Nutrient pollution in the coastal environment has been accelerated by progressively intensifying ... more Nutrient pollution in the coastal environment has been accelerated by progressively intensifying aquaculture activities. Excessive nutrients can lead to coastal eutrophication with serious economic and ecological consequences. In this study, we studied coastal planktonic microbial community over a year to understand the aquaculture impact on coastal water quality and function. We observed increased total inorganic nitrogen concentrations in active fish farms to favor the diverse Alpha- and Gammaproteobacteria. Bacterial community alpha diversity in fish farms was positively correlated with total inorganic nitrogen, and active fish farming co-influenced the bacterial structural composition and regional beta diversity. By analyzing the nitrogen cycle-related functional compositions and pathways using PICRUSt2 prediction on inferred genomes, we identified the contribution of over 600 bacterial species to four major pathways. Enhanced nitrogen load in active fish farms was positively co...
The twilight zone is an important depth of the ocean where particulate organic matter (POM) remin... more The twilight zone is an important depth of the ocean where particulate organic matter (POM) remineralization takes place, and prokaryotes contribute to more than 70% of the estimated remineralization. However, little is known about the microbial community and metabolic activity associated with different particles in the twilight zone. The composition and distribution of particle-attached prokaryotes in the twilight zone of the South China Sea (SCS) were investigated using high-throughput sequencing and quantitative PCR, together with the Biolog Ecoplate™ microplates culture to analyze the microbial metabolic activity. We found that α- and γ-Proteobacteria dominating at the lower and upper boundary of the twilight zone, respectively; Methanosarcinales and Halobacteriales of the Euyarchaeota occupied in the larger particles at the upper boundary. Similar microbial community existed between euphotic layer and the upper boundary. Higher amount of shared Operational Taxonomic Units (OTUs...
Euglena gracilis is one of the few permitted edible microalgae. Considering consumer acceptance, ... more Euglena gracilis is one of the few permitted edible microalgae. Considering consumer acceptance, E. gracilis grown heterotrophically with yellow appearances have wider food industrial applications such as producing meat analogs than green cells. However, there is much room to improve the protein content of heterotrophic culture cells. In this study, the effects of nitrogen sources, temperature, initial pH, and C/N ratios on the protein production of E. gracilis were evaluated under heterotrophic cultivation. These results indicated that ammonium sulfate was the optimal nitrogen source for protein production. The protein content of E. gracilis cultured by ammonium sulfate increased by 113% and 44.7% compared with that cultured by yeast extract and monosodium glutamate, respectively. The manipulation of the low C/N ratio further improved E. gracilis protein content to 66.10% (w/w), which was 1.6-fold of that in the C/N = 25 group. Additionally, amino acid analysis revealed that the ni...
Synechococcusis a major contributor to global marine primary production. Here, its spatio-tempora... more Synechococcusis a major contributor to global marine primary production. Here, its spatio-temporal variations in abundance and phylogenetic structure were studied at three stations of the South China Sea at both DNA and cDNA levels.Synechococcuscell abundance was lowest in March, but highest in October at two coastal stations. Its abundance was higher at the estuarine station, which reached a peak value of 1.36 × 105cells/ml in April, owing to the nitrogen nutrients discharged from the Sanya River. Gene and gene transcript abundances of fourSynechococcuslineages, clades II, III, VIII, and S5.3, were studied by quantitative PCR, which showed that clade II was the most abundant lineage at both DNA and cDNA levels. High-throughput sequencing revealed that, at the DNA level,Synechococcusassemblage was dominated by clade SY4 (a novel clade defined in this study), S5.2, and clade II in the coastal waters and was dominated by freshwater/S5.2Synechococcus, reaching a value up to 88.61% in J...
