Differences in peptide decomposition rates and pathways between hypoxic and oxic coastal environments

Liu, Zhanfei; Liu, Shuting; Liu, Jiqing; Gardner, Wayne S.

doi:10.1016/j.marchem.2013.08.003

Cited by 38 publications

(100 citation statements)

References 49 publications

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“…The unique development of certain alphaproteobacterial and gammaproteobacterial genera may also explain the much lower production of AVFA fragments during the bottom water incubation compared to the surface water incubation ( Figures 2B,D ). Either these bacteria directly took up the peptide, or the hydrolysis and subsequent uptake of the fragments were tightly coupled (Fuhrman, 1987; Kuznetsova and Lee, 2002; Liu et al, 2013). These two processes cannot be differentiated with these data, but regardless, both pathways differ from that of the surface incubation, where hydrolysis and uptake seem uncoupled.…”

Section: Discussionmentioning

confidence: 99%

Different Bacterial Communities Involved in Peptide Decomposition between Normoxic and Hypoxic Coastal Waters

2017

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Proteins and peptides are key components of the labile dissolved organic matter pool in marine environments. Knowing which types of bacteria metabolize peptides can inform the factors that govern peptide decomposition and further carbon and nitrogen remineralization in marine environments. A 13C-labeled tetrapeptide, alanine-valine-phenylalanine-alanine (AVFA), was added to both surface (normoxic) and bottom (hypoxic) seawater from a coastal station in the northern Gulf of Mexico for a 2-day incubation experiment, and bacteria that incorporated the peptide were identified using DNA stable isotope probing (SIP). The decomposition rate of AVFA in the bottom hypoxic seawater (0.018–0.035 μM h-1) was twice as fast as that in the surface normoxic seawater (0.011–0.017 μM h-1). SIP experiments indicated that incorporation of 13C was highest among the Flavobacteria, Sphingobacteria, Alphaproteobacteria, Acidimicrobiia, Verrucomicrobiae, Cyanobacteria, and Actinobacteria in surface waters. In contrast, highest 13C-enrichment was mainly observed in several Alphaproteobacteria (Thalassococcus, Rhodobacteraceae, Ruegeria) and Gammaproteobacteria genera (Colwellia, Balneatrix, Thalassomonas) in the bottom water. These data suggest that a more diverse group of both oligotrophic and copiotrophic bacteria may be involved in metabolizing labile organic matter such as peptides in normoxic coastal waters, and several copiotrophic genera belonging to Alphaproteobacteria and Gammaproteobacteria and known to be widely distributed may contribute to faster peptide decomposition in the hypoxic waters.

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Section: Discussionmentioning

confidence: 99%

Different Bacterial Communities Involved in Peptide Decomposition between Normoxic and Hypoxic Coastal Waters

2017

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“…The total bacterial cells of preserved samples were counted using an Accuri C6 Flow Cytometer (FCM) system with a laser emitting at 480 mm using the SYBR ® Green I nucleic acid stain technique as previously described (Liu et al, 2013). Briefly, samples were stained and detected from their signatures in a plot of 90° side light scatter (SSC-H) vs. green fluorescence (FL1-H).…”

Section: Methodsmentioning

confidence: 99%

Potential Environmental Factors Affecting Oil-Degrading Bacterial Populations in Deep and Surface Waters of the Northern Gulf of Mexico

