Use of passive sampling in environmental DNA metabarcoding technology: Monitoring of fish diversity in the Jiangmen coastal waters

Environmental DNA (eDNA) metabarcoding technology is proving to be the most up-to-date and promising method for monitoring marine fish diversity. Fish eDNA is usually collected on a filter membrane after the filtration of water. Not only does this require the use of specialized equipment, but the amount of filtered water needed is also difficult to meet. The recently proposed passive eDNA collection method can expand the sampling scale, providing new perspectives for monitoring marine biodiversity. The role of collection methods in eDNA surveys, however, remains unclear. In this study, a low-cost custom framework with two types of filter membrane materials was used to conduct passive submersion samplings at the north and south ends of Shangchuan Island, Jiangmen, China. After defined periods of submersion, the filter membranes were recovered and eDNA extracted. Metabarcoding techniques were applied to detect fish species information in the eDNA samples. A total of 106 marine fish species from 27 orders, 53 families, and 92 genera, including one cartilaginous fish, were identified in the samples. The majority of fish detected by active filtration were also found in the passively collected samples, within the same location. Both sampling methods, therefore, showed similar species richness. Passive sampling was effective in identifying fish species diversity and provided a higher spatial resolution owing to the sample replicates. Passive sampling was also more sensitive in detecting species that differ significantly in abundance (biomarkers) between different sampling depths. When active filtration is not possible, or when large-scale sampling is the purpose of the study, passive sampling methods certainly provide a promising alternative. The findings of our study provide guidance for fish surveys and continuous bio-stereoscopic monitoring in coastal waters.

Inoculation with plant growth-promoting rhizobacteria improves seagrass Thalassia hemprichii photosynthesis performance and shifts rhizosphere microbiome

Plant growth-promoting rhizobacteria (PGPR) inoculation is a crucial strategy for maintaining the sustainability of agriculture and presents a promising solution for seagrass ecological restoration in the face of disturbances. However, the possible roles and functions of PGPRs in the seagrass rhizosphere remain unclear. Here, we isolated rhizosphere bacterial strains from both reef and coastal regions and screened two PGPR isolates regarding their in vivo functional traits. Subsequently, we conducted microcosm experiments to elucidate how PGPR inoculation affected seagrass photosynthesis and shape within each rhizosphere microbiome. Both screened PGPR strains, Raoultella terrigena NXT28 and Bacillus aryabhattai XT37, excelled at expressing a specific subset of plant-beneficial functions and increased the photosynthetic rates of the seagrass host. PGPR inoculation not only decreased the abundance of sulfur-cycling bacteria, it also improved the abundance of putative iron-cycling bacteria in the seagrass rhizosphere. Strain XT37 successfully colonized the seagrass rhizosphere and displayed a leading role in microbial network structure. As a nitrogen-fixing bacteria, NXT28 showed potential to change the microbial nitrogen cycle with denitrification in the rhizosphere and alter dissimilatory and assimilatory nitrate reduction in bulk sediment. These findings have implications for the development of eco-friendly strategies aimed at exploiting microbial communities to confer sulfide tolerance in coastal seagrass ecosystem.

Seagrass Thalassia hemprichii and associated bacteria co-response to the synergistic stress of ocean warming and ocean acidification

Seagrass meadows play vital ecological roles in the marine ecosystem. Global climate change poses considerable threats to seagrass survival. However, it is unclear how seagrass and its associated bacteria will respond under future complex climate change scenarios. This study explored the effects of ocean warming (+2 °C) and ocean acidification (-0.4 units) on seagrass physiological indexes and bacterial communities (sediment and rhizosphere bacteria) of the seagrass Thalassia hemprichii during an experimental exposure of 30 days. Results demonstrated that the synergistic effect of ocean warming and ocean acidification differed from that of one single factor on seagrass and the associated bacterial community. The seagrass showed a weak resistance to ocean warming and ocean acidification, which manifested through the increase in the activity of typical oxidoreductase enzymes. Moreover, the synergistic effect of ocean warming and ocean acidification caused a significant decrease in seagrass's chlorophyll content. Although the bacterial community diversity exhibited higher resistance to ocean warming and ocean acidification, further bacterial functional analysis revealed the synergistic effect of ocean warming and ocean acidification led to significant increases in SOX-related genes abundance which potentially supported the seagrass in resisting climate stress by producing sulfates and oxidizing hydrogen sulfide. More stable bacterial communities were detected in the seagrass rhizosphere under combined ocean warming and ocean acidification. While for one single environmental stress, simpler networks were detected in the rhizosphere. In addition, the observed significant correlations between several modules of the bacterial community and the physiological indexes of the seagrass indicate the possible intimate interaction between seagrass and bacteria under ocean warming and ocean acidification. This study extends our understanding regarding the role of seagrass associated bacterial communities and sheds light on both the prediction and preservation of the seagrass meadow ecosystems in response to global climate change.

