Jun Gong
Sun Yat-Sen University, School of Marine Sciences, Faculty Member
- Microbial Ecology, Microbial diversity, Ciliated Protozoa, Microbial Eukaryotes, Protistology, Arbuscular mycorrhizal fungi, and 12 moreMicrobial Oceanography, Coastal Processes, Pyrosequencing, Copy Number Variation of DNA, Protistan Ecology, 18s rDNA analysis, Phytoplankton Ecology, Marine Microbial Ecology, Environmental microbiology, Community Ecology, Nitrogen Cycle, and Aquatic Microbial Ecologyedit
Research Interests: Mycology, Decomposition, Aquatic Microbial Ecology, Biology, Ecology, and 15 moreMicrobial diversity, Biological Sciences, Environmental Sciences, Dynamics, Fungal ecology, Gradient, Habitat, Mariculture, Ecosystems, Fungal Genetics and Ecology, Ecological Succession, Nutrient, Benthos, Microbial Diversity, and Fungal Diversity
Research Interests: Earth Sciences, Environmental Science, Oceanography, Marine Microbial Ecology, Biology, and 15 moreHarmful algal blooms, Eutrophication, Biological Sciences, Phosphorus, Environmental Sciences, Nitrogen Fixation, Nutrient Enrichment, Atlantic Ocean, Biological Nitrogen Fixation, Community Structure, Nutrient Limitation, Marine Ecosystems, Algal Bloom, Coastal eutrophication, and North Pacific Ocean
SummaryLittle is known about the relative influence of historic processes and environmental gradients on shaping the diversity of single‐celled eukaryotes in marine benthos. By combining pyrosequencing of 18S ribosomal RNA genes with data... more
SummaryLittle is known about the relative influence of historic processes and environmental gradients on shaping the diversity of single‐celled eukaryotes in marine benthos. By combining pyrosequencing of 18S ribosomal RNA genes with data on multiple environmental factors, we investigated the diversity of microeukaryotes in surficial sediments of three basins of the Yellow Sea Large Marine Ecosystem. A considerable proportion (about 20%) of reads was affiliated with known parasitoid protists. Dinophyta and Ciliophora appeared dominant in terms of relative proportion of reads and operational taxonomic unit (OTU) richness. Overall, OTU richness of benthic microeukaryotes decreased with increasing water depth and decreasing pH. While community composition was significantly different among basins, partial Mantel tests indicated a depth–decay pattern of community similarity, whereby water depth, rather than geographic distance or environment, shaped β‐diversity of benthic microeukaryotes...
Research Interests: Marine Biology, Environmental microbiology, Coastal Processes, Marine Ecology, Community Ecology, and 15 moreAquatic Microbial Ecology, Biology, Ecology, Biogeochemical cycles, Biogeography, Biodiversity, Marine, High Throughput Sequencing, Community Structure, Marine biogeography, Benthos, Ciliophora, Deep Sea, Geologic Sediments, and Depth decay relationship
Nanociliates have been frequently found to be important players in the marine microbial loop, however, little is known about their diversity and distribution in coastal ecosystems. We investigated the molecular diversity and distribution... more
Nanociliates have been frequently found to be important players in the marine microbial loop, however, little is known about their diversity and distribution in coastal ecosystems. We investigated the molecular diversity and distribution patterns of nanoplanktonic oligotrich and choreotrich (OC) ciliates in surface water of three neritic basins of northern China, the South Yellow Sea (SYS), North Yellow Sea (NYS), and Bohai Sea (BS) in June and November 2011. SSU rRNA gene clone libraries generated from three summertime samples (sites B38, B4 and H8) were analyzed and revealed a large novel ribotype diversity, of which many were low-abundant phylotypes belonging to the subclass Oligotrichia, but divergent from described morphospecies. Based on the data of terminal-restriction fragment length polymorphism (T-RFLP) analysis of all 35 samples, we found that the T-RF richness was generally higher in the SYS than in the BS, and negatively correlated with the molar ratio of P to Si. Overall, multidimensional scaling and permutational multivariate analysis of variance of the community turnover demonstrated a distinct seasonal pattern but no basin-to-basin differentiation across all samples. Nevertheless, significant community differences among basins were recognized in the winter dataset. Mantel tests showed that the environmental factors, P:Si ratio, water temperature and concentration of dissolved oxygen (DO), determined the community across all samples. However, both biogeographic distance and environment shaped the community in winter, with DO being the most important physicochemical factor. Our results indicate that the stoichiometric ratio of P:Si is a key factor, through which the phytoplankton community may be shaped, resulting in a cascade effect on the diversity and community composition of OC nanociliates in the N-rich, Si-limited coastal surface waters, and that the Yellow Sea Warm Current drives the nanociliate community, and possibly the microbial food webs, in the coastal ecosystem in winter.
Research Interests: Marine Microbial Ecology, Biology, Ecology, Protistology, Medicine, and 15 moreMultidisciplinary, Mediterranean Sea, Phylogeny, Marine, Maximum Likelihood, Plankton, Community Structure, Species Richness, PLoS one, Spatial Distribution, Baltic Sea, Annual Cycle, Ciliophora, Multidisciplinary Sciences, and Oceans and Seas
Research Interests: Genetics, Zoology, Biology, Life Sciences, The, and 5 moreGene, ribosomal RNA, Tubulin, Phylogenetic Tree, and Ciliate
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Research Interests: Biology, Microbial diversity, Biodiversity, Medicine, Biological Sciences, and 15 morePhylogeny, Actinobacteria, Population, Communities, Archaea, Bacteria, Genetic variation, Microbial Diversity, Genome sequence, Firmicutes, Saline Soil, Alkaline, Meta Analysis and Systematic Review, Proteobacteria, and Crenarchaeota
ABSTRACT. The hypostome ciliates have been generally classified into two classes, Phyllopharyngea and Nassophorea. The status of Nassophorea and its relationship with Phyllopharyngea is one of the most controversial issues in ciliate... more
ABSTRACT. The hypostome ciliates have been generally classified into two classes, Phyllopharyngea and Nassophorea. The status of Nassophorea and its relationship with Phyllopharyngea is one of the most controversial issues in ciliate systematics. Here we focus on the phylogenetic interrelationships of Nassophorea and Phyllopharyngea based on small subunit ribosomal RNA gene sequences. The three nassophorean subgroups, synhymeniids, microthoracids, and nassulids, each emerged as monophyletic, with synhymeniids as a sister group of Phyllopharyngea, and microthoracids as a sister of the synhymeniids+Phyllopharyngea clade in all phylogenies. The exact placement of the nassulids, however, remains uncertain. Following a detailed analysis of phenotypic characters, we hypothesize that: (1) the Phyllopharyngea could have evolved from synhymeniids, with the further development of their subkinetal microtubules as one of the major events; and (2) the development of monokinetid structures, as we...
Research Interests: Evolutionary Biology, Microbiology, Phylogenetics, Taxonomy, Biology, and 15 moreSystematics, Medicine, Phylogeny, Sequence alignment, Animals, Polymerase Chain Reaction, Molecular Phylogenetics and Evolution, ribosomal RNA, Monophyly, Phylogenetic Tree, Ciliophora, Species Specificity, Eukaryotic microbiology, Subunit, and Molecular Sequence Data
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Research Interests: Botany, Microbiology, Community Ecology, Microbial Ecology, Biology, and 15 moreChina, Microbial diversity, Medicine, Arbuscular mycorrhizal fungi, AM fungi, Coastal Sand Dunes, Cluster Analysis, Community Structure, Environmental Variables, Grassland, Ecosystem, Glomus, Area, Microbial Diversity, and Biota
Research Interests: Evolutionary Biology, Evolutionary genetics, Biology, Chemical Evolution, Darwinism, and 15 moreArabidopsis thaliana, Ciliates, Cytology, Biogenesis, Biological evolution, Animal Phylogeny, Ciliated Protozoa, Animal evolution, Ciliophora, Amino Acid Sequence, Erythrocytes, Ciliate, Chromosomes, Cellular Biophysics, and Blood platelets
The relative abundances of nitrifying, denitrifying and anammox prokaryotes in sediments of three hyper‐nutrified estuarine tidal flats of Laizhou Bay, Bohai Sea, China were investigated. Quantitative PCR estimates indicated that in most... more
The relative abundances of nitrifying, denitrifying and anammox prokaryotes in sediments of three hyper‐nutrified estuarine tidal flats of Laizhou Bay, Bohai Sea, China were investigated. Quantitative PCR estimates indicated that in most cases archaeal (AOA) amoA genes were more abundant than bacterial (AOB) amoA genes, and ratio of AOA/AOB was correlated with pH, Cd, and Cu. Of the denitrifiers, nirK‐type outnumbered nirS‐type, with nosZ‐type being the lowest. Variation of the ratio between nirK and nirS abundance depends on pH, nitrite, nitrate, and Cd. The combination of (nirS + nirK‐nosZ), an indicator of genetic potentials for N2O emission, was only related to the temperature. Anammox bacterial 16S rRNA gene abundances were correlated with salinity, pH, nitrite, and Cu. In contrast, the contribution of anammox to N2 production, by using anammox bacterial 16S rRNA/nosZ ratio as a proxy, was correlated to temperature, ammonium and dissolved oxygen in the overlying water, ratio of...