Marine picocyanobacteria Synechococcus exhibit highly diverse pigment types (PTs) and hence posse... more Marine picocyanobacteria Synechococcus exhibit highly diverse pigment types (PTs) and hence possess great advantage to utilize different spectrum of light effectively and to occupy a wide range of light niches. In this study, we explored the diversity of Synechococcus PTs in the eastern Indian Ocean (EIO), surface water of Strait of Malacca (SSM), and coastal waters of Sri Lanka (SSL). All the detected PTs were phycourobilin (PUB) containing PT 3 and showed distinct distribution patterns. Low PUB PT 3a and partial chromatic acclimater PT 3eA dominated in coastal and shallow waters (SSM and SSL). In contrast, high PUB and chromatic acclimaters PT 3dA and PT 3c/3dB were mainly distributed in open ocean (EIO). PT 3dA and PT 3c/3dB occurred at similar depths of the lower euphotic layers but showed distinct distribution pattern that are partially exclusive, indicating that they compete with each other for the same light niche. Interestingly, the newly described PT 3f was detected with hi...
Mixotrophs are widely distributed in aquatic ecosystems and play critical roles in the planktonic... more Mixotrophs are widely distributed in aquatic ecosystems and play critical roles in the planktonic food web. However, how mixotrophs respond to projected ocean warming remains a debatable topic. To close the knowledge gap, we investigated the thermal responses of growth rate and functional traits of a mixotrophic dinoflagellate (Lepidodinium sp.) isolated from subtropical coastal waters. We found that Lepidodinium sp. is a facultative mixotroph with an obligate phototrophic lifestyle that adjusts its phagocytotic feeding according to inorganic nutrient concentrations. The thermal sensitivity in terms of activation energy (Ea, eV) of Lepidodinium sp. grown in mixotrophic mode (with sufficient prey, 0.69-0.89 eV) was significantly higher than in autotrophic mode (without prey, 0.30-0.37 eV). This finding is consistent with the results of predominantly heterotrophic mixotrophs, providing experimental evidence for the hypothesis that mixotrophs shift towards more heterotrophy with rising...
Coastal upwelling causes variations in temperature, salinity and inorganic nutrients in the water... more Coastal upwelling causes variations in temperature, salinity and inorganic nutrients in the water column, consequently leading to the shift of microbial populations and their metabolic activities. Impacts of the eastern Hainan upwelling (EHU) on the ammonia-oxidizing archaea (AOA) were investigated based on the amoA gene using pyrosequencing and quantitative PCR at both DNA and cDNA levels, together with the determination of the ammonia oxidation (AO) rate measured with 15N-labelled ammonium. By comparing stations with and without upwelling influence, we found that coastal upwelling correlated with an increase in amoA gene abundance, the dominance of distinct clades for AOA communities at the respective gene and transcript levels, and a large increase in the proportion of the SCM1-like (Nitrosopumilus maritimus-like) cluster as well. The AO rates were generally higher in the deeper water (~25 m), which was in significant positive correlation with the proportion of cluster Water Colu...
Liu, H., Dagg, J. M., Napp, J. M., and Sato, R. 2008. Mesozooplankton grazing in the coastal Gulf... more Liu, H., Dagg, J. M., Napp, J. M., and Sato, R. 2008. Mesozooplankton grazing in the coastal Gulf of Alaska: Neocalanus spp. vs. other mesozooplankton. – ICES Journal of Marine Science, 65: 351–360. Three species of large calanoid copepod, Neocalanus flemingeri, Neocalanus plumchrus, and Neocalanus cristatus, dominate the spring biomass of mesozooplankton in the Subarctic Pacific. We compared the grazing impact of Neocalanus species on phytoplankton with grazing by the remainder of the mesozooplankton community in the coastal and shelf waters of the Gulf of Alaska during spring and summer 2003. Neocalanus spp. and other mesozooplankton fed mainly on particles >20 µm, and phytoplankton in the smaller size-fractions (<20 µm) increased in the presence of mesozooplankton, possibly because of a trophic cascade resulting from mesozooplankton consumption of microzooplankton. Neocalanus spp. accounted for most of the mesozooplankton biomass and herbivory in the shelf water of the Gulf...