Construction and influencing factors of an early warning system for marine ranching ecological security: Experience from China's coastal areas

Marine ranching has been widely considered as a new mode of marine fishery production. Marine ranching ecological security (MRES) is the basis and premise to ensure the sustainable utilization of marine ranching functions. In this study, an MRES early warning system was constructed based on comprehensive marine ranching ecological security index (CMRESI) and system dynamic model to reveal the main factors affecting the development of marine ranching and explore the changes in MRES under different future development scenarios in China's coastal areas from 2011 to 2035. The results showed that (1) the mean CMRESI of China was only 0.3265 and spatial heterogeneity was significant, showing a general security state; (2) coupling and coordination degree of MRES subsystems was high in Jiangsu, Fujian, Shandong, and Guangdong, and resources was a major constraint on the coordinated development of MRES in the study area (63.6%); (3) Under the ecological priority development scenario, the CMRESI will be the highest in 2035; however, 27% of MRES (in Jiangsu, Fujian, and Hainan) will continue to issue serious early warnings. This study could provide a reference for construction planning, management maintenance, and decision-making of marine ranching.

The effect of acute toxicity from tributyltin on Liza haematocheila liver: Energy metabolic disturbance, oxidative stress, and apoptosis

Tributyltin (TBT), a highly toxic and persistent organic pollutant, is widely distributed in coastal waters. Liza haematocheila (L. haematocheila) is one of bony fish distributing coincident with TBT, and exposure risk of TBT to this fish is unknown. In this study, L. haematocheila was exposed to TBT of 0, 3.4, 6.8, and 17.2 μg/L for 48 h to explore hepatic response mechanism. Our results showed that Sn content in livers increased after 48 h of exposure. HSI and histological changes indicated that TBT suppressed liver development of L. haematocheila. TBT reduced ATPase activities. The increased RB in blood and the reduced TBC were measured after exposure to TBT. T-AOC and antioxidant enzymes SOD, CAT, and GPx activities were inhibited while MDA content was increased. Liver cells showed apoptosis characteristics after TBT exposure. Furthermore, transcriptome analysis of livers was performed and the results showed energy metabolism-related GO term (such as ATPase complex and ATPase dependent transmembrance transport complex), oxidative stress-related GO term (such as Celllular response to oxidative stress and Antioxidant activity), and apoptosis-related GO term (such as Regulation of cysteine-type endopeptidase activity involved in apoptosic signaling pathway). Moreover, we found six energy metabolism-related differentially expressed genes (DEGs) including three up-regulated DEGs (atnb233, cftr, and prkag2) and three down-regulated DEGs (acss1, abcd2, and smarcb1); five oxidative stress-related DEGs including one up-regulated DEG (mmp9) and four down-regulated DEG (prdx5, hsp90, hsp98, and gstf9); as well as six apoptosis-related DEGs including five up-regulated DEGs (casp8, cyc, apaf1, hccs, and dapk3) and one down-regulated DEG (bcl2l1). Our transcriptome data above further confirmed that acute stress of TBT led energy metabolic disturbance, oxidative stress, and apoptosis in L. haematocheila livers.

Impacts of conventional and biodegradable microplastics on juvenile Lates calcarifer: Bioaccumulation, antioxidant response, microbiome, and proteome alteration

Discarded plastic bag is a main component of marine debris, posing potential threats to marine biota. This study was conducted to assess the potential effects of microplastics on juvenile Lates calcarifer. Fish were exposed via diet to two microplastic types from conventional polyethylene (PE) and biodegradable (Bio) plastic bags for 21 days. Antioxidative enzymes activity, intestinal microbiome and proteome were determined. PE and Bio microplastics were found to accumulate in gastrointestinal tracts, and no mortality was observed. Microplastics exposure did not induce significant antioxidant response except for the glutathione reductase (GR) modulation. Intestinal microbiome diversity decreased significantly in PE group based on Simpson index. Both types of microplastics induced proteome modulation by down-regulating proteins associated with immune homeostasis. Bio microplastics maintained higher intestinal microbial diversity and induced more proteins alteration than PE microplastics. This study provides toxicological insights into the impacts of conventional and biodegradable microplastics on juvenile L. calcarifer.

Nitrogen removal in the sediments of the Pearl River Estuary, China: Evidence from the distribution and forms of nitrogen in the sediment cores

In this study, the spatial distribution and forms of nitrogen in sediment cores collected from the Pearl River Estuary were analyzed. Exchangeable nitrogen (N_ex) comprised only a small proportion of total nitrogen (N_tot), with a mean of 3.54% in the sediment cores. NH₄⁺ was the main form of N_ex. No obvious change was observed in the vertical content of fixed ammonia (N_fix) in the sediments, and the mean N_fix in all five sediment cores was 141.23 mg·kg^-1. The organic nitrogen (N_org), strongly related to organic carbon (C_org), was the main form in N_tot. The dissolved inorganic nitrogen in sediment pore water was much lower than that in estuarine water and no significant variation was observed from upstream to downstream. Our results indicated that most nitrogen deposited on surface sediments from overlying water was rapidly removed by a series of microbial processes, reducing the extent of nitrogen returning to overlying waters.

