Integrated Biogeography and Assembly Mechanisms of Microeukaryotic Communities in Coastal Waters Near Shellfish Cultivation.

The Lianjiang coast in the East China Sea is a typical subtropical marine ecosystem, and shellfish cultivation occupies almost all of the available tidal flats. Many studies have investigated the effects of shellfish cultivation on benthic organisms and sediments, while the impact of shellfish cultivation on plankton ecosystems is still poorly understood. This study investigated the biogeographical patterns of microeukaryotic communities from Lianjiang coastal waters in four seasons using 18S ribosomal RNA gene amplicon sequencing. Microeukaryotes were mainly comprised of Dinoflagellata, Diatomea, Arthropoda, Ciliophora, Chlorophyta, Protalveolata, Cryptophyceae, and Ochrophyta, and presented significant differences in three habitats (the aquaculture area, confluent area, and offshore area) and four seasons. Similarity percentage analysis revealed that Paracalanus parvus, Heterocapsa rotundata, Bestiolina similis, and five additional key taxa contributed to spatio-temporal differences. Seasonal environmental and spatial factors explained 27.47% of microeukaryotic community variation on average, with 11.11% of the variation shared. Environmental variables, particularly depth, pH, and nitrite concentration, were strongly associated with the microeukaryotic community compositions. The neutral community model further demonstrated that stochastic processes were sufficient in shaping substantial variation in microeukaryotic communities across four seasons, which may reveal the remaining unexplained microeukaryotic community variation. We further divided four seasons into the aquaculture stages and non-aquaculture stages, and speculated that aquaculture activities may increase the dispersal limitation of microeukaryotes in coastal waters, especially for the big bodied-microbes like Arthropoda. The results provide a better understanding of the biogeographical patterns, processes, and mechanisms of microeukaryotic communities near shellfish cultivation.

Microbial Community Structure and Metabolic Potential at the Initial Stage of Soil Development of the Glacial Forefields in Svalbard.

Microbial communities have been identified as the primary inhabitants of Arctic forefields. However, the metabolic potential of microbial communities in these newly exposed soils remains underexplored due to limited access. Here, we sampled the very edge of the glacial forefield in Svalbard and performed the 16S rRNA genes and metagenomic analysis to illustrate the ecosystem characteristics. Burkholderiales and Micrococcales were the dominant bacterial groups at the initial stage of soil development of glacial forefields. 214 metagenome-assembled genomes were recovered from glacier forefield microbiome datasets, including only 2 belonging to archaea. Analysis of these metagenome-assembled genomes revealed that 41% of assembled genomes had the genetic potential to use nitrate and nitrite as electron acceptors. Metabolic pathway reconstruction for these microbes suggested versatility for sulfide and thiosulfate oxidation, H2 and CO utilization, and CO2 fixation. Our results indicate the importance of anaerobic processes in elemental cycling in the glacial forefields. Besides, a range of genes related to adaption to low temperature and other stresses were detected, which revealed the presence of diverse mechanisms of adaption to the extreme environment of Svalbard. This research provides ecological insight into the initial stage of the soil developed during the retreating of glaciers.

Hypoxia and nutrient dynamics affected by marine aquaculture in a monsoon-regulated tropical coastal lagoon.

The Laoyehai (lagoon) is located at the east coast of Hainan Island in the South China Sea and has been subject to perturbations from human activities, notably marine aquaculture, and has eutrophic surface and hypoxic near-bottom waters. A lack of knowledge of hydrodynamic and biogeochemical processes is a challenge to the sustainable management of lagoon at the ecosystem level in science. Five field campaigns, including three during the southwest monsoon and two in the northeast monsoon periods, were carried out at the Laoyehai in 2008-2011. The aim of this study is to investigate the impacts of dynamic processes of hydrography and human activities on nutrient geochemistry and their relationships to the system eutrophication and hypoxia in the lagoon. In this coastal system, high levels of ammonium relative to nitrate are found, elevated phosphate skews the DIN/DIP relative to the Redfield ratio, and the dissolved silicate concentration is high because of submarine groundwater discharge. The organic fraction in the Laoyehai accounts for a large proportion of the total nutrients associated with the release of wastes from marine aquaculture. The hypoxia of near-bottom waters in the Laoyehai is created and maintained by heterotrophic processes that are fueled by organic matter, which are exacerbated by poor water exchange as a consequence of the geomorphology and weak tidal circulation.

