Response of particle-associated bacteria to long-term heavy metal contamination in a tropical estuary

Impact of environmental factors on diversity of fungi in sediments from the Shenzhen River Estuary

In this study, to explore the relationship between environmental factors and fungal diversity in the Shenzhen River ecosystem, multiple methods including chemical analysis, culture isolation, qPCR analysis of fungal ITS region and ITS-based Illumina next-generation-sequencing were integrated. A total of 115 isolates were finally isolated and could be classified into 23 genera. Top three abundant genera isolated were Meyerozyma (18 strains), Aspergillus (17 strains) and Penicillium (14 strains). Based on the Illumina sequencing approach, 829 OTUs were affiliated to seven phyla, 17 known classes, and 162 genera, indicating the Shenzhen estuary sediments are rich in fungal diversity. The major fungal genera were Meyerozyma, Trichoderma and Talaromyces. Environmental factors showed a gradient change in Shenzhen estuary, and fungal abundance was only significantly correlated with NH₄⁺. Shannon index was significantly correlated with pH and IC (P < 0.05). Principal coordinate analysis based on OTU level grouped into three clusters among sampling sites along with the IC and pH gradient. Functional guilds analysis suggests most of the fungi in this studying area were almost all saprotrophs, suggesting a large number of saprophytic fungi may play a significant role in the organic matter decomposition and nutrient cycling process. In summary, this study will deepen our understanding of fungi community in Shenzhen River ecosystem and their distribution and potential function shaped by environmental factors.

Impact of different environmental pollution processes on bacterial key-indicators in tropical rivers: scoping review

Freshwater ecosystems are an essential resource for human use and natural populations, but they are exposed to different sources of man-made pollution. This study analyses how different environmental pollution processes influence the structure of bacterial communities in tropical rivers. A scoping review was performed to characterize the bacterial communities in freshwater ecosystems in tropical regions that have been reported to be associated with pollution of different kinds. The statistical analyses allowed us to categorize the genera found into three large groups (pollution generalists, middle types, and pollution specialists) according to the types of pollutants with which they were associated. The results show that Escherichia has a greater association with fecal contamination, while Enterococcus is more associated with domestic wastewater and organic and synthetic chemicals. The present study proposes Streptomyces as a potential indicator of waters with microbial contamination, as well as some other genera as possible indicators of waters with heavy metal contamination.

Selective pressure governs the composition, antibiotic, and heavy metal resistance profiles of Aeromonas spp. isolated from Ba River in Northwest China

The selective pressure of the living surroundings is a key factor in the development of resistance profiles in pathogenic bacteria such as Aeromonas spp. In this study, Aeromonas species were isolated from the Ba River, and their composition, resistance profiles to antibiotics, and heavy metals (HMs) were investigated. The discovery revealed that selective pressure altered the diversity of Aeromonas spp., with Aeromonas veronii being more adaptable to contaminated waters. Long-term exposure to antibiotics or HMs exerts persistent selective pressure on Aeromonas species, leading to the increase in multiple antibiotic resistance (MAR) index and multidrug-resistant (MDR) strains. Furthermore, HMs could drive the co-selection of antibiotic resistance via co-resistance or cross-resistance. bla_TEM, bla_SHV, bla_CTX-M, sul1, czcA, mexA, and mexF were detected at high frequencies in Aeromonas species. Among these resistance phenotypes conferred genes, bla_TEM may be intrinsic in the genome of Aeromonas spp., while mexA and mexF may have been acquired from surrounding environments owing to selective pressure. Resistance genes evolved as a consequence of selective pressure and have been shown to be positively correlated with their prevalence. Our study suggests that the selective pressure of living surroundings significantly contributes to the composition and resistance profiles of Aeromonas spp. in the riverine ecosystem.

Phenotype profiles and adaptive preference of Acinetobacter johnsonii isolated from Ba River with different environmental backgrounds

Acinetobacter johnsonii is a potentially opportunistic pathogen widely distributed in nosocomial and natural environments, but little attention has been paid to this bacillus. Here A. johnsonii strains from Ba River with different pollution levels were isolated. In this study, we found that the increasing anthropogenic contaminants accounted for the emergence of multidrug-resistant (MDR) A. johnsonii strains. Correlation analysis results showed that the resistance phenotype of strains could be generated by co-selection of heavy metals or non-corresponding antibiotics. The whole genome sequence analysis showed that the relative heavy pollution of water selects strains containing more survival-relevant genes. We found that only some genes like bla_OXA-24 were responsible for its corresponding resistance profile. Additionally, the tolerance profiles toward heavy metals also attribute to the expression of efflux pumps rather than corresponding resistance genes. In summary, our finding revealed that the resistance profiles of A. johnsonii could be generated by cross or co-selection of anthropogenic contaminants and mediated by efflux pumps instead of corresponding resistance determinants. Our study also has deep-sight into the adaptive preference of bacteria in natural environments, and contributes to surveillance studies and MDR- A. johnsonii monitoring worldwide.

