Similar but different: Characterization of dddD gene-mediated DMSP metabolism among coral-associated Endozoicomonas.

Endozoicomonas are often predominant bacteria and prominently important in coral health. Their role in dimethylsulfoniopropionate (DMSP) degradation has been a subject of discussion for over a decade. A previous study found that Endozoicomonas degraded DMSP through the dddD pathway. This process releases dimethyl sulfide, which is vital for corals coping with thermal stress. However, little is known about the related gene regulation and metabolic abilities of DMSP metabolism in Endozoicomonadaceae. In this study, we isolated a novel Endozoicomonas DMSP degrader and observed a distinct DMSP metabolic trend in two phylogenetically close dddD-harboring Endozoicomonas species, confirmed genetically by comparative transcriptomic profiling and visualization of the change of DMSP stable isotopes in bacterial cells using nanoscale secondary ion spectrometry. Furthermore, we found that DMSP cleavage enzymes are ubiquitous in coral Endozoicomonas with a preference for having DddD lyase. We speculate that harboring DMSP degrading genes enables Endozoicomonas to successfully colonize various coral species across the globe.

Quantitatively deciphering the roles of sediment nitrogen removal in environmental and climatic feedbacks in two subtropical estuaries.

Sedimentary denitrification and anaerobic ammonium oxidation (anammox) are two microbially-mediated nitrogen removal pathways with distinct climatic feedbacks. Estuaries receive large fluxes of anthropogenic nitrogen and serve as hotspots for nitrogen loss. Applying 15N isotope pairing technique and sediment intact core incubation in two subtropical estuaries, the Yangtze River Estuary (YRE) and Jiulong River Estuary (JRE), we show that denitrification predominates the sedimentary nitrogen loss with a minor contribution (8.6 ± 7.5%) from anammox. Particulate organic matter degradation sustains the sedimentary nitrogen removal linking the nitrogen transformations between water column and sediment. Our results indicate that estuarine sediments exhibit high areal nitrogen removal rate, but play a relatively weak role in eliminating the nitrogen inputted from river basin due to the limited area. The riverine excess nitrogen will eventually enter into the adjacent continental shelf and be removed via phytoplankton assimilation-sedimentation-degradation-coupled nitrification-denitrification. In addition, sedimentary denitrification causes 1.8 ± 2.2% of nitrogen flow towards nitrous oxide (N2O) production and the derived N2O release flux accounts for 59% and 65% of the daily sea-air N2O emission in the YRE and JRE, respectively. These findings contribute to a better understanding of estuarine sedimentary nitrogen removal and associated climate feedbacks, and to the parameterization of Earth system models.

Sedimentary processes dominate nitrous oxide production and emission in the hypoxic zone off the Changjiang River estuary.

Coastal oceans, known as the major nitrous oxide (N2O) source to the atmosphere, are increasingly subject to eutrophication and concurrent near-bottom hypoxia. The natural nitrogen cycle is likely to be altered markedly in hypoxic coastal oceans. However, the processes responsible for N2O production and emission remain elusive because of lacking field rate measurements simultaneously conducted in the water column and sediment. Here, we quantified N2O production rates using a 15N-labeled technique in the water-column and surface sediments off the Changjiang (Yangtze) River estuary, the largest hypoxic zone in the Pacific margins. Our results showed that the estuarine surface sediments were the major source for N2O production, accounting for approximately 90% of the total water-column accumulation and consequent efflux of N2O in the hypoxic zone, whereas the water-column nitrification and denitrification combined only contributed <10%. More importantly, the coupling of nitrification and denitrification at the presence of abundant supply and remineralization of labile organic matter was the main driver of the N2O release from the sediment-water interface in this region. This study highlights the dominant role of benthic processes occurring at the sediment-water interface controlling the coastal N2O budget, as the anthropogenic eutrophication and hypoxia are expanding in coastal oceans.

Unusual Roles of Discharge, Slope and SOC in DOC Transport in Small Mountainous Rivers, Taiwan.