Unveiling changes in the complexation of dissolved organic matter with Pb(II) by photochemical and microbial degradation using fluorescence EEMs-PARAFAC.

Dissolved organic matter (DOM) is very important in determining the speciation, behaviors, and risk of metal pollutants in aquatic ecosystems. Photochemical and microbial degradation are key processes in the cycling of DOM, yet their effects on the DOM-Pb(II) interaction remain largely unknown. This was studied by examining the complexation of river DOM with Pb(II) after degradation, using fluorescence quenching titration and excitation-emission matrices-parallel factor analysis (EEMs-PARAFAC). Three humic-like and two protein-like components were identified, with strong removals of humic-like components and decreasing average molecular weight and humification degree of DOM by photo- and photo-microbial degradation. The changes in humic-like abundance and structure resulted in notable weakening of their interaction with Pb(II). The tryptophan-like C2 was also mainly removed by photo-degradation, while the tyrosine-like C3 could be either removed or accumulated. The Pb(II)-binding of protein-like components was generally weaker but was enhanced in some degradation groups, which might be related to the lowering competition from humic-like components. The binding parameters correlated significantly with the DOM indices, which were dominated by photo-degradation for humic-like components but by seasonal variations for the tyrosine-like component. These results have implications for understanding the key mechanisms underlying the variability of the DOM-metal interaction in aquatic environments.

Characterization of sediment organic matter in the outer Yangtze River Estuary using stable isotopes, optical techniques, and FT-ICR-MS: Implications for the carbon burial mechanism.

The burial of sediment organic matter (SOM) in the estuary and shelf plays an important role in the global carbon cycle. However, it is challenging to determine the source, composition, and burial of SOM in the coastal sea, especially at the molecular level. This was explored in the coastal area outside the largest Yangtze River of China with multiple techniques including elemental and stable isotopic analysis, absorption spectroscopy, fluorescence excitation-emission matrices coupled with parallel factor analysis (EEMs-PARAFAC), and ultra-high resolution Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS). The end-member mixing analysis based on δ13C and δ15N showed a dominance of marine contribution (up to 70%) at most stations while the terrestrial contribution increased to >55% nearshore in summer at a high fluvial sediment flux. This was consistent with the offshore decreasing humic-like C1 and C2, humification index (HIX), %lignin-like compounds, and %CHO but increasing tryptophan-like C3, biological index (BIX), %protein-like compounds, and %CHOS from EEMs-PARAFAC and FT-ICR-MS analysis. The %clay correlated positively with SOM content, HIX, %lignin-like compounds, O/C, and modified aromaticity index (AImod) but correlated negatively with %C3, H/C, and the relative abundance of labile formulas (MLBL), while %silt showed contrasting correlations. These results indicated the fine clay sediments adsorbed more humified, aromatic, oxygenated, and terrestrial compounds that were probably more resistant to biodegradation and thus had a higher burial efficiency than those on the silty sediments. Principal component analysis based on SOM indices further revealed different characteristics of SOM in the nearshore, northern offshore, and southern offshore regions, which were probably dependent on the delivery by local current systems. Overall, these findings contributed to unraveling the source and molecular composition of SOM associated with different grain size sediments and local current delivery, which are fundamental for understanding the factors underlying carbon burial in the complex coastal environment.

Short-term sedimentary evidence for increasing diatoms in Arctic fjords in a warming world.