Mangrove forests are widespread along the subtropical and tropical coasts. They provide a habitat... more Mangrove forests are widespread along the subtropical and tropical coasts. They provide a habitat for a wide variety of plants, animals and microorganisms, and act as a buffer zone between the ocean and land. Along with other coastal environments, mangrove ecosystems are under increasing pressure from human activities, such as excessive input of nutrients and toxic pollutants. Despite efforts to understand the diversity of microbes in mangrove sediments, their metabolic capability in pristine and contaminated mangrove sediments remains largely unknown. By using metagenomic approach, we investigated the metabolic capacity of microorganisms in contaminated (CMS) and pristine (PMS) mangrove sediments at subtropical and tropical coastal sites. When comparing the CMS with PMS, we found that the former had a reduced diazotroph abundance and nitrogen fixing capability, but an enhanced metabolism that is related to the generation of microbial greenhouse gases via increased methanogenesis an...
Accurate estimates of bacterial carbon metabolic rates are indispensable for understanding the re... more Accurate estimates of bacterial carbon metabolic rates are indispensable for understanding the regulation of carbon fluxes in aquatic environments. Here, changes in bacterial growth, production, and cell volume in both pre-filtered and unfiltered seawater during 24 h incubation were monitored. The methodological artifacts during Winkler bacterial respiration (BR) measurements in subtropical Hong Kong coastal waters were assessed. Bacterial abundance increased by 3- and 1.8-fold in the pre-filtered and unfiltered seawater after incubation, respectively. Bacterial production (BP) and cell volume also showed significant enhancement. Compared with the BR measurements obtained by the Winkler method, the instantaneous free-living BR measurements, after correction, decreased by ~ 70%. The time-integrated free-living BR and BP during 24 h incubation in the pre-filtered sample provided an improved estimate of bacterial growth efficiency, which increased by ~ 52% compared to the common estima...
Toxic differences between antibacterial silver (either ionic Ag+ and nanoparticle – AgNPs) were r... more Toxic differences between antibacterial silver (either ionic Ag+ and nanoparticle – AgNPs) were related to the microbial metabolism of enriched organic matter in the gut.
Mixotrophic protists are widely observed in the aquatic ecosystems, while how they respond to ino... more Mixotrophic protists are widely observed in the aquatic ecosystems, while how they respond to inorganic nutrient imbalance and ocean warming remains understudied. We conducted a series of experiments on a mixotrophic dinoflagellate Lepidodinium sp. isolated from subtropical coastal waters to investigate the combined effect of temperature and medium nitrate to phosphate ratio (N:P ratio) on the ingestion activities of mixotrophic protists. We found Lepidodinium sp. displayed selective feeding behaviour with a higher ingestion rate on high-N prey (N-rich Rhodomonas salina) when the ambient inorganic N:P ratio was equal to or below the Redfield ratio. The Chesson selectivity index α increased with increasing temperature, suggesting that warming exacerbated the selective feeding of Lepidodinium sp. Under inorganic nitrogen sufficient conditions (N:P ratio = 64), no selective feeding was observed at 25 and 28°C, while it occurs at 31°C, which also indicates that warming alters the feedin...
Phytoplankton are diverse and abundant as primary producers in the ocean, with diversity and comm... more Phytoplankton are diverse and abundant as primary producers in the ocean, with diversity and community compositions varying spatially. How fundamental processes (e.g., selection, dispersal, and drift) regulate their global biogeography remains to be comprehensively explored.
Understanding the strategies developed by different microbial groups to adapt to specific niches ... more Understanding the strategies developed by different microbial groups to adapt to specific niches is critical. Through genome and transcriptome analyses of two newly isolated novel euryhaline Synechococcus strains, this study revealed that cluster 5 phycoerythrobilin-containing Synechococcus, which are thought to be strictly marine strains, could be abundant in low-salinity waters of the Pearl River estuary (salinity <15 ppt) and explained the molecular mechanisms that enabled them to adapt the low and fluctuating salinity in the estuarine environment.