Research Interests: Water resources, Microbial Ecology, Marine Microbial Ecology, Biology, Trace Metals, and 14 moreEnvironmental Chemistry, Nitrogen Cycle, Multidisciplinary, Estuarine Ecology, Heavy metals, Environmental Sciences, Heavy Metal Pollution, Heavy Metal, Marine sediments, Anammox, Nitrite Reductase, Estuary, Ecology and Environmental Sciences, and Bay
Research Interests: Chemistry, Microbial Ecology, BIOCHAR, Agriculture, Environmental Chemistry, and 15 moreBiological Sciences, Microbial Communities, Environmental Sciences, Incubation, Arbuscular mycorrhizal fungi, Archaea, Community Structure, Ammonia, Forest soils, Microbial Activity As Affected by Biochar Addition In Soil, Amendment, Ammonia Oxidation, Agricultural Soil, Microbial community, and Acidic soils
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Research Interests: Microbiology, Microbial Ecology, Biology, Biodiversity, Medicine, and 15 morePhylogeny, Ciliates, Polymerase Chain Reaction, North China, Ciliated Protozoa, Molecular Characterization, Genetic variation, Ciliophora, Microbial Eukaryotes, Base Sequence, Ciliate, Environmental DNA, Molecular Detection, Oligohymenophorea, and Molecular Sequence Data
Understanding consistencies and discrepancies in characterizing diversity and quantity of phytoplankton is essential for better modeling ecosystem change. In this study, eukaryotic phytoplankton in the Pearl River Estuary, South China Sea... more
Understanding consistencies and discrepancies in characterizing diversity and quantity of phytoplankton is essential for better modeling ecosystem change. In this study, eukaryotic phytoplankton in the Pearl River Estuary, South China Sea were investigated using nuclear 18S rRNA and plastid 16S or 23S rRNA genes and pigment analysis. It was found that 18S abundance poorly explained the variations in total chlorophyll a (Chl-a). However, the ratios of log-transformed 18S abundance to Chl-a in the major phytoplankton groups were generally environment dependent, suggesting that the ratio has potential as an indicator of the physiological state of phytoplankton. The richness of 18S-based operational taxonomic units was positively correlated with the richness of 16S-based amplicon sequence variants of the whole phytoplankton community, but insignificant or weak for individual phytoplankton groups. Overall, the 18S based, rather than the 16S based, community structure had a greater similarity to pigment-based estimations. Relative to the pigment data, the proportion of haptophytes in the 18S dataset, and diatoms and cryptophytes in the 16S dataset, were underestimated. This study highlights that 18S metabarcoding tends to reflect biomass-based community organization of eukaryotic phytoplankton. Because there were lower copy numbers of plastid 16S than 18S per genome, metabarcoding of 16S probably approximates cell abundance-based community organization. Changes in biomass organization of the pigment-based community were sensitive to environmental changes. Taken together, multiple methodologies are recommended to be applied to more accurately profile the diversity and community composition of phytoplankton in natural ecosystems.
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Biotic interactions are known as a major control on microbial diversity. However, biotic interactions have rarely been quantified in an adequate manner, often leaving much residual variation unexplained in microbial biogeographic studies.... more
Biotic interactions are known as a major control on microbial diversity. However, biotic interactions have rarely been quantified in an adequate manner, often leaving much residual variation unexplained in microbial biogeographic studies. Herein, we propose a holistic approach to disentangle the relative importance of interdomain interactions in shaping microbial diversity by incorporating community-level characteristics. Taking coastal bacterioplankton on a regional scale as an example, we designated a range of community characteristics of pico-and nanoeukaryotes derived from metabarcoding and flow cytometric data as inter-domain interacting proxies, which were then considered in statistical modeling. We found that the bacterial diversity indices and community structure were much more accurately explained by a number of eukaryotic characteristics than by the measured environmental variables and/or spatial variables alone, as were the richness, relative abundances, and assemblage structures of major bacterial taxa. In co-occurrence networks, the nodes of characteristics that had more edges (links) were frequently the best explanatory variables for bacterial diversity indices. Over 70% of total variation in bacterial community structure could be explained by three categories of biotic interactions: parasitism (27%), fungi-bacterial competition (32%), and trophic structure and bacterivory (13%). This study showcases a methodological framework to infer different types of inter-domain interactions at play, and stresses the importance of non-grazing interacting processes in shaping bacterial diversity and community assembly.
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Microbial communities are commonly characterised through the metabarcoding of environmental DNA. This DNA originates from both viable (including dormant and active) and dead organisms, leading to recent efforts to distinguish between... more
Microbial communities are commonly characterised through the metabarcoding of environmental DNA. This DNA originates from both viable (including dormant and active) and dead organisms, leading to recent efforts to distinguish between these states. In this study, we further these approaches by distinguishing not only between viable and dead cells but also between dormant and actively growing cells. This is achieved by sequencing both rRNA and rDNA, in conjunction with propidium monoazide cross-linked rDNA, to partition the active, dormant and relic fractions in environmental samples. We apply this method to characterise the diversity and assemblage structure of these fractions of microeukaryotes in intertidal sediments during a wet-dry-rewet incubation cycle. Our findings indicate that a significant proportion of microeukaryotic phylotypes detected in the total rDNA pools originate from dormant and relic microeukaryotes in the sediments, both in terms of richness (dormant, 13 ± 2%; relic, 47 ± 5%) and read abundance (dormant, 20 ± 7%; relic, 14 ± 5%). The richness and sequence proportion of dormant microeukaryotes notably increase during the transition from wet to dry conditions. Statistical analyses suggest that the dynamics of diversity and assemblage structure across different activity fractions are influenced by various environmental drivers. Our strategy offers a versatile approach that can be adapted to characterise other microbes in a wide range of environments.
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We investigated spatial heterogeneity and diel variations in bacterioplankton and pico-nanoeukaryote communities, and potential biotic interactions at the extinction stage of the Ulva prolifera bloom in the Jiaozhou Bay, Yellow Sea. It... more
We investigated spatial heterogeneity and diel variations in bacterioplankton and pico-nanoeukaryote communities, and potential biotic interactions at the extinction stage of the Ulva prolifera bloom in the Jiaozhou Bay, Yellow Sea. It was found that the presence of Ulva canopies significantly promoted the cell abundance of heterotrophic bacteria, raised evenness, and altered the community structure of bacterioplankton. A diel pattern was solely significant for pico-nanoeukaryote community structure. >50 % of variation in the heterotrophic bacterial abundance was accounted for by the ratio of Bacteroidota to Firmicutes, and dissolved organic nitrogen effectively explained the variations in cell abundances of phytoplankton populations. The factors representing biotic interactions frequently contributed substantially more than environmental factors in explaining the variations in diversity and community structure of both bacterioplankton and pico-nanoeukaryotes. There were higher proportions of eukaryotic pathogens compared to other marine systems, suggesting a higher ecological risk associated with the Ulva blooms.
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Marine Synechococcus are an ecologically important picocyanobacterial group widely distributed in various oceanic environments. Little is known about the dynamics and distribution of Synechococcus abundance and genotypes during seasonal... more
Marine Synechococcus are an ecologically important picocyanobacterial group widely distributed in various oceanic environments. Little is known about the dynamics and distribution of Synechococcus abundance and genotypes during seasonal hypoxia in coastal zones. In this study, an investigation was conducted in a coastal marine ranch along two transects in Muping, Yantai, where hypoxic events (defined here as the dissolved oxygen concentration <3 mg L−1) occurred in the summer of 2015. The hypoxia occurred in the bottom waters from late July and persisted until late August. It was confined at nearshore stations of the two transects, one running across a coastal ranch and the other one outside. During this survey, cell abundance of Synechococcus was determined with flow cytometry, showing great variations ranging from 1 × 104 to 3.0 × 105 cells mL−1, and a bloom of Synechococcus occurred when stratification disappeared and hypoxia faded out outside the ranch. Regression analysis in...
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Relationships between ribotypic and phenotypic traits of protists across life-cycle stages remain largely unknown. Herein, we used single cells of two soil and two marine ciliate species to examine phenotypic and ribotypic traits and... more
Relationships between ribotypic and phenotypic traits of protists across life-cycle stages remain largely unknown. Herein, we used single cells of two soil and two marine ciliate species to examine phenotypic and ribotypic traits and their relationships across lag, log, plateau, cystic stages and temperatures. We found that Colpoda inflata and C. steinii demonstrated allometric relationships between 18S rDNA copy number per cell (CNPC), cell volume (CV), and macronuclear volume across all life-cycle stages. Integrating previously reported data of Euplotes vannus and Strombidium sulcatum indicated taxon-dependent rDNA CNPC–CV functions. Ciliate and prokaryote data analysis revealed that the rRNA CNPC followed a unified power-law function, only if the rRNA-deficient resting cysts were not considered. Hence, a theoretical framework was proposed to estimate the relative quantity of resting cysts in the protistan populations with total cellular rDNA and rRNA copy numbers. Using rDNA CNPC...
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Pico-/nanoeukaryotes (P/NEs) comprise both primary producers and bacterial predators, playing important biogeochemical and ecological roles in the marine microbial loop. Besides the difference in size, these small-sized fractions can be... more
Pico-/nanoeukaryotes (P/NEs) comprise both primary producers and bacterial predators, playing important biogeochemical and ecological roles in the marine microbial loop. Besides the difference in size, these small-sized fractions can be distinguished from microplankton by certain functional and ecological traits. Nevertheless, little information is available regarding patterns of their taxonomic and functional diversity and community composition along environmental gradients in coastal marine ecosystems. In this study, we applied high-throughput sequencing of 18S rRNA gene to assess the taxonomic species richness and community composition of P/NEs in surface waters of Bohai Sea and North Yellow Sea, northern China spanning a 600-km distance during summer and winter of 2011. The richness of operational taxonomic units (OTUs) formed a U-shaped relationship with concentration of chlorophyll a (Chl-a, a proxy of primary productivity), but a stronger, negative relationship with concentra...
