Identification of suspended particulate matters as the hotspot of polycyclic aromatic hydrocarbon degradation-related bacteria and genes in the Pearl River Estuary using metagenomic approaches

Evidence of transboundary movement of chemicals from Mexico to the U.S. in Tijuana River Estuary sediments

The Tijuana River Estuary (TRE) has been a public health hazard and point of contention between the United States and Mexico for decades, with sources of pollution on both sides of the border. The goal of our study is to determine the presence and dynamics of chemical contamination in the TRE. We sampled sediment from four TRE locations in the U.S. during stable dry conditions and immediately after a wet weather period. Organic chemicals were initially screened with non-targeted analysis using gas chromatography high-resolution mass spectrometry (GC/HRMS) that tentatively identified 6978 chemicals in the NIST 20 database. These tentative identifications were filtered using the USEPA CompTox database to guide quantitative targeted analysis at detection limits below 1 ng/g dry weight sediment. Quantitative targeted analysis of 152 organic pollutants and 18 inorganic elements via GC/HRMS revealed generally higher concentrations of contaminants in dry weather sediments compared to wet weather sediments. The highest concentrations of all chemical classes were detected at the site closest to the U.S.-Mexico border, followed by an urban area near Imperial Beach, California, U.S. All sites exhibited a mixture of petrogenic and pyrogenic polycyclic aromatic hydrocarbons (PAHs). Current-use pesticides were dominated by pyrethroid insecticides and the thiocarbamate herbicide s-Ethyl dipropylthiocarbamate (EPTC), while the U.S.-banned organochlorine pesticides were dominated by chlordanes, dieldrin, and dichlorodiphenyltrichloroethane (DDT) and its degradation byproducts. Polychlorinated biphenyl (PCB) concentrations were greatest at the site closest to the U.S.-Mexico border but in the low nanogram-per-gram range. Phthalates were only found at the same site, with relatively high concentrations of bis(2-ethylhexyl) phthalate. This study provides positive identification and quantitative concentrations for organic pollutants in TRE sediments. Our data suggest that there are multiple sources of chemical contamination in the estuary, including possible transboundary movement of pollutants from Mexico.

Characterization of metal resistance genes carried by waterborne free-living and particle-attached bacteria in the Pearl River Estuary

Toxic metals can substantially change the bacterial community and functions thereof in aquatic environments. Herein, metal resistance genes (MRGs) are the core genetic foundation for microbial responses to the threats of toxic metals. In this study, waterborne bacteria collected from the Pearl River Estuary (PRE) were separated into the free-living bacteria (FLB) and particle-attached bacteria (PAB), and analyzed using metagenomic approaches. MRGs were ubiquitous in the PRE water and mainly related to Cu, Cr, Zn, Cd and Hg. The levels of PAB MRGs in the PRE water ranged from 8.11 × 10⁹ to 9.93 × 10¹² copies/kg, which were significantly higher than those of the FLB (p < 0.01). It could be attributed to a large bacterial population attached on the suspended particulate matters (SPMs), which was evidenced by a significant correlation between the PAB MRGs and 16S rRNA gene levels in the PRE water (p < 0.05). Moreover, the total levels of PAB MRGs were also significantly correlated with those of FLB MRGs in the PRE water. The spatial pattern of MRGs of both FLB and PAB exhibited a declining trend from the low reaches of the PR to the PRE and on to the coastal areas, which was closely related to metal pollution degree. MRGs likely carried by plasmids were also enriched on the SPMs with a range from to 3.85 × 10⁸ to 3.08 × 10¹² copies/kg. MRG profiles and taxonomic composition of the predicted MRG hosts were significantly different between the FLB and PAB in the PRE water. Our results suggested that FLB and PAB could behave differential response to heavy metals in the aquatic environments from the perspective of MRGs.

Medium-chain alkane biodegradation and its link to some unifying attributes of alkB genes diversity

Hydrocarbon footprints in the environment, via biosynthesis, natural seepage, anthropogenic activities and accidents, affect the ecosystem and induce a shift in the healthy biogeochemical equilibrium that drives needed ecological services. In addition, these imbalances cause human diseases and reduce animal and microorganism diversity. Microbial bioremediation, which capitalizes on functional genes, is a sustainable mitigation option for cleaning hydrocarbon-impacted environments. This review focuses on the bacterial alkB functional gene, which codes for a non-heme di‑iron monooxygenase (AlkB) with a di‑iron active site that catalyzes C₈-C₁₆ medium-chain alkane metabolism. These enzymes are ubiquitous and share common attributes such as being controlled by global transcriptional regulators, being a component of most super hydrocarbon degraders, and their distributions linked to horizontal gene transfer (HGT) events. The phylogenetic approach used in the HGT detection suggests that AlkB tree topology clusters bacteria functionally and that a preferential gradient dictates gene distribution. The alkB gene also acts as a biomarker for bioremediation, although it is found in pristine environments and absent in some hydrocarbon degraders. For instance, a quantitative molecular method has failed to link alkB copy number to contamination concentration levels. This limitation may be due to AlkB homologues, which have other functions besides n-alkane assimilation. Thus, this review, which focuses on Pseudomonas putida GPo1 alkB, shows that AlkB proteins are diverse but have some unifying trends around hydrocarbon-degrading bacteria; it is erroneous to rely on alkB detection alone as a monitoring parameter for hydrocarbon degradation, alkB gene distribution are preferentially distributed among bacteria, and the plausible explanation for AlkB affiliation to broad-spectrum metabolism of hydrocarbons in super-degraders hitherto reported. Overall, this review provides a broad perspective of the ecology of alkB-carrying bacteria and their directed biodegradation pathways.