Effect of temperature on the accumulation of marine biogenic gels in the surface microlayer near the outlet of nuclear power plants and adjacent areas in the Daya Bay, China

The surface microlayer (SML) in marine systems is often characterized by an enrichment of biogenic, gel-like particles, such as the polysaccharide-containing transparent exopolymer particles (TEP) and the protein-containing Coomassie stainable particles (CSP). This study investigated the distribution of TEP and CSP, in the SML and underlying water, as well as their bio-physical controlling factors in Daya Bay, an area impacted by warm discharge from two Nuclear power plants (Npp’s) and aquaculture during a research cruise in July 2014. The SML had higher proportions of cyanobacteria and of pico-size Chl a contrast to the underlayer water, particularly at the nearest outlet station characterized by higher temperature. Diatoms, dinoflagellates and chlorophyll a were depleted in the SML. Both CSP and TEP abundance and total area were enriched in the SML relative to the underlying water, with enrichment factors (EFs) of 1.5–3.4 for CSP numbers and 1.32–3.2 for TEP numbers. Although TEP and CSP showed highest concentration in the region where high productivity and high nutrient concertation were observed, EFs of gels and of dissolved organic carbon (DOC) and dissolved acidic polysaccharide (> 1 kDa), exhibited higher values near the outlet of the Npp’s than in the adjacent waters. The positive relation between EF’s of gels and temperature and the enrichment of cyanobacteria in the SML may be indicative of future conditions in a warmer ocean, suggesting potential effects on adjusting phytoplankton community, biogenic element cycling and air-sea exchange processes.

A rapid and high-throughput microplate spectrophotometric method for field measurement of nitrate in seawater and freshwater

The well-known zinc-cadmium reduction method is frequently used for determination of nitrate. However, this method is seldom to be applied on field research of nitrate due to the long time consuming and large sample volume demand. Here, we reported a modified zinc-cadmium reduction method (MZCRM) for measurement of nitrate at natural-abundance level in both seawater and freshwater. The main improvements of MZCRM include using small volume disposable tubes for reaction, a vortex apparatus for shaking to increase reduction rate, and a microplate reader for high-throughput spectrophotometric measurements. Considering salt effect, two salinity sections (5~10 psu and 20~35 psu) were set up for more accurate determination of nitrate in low and high salinity condition respectively. Under optimized experimental conditions, the reduction rates were stabilized on 72% and 63% on the salinity of 5 and 20 psu respectively. The lowest detection limit for nitrate was 0.5 μM and was linear up to 100 μM (RSDs was 4.8%). Environmental samples assay demonstrated that MZCRM was well consistent with conventional zinc-cadmium reduction method. In total, this modified method improved accuracy and efficiency of operations greatly, and would be realized a rapid and high-throughput determination of nitrate in field analysis of nitrate with low cost.

Developing a salinity-based approach for the evaluation of DIN removal rate in estuarine ecosystems

Estuaries play an important role in the removal of overloading nitrogen to relieve the eutrophic pressure of coastal seawater. However, the exact amount of nitrogen removed in estuarine ecosystems is difficult to be estimated because of the complex dynamic mixing process between riverine water and coastal seawater. In this study, a new method was developed to calculate the removal rate of dissolved inorganic nitrogen (DIN) in estuarine waters attributed to the mixing process and was based on the assumption that relative salinity can serve as an indicator of the degree of mixing. This assumption was supported by the experimental results that demonstrated a linear regression relationship between DIN decline and salinity increase Thus, the decreased amount of DIN in mixing waters attributed to the dilution effect could be determined with the salinity as an index. With this model, the DIN removal rate in both Chesapeake Bay and Pearl River Estuary were defined. As predicted, our analysis demonstrated that the DIN removal rate increased gradually from upstream to downstream in both studied estuaries with obvious seasonable variation pattern: high in warm seasons and low in cold seasons. The practical application of this method might be affected by multiple factors, including the geographic landform of estuaries, initial estuaries DIN concentration, the DIN concentration in seawater, DIN importing from tributaries, sewage discharge and hydrodynamic mixing. Therefore, the results supported the hypothesis that estuaries have a strong capability to remove the nitrogen inputted from human activities, especially in warm season and therefore should play an important role in regulating the balance of global nitrogen biogeochemical cycle.

