Genes In Sediments Research Articles

Macrogenomics Reveals Effects on Marine Microbial Communities during Oplegnathus punctatus Enclosure Farming.

(1) Background: Laizhou Bay is an important aquaculture area in the north of China. Oplegnathus punctatus is one of the species with high economic benefits. In recent years, the water environment of Laizhou Bay has reached a mild eutrophication level, while microorganisms are an important group between the environment and species. In this study, we evaluated alterations in environmental elements, microbial populations, and antibiotic resistance genes (ARGs) along with their interconnections during Oplegnathus punctatus net culture. (2) Methods: A total of 142 samples from various water layers were gathered for metagenome assembly analysis. Mariculture increases the abundance of microorganisms in this culture area and makes the microbial community structure more complex. The change had more significant effects on sediment than on seawater. (3) Results: Certain populations of cyanobacteria and Candidatus Micrarchaecta in seawater, and Actinobacteria and Thaumarchaeota in sediments showed high abundance in the mariculture area. Antibiotic resistance genes in sediments were more sensitive to various environmental factors, especially oxygen solubility and salinity. (4) Conclusions: These findings highlight the complex and dynamic nature of microorganism-environment-ARG interactions, characterized by regional specificity and providing insights for a more rational use of marine resources.

Antibiotic Pollution and Its Effects on the Spatiotemporal Variation in Microbial Community Structure and Functional Genes in Sediment of Baiyangdian Lake

Microbial communities play an important role in water quality regulation and biogeochemical cycles in lakes, and their community structure and function are affected by environmental factors. Therein, antibiotics affect the abundance, diversity, composition, and function of microbial communities. In this study, Baiyangdian Lake was selected as the study area. Sediment samples of 16 sites were collected in August 2018 and April 2019, respectively. Ultra-high performance liquid chromatography-mass spectrometry （HPLC-MS/MS） was used to determine the content of typical antibiotics-quinolones （QNs） in sediment. Through high-throughput sequencing technology, the structure and function of microbial communities was analyzed in the sediments to explore the spatiotemporal variation. Thereinto, redundancy analysis （RDA） was used to identify the key influencing factors of spatiotemporal variation of microbial communities. The results showed that： ① From August to April, the average ω（QNs） showed an increasing trend, and its mean value changed from 3.91 ng·g-1 to 6.34 ng·g-1, with significant seasonal differences in oxolinic acid （OXO） and total QNs content （P < 0.05）. ② In terms of temporal variation, the dominant bacteria were Proteobacteria and Chloroflexi. The relative abundance of Proteobacteria showed a decreasing trend, whereas Chloroflexi showed an increasing trend； at the genus level, the dominant bacteria genera in August were norank_ f__Anaerolineaceae and Thiobacilus, and the dominant bacteria genera in April were Acinetobacter and norank_ f_Anaerolineaceae, and the dominant bacteria genera had significant seasonal differences （P < 0.05）. ③ In terms of temporal variation, the index of Simpson, Chao, Ace, and OTU number all showed an increasing trend, and the seasonal differences were significant （P < 0.05）. ④ In terms of spatial variation, there were no significant spatial differences among functional genes of COG. In terms of temporal variation, there were significant seasonal differences in functional genes of energy production and conversion, carbohydrate transport and metabolism, transcription, cell wall/membrane/envelope biogenesis, and signal transduction mechanisms （P < 0.01 and P < 0.05）. ⑤ Microbial community structure and functional genes were significantly correlated with QNs （P < 0.01 and P < 0.05）, and QNs were the main influencing factors. Therefore, QNs were the main factor affecting the changes in microbial community structure and functional genes in sediments of Baiyangdian Lake. Thus, comprehensive control of antibiotic pollution in sediments should be further strengthened.

A comparison of microbial diversity, distribution patterns, and halogenated aromatics biodegrading genes in sediments of two urban rivers

Urban river sediments often serve as reservoirs of halogenated aromatic pollutants, such as polychlorinated biphenyls (PCBs), leading to significantly alterations in the biological characteristics of this ecosystem. Various microbes can degrade halogenated aromatics, serving as a crucial detoxification mechanism that converts toxic pollutants into common metabolites to complete the carbon cycle. However, the impact of PCBs on the diversity and structure of microbial communities in urban rivers has remained largely unexplored. Understanding the dynamics of microbial community structure and function is essential for unraveling biodegradation pathways and interactions of these microbial degraders in PCB-contaminated urban river sediments. In this study, a thorough analysis of microbial diversity and distribution patterns was conducted using 16S rRNA gene-based sequencing in the sediments of two urban rivers, the Dasha River and Maozhou River. Our results unveiled distinct community variances between the two rivers, primarily influenced by environmental factors. The detailed composition and abundance of halogenated aromatic biodegradation related genes were elucidated using metagenomics, mainly contributed by Proteobacteria, Desulfobacterota, and Chloroflexi. Network analysis revealed close interactions among these microbes within each river, indicating a cooperative propensity for PCBs biodegradation, which underscores the interactions as the mode of metabolism and common survival strategy in contaminated rivers.

