Metagenomics-Based Microbial Ecological Community Threshold and Indicators of Anthropogenic Disturbances in Estuarine Sediments.

Spatial gradients and molecular transformations of DOM, DON and DOS in human-impacted estuarine sediments

Distribution, source and enrichment of some chemical elements in sediments of the Pearl River Estuary, China

Denitrification, an important process in microbial mediated nitrogen cycle, plays important roles in nitrogen loss in estuarine sediments. However, the function of denitrifiers in the estuarine subsurface sediments remained poorly understood. In this study, we analyzed the potential activity, abundance and community structure of nirS-type denitrifiers using 15N-labeled incubation quantitative-PCR and high throughput sequencing techniques in sediment cores from Pearl River Estuary (PRE). Results showed that subsurface sediments had nearly same level denitrification potential activity compare to surface sediments, although the abundance of nirS gene decreased sharply from surface to bottom in sediment cores. Meanwhile, nirS gene abundance exhibit significant temporal variations, which is consistent with denitrification potential activity. Moreover, the community structure and diversity of nirS-type denitrifiers in sediment cores exhibited remarkable temporal shift pattern. For spatial variation, no significant difference was observed of denitrifiers community structure in each sediment core from the surface to the subsurface, while there were significant different diversity characteristic among different cores. Redundancy analysis (RDA) showed that multiple environmental factors including salinity, pH, oxidation-reduction potential, nutrient content and organic substances synergistically shaped the diversity and distribution of nirS-type denitrifers in PRE sediments. Our results showed that nirS-type denitrifers played important roles in the nitrogen removal in subsurface sediments of PRE.

The effects of anthropogenic disturbances and hydrological activity of a river on soil Collembola communities in an urbanized zone

Niche specificity and potential terrestrial organic carbon utilization of benthic Bathyarchaeota in a eutrophic subtropic estuarine system

Riparian soils are affected by both natural and anthropogenic disturbances occurring in the water bodies and on the catchment area. These riparian areas are also rich in microhabitats and therefore host various soil biota, including diatoms. Diatoms are known for their bioindication abilities in water and could potentially be used in that context in the riparian zone. Therefore the possibility of riparian soil diatoms acting as indicators of both terrestrial and aquatic disturbances is worth discussion. We analysed diatom community structure and their variability between different study areas and sites. We also quantified diatom species diversity and richness and evenness of the riparian topsoils. Possible effects of various anthropogenic disturbances on diatom communities, alkaline air pollution, and the effects of mining waters pumped into the area were studied in north-eastern Estonia. These results were compared with results from an area with low human influence in south-eastern Estonia. Additionally, we evaluated the potential of diatoms as indicators of various anthropogenic disturbance levels and a water contamination gradient based on sulphate concentrations. Community parameters, including species richness, diversity, and evenness, indicated some differences between the studied communities both when the separate study sites and distinguishable anthropogenic disturbance levels were compared. Diatom assemblages also showed moderate variability between the study sites, which could be influenced by variable moisture conditions, variable organic matter content, and the trophic level of the water body. Despite the variable levels of human influence the two compared areas shared about 51.4% of the species. Our findings show that the diatom community composition of riparian soils could potentially indicate anthropogenic disturbance levels, especially through the abundance, absence, or presence of specific species (e.g. Hantzschia amphioxys, Fragilaria zeilleri var. elliptica, Pinnularia lata).

ABSTRACTComplete ammonia oxidizers (comammox) have been widely detected in riverine and estuarine ecosystems. However, knowledge about the process of comammox community assembly from freshwater to marine environments is still limited. Here, based on deep sequencing, we investigated the community composition of comammox along a salinity gradient in the Pearl River Estuary (PRE), South China. Our results showed that comammox microorganisms in the PRE sediments were extremely diverse and displayed distinct distributional patterns between upstream and downstream habitats. Quantitative PCR demonstrated that comammox was the dominant ammonia-oxidizing microorganism (AOM) in the PRE upstream sediments, and ammonia-oxidizing archaea (AOA) dominated the PRE downstream sediments, while ammonia-oxidizing bacteria (AOB) were not dominant in any section of the PRE. Neutral modeling revealed that stochastic processes explained a limited part of the variation in the comammox community. The majority of beta nearest-taxon index values were higher than 2, indicating that comammox community assembly in the PRE sediments was better explained through a deterministic process than through a stochastic process. Salinity and total nitrogen were the most important contributing factors that shaped the comammox community. This study expanded the current knowledge of the diversity and niche preference of comammox in the estuarine ecosystem, and further enhances our understanding of the assembly of comammox community from freshwater to marine environments.IMPORTANCE Microbial communities are shaped by stochastic (emigration, immigration, birth, death, and genetic drift of species) and deterministic (e.g., environmental factors) processes. However, it remains unknown as to which type of process is more important in influencing the comammox community assembly from freshwater to marine environments. In this study, we compared the relative importance of stochastic and deterministic processes in shaping the assembly of the comammox community, which demonstrated that the deterministic process was more important in determining the community assembly patterns in the PRE ecosystem.