Arctic fjords are hotspots of marine carbon burial, with diatoms playing an essential role in the biological carbon pump. Under the background of global warming, the proportion of diatoms in total phytoplankton communities has been declining in many high-latitude fjords due to increased turbidity and oligotrophication resulting from glacier melting. However, due to the habitat heterogeneity among Svalbard fjords, diatom responses to glacier melting are also expected to be complex, which will further lead to changes in the biological carbon pumping and carbon sequestration. To address the complexity, three short sediment cores were collected from three contrasting fjords in Svalbard (Krossfjorden, Kongsfjorden, Gronfjorden), recording the history of fjord changes in recent decades during significant glacier melting. The amino acid molecular indicators in cores K4 and KF1 suggested similar organic matter degradation states between these two sites. In contrast to the turbid Kongsfjorden and Gronfjorden, preserved fucoxanthin in Krossfjorden indicated a continuous increase in diatoms since the mid-1980s, corresponding to a 59 % increase in biological carbon pumping, as quantified by the δ13C of sedimentary organic carbon. The increasing biological carbon pumping in Krossfjorden is further attributed to its hard rock types in the glacier basin, compared to Kongsfjorden and Gronfjorden, which are instead covered by soft rocks, as confirmed by a one-dimensional model. Given the distribution of rock types among basins in Svalbard, we extrapolate our findings and propose that approximately one-fifth of Svalbard's fjords, especially those with hard rock basins and persistent marine-terminated glaciers, still have the potential for an increase in diatom fractions and efficient biological carbon pumping. Our findings reveal the complexity of fjord phytoplankton responses and biological carbon pumping to increasing glacier melting, and underscore the necessity of modifying Arctic marine carbon feedback to climate change based on results from fjords underlain by hard rocks.

The hidden acceleration pump uncovers the role of shellfish in oceanic carbon sequestration.

Whether shellfish mariculture should be included in the blue carbon profile as a strategy to combat climate change has been controversial. It is highly demanding not only to provide calibration quantitation, but also to provide an ecosystem-based mechanism. In this study, we chose mussel farms as a case study to evaluate their contributions to carbon sinks and their responses to sedimentary carbon fixation and sequestration. First, we quantified the air-sea CO2 flux in the mussel aquacultural zone and observed a weak carbon sink (-0.15 ± 0.07 mmol·m-2·d-1) during spring. Next, by analyzing the carbon composition in the sediment, we recorded a noticeable and unexpected increase in the sedimentary recalcitrant carbon (RC) content in the mussel farming case. To address this surprising sedimentary phenomenon, a long-term indoor experimental test was conducted to distinguish the consequences of mussel engagement with sedimentary RC. Our observational data support the idea that mussel engagement promotes accumulation of RC in sediments by 2.5-fold. Furthermore, the relative intensity of carboxylic-rich alicyclic molecule (CRAM)-like compounds (recalcitrant dissolved organic matter (RDOM)) increased by 451.4 % in the mussel-engaged sedimentary dissolved organic matter (DOM) in comparison to the initial state. Mussel engagement had a significantly positive effect on the abundance of sedimentary carbon-fixing genes. Therefore, we definitively conclude that mussel farming is blue carbon positive and propose a new alternative theory that mussel farming areas may have high carbon sequestration potential via an ecologically integrated "3 M" (microalgae-mussel-microbiota) consortium. The "mussel pump" accelerates carbon sequestration and enhances climate-related ecosystem services.

Capturing the influence of submarine groundwater discharge on nutrient speciation dynamics within an estuarine aquaculture ecosystem.

Submarine groundwater discharge (SGD) plays a crucial role in nutrient dynamics and eutrophication status of the typical estuarine ecosystems, which are hotspots for groundwater-borne nutrient and are sensitive to aquaculture activities. To evaluate the significant role of SGD in regulating nutrient dynamics in an aquaculture estuary, a radium mass balance model combined biological feeding experiment was carried out in the present study. The results demonstrated that SGD fluxes were estimated to be 15.9 ± 9.41 cm d-1, 18.1 ± 8.51 cm d-1, and 23.0 ± 13.7 cm d-1 during July 2019, October 2019 and April 2021, and the SGD-driven dissolved inorganic/organic nutrient fluxes were 0.6-3.1-fold, 0.2-0.9-fold and 0.4-29-fold higher than those of riverine input, respectively. Seasonal variabilities of SGD rates indicated that saline SGD is dominated and is primarily modified by the oceanic forcing stimulated by tidal and wave dynamics. The contrasting conditions between bottom-up (groundwater- and river-derived nutrient fluxes) and top-down (nutrient responses in estuarine waters), showed the significance of seasonal differences in the biochemical mechanisms and aquaculture effects of modifying nitrogen dynamics. Dissimilatory nitrate reduction to ammonium and nitrification were responsible for the contrasting NOx- (NO2- and NO3-) and NH4+ conditions in July and October, respectively, and these factors jointly regulated NOx- and NH4+ in April. Dissolved organic nitrogen (DON) was the predominant component among the three seasons, except for DON degeneration in October, and it increased due to NH4+ assimilation by the phytoplankton community. These findings indicated that biochemical transformation has potential ramifications for the dynamics of SGD-driven nutrients and the management in marine aquaculture ecosystems.