Nutrient pollution in the coastal environment has been accelerated by progressively intensifying ... more Nutrient pollution in the coastal environment has been accelerated by progressively intensifying aquaculture activities. Excessive nutrients can lead to coastal eutrophication with serious economic and ecological consequences. In this study, we studied coastal planktonic microbial community over a year to understand the aquaculture impact on coastal water quality and function. We observed increased total inorganic nitrogen concentrations in active fish farms to favor the diverse Alpha- and Gammaproteobacteria. Bacterial community alpha diversity in fish farms was positively correlated with total inorganic nitrogen, and active fish farming co-influenced the bacterial structural composition and regional beta diversity. By analyzing the nitrogen cycle-related functional compositions and pathways using PICRUSt2 prediction on inferred genomes, we identified the contribution of over 600 bacterial species to four major pathways. Enhanced nitrogen load in active fish farms was positively co...
The twilight zone is an important depth of the ocean where particulate organic matter (POM) remin... more The twilight zone is an important depth of the ocean where particulate organic matter (POM) remineralization takes place, and prokaryotes contribute to more than 70% of the estimated remineralization. However, little is known about the microbial community and metabolic activity associated with different particles in the twilight zone. The composition and distribution of particle-attached prokaryotes in the twilight zone of the South China Sea (SCS) were investigated using high-throughput sequencing and quantitative PCR, together with the Biolog Ecoplate™ microplates culture to analyze the microbial metabolic activity. We found that α- and γ-Proteobacteria dominating at the lower and upper boundary of the twilight zone, respectively; Methanosarcinales and Halobacteriales of the Euyarchaeota occupied in the larger particles at the upper boundary. Similar microbial community existed between euphotic layer and the upper boundary. Higher amount of shared Operational Taxonomic Units (OTUs...
Euglena gracilis is one of the few permitted edible microalgae. Considering consumer acceptance, ... more Euglena gracilis is one of the few permitted edible microalgae. Considering consumer acceptance, E. gracilis grown heterotrophically with yellow appearances have wider food industrial applications such as producing meat analogs than green cells. However, there is much room to improve the protein content of heterotrophic culture cells. In this study, the effects of nitrogen sources, temperature, initial pH, and C/N ratios on the protein production of E. gracilis were evaluated under heterotrophic cultivation. These results indicated that ammonium sulfate was the optimal nitrogen source for protein production. The protein content of E. gracilis cultured by ammonium sulfate increased by 113% and 44.7% compared with that cultured by yeast extract and monosodium glutamate, respectively. The manipulation of the low C/N ratio further improved E. gracilis protein content to 66.10% (w/w), which was 1.6-fold of that in the C/N = 25 group. Additionally, amino acid analysis revealed that the ni...
Synechococcusis a major contributor to global marine primary production. Here, its spatio-tempora... more Synechococcusis a major contributor to global marine primary production. Here, its spatio-temporal variations in abundance and phylogenetic structure were studied at three stations of the South China Sea at both DNA and cDNA levels.Synechococcuscell abundance was lowest in March, but highest in October at two coastal stations. Its abundance was higher at the estuarine station, which reached a peak value of 1.36 × 105cells/ml in April, owing to the nitrogen nutrients discharged from the Sanya River. Gene and gene transcript abundances of fourSynechococcuslineages, clades II, III, VIII, and S5.3, were studied by quantitative PCR, which showed that clade II was the most abundant lineage at both DNA and cDNA levels. High-throughput sequencing revealed that, at the DNA level,Synechococcusassemblage was dominated by clade SY4 (a novel clade defined in this study), S5.2, and clade II in the coastal waters and was dominated by freshwater/S5.2Synechococcus, reaching a value up to 88.61% in J...