Spatial distribution of gut juice extractable Cu, Pb and Zn in sediments from the Pearl River Estuary, Southern China

Key messageHere, we present a workflow for determining the optimal tree height model and calibration design for forests affected to varying degrees by anthropogenic disturbance. For mixed Araucaria-Nothofagus forests, tree height predictions in newly surveyed stands are most accurate and effective when the height of up to five random trees is measured to recalibrate predefined nonlinear mixed-effects models.ContextAraucaria-Nothofagus forests in Chile are affected by anthropogenic disturbances such as intentional forest fires, grazing, and seed harvesting, causing forest structure to become more heterogeneous. This also challenges tree height predictions, which are required for yield estimations, carbon accounting, and forest management, since height measurements of standing trees are often considered too costly, difficult, and imprecise.AimsHow does the structure of these forests vary by different levels of anthropogenic disturbance? Which models for estimating tree height of Araucaria araucana and Nothofagus pumilio are most reliable and generally usable? And considering their application in stands they have not been fitted to, which calibration design is optimal for these models?MethodsTwelve stands were surveyed and classified into four different intensities of anthropogenic disturbance. In 25 to 36 plots per stand, horizontal point sampling measurements of stem diameter as well as of height of selected trees were carried out. Different quantitative stand-level properties were calculated to determine forest structure, which was compared among stands by cluster analysis. To identify the optimal height-diameter (H–D) model, simple models including diameter only as well as generalized models including stand variables were tested, each additionally extended by a nonlinear mixed-effects (NLME) modeling framework accounting for nested and random effects. To further determine tree height in new stands, the optimal model calibration design was identified involving the empirical best unbiased predictor technique.ResultsForest structure greatly varied among stands affected by different levels of anthropogenic disturbance, which challenged the development of tree height prediction models. Of all the simple H–D models considered, the Gompertz model was the best for A. araucana and the Näslund model for N. pumilio. The models progressively improved by adding stand variables and using NLME techniques. However, our final model comparisons indicate that a calibrated simple NLME model without stand variables should be preferred. It was further found that the optimal calibration design is to use five randomly selected trees.ConclusionAlthough anthropogenic disturbances can have a complex effect on height-diameter relationships, the same H–D model can be used for stands representing different anthropogenic disturbance levels and recalibrated by cost-effective measurements.

Spatiotemporal variations of halogenated polycyclic aromatic hydrocarbons in sediments of Pearl River Estuary: Occurrence, sources, and potential ecological risks.

High productivity and accessibility have made coastal wetlands attractive sites for human settlements. This study analyzed the patterns of wetland landscapes in Galveston Bay, Texas, USA. The first objective of the study was to describe the relationships between the fractal dimension of wetland boundaries and those factors which affect the wetland landscapes (e.g., land use, type of vegetation, size, location, and level of human disturbance). The second objective was to construct a historical database to contrast wetland areas which had experienced different levels of disturbance between 1956 and 1989. The fractal dimension, a measure of how much of the geographical space is filled by boundaries, was measured by the perimeter-area method. The fractal dimension of wetlands was significantly affected by land use, type of vegetation, size, and level of anthropogenic disturbance. In addition, increasing the size of buffers around roads did not significantly affect the fractal dimension of wetlands. Landscape indices, such as fractal dimension, dominance, and diversity, were used to characterize spatial heterogeneity in the historical database. Lake Stephenson, an area of low anthropogenic disturbance, experienced no changes in wetland composition and abundance over time. Anahuac, an area of medium disturbance, experienced changes in both wetland composition and abundance. Texas City, an area of high disturbance, experienced a change in wetland composition. These differences can be associated with the type and level of disturbance present; however, more evidence is needed to determine whether certain landscape patterns have stable, intrinsic properties which allow persistence in the face of disturbance. These results will be informative to resource managers determining how wetlands can be managed as natural resources and nature reserves.