Soil microorganisms and methane emissions in response to short-term warming field incubation in Svalbard.

Introduction: Global warming is caused by greenhouse gases (GHGs). It has been found that the release of methane (CH4) from Arctic permafrost, soil, ocean, and sediment is closely related to microbial composition and soil factors resulting from warming over several months or years. However, it is unclear for how long continuous warming due to global warming affects the microbial composition and GHG release from soils along Arctic glacial meltwater rivers. Methods: In this study, the soil upstream of the glacial meltwater river (GR) and the estuary (GR-0) in Svalbard, with strong soil heterogeneity, was subjected to short-term field incubation at 2°C (in situ temperature), 10°C, and 20°C. The incubation was carried out under anoxic conditions and lasted for few days. Bacterial composition and CH4 production potential were determined based on high-throughput sequencing and physiochemical property measurements. Results: Our results showed no significant differences in bacterial 16S rRNA gene copy number, bacterial composition, and methanogenic potential, as measured by mcrA gene copy number and CH4 concentration, during a 7- and 13-day warming field incubation with increasing temperatures, respectively. The CH4 concentration at the GR site was higher than that at the GR-0 site, while the mcrA gene was lower at the GR site than that at the GR-0 site. Discussion: Based on the warming field incubation, our results indicate that short-term warming, which is measured in days, affects soil microbial composition and CH4 concentration less than the spatial scale, highlighting the importance of warming time in influencing CH4 release from soil. In summary, our research implied that microbial composition and CH4 emissions in soil warming do not increase in the first several days, but site specificity is more important. However, emissions will gradually increase first and then decrease as warming time increases over the long term. These results are important for understanding and exploring the GHG emission fluxes of high-latitude ecosystems under global warming.

Effects of coastal aquaculture on sediment organic matter: Assessed with multiple spectral and isotopic indices.

Sediment organic matter (SOM) is important in the biogeochemical cycling of carbon, nutrients, and pollutants in the coastal environment, which is increasingly disturbed by aquaculture that is particularly intense in China. However, the identification of aquaculture signals in SOM is rather challenging in the complex coastal environment that receives materials from a variety of sources. This was studied in a typical culture area of shellfish and algae in SE China from July 2019 to October 2020, using a combination of elemental (OC, TN, N/C), isotopic (δ13C and δ15N), spectral (absorption spectroscopy and fluorescence EEMs-PARAFAC), and statistical analysis (principal component analysis, PCA). All indices of SOM quantity and several spectral indices for the SOM composition correlated significantly with grain size, with lower SOM quantity and higher autochthonous contribution in coarse sediments. The strong correlations between elemental and spectral indices suggested that optical analysis could provide valuable indices for assessing the quantity of bulk organic matter. The comparison of SOM indices between different zones and between different months showed an overall limited influence of shellfish and laver culture. This indicated the sustainability of these types of aquaculture that require no manual addition of feeds and thus are generally clean. The further applications of end-member mixing analysis using the IsoSource program and PCA were more sensitive, which identified the removal of SOM by shellfish in the growing season and the contribution from shellfish residuals after the harvest and the cultured laver at some locations. Overall, our results have implications for a better understanding of the biogeochemical processes and ecosystem sustainability in the coastal environment under intense aquaculture activities.

Reconstruction of the main phytoplankton population off the Changjiang Estuary in the East China Sea and its assemblage shift in recent decades: From observations to simulation.

Under eutrophication background, the increasing dinoflagellates blooms relative to diatoms blooms off the Changjiang Estuary has caused much concern. We have provided sediment evidence for the first time that the time window of diatoms-to-dinoflagellates shift off the Changjiang Estuary in the East China Sea is early 1990s. Investigations to the water column revealed different surface-bottom concentration matchup patterns between peridinin (dinoflagellates) and fucoxanthin (diatoms), which suggests that the diatoms-dinoflagellates shift recorded in the sediment may have come from more dinoflagellate blooms since 1990s. Physical-biogeochemical 3D numerical simulations for the past decades suggest that the effect of increasing spring sea surface temperature and increasing N/P ratio on the diatoms-dinoflagellates shift is dominant and recessive, respectively.

