Rise and fall of an avian oasis: Tracking the impacts of land use change in a key coastal wetland in the world's largest megalopolis

Tropical estuaries support wetlands with high biodiversity value and provide essential ecosystem services. Many of these systems, however, are global hotspots for urbanization, particularly in Asia, where this process has resulted in rapid conversion, fragmentation, and degradation of 80 % of the wetlands along the East Asian-Australasian Flyway (EAAF) for migratory birds. However, the impact of such landscape scale changes on migratory birds at a key stopover site along the EAAF has not been evaluated. Here, we used long-term data (> 40 years) from Deep Bay (Hong Kong), a shallow embayment in the Pearl River estuary (PRE) in south China, to investigate the impact of urbanization on (1) catchment land use and water quality, and (2) its impact on the capacity of the wetland to support populations of migratory waterbirds. Deep Bay supports the largest remnants of mangrove forests and tidal mudflats in the PRE and is an important refueling ground along the EAAF. It is also part of the Greater Bay Area (GBA, population 86 million), the world's largest megalopolis. The principal component analysis highlighted the nutrient loading and cleansing effect from seasonal flushing as characterizing variation in water quality in Deep Bay over four decades. Major shifts in water quality during the study period were accompanied by contemporaneous changes in wintering waterbirds numbers. Prior to 2003, the main drivers of water quality were organic nutrients from animal husbandry. Following large-scale reclamation and increases in impervious surface cover post-2003, primarily due to the development of the megacity of Shenzhen (population 17.7 million), the hydrodynamics of Deep Bay have changed, with knock-on effects of sedimentation, input of pollutants, and changes in the macrobenthos. The wintering waterbirds community responded to these changes both in total numbers and the relative importance of feeding guilds. Where total bird counts are positively influenced by benthic biomass, and the benthic biomass is positively correlated to the water quality that is driven by the cleansing effect of tidal flushing. These anthropogenic drivers have negatively impacted migratory birds that use Deep Bay as a refueling station. This study highlights the need for policymakers to control these drivers and limit the level to which sensitive coastlines are urbanized.

Unlocking foraminiferal genetic diversity on estuarine mudflats with eDNA metabarcoding

Environmental biomonitoring is a prerequisite for efficient evaluation and remediation of ecosystem degradation due to anthropogenic pressure or climate change. Estuaries are key habitats subject to multiple anthropogenic and natural stressors. Due to these multiple stressors, the detection of anthropogenic pressure is challenging. The fact that abundant natural stressors often lead to negative quality assessments has been coined the "estuarine quality paradox". To solve this issue, the application of molecular approaches with successful bioindicators like foraminifera is promising. However, sampling protocols, molecular procedures and data analyses need to be validated before such tools can be routinely applied. We conducted an environmental DNA survey of estuarine mudflats along the French Atlantic coast, using a metabarcoding approach targeting foraminifera. Our results demonstrate that estuarine environments have only a few active OTUs dominating the community composition and a large stock of dormant or propagule stages. This last genetic diversity components constitute an important reservoir, with different species which can potentially develop in response to the temporal variability of the multiple stressors. In fact, different OTUs were dominant in the studied estuaries. Our statistical model shows that the physical and chemical characteristics of the sediment and the climatic conditions explain only 43 % of the community composition variance. This suggests that other, less easily quantifiable factors, such as the history and use of the estuaries or the ecological drift could play an important role as well. Environmental DNA biomonitoring opens new perspectives to better characterize the genetic diversity in estuaries.