Seasonal changes in N-cycling functional genes in sediments and their influencing factors in a typical eutrophic shallow lake, China.

N-cycling processes mediated by microorganisms are directly linked to the eutrophication of lakes and ecosystem health. Exploring the variation and influencing factors of N-cycling-related genes is of great significance for controlling the eutrophication of lakes. However, seasonal dynamics of genomic information encoding nitrogen (N) cycling in sediments of eutrophic lakes have not yet been clearly addressed. We collected sediments in the Baiyangdian (BYD) Lake in four seasons to explore the dynamic variation of N-cycling functional genes based on a shotgun metagenome sequencing approach and to reveal their key influencing factors. Our results showed that dissimilatory nitrate reduction (DNRA), assimilatory nitrate reduction (ANRA), and denitrification were the dominant N-cycling processes, and the abundance of nirS and amoC were higher than other functional genes by at least one order of magnitude. Functional genes, such as nirS, nirK and amoC, generally showed a consistent decreasing trend from the warming season (i.e., spring, summer, fall) to the cold season (i.e., winter). Furthermore, a significantly higher abundance of nitrification functional genes (e.g., amoB, amoC and hao) in spring and denitrification functional genes (e.g., nirS, norC and nosZ) in fall were observed. N-cycling processes in four seasons were influenced by different dominant environmental factors. Generally, dissolved organic carbon (DOC) or sediment organic matter (SOM), water temperature (T) and antibiotics (e.g., Norfloxacin and ofloxacin) were significantly correlated with N-cycling processes. The findings imply that sediment organic carbon and antibiotics may be potentially key factors influencing N-cycling processes in lake ecosystems, which will provide a reference for nitrogen management in eutrophic lakes.

Co-exposure of microplastics and sulfamethoxazole propagated antibiotic resistance genes in sediments by regulating the microbial carbon metabolism

The concerns on the carriers of microplastics (MPs) on co-existing pollutants in aquatic environments are sharply rising in recent years. However, little is known about their interactions on the colonization of microbiota, especially for the spread of pathogens and antibiotic resistance genes (ARGs). Therefore, this study aimed to investigate the influences on the propagation of ARGs in sediments by the co-exposure of different MPs and sulfamethoxazole (SMX). The results showed that the presence of MPs significantly enhanced the contents of total organic carbon, while having no effects on the removal of SMX in sediments. Exposure to SMX and MPs obviously activated the microbial carbon utilization capacities based on the BIOLOG method. The propagation of ARGs in sediments was activated by SMX, which was further promoted by the presence of polylactic acid (PLA) MPs, but significantly lowered by the co-exposed polyethylene (PE) MPs. This apparent difference may be attributed to the distinct influence on the antibiotic efflux pumps of two MPs. Moreover, the propagation of ARGs may be also dominated by microbial carbon metabolism in sediments, especially through regulating the carbon sources of carboxylic acids, carbohydrates, and amino acids. This study provides new insights into the carrier effects of MPs in sediments.

Nitrogen-cycling genes in oyster reefs and surrounding sediments: Relationships with environmental factors and respective nitrogen rates

To investigate nitrogen (N) cycling in oyster reef habitats along the East coast of Australia, we assessed N-cycling gene abundances in oyster shell biofilms and surrounding sediments, and explored their correlation with environmental factors and respective N rates. We found higher abundances of the denitrification gene nosZII in oyster shell biofilms, while there were not significant differences in the denitrification genes nirS and nirK between oyster biofilms and sediments. Additionally, oyster shell biofilms had a lower (nirS + nirK)/nosZII ratio, indicating a greater capacity for N removal and limited nitrous oxide release compared to sediments. Abundance of nirS, nirK, and dissimilatory nitrate reduction to ammonium (nrfA) genes in sediments decreased with increasing content of organic material, suggesting the influence of large-scale environmental conditions. N-cycling gene abundances did not relate to N rates, emphasising the importance of investigating microbial genes to enhance our understanding of the N cycle in oyster reef habitats.

Microecological health assessment of water environment and sediment based on metagenomics: a case study of Guixi River in Chongqing, China.