Riverine dissolved organic carbon (DOC), responsible for riverine productivity, is rarely documented in subtropical small mountainous rivers (SMRs) where high rainfall and steep slopes are the main features. This study investigated the DOC export at eight sites in three Taiwan SMRs to characterize the dynamics and controlling factors of DOC transport. Results showed that the mean DOC concentration of ~0.78 mg L-1 is much lower than the global average of ~5.29 mg L-1. However, the mean DOC yield, ~22.51 kg-C ha-1 yr-1, is higher than the global average of 14.4-19.3 kg-C ha-1 yr-1. Comparing with worldwide rivers from literature, the annual discharge, slope, and SOC (soil organic carbon) are controlling factors as expected, though they influence in different ways. SOC stock likely regulated by elevation-dependent biomes dominate the DOC supply, while slope restrains the DOC generation due to shallow soil depth and fast runoff velocity. However, the abundant discharge flushing this persistent low supply leads to a large DOC export in the SMRs. Furthermore, the DOC dynamics during typhoon periods showed a clockwise hysteresis, suggesting that the DOC is mainly from the riparian zone or downslope area during the rising limb of the hydrograph. This study elucidates the DOC transport in SMRs and provides an atypical yet significant piece of understanding on DOC transport in a global context.

Organic matter decomposition sustains sedimentary nitrogen loss in the Pearl River Estuary, China.

The Pearl River Estuary (PRE) has long received tremendous amounts of anthropogenic nitrogen, and is facing severe environmental problems. Denitrification and anaerobic ammonium oxidation (anammox) are known to be two major nitrogen removal pathways in estuarine sediments. Through the use of slurry and intact sediment core incubations, we examined the nitrogen removal pathways and quantified the in situ denitrification and anammox with associated gaseous nitrogen production rates. Sedimentary nitrogen removal was predominated by denitrification (93-100%) relative to a minimal contribution (<7%) from anammox. Among the detected environmental factors, salinity, bottom water NOx- (nitrate and nitrite) concentration, sedimentary organic matter and dissolved oxygen consumption rates showed good correlations with denitrification and anammox rates. Sedimentary nitrogen loss was mainly supported by endogenic coupled nitrification-denitrification (6.0 ±â€¯1.5 × 106 mol N d-1), with water-column-delivered NOx- (2.1 ±â€¯0.6 × 106 mol N d-1) as the secondary source. Such results suggested that sedimentary nitrogen removal involved mainly particulate organic form (allochthonous or autochthonous) deposited onto sediments, rather than inorganic forms in overlying water. Meanwhile, total N2O production from sediments was estimated to be 7.3 ±â€¯2.1 × 104 mol N d-1, equivalent to ~35% of the daily N2O emissions in the PRE.

Nitrogen transformations and removal efficiency enhancement of a constructed wetland in subtropical Taiwan.

Urbanization condenses reactive nitrogen into cities leaving threats of nitrogen pollution onto nearby environments when sewage is not properly treated. Constructed wetland is an ecological and economical way to remove reactive nitrogen. We investigated the seasonal nitrogen transformations and removal pathways in a surface-flow constructed wetland (93,000m2 with five treatment cells), which treats domestic wastewater in subtropical Taiwan. By using isotopic pairing technique, we found denitrification exceeds anammox dominated the nitrogen removal pathway throughout seasons. The potential denitrification (0.09 to 2.84gNm-2d-1) in the overlying water was in the same magnitude relative to that in sediments (1.26 to 4.14gNm-2d-1). The denitrification rates in sediments were highest in summer followed by autumn and winter. The concentration removal efficiencies of ammonium and dissolved inorganic nitrogen (DIN) were both highest in summer, then decreased significantly in autumn and winter. Temperature is a significant regulator for seasonal nitrogen removal. However, a positive correlation was observed between the potential denitrification rates and the amount of 15NO3- addition, indicating that nitrate addition may still stimulate denitrification under low temperature condition in winter (15.2-16.3°C). Since nitrate concentrations in porewater were much lower than that in water column for autumn and winter, we speculated NOx--N (nitrite and nitrate) supply to the sediments was a limiting factor for low DIN removal efficiency. We proposed to enhance nitrate removal efficiency via denitrification by physically promoting NOx--N and oxygen exchanges through the sediment-water interface.