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Seagrass colonization alters sediment physicochemical properties by depositing seagrass fibers and releasing organic carbon and oxygen from the roots. How this seagrass colonization-induced spatial heterogeneity affects archaeal community... more
Seagrass colonization alters sediment physicochemical properties by depositing seagrass fibers and releasing organic carbon and oxygen from the roots. How this seagrass colonization-induced spatial heterogeneity affects archaeal community structure and abundance remains unclear. In this study, we investigated archaeal abundance, diversity, and composition in both vegetated and adjacent bare surface sediments of a Zostera marina meadow. High-throughput sequencing of 16S rDNA showed that Woesearchaeota, Bathyarchaeota, and Thaumarchaeota were the most abundant phyla across all samples, accounting for approximately 42%, 21%, and 17% of the total archaeal communities, respectively. In terms of relative abundance, Woesearchaeota and Bathyarchaeota were not significantly different between these two niches; however, specific subclades (Woese-3, Woese-21, Bathy-6, Bathy-18) were significantly enriched in vegetated sediments (P<0.05), while Thaumarchaeota was favored in unvegetated sites ...
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Bacterivory is an important ecological function of protists in natural ecosystems. However, there are diverse bacterial species resistant to protistan digestion, which reduces the carbon flow to higher trophic levels. So far, a molecular... more
Bacterivory is an important ecological function of protists in natural ecosystems. However, there are diverse bacterial species resistant to protistan digestion, which reduces the carbon flow to higher trophic levels. So far, a molecular biological view of metabolic processes in heterotrophic protists during predation of bacterial preys of different digestibility is still lacking. In this study, we investigated the growth performance a ciliated protozoan Tetrahymena thermophila cultivated in a bacteria-free Super Proteose Peptone (SPP) medium (control), and in the media mixed with either a digestion-resistant bacterial species (DRB) or a digestible strain of E. coli (ECO). We found the protist population grew fastest in the SPP and slowest in the DRB treatment. Fluorescence in situ hybridization confirmed that there were indeed non-digested, viable bacteria in the ciliate cells fed with DRB, but none in other treatments. Comparative analysis of RNA-seq data showed that, relative to ...
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Marine benthic nitrogen (N)-cycling may vary widely across space and seasons; it is thus needed to make high-resolution estimations of these important ecosystem processes with a reasonable number of variables. In this study, we determined... more
Marine benthic nitrogen (N)-cycling may vary widely across space and seasons; it is thus needed to make high-resolution estimations of these important ecosystem processes with a reasonable number of variables. In this study, we determined the benthic denitrification and anammox potentials in two basins, the Bohai Sea (BS) and the North Yellow Sea (NYS) of China in May and November, and evaluated models in predicting these functions with environmental factors and/or microbial gene-based functional traits. We found that denitrification generally dominated the N-loss (54% to 98%), and that the denitrification rate varied greatly between basins and seasons. The anammox rate was generally higher in the BS than in the NYS in both seasons, and it made a greater contribution in November (22%) than in May (16%). Among the measured environmental factors, chlorophyll a in bottom waters and sedimentary organic carbon content were the most influential for predicting denitrification and anammox rates, respectively. On the other hand, the alpha diversities and gene abundances of involved bacteria were poorly correlated with the function potentials, indicating that these functional traits could not well explain the functions alone. Upon the incorporation of two gene copy number ratios [nosZ/(nirS+nirK) and nirK/bacterial 16S rRNA genes] into the environmental factor-parameterized models, however, we found the predictive powers of the regression models for total N-loss, denitrification and anammox rates, and contributions of anammox increased substantially, indicating that taking microbial functional traits into account could make estimations of these N-cycling functions in coastal ecosystems more accurate.
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Ｍａｒｉｎｅ ｍａｃｒｏａｌｇａｌ ｂｌｏｏｍｓ ｉｎ ｃｏａｓｔａｌ ｅｕｔｒｏｐｈｉｃ ｗａｔｅｒｓ ａｆｆｅｃｔ ｔｈｅ ｐｈｙｓｉｏｌｏｇｙ ａｎｄ ｅｃｏｌｏｇｙ ｏｆ ｔｈｅ ｃｕｌｔｕｒｅｄ ｏｒｇａｎｉｓｍｓ，ｃａｕｓｉｎｇ ｍａｓｓｉｖｅ ｄｅａｔｈ ｏｆ ｔｈｅｓｅ ａｎｉｍａｌｓ ｓｏｍｅｔｉｍｅｓ．Ｋｎｏｗｉｎｇ ｔｈｅ ｑｕａｎｔｉｔｙ ａｎｄ ｖａｒｉａｔｉｏｎ... more
Ｍａｒｉｎｅ ｍａｃｒｏａｌｇａｌ ｂｌｏｏｍｓ ｉｎ ｃｏａｓｔａｌ ｅｕｔｒｏｐｈｉｃ ｗａｔｅｒｓ ａｆｆｅｃｔ ｔｈｅ ｐｈｙｓｉｏｌｏｇｙ ａｎｄ ｅｃｏｌｏｇｙ ｏｆ ｔｈｅ
ｃｕｌｔｕｒｅｄ ｏｒｇａｎｉｓｍｓ，ｃａｕｓｉｎｇ ｍａｓｓｉｖｅ ｄｅａｔｈ ｏｆ ｔｈｅｓｅ ａｎｉｍａｌｓ ｓｏｍｅｔｉｍｅｓ．Ｋｎｏｗｉｎｇ ｔｈｅ ｑｕａｎｔｉｔｙ ａｎｄ ｖａｒｉａｔｉｏｎ
ｏｆ ｔｈｅ ａｌｇａｌ ｓｐｏｒｅｓ ｏｒ ｇａｍａｔｅｓ ｉｎ ｔｈｅ ａｑｕａｔｉｃ ｓｙｓｔｅｍｓ ｉｓ ｃｒｕｃｉａｌ ｉｎ ｕｎｄｅｒｓｔａｎｄｉｎｇ ｔｈｅ ｂｉｏｌｏｇｉｃａｌ ａｎｄ ｅｃｏｌｏｇｉｃａｌ
ｍｅｃｈａｎｉｓｍｓ ｕｎｄｅｒｌｙｉｎｇ ａｌｇａｌ ｏｕｔｂｒｅａｋｓ ａｎｄ ｉｎ ｄｅｖｅｌｏｐｉｎｇ ｓｔｒａｔｅｇｉｅｓ ｏｆ ｐｒｅｖｅｎｔｉｏｎ．Ｉｎ ｔｈｉｓ ｓｔｕｄｙ，
ｗｅ ｎｅｗｌｙ ｄｅｓｉｇｎｅｄ ｓｐｅｃｉｆｉｃ ＰＣＲ ｐｒｉｍｅｒｓ ｔａｒｇｅｔｉｎｇ ｔｈｅ ｉｎｔｅｒｎａｌ ｔｒａｎｓｃｒｉｐｔ ｒｅｇｉｏｎ（ＩＴＳ）ｏｆ ｔｈｅ ｒｉｂｏｓｏｍａｌ