River sediment is vital in containing water pollution and strengthening water remediation. This paper has conducted a study on the microecological health assessment of the sediment and water body of Guixi River in Dianjiang, Chongqing, China, using metagenomics sequencing and microbial biological integrity index (M-IBI) technology. The analysis of physical and chemical characteristics shows that the concentration of TN varies from 2.62 to 9.76mg/L in each sampling section, and the eutrophication of the water body is relatively severe. The proportion of Cyanobacteria in the sampling section at the sink entrance is higher than that of other sites, where there are outbreaks of water blooms and potential hazards to human health. The dominant functions of each site include carbon metabolism, TCA cycle, and pyruvate metabolism. In addition, the main virulence factors and antibiotic resistance genes in sediment are Type IV pili (VF0082), LOS (CVF494), MymA operon (CVF649), and macrolide resistance genes macB, tetracyclic tetA (58), and novA. Correlation analysis of environmental factors and microorganisms was also performed, and it was discovered that Thiothrix and Acidovorax had obvious gene expression in the nitrogen metabolism pathway, and the Guixi River Basin had a self-purification capacity. Finally, based on the microecological composition of sediment and physical and chemical characteristics of the water body, the health assessment was carried out, indicating that the main pollution area was Dianjiang Middle School and the watershed near the sewage treatment plant. The findings should theoretically support an in-depth assessment of the water environment's microecological health.

Profiles and spatial distributions of heavy metals, microbial communities, and metal resistance genes in sediments from an urban river.

The occurrence and propagation of resistance genes due to exposure to heavy metals (HMs) in rivers is an emerging environmental issue. Little is known about resistance genes in microbial communities in river sediments with low HM concentrations. The profiles and spatial distributions of HMs, the microbial community, and metal resistance genes (MRGs) were analyzed in sediment samples from the Zhilong River basin in Yangjiang city, near the Pearl River Delta. Concentrations of copper (Cu), cadmium (Cd), lead (Pb), chromium (Cr), and nickel (Ni) were relatively low compared with those in other urban river sediments in China. HM chemical composition and fractions and the structure of the microbial community varied along the main channel, but the composition and abundance of MRGs were relatively homogeneous. Variations in HMs and microbial communities in mid- to upstream areas were related to the presence of tributaries, whose inputs were one of the major factors affecting HM chemical fractions and genera structure in mainstream sediments. There were no significant correlations (p < 0.05) between HM concentrations, bacterial communities, and the MRG profiles; thus, HM concentrations were not the main factor affecting MRGs in sediments. These results contribute to understanding the propagation of MRGs in urban rivers in developing cities.

Cadaverine and putrescine exposure influence carbon and nitrogen cycling genes in water and sediment of the Yellow River

The response patterns of microbial functional genes involved in biogeochemical cycles to cadaver decay is a central topic of recent environmental sciences. However, the response mechanisms and pathways of the functional genes associated with the carbon (C) and nitrogen (N) cycling to cadaveric substances such as cadaverine and putrescine remain unclear. This study explored the variation of functional genes associated with C fixation, C degradation and N cycling and their influencing factors under cadaverine, putrescine and mixed treatments. Our results showed only putrescine significantly increased the alpha diversity of C fixation genes, while reducing the alpha diversity of N cycling genes in sediment. For the C cycling, the mixed treatment significantly decreased the total abundance of reductive acetyl-CoA pathway genes (i.e., acsB and acsE) and lig gene linked to lignin degradation in water, while only significantly increasing the hydroxypropionate-hydroxybutylate cycle (i.e., accA) gene abundance in sediment. For the N cycling, mixed treatment significantly decreased the abundance of the nitrification (i.e., amoB), denitrification (i.e., nirS3) genes in water and the assimilation pathway gene (i.e., gdhA) in sediment. Environmental factors (i.e., total carbon and total nitrogen) were all negatively associated with the genes of C and N cycling. Therefore, cadaverine and putrescine exposure may inhibit the pathway in C fixation and N cycling, while promoting C degradation. These findings can offer some new insight for the management of amine pollution caused by animal cadavers.

Microbial community structure and antibiotic resistance profiles in sediments with long-term aquaculture history