Modeling the terrestrial N processes in a small mountain catchment through INCA-N: A case study in Taiwan.

Riverine dissolved inorganic nitrogen (DIN) is an important indicator of trophic status of aquatic ecosystems. High riverine DIN export in Taiwan, ~3800kg-Nkm-2yr-1, which is ~18 times higher than the global average, urges the need of thorough understanding of N cycling processes. We applied INCA-N (Integrated Nitrogen Catchment Model) to simulate riverine DIN export and infer terrestrial N processes using weekly rainwater and streamwater samples collected at the Fushan Experimental Forest (FEF) of northern Taiwan. Results showed that the modeled discharge and nitrate export are in good agreement with observations, suggesting the validity of our application. Based on our modeling, the three main N removal processes, in the order of descending importance, were plant uptake, riverine N transport and denitrification at FEF. The high plant uptake rate, 4920kg-Nkm-2yr-1, should have led to accumulation of large biomass but biomass at FEF was relatively small compared to other tropical forests, likely due to periodic typhoon disruptions. The low nitrate concentration but high DIN export highlights the importance of hydrological control over DIN export, particularly during typhoons. The denitrification rate, 750kg-Nkm-2yr-1, at FEF was also low compared to other tropical forest ecosystems, likely resulting from quick water drainage through the coarse-loamy top soils. The high DIN export to atmospheric deposition ratio, 0.45, suggests that FEF may be in advanced stages of N excess. This simulation provides useful insights for establishing monitoring programs and improves our understanding N cycling in subtropical watersheds.

Prokaryotic assemblages and metagenomes in pelagic zones of the South China Sea.

BACKGROUND: Prokaryotic microbes, the most abundant organisms in the ocean, are remarkably diverse. Despite numerous studies of marine prokaryotes, the zonation of their communities in pelagic zones has been poorly delineated. By exploiting the persistent stratification of the South China Sea (SCS), we performed a 2-year, large spatial scale (10, 100, 1000, and 3000 m) survey, which included a pilot study in 2006 and comprehensive sampling in 2007, to investigate the biological zonation of bacteria and archaea using 16S rRNA tag and shotgun metagenome sequencing. RESULTS: Alphaproteobacteria dominated the bacterial community in the surface SCS, where the abundance of Betaproteobacteria was seemingly associated with climatic activity. Gammaproteobacteria thrived in the deep SCS, where a noticeable amount of Cyanobacteria were also detected. Marine Groups II and III Euryarchaeota were predominant in the archaeal communities in the surface and deep SCS, respectively. Bacterial diversity was higher than archaeal diversity at all sampling depths in the SCS, and peaked at mid-depths, agreeing with the diversity pattern found in global water columns. Metagenomic analysis not only showed differential %GC values and genome sizes between the surface and deep SCS, but also demonstrated depth-dependent metabolic potentials, such as cobalamin biosynthesis at 10 m, osmoregulation at 100 m, signal transduction at 1000 m, and plasmid and phage replication at 3000 m. When compared with other oceans, urease at 10 m and both exonuclease and permease at 3000 m were more abundant in the SCS. Finally, enriched genes associated with nutrient assimilation in the sea surface and transposase in the deep-sea metagenomes exemplified the functional zonation in global oceans. CONCLUSIONS: Prokaryotic communities in the SCS stratified with depth, with maximal bacterial diversity at mid-depth, in accordance with global water columns. The SCS had functional zonation among depths and endemically enriched metabolic potentials at the study site, in contrast to other oceans.

Microbial and viral metagenomes of a subtropical freshwater reservoir subject to climatic disturbances.