Views from 'crabworld': the spatial distribution of light in a tropical mudflat

Natural scene analysis has been extensively used to understand how the invariant structure of the visual environment may have shaped biological image processing strategies. This paper deals with four crucial, but hitherto largely neglected aspects of natural scenes: (1) the viewpoint of specific animals; (2) the fact that image statistics are not independent of the position within the visual field; (3) the influence of the direction of illumination on luminance, spectral and polarization contrast in a scene; and (4) the biologically relevant information content of natural scenes. To address these issues, I recorded the spatial distribution of light in a tropical mudflat with a spectrographic imager equipped with a polarizing filter in an attempt to describe quantitatively the visual environment of fiddler crabs. The environment viewed by the crabs has a distinct structure. Depending on the position of the sun, the luminance, the spectral composition, and the polarization characteristics of horizontal light distribution are not uniform. This is true for both skylight and for reflections from the mudflat surface. The high-contrast feature of the line of horizon dominates the vertical distribution of light and is a discontinuity in terms of luminance, spectral distribution and of image statistics. On a clear day, skylight intensity increases towards the horizon due to multiple scattering, and its spectral composition increasingly resembles that of sunlight. Sky-substratum contrast is highest at short wavelengths. I discuss the consequences of this extreme example of the topography of vision for extracting biologically relevant information from natural scenes.

Intra- and inter-habitat variation in sediment heavy metals, antibiotics and ecological risks in Mai Po RAMSAR, China

Distribution of heavy metals (HMs) and antibiotics (ABs) in surface sediments of three habitats: mudflat, mangrove and gei wai (inter-tidal shrimp ponds), at Mai Po RAMSAR were determined with inductively coupled plasma and liquid chromatograph tandem - mass spectrometry, respectively. Eight HMs (Cr, As, Pb, Cd, Mn, Ni, Cu and Zn), and ten ABs (tetracyclines, quinolones, macrolides and sulphonamides) were detected in all habitats, with relatively lower concentration in gei wai. Ecological risk assessment based on PNEC revealed that HMs posed a higher ecological risk to microorganisms than ABs. All metals except Mn were above their respective threshold effect levels according to sediment quality guidelines, indicating their potential toxicity to benthos. The enrichment factor and geo-accumulation index on background values suggested sediments were moderately polluted by Zn, Cu and Cd, possibly from anthropogenic inputs. This study implies that HMs pollution must be prevented through proper regulation of agricultural and industrial discharge.

Adverse impacts of high-density microplastics on juvenile growth and behaviour of the endangered tri-spine horseshoe crab Tachypleus tridentatus

The impacts of high-density microplastics, namely polyamine 6,6 (nylon), polymethyl methacrylate (PMMA) and polyethylene terephthalate (PET), on growth and behaviour of the endangered tri-spine horseshoe crab Tachypleus tridentatus were investigated for 100 days. Negative changes in wet weight and prosomal width of the juveniles were observed in all treatments of microplastics, but significant difference was only detected in prosomal width between control and PMMA. T. tridentatus became significantly less active upon exposure to nylon and PET. The extent of burrowing by T. tridentatus did not significantly differ among the treatments but was overall significantly reduced towards day 100. T. tridentatus exposed to PET significantly showed the lowest survival probability (30 %), compared to the other treatments (70-90 %). In conclusion, high-density microplastics compromised growth and behaviour of juvenile horseshoe crabs. Among the polymers that were tested, PET was considered more harmful and associated with higher mortality.

Contamination status and associated ecological risk assessment of heavy metals in different wetland sediments from an urbanized estuarine ecosystem

Sediment samples of different wetland types (saltmarsh, mangrove, tidal pool, mudflat and sandflat) from an urbanized estuary were analyzed to evaluate the contamination level and ecological risks of five heavy metals (Pb, Fe, Zn, Ni and Cr). The findings showed that the mean concentration (mg/kg) of heavy metals followed the order of Fe > Zn > Ni > Pb > Cr, while Pb and Fe concentrations exceeded the recommended guidelines. Heavy metals levels were highest in saltmarsh and mudflats. Contamination assessment indices e.g., contamination factor (CF), degree of contamination (CD), enrichment factor (EF), and geo-accumulation index (Igeo) revealed that the studied wetlands had low to moderate levels of pollution, meaning these sites receive medium levels of anthropogenic contamination compared with background values. For some of the studied metals, such as Pb, Zn, Fe, and Ni, the EF value was >1 in certain types of wetland, indicating anthropogenic sources, while Cr was <1 indicating natural sources. The pollution load index (PLI) value was determined to be <1, indicating perfection of soil, and was in the following order: mudflat> saltmarsh> tidal pool> mangrove > sandflat. The ecological risk (RI) value was the highest for saltmarsh and the lowest for sandflats. However, the RI value for Cr, Zn, Ni, and Pb was <30 suggesting that these metals pose a low risk in the local ecosystem. Cluster analysis (CA), principal component analysis (PCA), and Pearson's correlation specified that anthropogenic sources of metals.