ＲＮＡ ｇｅｎｅｓ（ｒＤＮＡ）ｏｆ ｔｈｒｅｅ ｍａｃｒｏａｌｇａｌ ｓｐｅｃｉｅｓ，Ｕｌｖａ ｃｆ．ｌｉｎｚａ，Ｕｌｖａ ｓｐ．，ａｎｄ Ｓｃｙｔｏｓｉｐｈｏｎ ｌｏｍｅｎｔａｒｉａ，
ｗｈｉｃｈ ａｌｌ ａｒｅ ｋｎｏｗｎ ｔｏ ｂｅ ｐｏｔｅｎｔｉａｌｌｙ ｂｌｏｏｍｉｎｇ ｓｐｅｃｉｅｓ ｉｎ ｍａｒｉｃｕｌｔｕｒｅ ｐｏｎｄｓ．Ｔｈｅ ｓｐｅｃｉｆｉｃｉｔｙ ｏｆ ｔｈｅｓｅ ｐｒｉｍｅｒｓ
ｗａｓ ｖｅｒｉｆｉｅｄ ｉｎ ｓｉｌｉｃｏ，ｉｎ ｖｉｔｒｏ ａｎｄ ｉｎ ｓｉｔｕ．Ｒｅａｌ－ｔｉｍｅ ｑｕａｎｔｉｔａｔｉｖｅ ＰＣＲ（ｑＰＣＲ）ａｓｓａｙｓ ｗｉｔｈ ｔｈｅｓｅ ｐｒｉｍｅｒｓ
ｗｅｒｅ ｄｅｖｅｌｏｐｅｄ ａｎｄ ｖｅｒｉｆｉｅｄ，ｓｈｏｗｉｎｇ ａ ｄｅｔｅｃｔｉｏｎ ｌｉｍｉｔａｔｉｏｎ ａｓ ｌｏｗ ａｓ ２００～４００ＩＴＳ ｃｏｐｙ ｎｕｍｂｅｒｓ ｏｆ
ｔｈｅ ａｌｇａｌ ｇｅｎｏｍｉｃ ＤＮＡ．Ｔｈｅ ｎｅｗｌｙ ｄｅｖｅｌｏｐｅｄ ａｓｓａｙｓ ｗｅｒｅ ｆｕｒｔｈｅｒ ａｐｐｌｉｅｄ ｔｏ ｑｕａｎｔｉｆｙ ｔｈｅ ｓｐｏｒｅｓ／ｇａｍａｔｅｓ
ｏｆ Ｓ．ｌｏｍｅｎｔａｒｉａｉｎ ｓｕｒｆａｃｅ ｗａｔｅｒｓ ｏｆ ａ ｆａｒｍｉｎｇ ｐｏｎｄ ｆｏｒ ｓｅａ ｃｕｃｕｍｂｅｒｓ．Ｔｈｅ ｑｕａｎｔｉｆｉｃａｔｉｏｎ ｏｆ ｔｈｅ ｓｐｏｒｅｓ ｏｆ
Ｓ．ｌｏｍｅｎｔａｒｉａｄｕｒｉｎｇ ａ １６－ｍｏｎｔｈ ｐｅｒｉｏｄ（ｆｒｏｍ Ｄｅｃｅｍｂｅｒ ｏｆ ２０１４ｔｏ Ｍａｒｃｈ ｏｆ ２０１６）ｓｈｏｗｅｄ ｔｈａｔ ｔｈｅ ＩＴＳ
ｒＤＮＡ ｃｏｐｙ ｎｕｍｂｅｒ ｏｆ ｔｈｉｓ ｓｐｅｃｉｅｓ ｗａｓ ｒｅｌａｔｉｖｅｌｙ ｈｉｇｈ ｉｎ Ｄｅｃｅｍｂｅｒ ｏｆ ２０１５，ｗｈｉｃｈ ｗａｓ ｉｎ ｃｏｉｎｃｉｄｅｎｃｅ ｗｉｔｈ
ｔｈｅ ｏｂｓｅｒｖｅｄ ｂｌｏｏｍｉｎｇ ｏｆ ｔｈｅ ｓｐｅｃｉｅｓ ｉｎ Ｍａｒｃｈ ｏｆ ２０１６，ｓｕｇｇｅｓｔｉｎｇ ａ ｌｉｎｋ ｂｅｔｗｅｅｎ ｔｈｅ ｈｉｇｈ ｓｐｏｒｅ ａｂｕｎｄａｎｃｅ
ｉｎ ｔｈｅ ｗｉｎｔｅｒ ａｎｄ ｔｈｅ ｂｌｏｏｍ ｏｆ ｔｈｅ ｍａｃｒｏａｌｇａ ｉｎ ｔｈｅ ｅａｒｌｙ ｓｐｒｉｎｇ ｏｆ ｎｅｘｔ ｙｅａｒ．
ｃｕｌｔｕｒｅｄ ｏｒｇａｎｉｓｍｓ，ｃａｕｓｉｎｇ ｍａｓｓｉｖｅ ｄｅａｔｈ ｏｆ ｔｈｅｓｅ ａｎｉｍａｌｓ ｓｏｍｅｔｉｍｅｓ．Ｋｎｏｗｉｎｇ ｔｈｅ ｑｕａｎｔｉｔｙ ａｎｄ ｖａｒｉａｔｉｏｎ
ｏｆ ｔｈｅ ａｌｇａｌ ｓｐｏｒｅｓ ｏｒ ｇａｍａｔｅｓ ｉｎ ｔｈｅ ａｑｕａｔｉｃ ｓｙｓｔｅｍｓ ｉｓ ｃｒｕｃｉａｌ ｉｎ ｕｎｄｅｒｓｔａｎｄｉｎｇ ｔｈｅ ｂｉｏｌｏｇｉｃａｌ ａｎｄ ｅｃｏｌｏｇｉｃａｌ
ｍｅｃｈａｎｉｓｍｓ ｕｎｄｅｒｌｙｉｎｇ ａｌｇａｌ ｏｕｔｂｒｅａｋｓ ａｎｄ ｉｎ ｄｅｖｅｌｏｐｉｎｇ ｓｔｒａｔｅｇｉｅｓ ｏｆ ｐｒｅｖｅｎｔｉｏｎ．Ｉｎ ｔｈｉｓ ｓｔｕｄｙ，
ｗｅ ｎｅｗｌｙ ｄｅｓｉｇｎｅｄ ｓｐｅｃｉｆｉｃ ＰＣＲ ｐｒｉｍｅｒｓ ｔａｒｇｅｔｉｎｇ ｔｈｅ ｉｎｔｅｒｎａｌ ｔｒａｎｓｃｒｉｐｔ ｒｅｇｉｏｎ（ＩＴＳ）ｏｆ ｔｈｅ ｒｉｂｏｓｏｍａｌ
ＲＮＡ ｇｅｎｅｓ（ｒＤＮＡ）ｏｆ ｔｈｒｅｅ ｍａｃｒｏａｌｇａｌ ｓｐｅｃｉｅｓ，Ｕｌｖａ ｃｆ．ｌｉｎｚａ，Ｕｌｖａ ｓｐ．，ａｎｄ Ｓｃｙｔｏｓｉｐｈｏｎ ｌｏｍｅｎｔａｒｉａ，
ｗｈｉｃｈ ａｌｌ ａｒｅ ｋｎｏｗｎ ｔｏ ｂｅ ｐｏｔｅｎｔｉａｌｌｙ ｂｌｏｏｍｉｎｇ ｓｐｅｃｉｅｓ ｉｎ ｍａｒｉｃｕｌｔｕｒｅ ｐｏｎｄｓ．Ｔｈｅ ｓｐｅｃｉｆｉｃｉｔｙ ｏｆ ｔｈｅｓｅ ｐｒｉｍｅｒｓ
ｗａｓ ｖｅｒｉｆｉｅｄ ｉｎ ｓｉｌｉｃｏ，ｉｎ ｖｉｔｒｏ ａｎｄ ｉｎ ｓｉｔｕ．Ｒｅａｌ－ｔｉｍｅ ｑｕａｎｔｉｔａｔｉｖｅ ＰＣＲ（ｑＰＣＲ）ａｓｓａｙｓ ｗｉｔｈ ｔｈｅｓｅ ｐｒｉｍｅｒｓ
ｗｅｒｅ ｄｅｖｅｌｏｐｅｄ ａｎｄ ｖｅｒｉｆｉｅｄ，ｓｈｏｗｉｎｇ ａ ｄｅｔｅｃｔｉｏｎ ｌｉｍｉｔａｔｉｏｎ ａｓ ｌｏｗ ａｓ ２００～４００ＩＴＳ ｃｏｐｙ ｎｕｍｂｅｒｓ ｏｆ
ｔｈｅ ａｌｇａｌ ｇｅｎｏｍｉｃ ＤＮＡ．Ｔｈｅ ｎｅｗｌｙ ｄｅｖｅｌｏｐｅｄ ａｓｓａｙｓ ｗｅｒｅ ｆｕｒｔｈｅｒ ａｐｐｌｉｅｄ ｔｏ ｑｕａｎｔｉｆｙ ｔｈｅ ｓｐｏｒｅｓ／ｇａｍａｔｅｓ
ｏｆ Ｓ．ｌｏｍｅｎｔａｒｉａｉｎ ｓｕｒｆａｃｅ ｗａｔｅｒｓ ｏｆ ａ ｆａｒｍｉｎｇ ｐｏｎｄ ｆｏｒ ｓｅａ ｃｕｃｕｍｂｅｒｓ．Ｔｈｅ ｑｕａｎｔｉｆｉｃａｔｉｏｎ ｏｆ ｔｈｅ ｓｐｏｒｅｓ ｏｆ
Ｓ．ｌｏｍｅｎｔａｒｉａｄｕｒｉｎｇ ａ １６－ｍｏｎｔｈ ｐｅｒｉｏｄ（ｆｒｏｍ Ｄｅｃｅｍｂｅｒ ｏｆ ２０１４ｔｏ Ｍａｒｃｈ ｏｆ ２０１６）ｓｈｏｗｅｄ ｔｈａｔ ｔｈｅ ＩＴＳ
ｒＤＮＡ ｃｏｐｙ ｎｕｍｂｅｒ ｏｆ ｔｈｉｓ ｓｐｅｃｉｅｓ ｗａｓ ｒｅｌａｔｉｖｅｌｙ ｈｉｇｈ ｉｎ Ｄｅｃｅｍｂｅｒ ｏｆ ２０１５，ｗｈｉｃｈ ｗａｓ ｉｎ ｃｏｉｎｃｉｄｅｎｃｅ ｗｉｔｈ
ｔｈｅ ｏｂｓｅｒｖｅｄ ｂｌｏｏｍｉｎｇ ｏｆ ｔｈｅ ｓｐｅｃｉｅｓ ｉｎ Ｍａｒｃｈ ｏｆ ２０１６，ｓｕｇｇｅｓｔｉｎｇ ａ ｌｉｎｋ ｂｅｔｗｅｅｎ ｔｈｅ ｈｉｇｈ ｓｐｏｒｅ ａｂｕｎｄａｎｃｅ
ｉｎ ｔｈｅ ｗｉｎｔｅｒ ａｎｄ ｔｈｅ ｂｌｏｏｍ ｏｆ ｔｈｅ ｍａｃｒｏａｌｇａ ｉｎ ｔｈｅ ｅａｒｌｙ ｓｐｒｉｎｇ ｏｆ ｎｅｘｔ ｙｅａｒ．
Research Interests:
The combined effects of intertidal zonation and mangrove vegetation on benthic bacterial communities and ecological functions were studied. MiSeq sequencing of the 16S rRNA gene and PICRUSt predictive functional profiles were used to... more
The combined effects of intertidal zonation and mangrove vegetation on benthic bacterial communities and ecological functions were studied. MiSeq sequencing of the 16S rRNA gene and PICRUSt predictive functional profiles were used to investigate the diversity, community structure and potential metabolic functions of benthic bacteria in surface sediments of a mangrove ecosystem. Compared with the lower intertidal zone, bacterial alpha diversity and richness were significantly higher in the upper intertidal zone and highly associated with sediment organic matter. The upper zone was occupied by higher proportions of heterotrophic bacteria involved in the degradation of organic compounds. These included Desulfobacterales, Anaerolineae and Acidobacteria, while the proportion of Rhodobacterales and Xenococcaceae was greatly increased in the lower zone. No significant
difference of either alpha diversity or community composition was found between rhizosphere and bulk sediments, except that higher relative proportions of Rhizobiales and Actinobacteria occurred in rhizosphere sediments. The shift in bacterial community structure was mainly driven by changes in sediment Pb and NH4+ concentrations. Among the major carbon, nitrogen and sulfur cycling processes examined, higher potentials of cellulose and hemicellulose degradation, dissimilatory sulfate reduction, and nitrate or nitrite reduction occurred in the upper intertidal zone. Assimilatory sulfate reduction and sulfur oxidation potentials were higher in the root-associated sediments than in the bulk sediments. This study indicated that intertidal zonation was more important than root effects in modulating benthic bacterial diversity and functional potentials in a mangrove ecosystem.
difference of either alpha diversity or community composition was found between rhizosphere and bulk sediments, except that higher relative proportions of Rhizobiales and Actinobacteria occurred in rhizosphere sediments. The shift in bacterial community structure was mainly driven by changes in sediment Pb and NH4+ concentrations. Among the major carbon, nitrogen and sulfur cycling processes examined, higher potentials of cellulose and hemicellulose degradation, dissimilatory sulfate reduction, and nitrate or nitrite reduction occurred in the upper intertidal zone. Assimilatory sulfate reduction and sulfur oxidation potentials were higher in the root-associated sediments than in the bulk sediments. This study indicated that intertidal zonation was more important than root effects in modulating benthic bacterial diversity and functional potentials in a mangrove ecosystem.