Anaerobic ammonium oxidation (anammox) is an important pathway for the removal of fixed nitrogen from aquatic and terrestrial ecosystems. Previous studies on anammox were focused on the surface sediments in estuaries, but the activity and community composition of anammox bacteria in the estuarine subsurface sediments remained unknown. In this study, we used high-throughput sequencing of 16S rRNA gene combined with 15N isotope tracing method to investigate the activity, diversity, and spatio-temporal distribution of anammox bacteria in sediment cores of the Pearl River Estuary (PRE). Our results indicated that anammox in the subsurface sediments has significant potential activity, contributing to approximately 17.49% of the total microbial nitrogen loss. A variety of anammox bacteria, including Candidatus Scalindua, Ca. Brocadia, Ca. Jettenia, and Ca. Kuenenia, were all detected in the subsurface sediments. Moreover, the anammox bacterial community had a significant specific geographic distribution but no obvious difference along the sediment depth. Multiple environmental factors including salinity, and NH4+ and NO3− contents, synergistically shaped the diversity and distribution of anammox bacteria in PRE sediments.

Knowledge of the origins and dissemination of antibiotic resistance genes (ARGs) is essential for understanding modern resistomes in the environment. The mechanisms of the dissemination of ARGs can be revealed through comparative studies on the metagenomic profiling of ARGs between relatively pristine and human-impacted environments. The deep ocean bed of the South China Sea (SCS) is considered to be largely devoid of anthropogenic impacts, while the Pearl River Estuary (PRE) in south China has been highly impacted by intensive human activities. Commonly used antibiotics (sulfamethazine, norfloxacin, ofloxacin, tetracycline, and erythromycin) have been detected through chemical analysis in the PRE sediments, but not in the SCS sediments. In the relatively pristine SCS sediments, the most prevalent and abundant ARGs are those related to resistance to macrolides and polypeptides, with efflux pumps as the predominant mechanism. In the contaminated PRE sediments, the typical ARG profiles suggest a prevailing resistance to antibiotics commonly used in human health and animal farming (including sulfonamides, fluoroquinolones, and aminoglycosides), and higher diversity in both genotype and resistance mechanism than those in the SCS. In particular, antibiotic inactivation significantly contributed to the resistance to aminoglycosides, β-lactams, and macrolides observed in the PRE sediments. There was a significant correlation in the levels of abundance of ARGs and those of mobile genetic elements (including integrons and plasmids), which serve as carriers in the dissemination of ARGs in the aquatic environment. The metagenomic results from the current study support the view that ARGs naturally originate in pristine environments, while human activities accelerate the dissemination of ARGs so that microbes would be able to tolerate selective environmental stress in response to anthropogenic impacts.

Urbanization is a major threat to wildlife with its cohort of environmental stressors. Urban remnant vegetation can help mitigate these impacts, but such remnants are subject to stressors that might be detrimental for some species. Habitat generalists have flexible diets and broader habitat tolerances that could favour their persistence in these remnants. Marmosets (Callithrix jacchus) and sloths (Bradypus variegatus) differ in their ecological and behavioural plasticity and both occur in urban areas. We predict marmosets to be less affected than sloths, a specialist species, by anthropogenic disturbance. We estimated their densities in urban forest fragments of semi-deciduous Atlantic forest in Paraiba, NE Brazil, with contrasting levels of urbanization. Using the distance sampling methodology, we surveyed 12 trails in a larger and less impacted fragment (515 ha) and 13 trails across nine smaller forest patches (2.1–8.0 ha) with a greater level of anthropogenic disturbance. Density of marmoset’s groups was higher in the area with lower anthropogenic disturbance, whereas sloths’ density was significantly higher in the more urbanized fragments. Marmosets seemed to be more impacted by noise than sloths. The density of both species in forest patches with higher level of anthropogenic disturbance was similar or even higher than densities from non-urban and less disturbed areas. Despite the negative impacts on wildlife, urbanization seems to cause a reduction of predators and an increase in availability of food resources that favour some species. Our results show the importance of small urban forest fragment for the persistence of marmosets and sloths in Neotropical cities.

Anthropogenic disturbances alter the relationships between environmental heterogeneity and biodiversity of stream insects