Differentiating the role of different-sized microorganisms in peptide decomposition during incubations using size-fractioned coastal seawater

Abstract

Peptide decomposition by different-sized microorganisms was compared by incubating tetrapeptide alanine-valine-phenylalanine-alanine (AVFA), a fragment of RuBisCO, in coastal seawater after size-fraction by filtration. The size-fractioned seawater included <0.8-µm filtered (free-living bacteria), <5-µm filtered (free-living bacteria + heterotrophic nanoflagellates), <20µm filtered (free-living and particle-attached bacteria + heterotrophic nanoflagellates + other small protists), and unfiltered whole water collected from Texas coast in the western Gulf of Mexico. Decomposition rates of AVFA in the <20-µm and unfiltered seawater were significantly higher than those in the <0.8-µm and <5-µm seawater in the December 2011 incubation. The higher decomposition rate in the large size fractions can be attributed to activities of particleattached bacteria and/or large-size microorganisms, such as osmotrophic protists. However, the role of particle-attached bacteria in explaining this decomposition difference might be limited, as bacterial abundance and community structure did not differ much among the 4 treatments. Consistently, the June 2013 incubation indicated that AVFA decomposed most rapidly in the unfiltered seawater with >20-μm microorganisms. This study provides insights into the relative role of different-sized microorganisms in regulating the recycling of labile organic matter in coastal waters.

Distinct capabilities of different Gammaproteobacterial strains on utilizing small peptides in seawater

“…As there is ecological difference among bacterial strains even within the same species 96 , we used four Gammaproteobacterial strains as models for their corresponding bacterial species to demonstrate their potential capability of peptide decomposition. The rapid responses of these bacterial strains (Pseudoalteromonas and Alteromonas) to peptides are consistent to field studies of peptide decomposition using natural bacterial assemblages containing these species 16,25,43 , indicating our chosen bacterial strains can represent in some degree their corresponding species in peptide decomposition. In contrast, while Marinobacterium and Amphritea showed rapid increase in natural assemblages when incubated with AVFA 16,45 , they did not grow as single strain incubations, indicating they were using byproducts from AVFA decomposition by other bacteria in natural assemblages.…”

“…The initial bacterial abundance was inoculated to be ca. 5 × 10 5 cells/mL that is close to the natural abundance in the ship channel 43 . To ensure no bacteria contamination was introduced from peptide amendment, AVFA stock solution was filtered twice through 0.2 μm sterile polyvinylidene difluoride (PVDF) filters (Whatman, dia.…”

“…Four Gammaproteobacterial strains were chosen for this study based on previous studies, including Pseudoalteromonas atlantica T2a (ATCC 43666), Alteromonas sp. B-207 (ATCC 33524), Marinobacterium jannaschii 207 (ATCC 27135), and Amphritea japonica JAMM 1866 (ATCC BAA-1530) 11,16,43 . Bacterial strain pellets were activated in 50 mL autoclaved Difco marine broth 2216 (BD) at 30 °C (for Pseudoalteromonas, Altermonas, Marinobacterium) in an incubator shaker with the speed of 120 rpm or at 20 °C (for Amphritea) for 24-45 h. Bacterial growth was checked occasionally during the activation.…”

“…AVFA is a fragment of ribulose-1,5-biphosphate carboxylase/oxygenase (RuBisCO) that is ubiquitously involved in photosynthesis, and has been applied in our previous peptide decomposition studies 16,25 . These four bacterial strains were chosen because their growth has been often observed in substrate addition incubations in coastal waters [41][42][43][44][45] 100 fold change of relative abundance from amplicon sequencing, Table 1). We aim to obtain direct correlations between individual bacterial strains and their peptide decomposition rates and pathways, which can offer key insights into peptide decomposition in natural seawater.…”

Characterization of particle-associated and free-living bacterial and archaeal communities along the water columns of the South China Sea

“…Although bacteria attaching to particles are of relatively lower abundance compared to free-living cells in the pelagic ocean, they are consistently metabolically more active with higher extracellular enzymatic activities (Karner and Herndl, 1992) and cell-specific thymidine incorporation rates (Turley and Mackie, 1994;Turly and Stutt, 2000). Therefore, PA bacteria often play a comparable role to free-living bacteria in hydrolysis or decomposition of marine organic matter, biomass production and carbon cycling (Griffith et al, 1994;Turly and Stutt, 2000;Liu et al, 2015). The decline of bacterial abundance and richness along the depth profile is largely owing to the gradual decreasing availability of usable organic carbon (Smith, 1992;Turly and Stutt, 2000;Jiao et al, 2014).…”