nov., isolated from mudflat

A Gram-negative, nonmotile, rod-shaped bacterium, designated strain CAU 1631^T, was isolated from a mudflat sample in the Republic of Korea. Strain CAU 1631^T grew optimally at 30 °C, pH 6.5, and 1% (w/v) NaCl solution. Phylogenetic analysis based on 16S rRNA gene sequencing and 92 core genes indicated that strain CAU 1631^T is a member of the genus Muricauda and most closely related to Muricauda oceanensis 40DY170^T and Muricauda lutimaris SMK-108^T (98.1%, both). The draft genome was 3.4 Mb with 3064 protein-coding genes, and the DNA G + C content was 43.3 mol%. The major fatty acids were iso-C_15:0, iso-C_17:0 3-OH, and iso-C_15:0 G, and the major polar lipid was phosphatidylethanolamine. The predominant respiratory quinone was MK-6. Based on the comprehensive taxonomic characterization, strain CAU 1631^T is a novel species, for which the name Muricauda lutisoli sp. nov. has been proposed. The type strain is CAU 1631^T (= KCTC 82456^T = MCCC 1K06088^T).

Comparing the importance of freshwater flows driving primary production in three tropical estuaries

Estuaries in the tropical Gulf of Carpentaria (GOC) in Australia are under increasing pressure from catchment water development, potentially affecting productivity. We examined the potential effect of changes in freshwater inputs on the primary productivity of three estuaries (Flinders, Gilbert and Mitchell Rivers). The addition of nutrients stimulated mudflat primary production in all estuaries at multiple sampling times, suggesting chronic nutrient limitation. All three estuaries were productive with the Flinders estuary being the most productive of the three estuaries, compared to the Gilbert and Mitchell estuaries. This is despite the fact that the Flinders estuary has the shortest period of freshwater flow and more variable flows from year-to-year compared with the other estuaries. This makes the Flinders highly vulnerable to excessive water development. This study suggests that water extraction which significantly reduces freshwater inputs and associated nutrients has the potential to impact on productivity within these estuaries.

The changes in antibiotic resistance genes during 86 years of the soil ripening process without anthropogenic activities

This study aimed to reveal the baseline of natural variations in antibiotic resistance genes (ARGs) in soil without anthropogenic activities over the decades. Nine soil samples with different time of soil formation were taken from the Yancheng Wetland National Nature Reserve, China. ARGs and mobile genetic elements (MGEs) were characterized using metagenomic analysis. A total of 196 and 192 subtypes of ARGs were detected in bulk soil and rhizosphere, respectively. The diversity and abundance of ARGs were stable during 69 years probably due to the alkaline pH soil environment but not due to antibiotics. Increases in ARGs after 86 years were probably attributed to more migrant birds inhabited compared with other sampling sites. Multidrug was the most abundant type, and largely shared by soil samples. It was further shown that soil samples could not be clearly distinguished, suggesting a slow process of succession of ARGs in the mudflat. The variation partitioning analysis revealed that the ARG profile was driven by the comprehensive effects exhibited by the bacterial community, MGEs, and environmental factors. Besides, pathogenic bacteria containing ARGs mediated by migrant birds in the area with 86 years of soil formation history nearing human settlements needed special attention. This study revealed the slow variations in ARGs in the soil ripening process without anthropogenic activities over decades, and it provided information for assessing the effect of human activities on the occurrence and dissemination of ARGs.