Marine picocyanobacteria Synechococcus exhibit highly diverse pigment types (PTs) and hence posse... more Marine picocyanobacteria Synechococcus exhibit highly diverse pigment types (PTs) and hence possess great advantage to utilize different spectrum of light effectively and to occupy a wide range of light niches. In this study, we explored the diversity of Synechococcus PTs in the eastern Indian Ocean (EIO), surface water of Strait of Malacca (SSM), and coastal waters of Sri Lanka (SSL). All the detected PTs were phycourobilin (PUB) containing PT 3 and showed distinct distribution patterns. Low PUB PT 3a and partial chromatic acclimater PT 3eA dominated in coastal and shallow waters (SSM and SSL). In contrast, high PUB and chromatic acclimaters PT 3dA and PT 3c/3dB were mainly distributed in open ocean (EIO). PT 3dA and PT 3c/3dB occurred at similar depths of the lower euphotic layers but showed distinct distribution pattern that are partially exclusive, indicating that they compete with each other for the same light niche. Interestingly, the newly described PT 3f was detected with hi...
Mixotrophs are widely distributed in aquatic ecosystems and play critical roles in the planktonic... more Mixotrophs are widely distributed in aquatic ecosystems and play critical roles in the planktonic food web. However, how mixotrophs respond to projected ocean warming remains a debatable topic. To close the knowledge gap, we investigated the thermal responses of growth rate and functional traits of a mixotrophic dinoflagellate (Lepidodinium sp.) isolated from subtropical coastal waters. We found that Lepidodinium sp. is a facultative mixotroph with an obligate phototrophic lifestyle that adjusts its phagocytotic feeding according to inorganic nutrient concentrations. The thermal sensitivity in terms of activation energy (Ea, eV) of Lepidodinium sp. grown in mixotrophic mode (with sufficient prey, 0.69-0.89 eV) was significantly higher than in autotrophic mode (without prey, 0.30-0.37 eV). This finding is consistent with the results of predominantly heterotrophic mixotrophs, providing experimental evidence for the hypothesis that mixotrophs shift towards more heterotrophy with rising...
Coastal upwelling causes variations in temperature, salinity and inorganic nutrients in the water... more Coastal upwelling causes variations in temperature, salinity and inorganic nutrients in the water column, consequently leading to the shift of microbial populations and their metabolic activities. Impacts of the eastern Hainan upwelling (EHU) on the ammonia-oxidizing archaea (AOA) were investigated based on the amoA gene using pyrosequencing and quantitative PCR at both DNA and cDNA levels, together with the determination of the ammonia oxidation (AO) rate measured with 15N-labelled ammonium. By comparing stations with and without upwelling influence, we found that coastal upwelling correlated with an increase in amoA gene abundance, the dominance of distinct clades for AOA communities at the respective gene and transcript levels, and a large increase in the proportion of the SCM1-like (Nitrosopumilus maritimus-like) cluster as well. The AO rates were generally higher in the deeper water (~25 m), which was in significant positive correlation with the proportion of cluster Water Colu...
Liu, H., Dagg, J. M., Napp, J. M., and Sato, R. 2008. Mesozooplankton grazing in the coastal Gulf... more Liu, H., Dagg, J. M., Napp, J. M., and Sato, R. 2008. Mesozooplankton grazing in the coastal Gulf of Alaska: Neocalanus spp. vs. other mesozooplankton. – ICES Journal of Marine Science, 65: 351–360. Three species of large calanoid copepod, Neocalanus flemingeri, Neocalanus plumchrus, and Neocalanus cristatus, dominate the spring biomass of mesozooplankton in the Subarctic Pacific. We compared the grazing impact of Neocalanus species on phytoplankton with grazing by the remainder of the mesozooplankton community in the coastal and shelf waters of the Gulf of Alaska during spring and summer 2003. Neocalanus spp. and other mesozooplankton fed mainly on particles >20 µm, and phytoplankton in the smaller size-fractions (<20 µm) increased in the presence of mesozooplankton, possibly because of a trophic cascade resulting from mesozooplankton consumption of microzooplankton. Neocalanus spp. accounted for most of the mesozooplankton biomass and herbivory in the shelf water of the Gulf...