Different hydrodynamic processes regulated on water quality (nutrients, dissolved oxygen, and phytoplankton biomass) in three contrasting waters of Hong Kong

The subtropical Hong Kong (HK) waters are located at the eastern side of the Pearl River Estuary. Monthly changes of water quality, including nutrients, dissolved oxygen (DO), and phytoplankton biomass (Chl-a) were routinely investigated in 2003 by the Hong Kong Environmental Protection Department in three contrasting waters of HK with different prevailing hydrodynamic processes. The western, eastern, and southern waters were mainly dominated by nutrient-replete Pearl River discharge, the nutrient-poor coastal/shelf oceanic waters, and mixtures of estuarine and coastal seawater and sewage effluent of Hong Kong, respectively. Acting in response, the water quality in these three contrasting areas showed apparently spatial–temporal variation pattern. Nutrients usually decreased along western waters to eastern waters. In the dry season, the water column was strongly mixed by monsoon winds and tidal currents, which resulted in relatively low Chl-a (<5 μg l(−1)) and high bottom DO (>4 mg l(−1)), suggesting that mixing enhanced the buffering capacity of eutrophication in HK waters. However, in the wet season, surface Chl-a was generally >10 μg l(−1) in southern waters in summer due to halocline and thermohaline stratification, adequate nutrients, and light availability. Although summer hypoxia (DO <2 mg l(−1)) was episodically observed near sewage effluent site and in southern waters induced by vertical stratification, the eutrophication impacts in HK waters were not as severe as expected owing to P limitation and short water residence time in the wet season.

[Distribution characteristics of nitrogen and its source in core sediments from Pearl River Estuary]

Based on the measurement of the concentration of nitrogen in four core sediments from Pear River Estuary, the forms and the depth-dependent changes characteristics of nitrogen were studied, and the possible sources of nitrogen in the sediments were discussed. The results indicate that the content of total nitrogen ranged from 850.62mg/kg to 2 340.85mg/kg, with mean content of 1 502.73mg/kg. There is a general tendency for an upward increase in core sediments, which is more evident in the middle than in two ends. Organic nitrogen had a range of content from 655.42mg/kg to 2 029.86mg/kg, with mean content of 1 187.86mg/kg. And the content of organic nitrogen decreases gradually with the increase of depth or lower in the middle than in two ends. The content of NH4-N was relatively high, ranging from 47.59mg/kg to 739.61mg/kg, with mean content of 271.69mg/kg, and increases obviously with the increase of depth. The TOC/TN ratios were most between 5 and 17, which show organic matter is the mixture of aquatic and terrestrial sources. The total nitrogen has distinct synchronization phenomenon with the organic nitrogen in sedimentation course,but has little relativity with the NH4-N. There is large difference of synchronization phenomenon between total nitrogen and NH4-N at different sites.

[Accumulation of heavy metals in the sediments of Shenzhen Bay, south China]

Heavy metals concentrations in marine sediment cores of Shenzhen Bay were measured, and the profile distribution characteristic of heavy metals was discussed. Combined with the 210 Pb dating results, the contamination history of heavy metals was studied in high resolution records, and the metal accumulation processes were also analyzed. The results indicated that the concentrations of heavy metals was relatively low compared with other area in the world, but the elements of Pb, Cu and Zn were obviously contaminated by anthropogenic impact. The rapid economical development of Shenzhen in the last 20 years and Hong Kong in 1960-1970s contributed much on accumulation of heavy metals in the sediments.

The characteristics of nutrients and eutrophication in the Pearl River estuary, South China

In the spring of 1998, 24-h time series and synchronization of vertical profiles of NO(3)-N, NO(2)-N, NH(3)-N, PO(4)-P, chlorophyll a, suspended substance, salinity, temperature and other chemical parameters were taken at 10 stations in the Pearl River estuary in order to analyze the status and characteristics of nutrients and eutrophication. The results indicated that dissolved inorganic nitrogen (DIN) mainly came from the four river channels in the main estuary, and NO(3)-N was the main form of DIN in most area. The concentration of DIN was general above 0.30 mg l(-1) in the estuary, and more than 0.50 mgl(-1) in most part. Phosphate from four river channels was not the main sources, but land-based sources from the area near Shenzhen Bay or along the estuary were obvious, and other land-based sources outside the estuary brought by coastal current and flood tide current were also the main contributions. The concentration of phosphate was generally about 0.015 mg l(-1) except the area near Shenzhen Bay. The ratio of N:P was generally high, and it was higher in the north than in the south. The highest ratio was higher than 300, and the lowest one was over 30. The concentration of chlorophyll a was about 0.8-7.8 mg m(-3), and turbidity and phosphate may be the main two limiting factors for algal bloom in the estuary. The concentration of nutrients decreased slightly in the past decade, but still stayed at a high level. The nutrients mainly came from domestic sewage, industrial wastewater, agriculture fertilizer and marine culture in the Pearl River estuary.