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The present study aimed to reveal the eukaryotic diets of two economically important marine sediment-inhabiting worms, Sipunculus nudus (peanut worm) and Urechis unicinctus (spoon worm), using clone libraries and phylogenetic analyses of... more
The present study aimed to reveal the eukaryotic diets of two economically important marine sediment-inhabiting worms, Sipunculus nudus (peanut worm) and Urechis unicinctus (spoon worm), using clone libraries and phylogenetic analyses of 18S rRNA genes. Fungal rDNA was also targeted and analyzed to reveal mycobiomes. Overall, we detected a wide range of eukaryotic phylotypes associated with the larvae of S. nudus and in the gut contents of both worms. These phylotypes included
ciliates, diatoms, dinoflagellates, eustigmatophytes, placidids, oomycetes, fungi, nematodes, flatworms, seaweeds, and higher
plants. Oomycetes were associated with the planktonic larvae of S. nudus. The composition of eukaryotic diets shifted greatly across the larval, juvenile, and adult stages of S. nudus, and among different gut sections in U. unicinctus, reflecting lifestyle changes during the ontogeny of the peanut worm and progressive digestion in the spoon worm. Malassezia-like fungi were prevalent in mycobiomes. Epicoccum and Trichosporon-related phylotypes dominated mycobiomes associated with larval individuals and in the gut contents of adults, respectively. The gut mycobiome of S. nudus was successively characterized through the midgut, aspiratory intestines, hindgut, and rectum as having a high proportion of Climacodon-Rhizochaete, Ceriporiopsis, Cladosporium-Pseudomicrostroma, and Malassezia-related species in the libraries. These results emphasize the dynamics of diets and gut mycobiomes in marine benthic animals.
ciliates, diatoms, dinoflagellates, eustigmatophytes, placidids, oomycetes, fungi, nematodes, flatworms, seaweeds, and higher
plants. Oomycetes were associated with the planktonic larvae of S. nudus. The composition of eukaryotic diets shifted greatly across the larval, juvenile, and adult stages of S. nudus, and among different gut sections in U. unicinctus, reflecting lifestyle changes during the ontogeny of the peanut worm and progressive digestion in the spoon worm. Malassezia-like fungi were prevalent in mycobiomes. Epicoccum and Trichosporon-related phylotypes dominated mycobiomes associated with larval individuals and in the gut contents of adults, respectively. The gut mycobiome of S. nudus was successively characterized through the midgut, aspiratory intestines, hindgut, and rectum as having a high proportion of Climacodon-Rhizochaete, Ceriporiopsis, Cladosporium-Pseudomicrostroma, and Malassezia-related species in the libraries. These results emphasize the dynamics of diets and gut mycobiomes in marine benthic animals.
Research Interests:
Little is known about the diversity, community composition, or distribution of benthic microbial eukaryotes in organic carbon (OC)-rich mangrove sediments.We hypothesized that the distribution of microeukaryotes was related to the spatial... more
Little is known about the diversity, community composition, or distribution of benthic microbial eukaryotes in organic carbon (OC)-rich mangrove sediments.We hypothesized that the distribution of microeukaryotes was related to the spatial heterogeneity of mangrove sediment geochemistry due to tidal zonation and the rhizosphere effect. A range of geochemical properties of surface sediments were characterized, and alpha and beta diversities of microeukaryotes in a
mangrove ecosystem were investigated using MiSeq sequencing of 18S rRNA genes. We found that the sequence proportions of Chlorophyta and Bacillariophyta were notably high in the datasets. Both operational taxonomic unit (OTU) richness and microeukaryotic community structure (MCS) were significantly different between the OC-rich upper tidal zone and the sulfate- and ammonium-rich lower tidal zone, indicating a strong response of microeukaryotic diversity to tidal zonation. The zonewise community differences were characterized by distinct shifts in the proportions and OTUs of chlorophytes, diatoms, and fungi. However, neither OTU richness nor MCS was significantly different between near-root and bulk sediments, though several geochemical parameters varied.
Similarly, the assemblages of fungi showed a pattern of tidal zonation. Overall, variations in MCS in mangrove sediments were mainly driven by the quantity and quality of organic matter, grain size, and concentration of sulfate.
mangrove ecosystem were investigated using MiSeq sequencing of 18S rRNA genes. We found that the sequence proportions of Chlorophyta and Bacillariophyta were notably high in the datasets. Both operational taxonomic unit (OTU) richness and microeukaryotic community structure (MCS) were significantly different between the OC-rich upper tidal zone and the sulfate- and ammonium-rich lower tidal zone, indicating a strong response of microeukaryotic diversity to tidal zonation. The zonewise community differences were characterized by distinct shifts in the proportions and OTUs of chlorophytes, diatoms, and fungi. However, neither OTU richness nor MCS was significantly different between near-root and bulk sediments, though several geochemical parameters varied.
Similarly, the assemblages of fungi showed a pattern of tidal zonation. Overall, variations in MCS in mangrove sediments were mainly driven by the quantity and quality of organic matter, grain size, and concentration of sulfate.
Research Interests:
This study explored the molecular diversity and biogeography of benthic ciliates in Chinese marginal seas, the Bohai Sea (BHS), North Yellow Sea (NYS) and South Yellow Sea (SYS). From a previous 18S rRNA gene pyrosequencing dataset of the... more
This study explored the molecular diversity and biogeography of benthic ciliates in Chinese marginal seas, the Bohai Sea (BHS), North Yellow Sea (NYS) and South Yellow Sea (SYS). From a previous 18S rRNA gene
pyrosequencing dataset of the benthic microeukaryotes, we retrieved the sequences affiliated with phylum Ciliophora and analyzed alpha and beta diversities of ciliate communities. We found that BHS had the highest
ciliate operational taxonomic unit (OTU) richness than NYS and SYS, whereas the richness was not significantly different between summer and winter. Among all the measured environmental variables, water depth showed consistently the strongest correlations with alpha diversities. Overall, the class Spirotrichea (mostly Choreotrichia
and unassigned lineages within the class) dominated the communities in terms of both relative proportion of sequences (77.0%) and OTU richness (66.5%). OTU-level ciliate community structure was significant different
among the three basins, but not between the seasons. Structurally, significant differences in relative proportion among the basins were detected for the class Litostomatea, but not for other classes. Partial Mantel tests demonstrated that water depth difference was more important than geographic and environment distances in shaping the community structure of benthic ciliates in the studied area. About 60% OTUs were not assigned at a class or order level and at least 45% OTUs shared a sequence similarity no more than 97% with the described
species, indicating a great potential for ciliate species discovery in the offshore sediments. Compared with previous morphology-based surveys, the spatial pattern of ciliate diversity (decreasing from NYS to SYS) is also identified in the present study. Nevertheless, structurally, the dominant class appeared to be Spirotrichea in the sequencing dataset, which differs from previous morphology-based results (dominance of classes Prostomatea and Karyorelictea in biomass). The potential causes for the discrepancies between molecular and morphological
findings are also discussed.
pyrosequencing dataset of the benthic microeukaryotes, we retrieved the sequences affiliated with phylum Ciliophora and analyzed alpha and beta diversities of ciliate communities. We found that BHS had the highest
ciliate operational taxonomic unit (OTU) richness than NYS and SYS, whereas the richness was not significantly different between summer and winter. Among all the measured environmental variables, water depth showed consistently the strongest correlations with alpha diversities. Overall, the class Spirotrichea (mostly Choreotrichia
and unassigned lineages within the class) dominated the communities in terms of both relative proportion of sequences (77.0%) and OTU richness (66.5%). OTU-level ciliate community structure was significant different
among the three basins, but not between the seasons. Structurally, significant differences in relative proportion among the basins were detected for the class Litostomatea, but not for other classes. Partial Mantel tests demonstrated that water depth difference was more important than geographic and environment distances in shaping the community structure of benthic ciliates in the studied area. About 60% OTUs were not assigned at a class or order level and at least 45% OTUs shared a sequence similarity no more than 97% with the described
species, indicating a great potential for ciliate species discovery in the offshore sediments. Compared with previous morphology-based surveys, the spatial pattern of ciliate diversity (decreasing from NYS to SYS) is also identified in the present study. Nevertheless, structurally, the dominant class appeared to be Spirotrichea in the sequencing dataset, which differs from previous morphology-based results (dominance of classes Prostomatea and Karyorelictea in biomass). The potential causes for the discrepancies between molecular and morphological
findings are also discussed.
Research Interests:
Peritrich ciliates are highly diverse and can be important bacterial grazers in aquatic ecosystems. Morphological identifications of peritrich species and assemblages in the environment are time-consuming and expertise-demanding. In this... more
Peritrich ciliates are highly diverse and can be important bacterial grazers in aquatic ecosystems. Morphological identifications of peritrich species and assemblages in the environment are time-consuming and expertise-demanding. In this study, two peritrich-specific PCR primers were newly designed to amplify a fragment including the internal transcribed spacer (ITS) region of ribosomal rDNA from environmental samples. The primers showed high specificity in silico, and in tests with peritrich isolates and environmental DNA. Application of these primers in clone library construction and sequencing yielded exclusively sequences of peritrichs for water and sediment samples. We also found the ITS1, ITS2, ITS, D1 region of 28S rDNA, and ITS+D1 region co-varied with, and generally more variable than, the V9 region of 18S rDNA in peritrichs. The newly designed specific primers thus provide additional tools to study the molecular diversity, community composition, and phylogeography of these ecologically important protists in different systems.