The Vital Role of ShTHIC from the Endophyte OsiSh-2 in Thiamine Biosynthesis and Blast Resistance in the OsiSh-2-Rice Symbiont.

Endophytes can benefit the growth and stress resistance of host plants by secreting bioactive components. Thiamine is an essential vitamin involved in many metabolic pathways and can only be synthesized by microbes and plants. In this study, we found that thiamine could inhibit the development of the phytopathogen Magnaporthe oryzae and decrease the rice blast index under field conditions. In the thiamine biosynthesis pathway, the key enzyme ShTHIC of an endophyte Streptomyces hygroscopicus OsiSh-2 and OsTHIC of rice (Oryza sativa) were highly homologous. Gene overexpression or knockout approaches revealed that both THIC contributed to thiamine synthesis and resistance to M. oryzae. Furthermore, S. hygroscopicus OsiSh-2 colonization led to a decrease in the thiamine synthesis level of rice but still maintained thiamine homeostasis in rice. However, inoculation with the ShTHIC knockout strain ΔTHIC reduced the thiamine content in rice, although the thiamine synthesis level of rice was increased. After infection with M. oryzae, blast resistance was dramatically improved in OsiSh-2-inoculated rice but decreased in ΔTHIC-inoculated rice compared with non-inoculated rice. This result demonstrated that ShTHIC could regulate thiamine biosynthesis and consequently assist blast resistance in the OsiSh-2-rice symbiont. Our results revealed a novel blast-resistance mechanism mediated by a key thiamine biosynthetic enzyme from an endophyte OsiSh-2.

Effects of nutrient-rich submarine groundwater discharge on marine aquaculture: A case in Lianjiang, East China Sea.

Submarine groundwater discharge (SGD) and associated nutrient have long been received insufficient attention in the aquaculture areas of Lianjiang, East China Sea. In this study, we used 224Ra mass balance model to evaluate the importance of SGD in the aquaculture areas of Lianjiang in different seasons. The results showed that SGD fluxes were 0.14 ± 0.070 m3 m-2 d-1 in July and 0.077 ± 0.040 m3 m-2 d-1 in October 2019, which corresponded to approximately 22% and 32% of the river discharge, respectively. Nevertheless, the dissolved inorganic nitrogen (DIN) and phosphorus (DIP) fluxes contributed by SGD over total nutrient inputs were approximately 58% and 73%, respectively in July, 11% and 33%, respectively in October 2019. The ratio of DIN to DIP in seawater was slightly higher than that derived from SGD in July and significantly lower than that derived from the river and SGD in October, which was prone to profound modulated by shellfish (e.g., clam Ruditapes philippinarum and Sinonovacula constricta) and nori (e.g., Pyropia haitanensis) that selectively acquire nitrogen and phosphorous, suggesting that SGD could affect the nutrient structure and aquaculture activities in Lianjiang. Moreover, the new primary production via SGD yielded (2.47 ± 1.32) × 103 mg C m-2 d-1 in July and (3.52 ± 1.76) × 102 mg C m-2 d-1 in October 2019, which were approximately 8-25% and 10-31% of the production in the entire study area. These meaningful discoveries indicated that SGD and associated nutrient are the predominant regulator of nutrient and aquaculture structure under significant seasonal differences.

Effects of fish culture on particulate organic matter in a reservoir-type river as revealed by absorption spectroscopy and fluorescence EEM-PARAFAC.