Microbial community assembly responses to polycyclic aromatic hydrocarbon contamination across water and sediment habitats in the Pearl River Estuary

Along with rapid urbanization and intensive human activities, polycyclic aromatic hydrocarbon (PAH) pollution in the Pearl River Estuary (PRE) and its effects on the microbial community have attracted extensive attention. However, the potential and mechanism of microbial degradation of PAHs across water and sediment habitats remain obscure. Herein, the estuarine microbial community structure, function, assembly process and co-occurrence patterns impacted by PAHs were comprehensively analyzed using environmental DNA-based approaches. The contamination and distribution of PAHs were jointly affected by anthropogenic and natural factors. Some of the keystone taxa were identified as PAH-degrading bacteria (i.e., genera Defluviimonas, Mycobacterium, families 67-14, Rhodobacteraceae, Microbacteriaceae and order Gaiellales in water) or biomarkers (i.e., Gaiellales in sediment) that were significantly correlated with PAH levels. The proportion of deterministic process in the high PAH-polluted water (76%) was much higher than that in the low pollution area (7%), confirming the significant effect of PAHs on the microbial community assembly. In sediment, the communities with high phylogenetic diversity demonstrated a great extent of niche differentiation, exhibited a stronger response to environmental variables and were strongly influenced by deterministic processes (40%). Overall, deterministic and stochastic processes are closely related to the distribution and mass transfer of pollutants, and substantially affect the biological aggregation and interspecies interaction within communities in the habitats.

Impact of Particulate Pollution on Aquatic Invertebrates

A serious global problem, air pollution poses a risk to both human and environmental health. It contains hazardous material like heavy metals, nanoparticles, and others that can create an impact on both land and marine environments. Particulate pollutants, which can enter water systems through a variety of ways, including precipitation and industrial runoff, can have a particularly adverse influence on aquatic invertebrates. Once in the water, these particles can harm aquatic invertebrates physically, physiologically, and molecularly, resulting in developmental problems and multi-organ toxicity. Further research at the cellular and molecular levels in numerous locations of the world is necessary to completely understand the impacts of particle pollution on aquatic invertebrates. Understanding how particle pollution affects aquatic invertebrates is vital as the significance of ecotoxicological studies on particulate contaminants increases. This review gives a comprehensive overview of the current understanding of how particle pollution affects aquatic invertebrates.

Seasonal occurrence of multiple classes of antibiotics in East China rivers and their association with suspended particulate matter

Understanding the occurrence and fate of antibiotics from different categories is vital to predict their environmental exposure and risks. This study presents the spatiotemporal occurrence of 45 multi-class antibiotics and their associations with suspended particulate matter (SPM) in Xiaoqing River (XRB) and Yellow River (YRB) via 10-month monitoring in East China. Thirty-five and 31 antibiotics were detected in XRB and YRB, respectively. Among them, fluoroquinolones (FQs) had the highest total mean concentration (up to 24.8 μg/L in XRB and 15.4 μg/L in YRB), followed by sulfonamides (SAs) (14.0 μg/L and 15.4 μg/L) and macrolides (MLs) (1.1 μg/L and 1.6 μg/L). Significant spatial-temporal variations were found in both rivers where higher concentrations of antibiotics were observed in urban and densely populated areas during winter and spring. Hydrological factors such as river flow and water volume, instream attenuation and antibiotic usage may cause the observed variabilities in the seasonal patterns of antibiotic pollution. Using linear regression analysis, for the first time, this study confirmed that the total concentrations of MLs (p < 0.05), FQs (p < 0.001) and SAs (p < 0.001) were strongly correlated with the turbidity/total suspended solids in the studied rivers (except MLs in YRB). It is thus suggested that partitioning processes onto SPM might affect the distribution of detected antibiotics in rivers, which are largely dependent on SPM composition and characteristics. The risk quotient (RQ) determined for up to 87 % of individual compound was below 0.1 in both rivers; however, the high joint toxicity reflected by the mixed RQs of detected antibiotics may rise risk alarm for aquatic species. Further aspects regarding active mechanisms of SPM-antibiotic interactions and ecological risks of coexistence of multiple antibiotics need to be investigated.

Seasonal and inter-annual variability of bacterioplankton communities in the subtropical Pearl River Estuary, China

It is widely recognized that environmental factors substantially influence on the seasonal and inter-annual variability of bacterioplankton communities, yet little is known about the seasonality of bacterioplankton communities in subtropical estuaries at longer-term time scales. Here, the bacterioplankton communities from the eight major outlets of the subtropical Pearl River Estuary were investigated across 3 years (2017-2019) using full-length 16S rRNA gene sequencing. Significant seasonal and inter-annual variation was observed in bacterioplankton community compositions across the 3 years (p < 0.05). In addition, the inferred functional composition of the communities varied with seasons, although not significantly, suggesting that functional redundancy existed among communities and across seasons that could help to cope with environmental changes. Five evaluated environmental parameters (temperature, salinity, pH, total dissolved solids (TDS), total phosphorus (TP)) were significantly correlated with community composition variation, while only three environmental parameters (temperature, pH, and TDS) were correlated with variation in inferred functional composition. Moreover, community composition tracked the seasonal temperature gradients, indicating that temperature was a key environmental factor that affected bacterioplankton community's variation along with seasonal succession patterns. Gammaproteobacteria and Alphaproteobacteria were the most dominant classes in the surface waters of Pearl River Estuary, and their members exhibited divergent responses to temperature changes, while several taxa within these group could be indicators of low and high temperatures that are associated with seasonal changes. These results strengthen our understanding of bacterioplankton community variation in association with temperature-dependent seasonal changes in subtropical estuarine ecosystems.