Research Interests:
Benthic fungal diversities in Bohai Sea and North Yellow Sea were investigated using pyrosequencing of 18S rDNA. Overall, Chytridiomycota dominated, followed by Basidiomycota, Ascomycota and Cryptomycota, in terms of alpha diversities... more
Benthic fungal diversities in Bohai Sea and North Yellow Sea were investigated using pyrosequencing of 18S rDNA. Overall, Chytridiomycota dominated, followed by Basidiomycota, Ascomycota and Cryptomycota, in terms of alpha diversities and relative abundance. The beta diversity of benthic fungi showed a significant seasonality but no regional differences, accounted for by contrasting relative abundances of Chytridiomycota and Basidiomycota. Significantly seasonal changes in Chytridiomycota and Basidiomycota assemblage structure were also observed, but not for Ascomycota and Cryptomycota. Environmental filtering was more important than water depth and geographic distance in shaping the distribution of benthic fungi in the neritic oceans. The overall fungal beta diversity co-varied with concentration of chlorophyll a, pH, and salinity, distance from land, and water depth. The assemblage structure of benthic Chytridiomycota, Basidiomycota, Ascomycota and Cryptomycota co-varied with different sets of environmental parameters, suggesting their niche differentiations in the coastal sediments.
Research Interests:
Recent advances in molecular technology have revolutionized research on all aspects of the biology of organisms, including ciliates, and created unprecedented opportunities for pursuing a more integrative approach to investigation of... more
Recent advances in molecular technology have revolutionized research on all aspects of the biology of organisms, including ciliates, and created unprecedented opportunities for pursuing a more integrative approach to investigation of biodiversity. However, this goal is complicated by large gaps and inconsistencies that still exist in the foundation of basic information about biodiversity of ciliates. The present paper reviews issues relating to the taxonomy of ciliates and presents specific recommendations for best practice in the observation and documentation of their biodiversity. This effort stems from a workshop that explored ways to implement six Grand Challenges proposed by the International Research Coordination Network for Biodiversity of Ciliates (IRCN-BC). As part of its commitment to strengthening the knowledge base that supports research on biodiversity of ciliates, the IRCN-BC proposes to populate The Ciliate Guide, an online database, with biodiversity-related data and metadata to create a resource that will facilitate accurate taxonomic identifications and promote sharing of data.
Research Interests:
To improve understanding of diversity, phylogeny, and evolution in tintinnid ciliates, it is essential to link multiple molecular markers with properly identified and documented morphospecies. Accordingly, 54 tintinnid... more
To improve understanding of diversity, phylogeny, and evolution in tintinnid ciliates, it is essential to link multiple molecular markers with properly identified and documented morphospecies. Accordingly, 54 tintinnid morphospecies/isolates mainly from the Yellow and East China Seas were collected and analysed. Using single-cell approaches, sequences were obtained for three rDNA loci (18S, ITS1-5.8S-ITS2, D1-D5 region of 28S). Twenty-six tintinnid morphospecies (29 isolates) are documented by micrographs, measurements, morphologically described, and compared with the original species description. Three rDNA loci-based phylogenetic analyses were then performed for these identified isolates. Sequences from 25 further, unidentified species/isolates were included in the comparison of the three rDNA loci. Ribosomal DNA genes of the genus Leprotintinnus were analysed for the first time, showing that Leprotintinnus is closely related to Tintinnopsis radix and branch distinctly apart from the family Tintinnidiidae. Four novel clades (VI to IX) of the Tintinnopsis complex emerged in the 18S genealogies. Analyses of the relative variability of the ITS and 28S regions versus the 18S rDNA showed that the ITS1-5.8S-ITS2 and ITS2 regions well co-varied with the 18S rDNA when the variations of the latter were less than 3%, whereas at difference of less than 1%, no correlation was found between the compared genes. These findings highlight the difficulties in using variable locus-based cut-off divergences in circumscribing tintinnid morphospecies.
Research Interests:
The morphology and infraciliature of a new ciliate, Metopus yantaiensis n. sp., discovered in coastal soil of northern China, were investigated. It is distinguished from its congeners by a combination of the following features: nuclear... more
The morphology and infraciliature of a new ciliate, Metopus yantaiensis n. sp., discovered in coastal soil of northern China, were investigated. It is distinguished from its congeners by a combination of the following features: nuclear apparatus situated in the preoral dome; 18–21 somatic ciliary rows, of which three extend onto the preoral dome (dome kineties); three to five distinctly elongated caudal cilia, and 21–29 adoral polykinetids. The 18S rRNA genes of this new species and two congeners, Metopus contortus and Metopus hasei, were sequenced and phylogenetically analyzed. The new species is more closely related to M. hasei and the clevelandellids than to other congeners; both the genus Metopus and the order Metopida are not monophyletic. In addition, the digestion-resistant bacteria in the cytoplasm of M. yantaiensis were identified, using a 16S rRNA gene clone library, sequencing, and fluorescence in situ hybridization. The detected intracellular bacteria are affiliated with Sphingomonadales, Rhizobiales, Rickettsiales (Alphaproteobacteria), Pseudomonas (Gammaproteobacteria), Rhodocyclales (Betaproteobacteria), Clostridiales (Firmicutes), and Flavobacteriales (Bacteroidetes).
Research Interests:
Peritrich ciliates are highly diverse and can be important bacterial grazers in aquatic ecosystems. Morphological identifications of peritrich species and assemblages in the environment are time-consuming and expertise-demanding. In this... more
Peritrich ciliates are highly diverse and can be important bacterial grazers in aquatic ecosystems. Morphological identifications of peritrich species and assemblages in the environment are time-consuming and expertise-demanding. In this study, two peritrich-specific PCR primers were newly designed to amplify a fragment including the internal transcribed spacer (ITS) region of ribosomal rDNA from environmental samples. The primers showed high specificity in silico, and in tests with peritrich isolates and environmental DNA. Application of these primers in clone library construction and sequencing yielded exclusively sequences of peritrichs for water and sediment samples. We also found the ITS1, ITS2, ITS, D1 region of 28S rDNA, and ITS+D1 region co-varied with, and generally more variable than, the V9 region of 18S rDNA in peritrichs. The newly designed specific primers thus provide additional tools to study the molecular diversity, community composition, and phylogeography of these ecologically important protists in different systems. Peri974F: 5'-GGAAACTCATCAGGRCAAGAAGATT -3' (Liu and Gong 2012) Peri1370F: 5'-TGATTACGTCCCTGCAA-3' (this study) PeriLsu1R: 5'-CCTTCGCAGAACTTGTAT -3' (this study)
Research Interests:
Ribosomal (r)RNA and rDNA have been golden molecular markers in microbial ecology. However, it remains poorly understood how ribotype copy number (CN)-based characteristics are linked with diversity, abundance and activity of protist... more
Ribosomal (r)RNA and rDNA have been golden molecular markers in microbial ecology. However, it remains poorly understood how ribotype copy number (CN)-based characteristics are linked with diversity, abundance and activity of protist populations and communities observed at organismal levels. Here, we applied a single-cell approach to quantify ribotype CNs in two ciliate species reared at different temperatures. We found that in actively growing cells, the per-cell rDNA and rRNA CNs scaled with cell volume (CV) to 0.44 and 0.58 powers, respectively. The modeled rDNA and rRNA concentrations thus appear to be much higher in smaller than in larger cells. The observed rRNA:rDNA ratio scaled with CV0.14. The maximum growth rate could be well predicted by a combination of per-cell ribotype CN and temperature. Our empirical data and modeling on single-cell ribotype scaling are in agreement with both the metabolic theory of ecology and the growth rate hypothesis, providing a quantitative framework for linking cellular rDNA and rRNA CNs with body size, growth (activity) and biomass stoichiometry. This study also demonstrates that the expression rate of rRNA genes is constrained by cell size, and favors biomass rather than abundance-based interpretation of quantitative ribotype data in population and community ecology of protists.
Highlights:
(1) Temperature selects body size and rDNA copy number variants of protists.
(2) Cell size imposes a strong constraint on the rDNA CN per genome in protists.
(3) The power law function for rDNA CN- ciliate cell size relationship we obtained in this study may not be applicable for prokaryotes and some small-sized eukaryotes.
(4) The scaling relationship between rRNA/ribosome content and cell size is valid and consistent within a wide size range of life across heterotrophic bacteria, protists, and macroorganisms.
(5) The smaller the cell, the faster the growth, the higher rRNA concentration, the higher P:C ratio, thus the higher requirment for nutirents, and the lower carbon content in the biomass.
(6) Per-cell rRNA and rDNA copy numbers and environmental temperature may be used to predict the growth rate of uncultured microorganisms.
(7) the ribotype quantity of a population is more related with their biomass rather than cell abundance, especially when there are large variations in cell size within this population;
(8) the relative proportion of a population, or between two populations, within a protist community reflects their proportion in biomass rather than cell abundance; (9) the diversity indices involving the relative abundance of ribotypes of species (e.g., Shannon and Simpson diversities) reflect also biomass-based diversity of the protist communities; and
(10) the effect of body size has to be considered when interpreting rRNA:rDNA data for protistan activities.
Highlights:
(1) Temperature selects body size and rDNA copy number variants of protists.
(2) Cell size imposes a strong constraint on the rDNA CN per genome in protists.
(3) The power law function for rDNA CN- ciliate cell size relationship we obtained in this study may not be applicable for prokaryotes and some small-sized eukaryotes.
(4) The scaling relationship between rRNA/ribosome content and cell size is valid and consistent within a wide size range of life across heterotrophic bacteria, protists, and macroorganisms.
(5) The smaller the cell, the faster the growth, the higher rRNA concentration, the higher P:C ratio, thus the higher requirment for nutirents, and the lower carbon content in the biomass.