Mangrove forests are widespread along the subtropical and tropical coasts. They provide a habitat... more Mangrove forests are widespread along the subtropical and tropical coasts. They provide a habitat for a wide variety of plants, animals and microorganisms, and act as a buffer zone between the ocean and land. Along with other coastal environments, mangrove ecosystems are under increasing pressure from human activities, such as excessive input of nutrients and toxic pollutants. Despite efforts to understand the diversity of microbes in mangrove sediments, their metabolic capability in pristine and contaminated mangrove sediments remains largely unknown. By using metagenomic approach, we investigated the metabolic capacity of microorganisms in contaminated (CMS) and pristine (PMS) mangrove sediments at subtropical and tropical coastal sites. When comparing the CMS with PMS, we found that the former had a reduced diazotroph abundance and nitrogen fixing capability, but an enhanced metabolism that is related to the generation of microbial greenhouse gases via increased methanogenesis an...
Accurate estimates of bacterial carbon metabolic rates are indispensable for understanding the re... more Accurate estimates of bacterial carbon metabolic rates are indispensable for understanding the regulation of carbon fluxes in aquatic environments. Here, changes in bacterial growth, production, and cell volume in both pre-filtered and unfiltered seawater during 24 h incubation were monitored. The methodological artifacts during Winkler bacterial respiration (BR) measurements in subtropical Hong Kong coastal waters were assessed. Bacterial abundance increased by 3- and 1.8-fold in the pre-filtered and unfiltered seawater after incubation, respectively. Bacterial production (BP) and cell volume also showed significant enhancement. Compared with the BR measurements obtained by the Winkler method, the instantaneous free-living BR measurements, after correction, decreased by ~ 70%. The time-integrated free-living BR and BP during 24 h incubation in the pre-filtered sample provided an improved estimate of bacterial growth efficiency, which increased by ~ 52% compared to the common estima...
Toxic differences between antibacterial silver (either ionic Ag+ and nanoparticle – AgNPs) were r... more Toxic differences between antibacterial silver (either ionic Ag+ and nanoparticle – AgNPs) were related to the microbial metabolism of enriched organic matter in the gut.
Mixotrophic protists are widely observed in the aquatic ecosystems, while how they respond to ino... more Mixotrophic protists are widely observed in the aquatic ecosystems, while how they respond to inorganic nutrient imbalance and ocean warming remains understudied. We conducted a series of experiments on a mixotrophic dinoflagellate Lepidodinium sp. isolated from subtropical coastal waters to investigate the combined effect of temperature and medium nitrate to phosphate ratio (N:P ratio) on the ingestion activities of mixotrophic protists. We found Lepidodinium sp. displayed selective feeding behaviour with a higher ingestion rate on high-N prey (N-rich Rhodomonas salina) when the ambient inorganic N:P ratio was equal to or below the Redfield ratio. The Chesson selectivity index α increased with increasing temperature, suggesting that warming exacerbated the selective feeding of Lepidodinium sp. Under inorganic nitrogen sufficient conditions (N:P ratio = 64), no selective feeding was observed at 25 and 28°C, while it occurs at 31°C, which also indicates that warming alters the feedin...
Phytoplankton are diverse and abundant as primary producers in the ocean, with diversity and comm... more Phytoplankton are diverse and abundant as primary producers in the ocean, with diversity and community compositions varying spatially. How fundamental processes (e.g., selection, dispersal, and drift) regulate their global biogeography remains to be comprehensively explored.
Understanding the strategies developed by different microbial groups to adapt to specific niches ... more Understanding the strategies developed by different microbial groups to adapt to specific niches is critical. Through genome and transcriptome analyses of two newly isolated novel euryhaline Synechococcus strains, this study revealed that cluster 5 phycoerythrobilin-containing Synechococcus, which are thought to be strictly marine strains, could be abundant in low-salinity waters of the Pearl River estuary (salinity <15 ppt) and explained the molecular mechanisms that enabled them to adapt the low and fluctuating salinity in the estuarine environment.
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Papers by Hongbin Liu