Extreme climatic activities, such as typhoons, are widely known to disrupt our natural environment. In particular, studies have revealed that typhoon-induced perturbations can result in several long-term effects on various ecosystems. In this study, we have conducted a 2-year metagenomic survey to investigate the microbial and viral community dynamics associated with environmental changes and seasonal variations in an enclosed freshwater reservoir subject to episodic typhoons. We found that the microbial community structure and the associated metagenomes continuously changed, where microbial richness increased after typhoon events and decreased during winter. Among the environmental factors that influenced changes in the microbial community, precipitation was considered to be the most significant. Similarly, the viral community regularly showed higher relative abundances and diversity during summer in comparison to winter, with major variations happening in several viral families including Siphoviridae, Myoviridae, Podoviridae and Microviridae. Interestingly, we also found that the precipitation level was associated with the terrestrial viral abundance in the reservoir. In contrast to the dynamic microbial community (L-divergence 0.73 ± 0.25), we found that microbial metabolic profiles were relatively less divergent (L-divergence 0.24 ± 0.04) at the finest metabolic resolution. This study provides for the first time a glimpse at the microbial and viral community dynamics of a subtropical freshwater ecosystem, adding a comprehensive set of new knowledge to aquatic environments.

The factor VIII C1 domain contributes to platelet binding.

Activated factor VIII (FVIIIa) forms a procoagulant complex with factor IXa on negatively charged membranes, including activated platelet surfaces. Membrane attachment involves the FVIII C2 domain; involvement of the adjacent C1 domain has not been established. Binding of recombinant FVIII C1C2 and C2 proteins to platelets was detected by flow cytometry using (1) anti-C2 monoclonal antibody ESH8 followed by a phycoerythrin-labeled secondary antibody; (2) biotinylated C1C2 detected by phycoerythrin-labeled streptavidin, and (3) C1C2 and C2 site-specifically labeled with fluorescein. Highest binding and lowest background were obtained using fluorescein-conjugated proteins. More than 90% of activated platelets bound C1C2, compared with approximately 50% for equimolar C2. Estimates using fluorescent microbeads indicated approximately 7,000 C1C2-binding sites per platelet, approximately 1,400 for C2, and approximately 3,000 for fluorescein-labeled FVIIIa. Unlike C2 or FVIII(a), C1C2 bound to approximately 700 sites/platelet before activation. C1C2 binding to activated platelets appeared independent of von Willebrand factor and was competed effectively by FVIII(a), but only partially by excess C2. Fluorescein-labeled FVIIIa was competed much more effectively by C1C2 than C2 for binding to activated platelets. Two monoclonal antibodies that inhibit C2 binding to membranes competed platelet binding of C2 more effectively than C1C2. Thus, the C1 domain of FVIII contributes to platelet-binding affinity.

Severe haemophilia B due to a 6 kb factor IX gene deletion including exon 4: non-homologous recombination associated with a shortened transcript from whole blood.

In genotyping a severe hemophilia B subject, exons 1-3 and 5-8 were normal. Exon 4 did not amplify, suggesting a partial gene deletion. Previously, a French family with an exon 4 deletion had severe haemophilia B with a circulating, dysfunctional factor IX protein missing its first growth factor-like domain; breakpoints were not analyzed. Using a 5' primer for exon 3 and a 3' primer for exon 5 fragments, the subject's factor IX gene amplified a 5 kb fragment whereas 11 kb was predicted, indicating a 6 kb deletion. Restriction endonucleases localized the 3' intron 4 deletion breakpoint to 1.2 kb 5' to exon 5. Sequencing through the breakpoints revealed a 5,969 bp deletion that included exon 4 and was accompanied by a 13 bp duplication inserted near the 3' breakpoint site. Haemophilia was familial; on testing, his mother was confirmed as a heterozygous carrier, whereas his sister was homozygous for the normal, larger fragments. As exons 4 and 5 of the factor IX gene are in frame, this deletion should produce a shortened transcript, missing 114 bp (38 codons from the first growth factor-like domain). Reverse transcription of mRNA prepared from whole blood and PCR identified the shorter cDNA fragment. Western blotting demonstrated a smaller factor IX protein.