2017

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Understanding bacterial community dynamics as a result of an oil spill is important for predicting the fate of oil released to the environment and developing bioremediation strategies in the Gulf of Mexico. In this study, we aimed to elucidate the roles of temperature, water chemistry (nutrients), and initial bacterial community in selecting oil degraders through a series of incubation experiments. Surface (2 m) and bottom (1537 m) waters, collected near the Deepwater Horizon site, were amended with 200 ppm light Louisiana sweet crude oil and bacterial inoculums from surface or bottom water, and incubated at 4 or 24°C for 50 days. Bacterial community and residual oil were analyzed by pyrosequencing and gas chromatography-mass spectrometry (GC-MS), respectively. The results showed that temperature played a key role in selecting oil-degrading bacteria. Incubation at 4°C favored the development of Cycloclasticus, Pseudoalteromonas, Sulfitobacter, and Reinekea, while 24°C incubations enhanced Oleibacter, Thalassobius, Phaeobacter, and Roseobacter. Water chemistry and the initial community also had potential roles in the development of hydrocarbon-degrading bacterial communities. Pseudoalteromonas, Oleibacter, and Winogradskyella developed well in the nutrient-enriched bottom water, while Reinekea and Thalassobius were favored by low-nutrient surface water. We revealed that the combination of 4°C, crude oil and bottom inoculum was a key factor for the growth of Cycloclasticus, while the combination of surface inoculum and bottom water chemistry was important for the growth of Pseudoalteromonas. Moreover, regardless of the source of inoculum, bottom water at 24°C was a favorable condition for Oleibacter. Redundancy analysis further showed that temperature and initial community explained 57 and 19% of the variation observed, while oil and water chemistry contributed 14 and 10%, respectively. Overall, this study revealed the relative roles of temperature, water chemistry, and initial bacterial community in selecting oil degraders and regulating their evolution in the northern Gulf of Mexico.

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“…Studies linking some microbial groups to LMW-DON (Alderkamp et al, 2006;Nikrad et al, 2012;Liu et al, 2013) and HMW-DON (Nagata et al, 1998;Cottrell and Kirchman, 2000) uptake have demonstrated important spatiotemporal variability in DON utilization, but have been limited in their ability to understand the full diversity of bacteria and archaea involved in DON cycling by the need for a priori selection of target groups. Nevertheless, a relatively large number of bacterial taxa in the ocean have been implicated in HWM-DOM turnover, either through experimental additions or following phytoplankton blooms, and some overlap should be expected between these taxa and those involved in HWM-DON cycling.…”

Section: Introductionmentioning

confidence: 99%

Diverse, uncultivated bacteria and archaea underlying the cycling of dissolved protein in the ocean

et al. 2016

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Dissolved organic nitrogen (DON) supports a significant amount of heterotrophic production in the ocean. Yet, to date, the identity and diversity of microbial groups that transform DON are not well understood. To better understand the organisms responsible for transforming high molecular weight (HMW)-DON in the upper ocean, isotopically labeled protein extract from Micromonas pusilla, a eukaryotic member of the resident phytoplankton community, was added as substrate to euphotic zone water from the central California Current system. Carbon and nitrogen remineralization rates from the added proteins ranged from 0.002 to 0.35 μmol C l − 1 per day and 0.03 to 0.27 nmol N l − 1 per day. DNA stable-isotope probing (DNA-SIP) coupled with high-throughput sequencing of 16S rRNA genes linked the activity of 77 uncultivated freeliving and particle-associated bacterial and archaeal taxa to the utilization of Micromonas protein extract. The high-throughput DNA-SIP method was sensitive in detecting isotopic assimilation by individual operational taxonomic units (OTUs), as substrate assimilation was observed after only 24 h. Many uncultivated free-living microbial taxa are newly implicated in the cycling of dissolved proteins affiliated with the Verrucomicrobia, Planctomycetes, Actinobacteria and Marine Group II (MGII) Euryarchaeota. In addition, a particle-associated community actively cycling DON was discovered, dominated by uncultivated organisms affiliated with MGII, Flavobacteria, Planctomycetes, Verrucomicrobia and Bdellovibrionaceae. The number of taxa assimilating protein correlated with genomic representation of TonB-dependent receptor (TBDR)-encoding genes, suggesting a possible role of TBDR in utilization of dissolved proteins by marine microbes. Our results significantly expand the known microbial diversity mediating the cycling of dissolved proteins in the ocean.

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Differences in peptide decomposition rates and pathways between hypoxic and oxic coastal environments

Cited by 38 publications

References 49 publications

Different Bacterial Communities Involved in Peptide Decomposition between Normoxic and Hypoxic Coastal Waters

Different Bacterial Communities Involved in Peptide Decomposition between Normoxic and Hypoxic Coastal Waters

Potential Environmental Factors Affecting Oil-Degrading Bacterial Populations in Deep and Surface Waters of the Northern Gulf of Mexico

Diverse, uncultivated bacteria and archaea underlying the cycling of dissolved protein in the ocean

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