacteria retrieved from the coastal (Inland Sea of Japan; Hamasaki et al., 2007) and the oceanic (western North Pacific) sites. The band names of green and blue letters represent phylotypes retrieved from coastal and oceanic environments respectively. Bootstrap values > 50% are indicated. The scale bar represents 2% estimated sequence divergence.

Mentions: We sequenced partial 16S rRNA genes of 32 bands excised from both total and BrdU-incorporated communities (Fig. 1). The migration position of DGGE bands were compared among all sampling stations and the presence and absence of these 32 phylotypes at each sampling station was determined (Table 2). Twenty-five out of 32 bands were referred to as BrdU-incorporated phylotypes, including five alphaproteobacteria, one betaproteobacterium, four gammaproteobacteria, five CFB group bacteria, six Gram-positive bacteria and four cyanobacteria. Four out of five alphaproteobacteria belonged to Rhodobacterales. One betaproteobacterium belonged to Burkholderiales. Although the closest match of relative of this betaproteobacterium was an uncultured ‘Pseudomonas sp.’ clone in the database, this should be miss identification of the registered clone, and it phylogenetically belonged to Betaproteobacteria (Fig. 3). One out of four gammaproteobacteria belonged to Vibrionales and others belonged to Alteromonadales. As for Gram-positive bacteria, four were high-GC group (three actinobacteria and one unidentified bacterium) and two were low-GC group (Lactobacillales bacteria). Also, we found that two phylotypes closely related to Prochlorococcus and other two phylotypes closely related to Synechococcus. There were five phylotypes (KH03–30B and KH03–7B of alphaproteobacteria, KH03–11B of betaproteobacteria, KH03–42B and KH03–24B of CFB group bacteria) widely distributed from north to south as BrdU-incorporated bacteria. Most of gammaproteobacteria, all Gram-positive bacteria, two alphaproteobacteria and Prochlorococcus were found only at southern and transitional stations. In contrast, five phylotypes (KH03–9B of alphaproteobacteria, KH03–13B, KH03–32B and KH03–38B of CFB group bacteria and KH03-77 of Synechococcus) were found only at northern and transitional stations.


Community structures of actively growing bacteria shift along a north-south transect in the western North Pacific.

Taniguchi A, Hamasaki K - Environ. Microbiol. (2007)

A neighbour-joining tree of 16S rRNA gene sequences of actively growing bacteria from members of the Alphaproteobacteria, Betaproteobacteria and Gammaproteobacteria retrieved from the coastal (Inland Sea of Japan; Hamasaki et al., 2007) and the oceanic (western North Pacific) sites. The band names of green and blue letters represent phylotypes retrieved from coastal and oceanic environments respectively. Bootstrap values > 50% are indicated. The scale bar represents 2% estimated sequence divergence.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2327212&req=5

fig03: A neighbour-joining tree of 16S rRNA gene sequences of actively growing bacteria from members of the Alphaproteobacteria, Betaproteobacteria and Gammaproteobacteria retrieved from the coastal (Inland Sea of Japan; Hamasaki et al., 2007) and the oceanic (western North Pacific) sites. The band names of green and blue letters represent phylotypes retrieved from coastal and oceanic environments respectively. Bootstrap values > 50% are indicated. The scale bar represents 2% estimated sequence divergence.
Mentions: We sequenced partial 16S rRNA genes of 32 bands excised from both total and BrdU-incorporated communities (Fig. 1). The migration position of DGGE bands were compared among all sampling stations and the presence and absence of these 32 phylotypes at each sampling station was determined (Table 2). Twenty-five out of 32 bands were referred to as BrdU-incorporated phylotypes, including five alphaproteobacteria, one betaproteobacterium, four gammaproteobacteria, five CFB group bacteria, six Gram-positive bacteria and four cyanobacteria. Four out of five alphaproteobacteria belonged to Rhodobacterales. One betaproteobacterium belonged to Burkholderiales. Although the closest match of relative of this betaproteobacterium was an uncultured ‘Pseudomonas sp.’ clone in the database, this should be miss identification of the registered clone, and it phylogenetically belonged to Betaproteobacteria (Fig. 3). One out of four gammaproteobacteria belonged to Vibrionales and others belonged to Alteromonadales. As for Gram-positive bacteria, four were high-GC group (three actinobacteria and one unidentified bacterium) and two were low-GC group (Lactobacillales bacteria). Also, we found that two phylotypes closely related to Prochlorococcus and other two phylotypes closely related to Synechococcus. There were five phylotypes (KH03–30B and KH03–7B of alphaproteobacteria, KH03–11B of betaproteobacteria, KH03–42B and KH03–24B of CFB group bacteria) widely distributed from north to south as BrdU-incorporated bacteria. Most of gammaproteobacteria, all Gram-positive bacteria, two alphaproteobacteria and Prochlorococcus were found only at southern and transitional stations. In contrast, five phylotypes (KH03–9B of alphaproteobacteria, KH03–13B, KH03–32B and KH03–38B of CFB group bacteria and KH03-77 of Synechococcus) were found only at northern and transitional stations.

Bottom Line: Change of BrdU-incorporated community structures reflected the change of water masses along a north-south transect from subarctic to subtropical gyres in the North Pacific.Our result revealed phylogenetic affiliation of AGB and their dynamic change along with north-south environmental gradients in open oceans.Different species of AGB utilize different amount and kinds of substrates, which can affect the change of organic matter fluxes along transect.

View Article: PubMed Central - PubMed

Affiliation: Graduate School of Biosphere Science, Hiroshima University, 1-4-4 Kagamiyama, Higashi-Hiroshima, Hiroshima, Japan. htrakito@hiroshima-u.ac.jp

ABSTRACT
Bacterial community structures and their activities in the ocean are tightly coupled with organic matter fluxes and thus control ocean biogeochemical cycles. Bromodeoxyuridine (BrdU), halogenated nucleoside and thymidine analogue, has been recently used to monitor actively growing bacteria (AGB) in natural environments. We labelled DNA of proliferating cells in seawater bacterial assemblages with BrdU and determined community structures of the bacteria that were possible key species in mediating biochemical reactions in the ocean. Surface seawater samples were collected along a north-south transect in the North Pacific in October 2003 and subjected to BrdU magnetic beads immunocapture and PCR-DGGE (BUMP-DGGE) analysis. Change of BrdU-incorporated community structures reflected the change of water masses along a north-south transect from subarctic to subtropical gyres in the North Pacific. We identified 25 bands referred to AGB as BrdU-incorporated phylotypes, belonging to Alphaproteobacteria (5 bands), Betaproteobacteria (1 band), Gammaproteobacteria (4 bands), Cytophaga-Flavobacterium-Bacteroides (CFB) group bacteria (5 bands), Gram-positive bacteria (6 bands), and Cyanobacteria (4 bands). BrdU-incorporated phylotypes belonging to Vibrionales, Alteromonadales and Gram-positive bacteria appeared only at sampling stations in a subtropical gyre, while those belonging to Roseobacter-related bacteria and CFB group bacteria appeared at the stations in both subarctic and subtropical gyres. Our result revealed phylogenetic affiliation of AGB and their dynamic change along with north-south environmental gradients in open oceans. Different species of AGB utilize different amount and kinds of substrates, which can affect the change of organic matter fluxes along transect.

Show MeSH
Related in: MedlinePlus