Fractionation and accumulation of selected metals in a tropical estuary, south-west coast of India

Estimating the fractional distribution of sediment-bound heavy metals is highly significant for its ecological risk assessment in contaminated aquatic systems, since environmental factors enhance the mobility of heavy metals and its accumulation in different ecological matrices. In this study, the fractional distribution of Zn, Cd, Pb and Cu in the sediments of the Cochin estuary, along the south-west coast of India, was estimated along with its accumulation in four edible crustaceans. The high mobility of heavy metals in the Cochin estuary was evident from the distribution in fractions other than residual fraction. The exchangeable fractions of Zn and Cd were high in the Cochin estuary, indicating its high bioavailability. Even though the exchangeable fraction is negligible, Pb poses the risk of bioaccumulation due to the presence of oxidisable and reducible fractions. The level of heavy metals varies in different species of edible prawns, and high accumulation of all metals was observed in Metapenaeus dobsoni. Various risk assessment indices show that Cd and Pb pose significant ecological and human health risks in the Cochin estuary.

Effect of copper sulfate on the external microbiota of adult common snook (Centropomus undecimalis)

BACKGROUND

The environment exerts a strong influence on the fish external microbiota, with lower diversity and increased abundances of opportunistic bacterial groups characterizing cultured fish compared to their wild counterparts. Deviation from a healthy external microbiota structure has been associated with increased susceptibility to bacterial pathogens. Treatment of wild-caught broodstock with copper sulfate for the removal of external parasites is a common aquaculture practice. Despite the microbiota's importance to fish health, the effects of copper sulfate on mucosal bacterial communities and their ability to recover following this chemical treatment have not been examined. The skin microbiota of adult common snook was characterized from wild individuals (Wild), and wild-caught fish maintained in recirculating aquaculture systems (RAS) immediately following a month-long copper sulfate treatment (Captive-1), and then two-weeks (Captive-2) and 2 years (Captive-3) after cessation of copper treatment.

RESULTS

The skin microbiota of wild fish were characterized by high diversity and taxa including Synechocococcus, SAR11, and a member of the Roseobacter clade. Bacterial diversity decreased in Captive individuals during the 2-year sampling period. Captive fish harbored greater abundances of Firmicutes, which may reflect glycan differences between aquaculture and natural feeds. Bacterial taxa with copper resistance mechanisms and indicative of metal contamination were enriched in Captive-1 and Captive-2 fish. Vibrionaceae were dominant in Captive fish, particularly immediately and 2 weeks following copper treatment. Based on our observations and previous literature, our results suggest putatively beneficial taxa amass over time in captivity. Within 2 years, Captive individuals harbored Bacillus which contains numerous probiotic candidates and the complex carbon degraders of the family Saprospiraceae. Predicted butanoate metabolism exceeded that of Wild fish, and its reported roles in immunity and energy provision suggest a prebiotic effect for fishes.

CONCLUSIONS

The mucosal microbiota contains bacterial taxa that may act as bioindicators of environmental pollution. Increases in mutualistic groups indicate a return to a beneficial skin microbiota following copper sulfate treatment. Our data also suggests that vastly different taxa, influenced by environmental conditions, can be associated with adult fish without noticeable health impairment, perhaps due to establishment of various mutualists to maintain fish mucosal health.

Aberrations in the microbiome of cyanobacteria from a tropical estuary polluted by heavy metals

The effect of heavy metal pollution on the microbiome of cyanobacteria in Cochin estuary (CE) on the southwest coast of India is reported in the study. Statistically significant difference in heavy metal concentration was observed between water, suspended particulate matter (SPM) and sediment. The Zn, Cd, Cu, Ni and Cr were 2-6 times higher in the SPM compared with the sediment, while Pb was 10 to 25 times higher. Although nearly 60% of the species diversity of microbiome was common between cyanobacteria enriched from the upstream (S1S) and downstream (S11B), there was a difference in the major groups of heterotrophic bacterial associates. Proteobacteria was the dominant phylum (>80%) in S1S, while it was second only (27.5%) after Planctomycetes (37.4%) in S11B. The results of the current study indicate that the pollution can influence an ecosystem at the micro-niche level.