Yuya Tada

Differing Growth Responses of Major Phylogenetic Groups of Marine Bacteria to Natural Phytoplankton Blooms in the Western North Pacific Ocean

ABSTRACT Growth and productivity of phytoplankton substantially change organic matter characteristics, which affect bacterial abundance, productivity, and community structure in aquatic ecosystems. We analyzed bacterial community structures and measured activities inside and outside phytoplankton blooms in the western North Pacific Ocean by using bromodeoxyuridine immunocytochemistry and fluorescence in situ hybridization (BIC-FISH). Roseobacter/Rhodobacter, SAR11, Betaproteobacteria, Alteromonas, SAR86, and Bacteroidetes responded differently to changes in organic matter supply. Roseobacter/Rhodobacter bacteria remained widespread, active, and proliferating despite large fluctuations in organic matter and chlorophyll a (Chl-a) concentrations. The relative contribution of Bacteroidetes to total bacterial production was consistently high. Furthermore, we documented the unexpectedly large contribution of Alteromonas to total bacterial production in the bloom. Bacterial abundance, productivity, and growth potential (the proportion of growing cells in a population) were significantly correlated with Chl-a and particulate organic carbon concentrations. Canonical correspondence analysis showed that organic matter supply was critical for determining bacterial community structures. The growth potential of each bacterial group as a function of Chl-a concentration showed a bell-shaped distribution, indicating an optimal organic matter concentration to promote growth. The growth of Alteromonas and Betaproteobacteria was especially strongly correlated with organic matter supply. These data elucidate the distinctive ecological role of major bacterial taxa in organic matter cycling during open ocean phytoplankton blooms.

Actively Growing Bacteria in the Inland Sea of Japan, Identified by Combined Bromodeoxyuridine Immunocapture and Denaturing Gradient Gel Electrophoresis

ABSTRACT A fundamental question in microbial oceanography concerns the relationship between prokaryote diversity and biogeochemical function in an ecosystem context. We combined bromodeoxyuridine (BrdU) magnetic bead immunocapture and PCR-denaturing gradient gel electrophoresis (BUMP-DGGE) to examine phylotype-specific growth in natural marine assemblages. We also examined a broad range of marine bacterial isolates to determine their abilities to incorporate BrdU in order to test the validity of the method for application to diverse marine assemblages. We found that 27 of 29 isolates belonging to different taxa could incorporate BrdU. BUMP-DGGE analysis revealed phylogenetic affiliations of DNA-synthesizing, presumably actively growing bacteria across a eutrophic to mesotrophic transect in the Inland Sea of Japan. We found that the BrdU-incorporating (growing) communities were substantially different from the total communities. The majority (34/56) of phylotypes incorporated BrdU and were presumably growing, and these phylotypes comprised 10 alphaproteobacteria, 1 betaproteobacterium, 11 gammaproteobacteria, 11 Cytophaga-Flavobacterium-Bacteroides group bacteria, and 1 unclassified bacterium. All BrdU-responsive alphaproteobacteria were members of the Rhodobacterales, suggesting that such bacteria were dominant in the growing alphaproteobacterial populations in our samples. The BrdU-responsive gammaproteobacteria belonged to the Oceanospirillales, the SAR86 cluster, the Pseudomonadales, the Alteromonadales, and the Vibrionales. Thus, contemporaneous cooccurrence of diverse actively growing bacterial taxa was a consistent pattern in our biogeochemically varied study area.

Bacterial contribution to dissolved organic matter in eutrophic Lake Kasumigaura, Japan

ABSTRACT Incubation experiments using filtered waters from Lake Kasumigaura were conducted to examine bacterial contribution to a dissolved organic carbon (DOC) pool. Bacterial abundance, bacterial production, concentrations of DOC, total dissolved amino acids (TDAA), and total dissolved neutral sugars (TDNS) were monitored during the experiments. Bacterial production during the first few days was very high (20 to 35 μg C liter−1 day−1), accounting for 40 to 70% of primary production. The total bacterial production accounted for 34 to 55% of the DOC loss during the experiment, indicating high bacterial activities in Lake Kasumigaura. The DOC degradation was only 12 to 15%, whereas the degradation of TDAA and TDNS ranged from 30 to 50%, suggesting the preferential usage of TDAA and TDNS. The contribution of bacterially derived carbon to a DOC pool in Lake Kasumigaura was estimated using d-amino acids as bacterial biomarkers and accounted for 30 to 50% of the lake DOC. These values were much higher than those estimated for the open ocean (20 to 30%). The ratio of bacterially derived carbon to bulk carbon increased slightly with time, suggesting that the bacterially derived carbon is more resistant to microbial degradation than bulk carbon. This is the first study to estimate the bacterial contribution to a DOC pool in freshwater environments. These results indicate that bacteria play even more important roles in carbon cycles in freshwater environments than in open oceans and also suggests that recent increases in recalcitrant DOC in various lakes could be attributed to bacterially derived carbon. The potential differences in bacterial contributions to dissolved organic matter (DOM) between freshwater and marine environments are discussed.