(6) Per-cell rRNA and rDNA copy numbers and environmental temperature may be used to predict the growth rate of uncultured microorganisms.
(7) the ribotype quantity of a population is more related with their biomass rather than cell abundance, especially when there are large variations in cell size within this population;
(8) the relative proportion of a population, or between two populations, within a protist community reflects their proportion in biomass rather than cell abundance; (9) the diversity indices involving the relative abundance of ribotypes of species (e.g., Shannon and Simpson diversities) reflect also biomass-based diversity of the protist communities; and
(10) the effect of body size has to be considered when interpreting rRNA:rDNA data for protistan activities.
Research Interests:
Species determination is crucial in biodiversity research. In tintinnids, identification is based almost exclusively on the lorica, despite its frequent intraspecific variability and interspecific similarity. We suggest updated procedures... more
Species determination is crucial in biodiversity research. In tintinnids, identification is based almost exclusively on the lorica, despite its frequent intraspecific variability and interspecific similarity. We suggest updated procedures for identification and, depending on the aim of the study, further steps to obtain morphological, molecular, and ecological data. Our goal is to help improving the collection of information (e.g., species re-/descriptions and DNA barcodes) that is essential for generating a natural tintinnid classification and a reliable reference for environmental surveys. These suggestions are broadly useful for protistologists because they exemplify data integration, quality/effort compromise, and the need for scientific collaborations.
Research Interests:
The phylum Ciliophora plays important roles in a wide range of biological studies. However, the evolutionary relationships of many groups remain unclear due to a lack of sufficient molecular data. In this study, molecular dataset was... more
The phylum Ciliophora plays important roles in a wide range of biological studies. However, the evolutionary relationships of many groups remain unclear due to a lack of sufficient molecular data. In this study, molecular dataset was expanded with representatives from 55 orders and all major lineages. The main findings are: (1) 14 classes were recovered including one new class, Protocruziea n. cl.; (2) in addition to the two main branches, Postciliodesmatophora and Intramacronucleata, a third branch, the Mesodiniea, is identified as being basal to the other two subphyla; (3) the newly defined order Discocephalida is revealed to be a sister clade to the euplotids, strongly suggesting the separation of discocephalids from the hypotrichs; (4) the separation of mobilids from the peritrichs is not supported; (5) Loxocephalida is basal to the main scuticociliate assemblage, whereas the thigmotrichs are placed within the order Pleuronematida; (6) the monophyly of classes Phyllopharyngea, Karyorelictea, Armophorea, Prostomatea, Plagiopylea, Colpodea and Heterotrichea are confirmed; (7) ambiguous genera Askenasia, CyclotrichiumParaspathidium and Plagiocampa show close affiliation to the well known plagiopyleans; (8) validity of the subclass Rhynchostomatia is supported, and (9) the systematic positions of Halteriida and Linconophoria remain unresolved and are thus regarded as incertae sedis within Spirotrichea.
Research Interests:
Protistan bacterivory, a microbial process involving ingestion and digestion, is ecologically important in the microbial loop in aquatic and terrestrial ecosystems. While bacterial resistance to protistan ingestion are relatively well... more
Protistan bacterivory, a microbial process involving ingestion and digestion, is ecologically important in the microbial loop in aquatic and terrestrial ecosystems. While bacterial resistance to protistan ingestion are relatively well understood, little is known about protistan digestion in which some ingested bacteria could not be digested in cells of major protistan grazers in the natural environment. Here we report the phylogenetic identities of digestion-resistant bacteria (DRB) that could survive starvation and form relatively stable associations with 11 marine and one freshwater ciliate species. Using clone library and sequencing of 16S rRNA genes, we found that the protistan predators could host a high diversity of DRB, most of which represented novel bacterial taxa that have not been cultivated. The localization inside host cells, quantity, and viability of these bacteria were checked using fluorescence in situ hybridization. The DRB were affiliated with Actinobacteria, Bacteroidetes, Firmicutes, Parcubacteria (OD1), Planctomycetes, and Proteobacteria, with Gammaproteobacteria and Alphaproteobacteria being the most frequently occurring classes. The dominance of Gamma- and Alphaproteobacteria corresponds well to a previous study of Global Ocean Sampling metagenomic data showing the widespread types of bacterial type VI and IV secretion systems (T6SS and T4SS) in these two taxa, suggesting a putatively significant role of secretion systems in promoting marine protist-bacteria associations. In the DRB assemblages, opportunistic bacteria such as Alteromonadaceae, Pseudoalteromonadaceae and Vibrionaceae often presented with high proportions, indicating these bacteria could evade protistan grazing thus persist and accumulate in the community, which, however, contrasts with the well-known rarity of these bacteria in nature. This begs the question whether viral lysis is significant in killing these indigestible bacteria in microbial communities. Taken together, our study on the identity of DRB sheds new light on microbial interactions and generates further hypothesis on the potential importance of bacterial protein secretion systems in structuring bacterial community composition and functioning of “microbial black box” in aquatic environments.
Research Interests: Marine Ecology, Microbial Ecology, Marine Microbial Ecology, Functional Ecology, Protistology, and 9 moreBacterial Pathogenesis, Grazing Ecology, Protistan Ecology, Microbial Interactions Between Marine Viruses, Protistan grazing rates, Bacteria-protist network, Protist-bacteria symbiosis, Protist-bacteria association, and Digestion-resistant bacteria
Seagrass colonization will change the chemistry and biogeochemical cycles mediated by microbes in coastal sediments. In this study, we molecularly characterized the diazotrophic assemblages and entire bacterial community in surface... more
Seagrass colonization will change the chemistry and biogeochemical cycles mediated by microbes in coastal sediments. In this study, we molecularly characterized the diazotrophic assemblages and entire bacterial community in surface sediments of a Zostera marina-colonized coastal lagoon in Northern China. Higher nitrogenase gene (nifH) copy numbers were detected in the vegetated sediments compared with the unvegetated sediments nearby. The detected nifH phylotypes were mostly affiliated with the Geobacteraceae, Desulfobulbus, Desulfocapsa and Pseudomonas. Redundancy analysis based on terminal restriction fragment length polymorphism analysis showed that the distribution of nifH genotypes was mostly shaped by the ratio of total organic carbon to nitrogen, the concentration of cadmium in the sediments, and the pH of the overlying water. High throughput sequencing and phylogenetic analyses of bacterial 16S rRNA genes also indicated the presence of Geobacteraceae and Desulfobulbaceae phylotypes in these samples. A comparison of these results with previous studies suggests the prevalence and predominance of iron(III)-reducing Geobacteraceae and sulfate-reducing Desulfobulbaceae diazotrophs in coastal sedimentary environments. Although the entire bacterial community structure was not significantly different between these two niches, Desulfococcus (δ-Proteobacteria) and Anaerolineae (Chloroflexi), presented with much higher proportions in the vegetated sediments, and Flavobacteriaceae (Bacteroidetes) occurred more frequently in the bare sediments. These data suggest that the high bioavailability of organic matter (indicated by relatively lower carbon-to-nitrogen ratios) and the less-reducing anaerobic condition in vegetated sediments may favor Desulfococcus and Anaerolineae lineages, which are potentially important populations in benthic carbon and sulfur cycling in the highly productive seagrass ecosystem.
Research Interests:
Little is known about the relative influence of historic processes and environmental gradients on shaping the diversity of single-celled eukaryotes in marine benthos. By combining pyrosequencing of 18S ribosomal RNA genes with data on... more
Little is known about the relative influence of historic processes and environmental gradients on shaping the diversity of single-celled eukaryotes in marine benthos. By combining pyrosequencing of 18S ribosomal RNA genes with data on multiple environmental factors, we investigated the diversity of microeukaryotes in surficial sediments of three basins of the Yellow Sea Large Marine Ecosystem. A considerable proportion (about 20%) of reads was affiliated with known parasitoid protists. Dinophyta and Ciliophora appeared dominant in terms of relative proportion of reads and OTU (operational taxonomic unit) richness. Overall, OTU richness of benthic microeukaryotes decreased with increasing water depth and decreasing pH. While community composition was significantly different among basins, partial Mantel tests indicated a depth-decay pattern of community similarity, whereby water depth, rather than geographic distance or environment, shaped beta-diversity of benthic microeukaryotes (including both the abundant and the rare biosphere) on a regional scale. Similar hydrographic and mineralogical factors contributed to the biogeography of both the abundant and the rare OTUs. The trace metal vanadium had a significant effect on the biogeography of the rare biosphere. Our study sheds new light on the composition, diversity patterns, and underlying mechanisms of single-celled eukaryote distribution in surficial sediments of coastal oceans.
Additional key words: depth-decay relationship; alpha diversity; beta diversity; protist and fungi; protozoa; parasitic protist; SSU ribotype diversity; continent shelf seafloor
Additional key words: depth-decay relationship; alpha diversity; beta diversity; protist and fungi; protozoa; parasitic protist; SSU ribotype diversity; continent shelf seafloor
Research Interests: Marine Biology, Oceanography, Coastal Processes, Marine Ecology, Community Ecology, and 10 moreMicrobial Ecology, Aquatic Microbial Ecology, Marine Microbial Ecology, Protistology, Ocean acidification, High Throughput Sequencing, Pyrosequencing, Marine biogeography, Protistan Ecology, and Depth decay relationship
Macroalgal blooms may lead to dramatic changes in physicochemical variables and biogeochemical cycling in affected waters. However, little is known about the effects of macroalgal blooms on marine bacteria, especially those functioning in... more
Macroalgal blooms may lead to dramatic changes in physicochemical variables and biogeochemical cycling in affected waters. However, little is known about the effects of macroalgal blooms on marine bacteria, especially those functioning in nutrient cycles. We measured environmental factors and investigated bacterial diazotrophs in two niches, surface waters that were covered (CC) and non-covered (CF) with massive macroalgal canopies of Ulva prolifera, in the Yellow Sea in the summer of 2011 using real-time PCR and clone library analysis of nifH genes. We found that heterotrophic diazotrophs (Gammaproteobacteria) dominated the communities and were mostly represented by Vibrio-related phylotypes in both CC and CF. Desulfovibrio-related phylotypes were only detected in CC. There were significant differences in community composition in these two environments (p < 0.001) and a much higher abundance of nifH in CC (4.55 x106 copies l-1) than in CF (2.49 x106 copies l-1). The nifH copy number was inversely related to concentrations of ammonium and dissolved inorganic nitrogen and to the stoichiometric ratios of N:P and N:Si. This indicates that macroalgal blooms significantly affect diazotrophic abundance and community composition and that vibrios and Desulfovibrio-related heterotrophic diazotrophs adapt well to the (N-rich but P-limited) environment during blooming. Potential ecological and microbiological mechanisms behind this scenario are discussed.