Dam construction and fish culture can change the biogeochemical processes in river, yet their impact on the spectral properties of particulate organic matter (POM) remains to be studied. This was investigated in a reservoir-type river (Minjiang river, SE China) using absorption spectroscopy and fluorescence excitation-emission matrices-parallel factor analysis (EEMs-PARAFAC). Five fluorescent components were identified from POM with PARAFAC. Four components C1-C4 were affected by the seasonal variations of rainfall and runoff, indicating the influences of hydrological condition and terrestrial inputs. The Chlorophyll a concentration (Chl a) correlated significantly with the humic-like C3 (p < 0.05) and the protein-like C4 (p < 0.01), indicating phytoplankton was an important source of C3 and C4. The Chl a and fluorescence intensities of C3-C4 were higher in the fish culture zones than in other areas, and the absorption coefficient a300 and C1-C4 were lower downstream the dam. These results indicated that fish farming in the reservoir probably promoted the production of POM. The a300 and C1 per unit mass of suspended particulate matter (a300/TSM and C1/TSM) correlated significantly with the median particle size (p < 0.01), which might be related to the contribution of micro-phytoplankton. The absorption spectra of POM showed a shoulder peak at ∼280 nm, and its intensity correlated significantly and positively with Chl a (p < 0.01). These results indicated that the peak was probably derived from phytoplankton production. Our results have implications for better understanding the influences of human activities on the dynamics of river POM.

Hypoxia off the Changjiang (Yangtze River) estuary and in the adjacent East China Sea: Quantitative approaches to estimating the tidal impact and nutrient regeneration.

Large areas of hypoxia have been reported off The Changjiang Estuary and in the East China Sea. Five cruises, covering winter, spring, and summer, were carried out from 2007 to 2013 in this region, and in August 2013 (summer), an extensive hypoxic event (11,150km2) was observed, which was characterized by an estimated bulk oxygen depletion of 5.1 million tons. A strong tidal impact was observed associated with the bottom oxygen depletion, with the periodicity of diel variations in dissolved oxygen being 12h (i.e., similar to the tidal cycle). A conservative estimate of nutrient regeneration suggested that during the hypoxic event of August 2013, the amount of regenerated nitrogen (as nitrate) and phosphorus (as dissolved inorganic phosphorus) was 27,000-30,000 tons and 1300-41,000tons, respectively. Estimates of the absolute (bulk) regenerated nutrient fluxes were much greater than the conservative estimates.

Bacterial diversity in the surface sediments of the hypoxic zone near the Changjiang Estuary and in the East China Sea.

Changjiang (Yangtze River) Estuary has experienced severe hypoxia since the 1950s. In order to investigate potential ecological functions of key microorganisms in relation to hypoxia, we performed 16S rRNA-based Illumina Miseq sequencing to explore the bacterial diversity in the surface sediments of the hypoxic zone near the Changjiang Estuary and in the East China Sea (ECS). The results showed that numerous Proteobacteria-affiliated sequences in the sediments of the inner continental shelf were related to both sulfate-reducing and sulfur-oxidizing bacteria, suggesting an active sulfur cycle in this area. Many sequences retrieved from the hypoxic zone were also related to Planctomycetes from two marine upwelling systems, which may be involved in the initial breakdown of sulfated heteropolysaccharides. Bacteroidetes, which is expected to degrade high-molecular-weight organic matter, was abundant in all the studied stations except for station A8, which was the deepest and possessed the largest grain size. In addition, dissolved organic carbon, water depth, percentage ratio of clay to silt, salinity, and sedimentary grain size were environmental effectors that shaped the sedimentary microbial community structure. Our results showed that putative Gammaproteobacteria-affiliated sulfur-oxidizing bacteria may not only detoxify hydrogen sulfide produced by sulfate-reducing prokaryotes, but also serve as the primary producers in the marine sediments. Specific groups of aerobic Bacteroidetes and Planctomycetes participated in degrading organic matter, which might contribute to the oxygen depletion in the hypoxic zones.

[Characteristics of dissolved oxygen and its affecting factors in the Yangtze Estuary].

The cruises on hypoxia research were carried out in the Yangtze Estuary and adjacent area of the East China Sea on June, August and October, 2006. DO, stability and the concentration of nitrate and phosphate in the section B were analyzed. The result indicates that there is distinct difference among the concentration of DO in the section B of the three cruises. The DO distribution is higher in surface water but lower in bottom. The oxygen minimum value (1.1 mg x L(-1)) is found at the bottom in August, and the apparent oxygen utilization (AOU) is higher than 2.79 mg x L(-1) in the section B. The strong halocline above the hypoxic zone, as a result of affluent water from the coastwise, Taiwan Warm Current, and the high concentration of organic substance are major factors causing the formation of the hypoxia. The stability of the seawater goes down, the vertical mixing affect the DO through its effect on stratification, in October. deltaDO is primarily affected by the stability and the concentration of deltaNO3-, deltaDIP.