Impacts of pollution, sex, and tide on the time allocations to behaviours of Uca arcuata in mangroves

Fiddler crabs (Uca) are ecosystem engineers in coastal ecosystems. Many anthropogenic and natural factors can affect the time allocated to various behaviours in Uca. However, the behaviour of U. arcuata, a widely distributed fiddler crab in Asia, has not been studied in mainland China. Here, we used binoculars to record the time budget of ten behaviours of U. arcuata to investigate the potential effects of sex, tides, and pollution on these behaviours. We found that the crabs spent 42.3%, 27.0%, and 10.6% of their time on feeding, feeding while walking, and stationary respectively. The crabs spent <1.5% of their time on copulation and grooming. The total foraging time (feeding + feeding while walking) did not differ among the three polluted sites. However, crabs spent more time on feeding but less time on feeding while walking. The feeding rate and probability of burrowing and grooming decreased while the possibility of locomotion and stay in burrow increased with increasing nutrient concentration. Females spent 13.9% more time on feeding and fed 54.9% faster than males. Males had a higher tendency to grooming and combat while they were less likely to walk than females. Regarding to the influence of tide, fiddler crabs fed 11.2% faster at ebb tides than at flood tides, and they were more likely to walk and stay in burrows at flood tides than at ebb tides. Our results indicated that nutrient pollution had stronger impacts on the behaviours of crabs than sex and tide. In polluted mangroves, increasing nutrient concentration reduced the quantity of sediment processed by fiddler crabs due to their smaller feeding area, slower feeding rate, and reduced frequency of burrowing activities. These results imply that mitigating nutrient pollution in mangroves may benefit the restoration and management of coastal ecosystems through the enhanced engineering functions of fiddler crabs.

Adaptations to the mudflat: Insights from physiological and transcriptional responses to thermal stress in a burrowing bivalve Sinonovacula constricta

Understanding physiological adaptations of organisms to temperature changes that characterize their habitat is the first step in predicting the putative effects of global climate change on population dynamics. Mudflats are an important part of the intertidal zone and experience extreme and fluctuating temperatures. Therein, species would be potentially susceptible to global warming. The present study explored physiological adaptations of burrowing species to life in an intertidal mudflat by analyzing the potential operative temperatures in the mudflat, and assessing cardiac performance and the transcriptional response to thermal stress by a typical burrowing bivalve, the razor clam Sinonovacula constricta in different thermal environments, mimicking conditions during low tides. Clams showed higher thermal sublethal limits in mud with overlying air than in mud with overlying water, indicating an adaptation to rapidly changing ambient temperatures and thermal environments during emersion. This sublethal limit was far above the maximum operative temperature in the actual habitat site and suggests a potential buffer zone to ensure survival under unexpected high temperatures, that could occur with global warming. In response to high temperature, S. constricta exhibited the common heat stress response by up-regulating expression of the Bcl2-associated athanogene 3 (BAG3) and heat shock proteins to cope with the adverse effects of high temperature on protein homeostasis. Increased expression of key genes, including molybdenum cofactor synthesis 3 (MOCS3), oligoribonuclease (REX2), and NFκappaB inhibitor alpha (NFIA) may further remit the effect of thermal stress during the emersion period and delay a situation where clams reach their thermal sublethal limit, thereby helping to endure high temperature during low tide. These results clearly illustrate significant adaptations of a burrowing bivalve to life in intertidal mudflats at both physiological and molecular levels and can provide insights into potential physiological or evolutionary responses that could aid survival of mudflat species in a changing global climate.