Research Interests:
The planktonic and benthic fungi in a sea cucumber farming system were simultaneously investigated on three sampling dates. Analyses of SSU rRNA gene libraries of four samples revealed 131 fungal operational taxonomic units, of which 58%... more
The planktonic and benthic fungi in a sea cucumber farming system were simultaneously investigated on three sampling dates. Analyses of SSU rRNA gene libraries of four samples revealed 131 fungal operational taxonomic units, of which 58% were potentially novel. Chytridiomycota, Blastocladiomycota and Monoblepharidomycota were detected only from sediment whereas ascomycetes and basidiomycetes dominated in sediment and water, respectively. Cryptomycota phylotypes were detected from both water and sediment samples. Based on terminal-restriction fragment length polymorphisms, distinct succession and contrasting community structure was found between planktonic and benthic habitats. Redundancy analysis indicated that the concentration of dissolved silicate in surface water and N:P in porewater were the most significant abiotic variables shaping the planktonic and benthic communities, respectively. This study indicates that plankton and benthos are distinct habitats for fungal distribution even in shallow coastal systems, and nutrients and stoichiometric ratios play important roles in driving succession of fungal communities.
Research Interests:
Exposure to pathogens in recreational, or drinking water is a serious public health concern. It is important to rapidly determine and identify trace levels of pathogens in real environmental samples. We report here on a label-free... more
Exposure to pathogens in recreational, or drinking water is a serious public health concern. It is important to rapidly determine and identify trace levels of pathogens in real environmental samples. We report here on a label-free potentiometric aptasensor for rapid, sensitive and selective detection of Listeria monocytogenes (LM), a pathogen widely distributed in the environment. An aptamer binds specifically to internalin A, a surface protein present in LM cells. The target-binding event prevents the aptamer from electrostatically interacting with protamine, which can be sensitively detected using a polycation-sensitive membrane electrode. Using this method, LM can be detected down to 10 CFU mL-1. Coupled to an online filtration system, the bioassay has been evaluated with spiked coastal seawater samples and shows good recovery and high accuracy. This work demonstrates the possibility of developing potentiometric aptasensors for determination and identification of various bacteria in environmental samples.
Research Interests:
The spatial and temporal patterns of diversity, community structure, and their drivers are fundamental issues in microbial ecology. This study aimed to investigate the relative importance of spatial and seasonal controls on the... more
The spatial and temporal patterns of diversity, community structure, and their drivers are fundamental issues in microbial ecology. This study aimed to investigate the relative importance of spatial and seasonal controls on the distribution of nitrogen cycling microbes in sediments of estuarine tidal flats, and to test the hypothesis that metals impact the distribution of nitrogen-cycling microbes in the coastal system. Two layers of sediment samples were collected from three estuarine tidal flats of Laizhou Bay in 2010 winter and 2011 summer. The alpha diversities (Shannon and Simpson indices) and community structure of ammonia oxidizing bacteria (AOB) and archaea (AOA), denitrifier and anammox bacteria (AMB) were revealed using denaturing gradient gel electrophoresis and clone library analysis of amoA, nosZ and 16S rRNA gene markers. We found that both AOB and AMB exhibited distinct seasonal patterns in either alpha diversity or community turnover; AOA had different alpha diversities in two layers, but neither spatial nor seasonal patterns were found for their community turnover. However, no distinct spatiotemporal pattern was observed for either diversity or community composition of nosZ-type denitrifiers. For correlations between alpha diversities and environmental factors, significant correlations were found between AOB and ammonium, temperature and As, between denitrifiers and nitrite, salinity and Pb, and between AMB and Pb, ratio of organic carbon to nitrogen, ammonium, pH and dissolved oxygen. Salinity and sediment grain size were the most important factors shaping AOB and AOA communities, respectively; whereas AMB community structure was mostly determined by temperature, dissolved oxygen, pH and heavy metals As and Cd. These results stress that ammonia oxidizers, denitrifiers and anammox bacteria have generally different distributional patterns across time and space, and heavy metals might have contributed to their differentiated distributions in coastal sediments.
Research Interests:
Nanociliates have been frequently found to be important players in the marine microbial loop, however, little is known about their diversity and distribution in coastal ecosystems. We investigated the molecular diversity and distribution... more
Nanociliates have been frequently found to be important players in the marine microbial loop, however, little is known about their diversity and distribution in coastal ecosystems. We investigated the molecular diversity and distribution patterns of nanoplanktonic oligotrich and choreotrich (OC) ciliates in surface water of three neritic basins of northern China, the South Yellow Sea (SYS), North Yellow Sea (NYS), and Bohai Sea (BS) in June and November 2011. SSU rRNA gene clone libraries generated from three summertime samples (sites B38, B4 and H8) were analyzed and revealed a large novel ribotype diversity, of which many were low-abundant phylotypes belonging to the subclass Oligotrichia, but divergent from described morphospecies. Based on the data of terminal-restriction fragment length polymorphism (T-RFLP) analysis of all 35 samples, we found that the T-RF richness was generally higher in the SYS than in the BS, and negatively correlated with the molar ratio of P to Si. Overall, multidimensional scaling and permutational multivariate analysis of variance of the community turnover demonstrated a distinct seasonal pattern but no basin-to-basin differentiation across all samples. Nevertheless, significant community differences among basins were recognized in the winter dataset. Mantel tests showed that the environmental factors, P:Si ratio, water temperature and concentration of dissolved oxygen (DO), determined the community across all samples. However, both biogeographic distance and environment shaped the community in winter, with DO being the most important physicochemical factor. Our results indicate that the stoichiometric ratio of P:Si is a key factor, through which the phytoplankton community may be shaped, resulting in a cascade effect on the diversity and community composition of OC nanociliates in the N-rich, Si-limited coastal surface waters, and that the Yellow Sea Warm Current drives the nanociliate community, and possibly the microbial food webs, in the coastal ecosystem in winter.
Research Interests:
Anaerobic ammonium oxidation (anammox) as an important process of nitrogen cycle has been studied in estuarine environments. However, knowledge about the dynamics of anammox bacteria and their interactions with associated activity remains... more
Anaerobic ammonium oxidation (anammox) as an important process of nitrogen cycle has been studied in estuarine environments. However, knowledge about the dynamics of anammox bacteria and their interactions with associated activity remains scarce in these environments. Here we report the anammox bacterial diversity, abundance, and activity in the Yangtze Estuary, using molecular and isotope-tracing techniques. The phylogenetic analysis of 16S rRNA indicated that high anammox bacterial diversity occurred in this estuary, including Scalindua, Brocadia, Kuenenia, and two novel clusters. The patterns of community composition and diversity of anammox bacteria differed across the estuary. Salinity was a key environmental factor defining the geographical distribution and diversity of the anammox bacterial community at the estuarine ecosystem. Temperature and organic carbon also had significant influences on anammox bacterial biodiversity. The abundance of anammox bacteria ranged from 2.63 × 106 and 1.56 × 107 gene copies g-1, and its spatiotemporal variations were related significantly to salinity, temperature, and nitrite content. The anammox activity was related to temperature, nitrite, and anammox bacterial abundance, with values of 0.94–6.61 nmolNg-1 h-1. The tight link between the anammox and denitrification processes implied that denitrifying bacteria may be a primary source of nitrite for the anammox bacteria in the estuarine marshes. On the basis of the 15N tracing experiments, the anammox process was estimated to contribute 6.6%–12.9% to the total nitrogen loss whereas the remainder was attributed to denitrification.
Research Interests:
The relative abundances of nitrifying, denitrifying and anammox prokaryotes in sediments of three hypernutrified estuarine tidal flats of Laizhou Bay, Bohai Sea, China were investigated. Quantitative PCR estimates indicated that in most... more
The relative abundances of nitrifying, denitrifying and anammox prokaryotes in sediments of three hypernutrified estuarine tidal flats of Laizhou Bay, Bohai Sea, China were investigated. Quantitative PCR estimates indicated that in most cases archaeal (AOA) amoA genes were more abundant than bacterial (AOB) amoA genes, and ratio of AOA/AOB was correlated with pH, Cd and Cu. Of the denitrifiers, nirK-type outnumbered nirS-type, with nosZ-type being the lowest. Variation of the ratio between nirK and nirS abundance depends on pH, nitrite, nitrate and Cd. The combination of (nirS+nirK-nosZ), an indicator of genetic potentials for N2O emission, was only related to the temperature. Anammox bacterial 16S rRNA gene abundances were correlated with salinity, pH, nitrite, and Cu. In contrast, the contribution of anammox to N2 production, by using anammox bacterial 16S rRNA/nosZ ratio as a proxy, was correlated to temperature, ammonium and dissolved oxygen in the overlying water, ratio of organic carbon to nitrogen and arsenic in sediments. Our study stresses that abundances of N-cycling functional groups respond differently to variations of environmental conditions, and multiple factors including heavy metals with relatively low concentrations may play a role in shaping nitrogen cycling processes in these estuarine tidal flats.