Growth and distribution patterns of Roseobacter/Rhodobacter, SAR11, and Bacteroidetes lineages in the Southern Ocean

Roseobacter/Rhodobacter and SAR11, affiliated with Alphaproteobacteria, and the phylum Bacteroidetes constitute a large proportion of marine planktonic bacteria, but information about their growth and distribution patterns in the Southern Ocean is scarce. The aim of the present study is to determine patterns in the biomass and productivity of Roseobacter/Rhodobacter, SAR11, and Bacteroidetes groups along the steep temperature, salinity, and organic matter gradients in the Southern Ocean by using catalyzed reporter deposition-fluorescence in situ hybridization and bromodeoxyuridine (BrdU) immunocytochemistry FISH. We found that Roseobacter/Rhodobacter, SAR11, and Bacteroidetes are prominent contributors to total bacterial biomass and production. SAR11 bacteria were the predominant lineage, but their biomass was low in the coldest regions. In contrast, the biomasses of Roseobacter/Rhodobacter and Bacteroidetes lineages were positively correlated with organic matter concentrations. The Roseobacter/Rhodobacter had the highest proportion of BrdU-positive (i.e., actively growing) cells among the three phylotypes at all stations, despite their low abundance. The relative contribution of Bacteroidetes to the total bacterial productivity (number of active cells) was negatively correlated with temperature. These results suggest that the growth and distribution patterns of Roseobacter/Rhodobacter, SAR11, and Bacteroidetes were determined by different environmental gradients (e.g., organic matter concentrations or temperature) in the Southern Ocean.

Production and Reutilization of Fluorescent Dissolved Organic Matter by a Marine Bacterial Strain, Alteromonas macleodii

The recalcitrant fraction of marine dissolved organic matter (DOM) plays an important role in carbon storage on the earth’s surface. Bacterial production of recalcitrant DOM (RDOM) has been proposed as a carbon sequestration process. It is still unclear whether bacterial physiology can affect RDOM production. In this study, we conducted a batch culture using the marine bacterial isolate Alteromonas macleodii, a ubiquitous gammaproteobacterium, to evaluate the linkage between bacterial growth and DOM production. Glucose (1 mmol C L-1) was used as the sole carbon source, and the bacterial number, the DOM concentration in terms of carbon, and the excitation–emission matrices (EEMs) of DOM were monitored during the 168-h incubation. The incubation period was partitioned into the exponential growth (0–24 h) and stationary phases (24–168 h) based on the growth curve. Although the DOM concentration decreased during the exponential growth phase due to glucose consumption, it remained stable during the stationary phase, corresponding to approximately 4% of the initial glucose in terms of carbon. Distinct fluorophores were not evident in the EEMs at the beginning of the incubation, but DOM produced by the strain exhibited five fluorescent peaks during exponential growth. Two fluorescent peaks were similar to protein-like fluorophores, while the others could be categorized as humic-like fluorophores. All fluorophores increased during the exponential growth phase. The tryptophan-like fluorophore decreased during the stationary phase, suggesting that the strain reused the large exopolymer. The tyrosine-like fluorophore seemed to be stable during the stationary phase, implying that the production of tyrosine-containing small peptides through the degradation of exopolymers was correlated with the reutilization of the tyrosine-like fluorophore. Two humic-like fluorophores that showed emission maxima at the longer wavelength (525 nm) increased during the stationary phase, while the other humic-like fluorophore, which had a shorter emission wavelength (400 nm) and was categorized as recalcitrant, was stable. These humic-like fluorophore behaviors during incubation indicated that the composition of bacterial humic-like fluorophores, which were unavailable to the strain, differed between growth phases. Our results suggest that bacterial physiology can affect RDOM production and accumulation in the ocean interior.

Changes in the community structure of free-living heterotrophic bacteria in the open tropical Pacific Ocean in response to microalgal lysate-derived dissolved organic matter

Dissolved organic matter derived from phytoplankton (DOMP) can affect the bacterial biomass and community structure in aquatic ecosystems. Here, we examined the community response of free-living heterotrophic bacteria, with respect to cellular nucleic acid levels, to the DOMP lysates derived from three phytoplankton strains in the open tropical Pacific. The free amino acid (FAA) composition of each DOMP lysate differed among the microalgal strains. Terminal restriction fragment-length polymorphism analyses with 16S rRNA genes revealed that the community shifts of high nucleic acid (HNA) and low nucleic acid (LNA) bacteria varied significantly with the different DOMP lysate treatments. Furthermore, the FAA composition in DOMP lysates significantly affected the bacterial community shifts in HNA and LNA. Similarity percentage analysis using 16S rRNA gene deep-sequencing revealed that the DOMP lysates from the pelagophyte Pelagomonas calceolata caused relatively large community shifts with Alcaligenes predominating in the HNA fraction. In contrast, the DOMP lysate from the diatom Thalassiosira oceanica induced a community shift in the LNA fraction with a predominance of uncultured Actinobacteria Thus, the data indicate that the DOMP lysates from different microalgae constitute a primary factor altering the dominant bacterial groups in the open ocean.