Petroleum biomarkers as tracers of low-level chronic oil contamination of coastal environments: A systematic approach in a subtropical mangrove

Petroleum biomarkers (hopanes, terpanes and steranes) are frequently assessed in estuarine sediments as tracers of oil input. In order to compare distinct patterns of hydrocarbon accumulation in mudflats, salt marsh and mangrove, sediments from two transects (control and impacted areas) were sampled in Paranaguá Bay, SW Atlantic. Concentrations of n-alkanes, polycyclic aromatic hydrocarbons (PAHs) and petroleum biomarkers (hopanes, terpanes and steranes) were determined, as well as bulk parameters (TOC, grain size and δ¹³C). N-alkanes concentrations were similar between control and impacted sites (respectively, 3.03 ± 1.20 μg g^-1 and 4.11 ± 3.02 μg g^-1) and reflected a high biogenic input. Conversely, PAHs and petroleum biomarker concentrations were three to six times higher in impacted site than the control site (respectively, 60.4 ± 23.3 ng g^-1 and 22.0 ± 25.0 ng g^-1 for PAHs and 197.7 ± 51.8 ng g^-1 and 40.2 ± 32. ng g^-1 for hopanes). Despite these differences, concentrations were lower than those reported for highly impacted areas worldwide. Diagnostic ratios and hydrocarbon parameters (e.g. total PAHs and total petroleum biomarkers) helped to distinguish human impact in the ecological zones, suggesting different sources and/or levels of weathering, confirmed by ANOVA tests. TOC played a fundamental role to the concentration of hydrocarbons, showing similar distributions along the transects. Petroleum biomarkers could clearly indicate the preferential sites of deposition and assign different levels of anthropic contamination by hydrocarbons, thus providing clear information about the chronic petroleum pollution in coastal sediments.

Monitoring bioturbation by a small marine polychaete using microcomputed tomography

Bioturbation is one of the principle biological processes involved in transporting particles and solutes within sediments, which contributes to the maintenance of biodiversity. In muddy polluted environments, bioturbation may increase pollutant flux at the water-sediment interface, thereby enhancing contaminant bioavailability. The behavior of organisms dictates bioturbation, and gallery shape influences the magnitude of solute transport. Thus, quantitative investigations of gallery shape are fundamental to understanding how pollutant and solute transport is enhanced by bioturbators in muddy sediments. However, there is a lack of tools for quantitatively analyzing gallery geometry, especially for assessing bioturbation and gallery properties through time. Despite the potential of microcomputed tomography (μCT) for quantitative analyses of bioturbation, few such studies have been carried out. Here, we aimed to investigate the potential of μCT for quantitatively assessing the shape and geometric properties of galleries made by small marine polychaetes and their evolution through time in muddy sediments. We focused on Laeonereis acuta (Treadwell, 1923) (Nereididae, Polychaeta), which is a key bioturbator in marine coastal ecosystems. Using 2D and 3D images generated from μCT, we evaluated L. acuta galleries and propose several indexes to quantitatively assess gallery evolution and the role of gallery parameters in bioturbation. Quantitative investigations of polychaete galleries using μCT can assist in monitoring how bioturbation influences sedimentary systems.

Influence of introduced Sonneratia apetala on nutrients and heavy metals in intertidal sediments, South China

To investigate the influence of Sonneratia apetala on nutrients and heavy metals in intertidal sediments, sediment cores of S. apetala marsh and mudflat in Shenzhen Bay, China were analyzed. The results showed that S. apetala improved sediment nutrient properties due to increased total carbon (TC), total nitrogen (TN), and total sulfur (TS). The levels of heavy metals were higher in S. apetala site than in mudflat, including chromium (Cr), nickel (Ni), copper (Cu), zinc (Zn), arsenic (As), cadmium (Cd), lead (Pb), and mercury (Hg). In S. apetala site, TC, TN, and TS were not positively correlated with Cr, Ni, As, Cd, and Pb, indicating their less important roles in trapping heavy metals. There were positive correlations among Ni, Cu, Zn, and Cd in both sites, suggesting similar anthropogenic source. Levels of As were higher than the probable effect level at both sites, indicating their toxicological importance. The geo-accumulation index and potential ecological risk index revealed higher metal contaminations in S. apetala site, especially for Cd, Hg, and As. Multivariate analysis implied that S. apetala alter the biogeochemical cycle of Cd and Cr to a certain extent. These findings indicate that S. apetala may improve soil nutrient properties and facilitate heavy metal accumulation in intertidal sediments.