The aim of this investigation was to examine the microbial populations and their resistance patterns towards antibiotics, including the impact of nitrogen metabolism in response to the reintroduction of antibiotics, as well as the presence of resistance genes in sediments from shrimp ponds that have been utilized for extended periods of 5, 15, and over 30 years. Results showed that the sediments exhibited a high prevalence of Proteobacteria, Bacteroidetes, Planctomycetes, Chloroflexi, and Oxyphotobacteria as the most abundant bacterial phyla, accounting for 70.35–77.43% of the total bacterial community. The five most abundant phyla of fungi detected in all sediments, namely Rozellomycota, Ascomycota, Aphelidiomycota, Basidiomycota, and Mortierellomycota, constituted 24.26–32.54% of the total fungal community. It was highly probable that the Proteobacteria and Bacteroidetes phyla serve as the primary reservoir of antibiotic-resistant bacteria (ARB) in the sediment, which included various genera like Sulfurovum, Woeseia, Sulfurimonas, Desulfosarcina, and Robiginitalea. Among these genera, Sulfurovum appeared to be the most widespread in the sediment of aquaculture ponds that have been in operation for more than three decades, while Woeseia dominated in ponds that have been recently reclaimed and have a 15-year aquaculture history. Antibiotic resistance genes (ARGs) were categorized into seven distinct groups according to their mechanism of action. The prevalence of multidrug-resistant ARGs was found to be the highest among all types, with an abundance ranging from 8.74 × 10−2 to 1.90 × 10−1 copies per 16S rRNA gene copies. The results of a comparative analysis of sediment samples with varying aquaculture histories indicated that the total relative abundance of ARGs was significantly diminished in sediment with a 15-year aquaculture history as opposed to sediment with either a 5-year or 30-year aquaculture history. Another assessment of antibiotic resistances in aquaculture sediments involved an examination of the effects of reintroducing antibiotics on nitrogen metabolism processes. The findings revealed that the rates of ammonification, nitrification, and denitrification in the sediment with a history of 5 years and 15 years, decreased as the concentration of oxytetracycline increased from 1 to 300, and 2000 mg/kg, and inhibitory effects were found to be less pronounced in sediments with a 5-year history compared to those with a 15-year history. In contrast, oxytetracycline exposure led to a significant decrease in the rates of these processes in aquaculture pond sediments with a >30 years of aquaculture history across all the concentrations tested. The emergence and dissemination of antibiotic resistance profiles in aquaculture environments requires attention in future aquaculture management.

Gaoshiqia sediminis gen. nov., sp. nov., isolated from coastal sediment.

A Gram-stain-negative, facultative anaerobic, motile, rod-shaped and orange bacterium, designated A06T, was obtained off the coast of Weihai, PR China. Cells were 0.4-0.5×0.6-1.0 µm in size. Strain A06T grew at 20-40 °C (optimum, 33 °C), at pH 6.0-8.0 (optimum, pH 6.5-7.0) and in the presence of 0-8 % NaCl (w/v) (optimum, 2 %). Cells were oxidase and catalase positive. Menaquinone-7 was detected as the major respiratory quinone. The dominant cellular fatty acids were identified as C15:0 2-OH, iso-C15:0, anteiso-C15:0 and iso-C15:1 ω6c. The DNA G+C content of strain A06T was 46.1 mol%. The polar lipids were phosphatidylethanolamine, one aminolipid, one glycolipid and three unidentified lipids. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain A06T is a member of the family Prolixibacteraceae and exhibited the highest sequence similarity to Mangrovibacterium diazotrophicum DSM 27148T (94.3 %). Based on its phylogenetic and phenotypic characteristics, strain A06T is considered to represent a novel genus in the family Prolixibacteraceae, for which the name Gaoshiqia gen. nov. is proposed. The type species is Gaoshiqia sediminis sp. nov., with type strain A06T (=KCTC 92029T=MCCC 1H00491T). The identification and acquisition of microbial species and genes in sediments will help broaden the understanding of microbial resources and lay a foundation for its application in biotechnology. Strain A06T uses an enrichment method, so the isolation of strain A06T is of great significance to the enrichment of marine microbial resources.

Sulfide intrusion in a habitat forming seagrass can be predicted from relative abundance of sulfur cycling genes in sediments

Sulfide intrusion from sediments is an increasingly recognized contributor to seagrass declines globally, yet the relationship between sediment microorganisms and sulfide intrusion has received little attention. Here, we use metagenomic sequencing and stable isotope (34S) analysis to examine this relationship in Cockburn Sound, Australia, a seagrass-dominated embayment with a gradient of sulfide stress and seagrass declines. There was a significant positive relationship between sulfide intrusion into seagrasses and sulfate reduction genes in sediment microbial communities, which was greatest at sites with long term seagrass declines. This is the first demonstration of a significant link between sulfur cycling genes present in seagrass sediments and sulfide intrusion in a habitat-forming seagrass that is experiencing long-term shoot density decline. Given that microorganisms respond rapidly to environmental change, the quantitative links established in this study can be used as a potential management tool to enable the prediction of sulfide stress on large habitat forming seagrasses; a global issue expected to worsen with climate change.

Occurrence and influencing factors of antibiotics and antibiotic resistance genes in sediments of the largest multi-habitat lakes in Northern China.

Baiyangdian Lake is a typical and largest multi-habitat lake in the North plain of China. To understand the generation and transmission of antibiotics resistance genes (ARGs) in multi-habitat lakes, the contents of nutrients (TC, TOC, TN, TP and TS), heavy metals (Zn, Cr, Ni, Cu, Pb, As, Cd and Hg), 22 antibiotics, 16S-rRNA(16S), Class I integron (intI1) and 20 ARGs were determined. Samples were taken from the Fuhe river, river estuaries, reed marshes, living area, fish ponds and open water of Baiyangdian Lake. The results showed that quinolones were the main pollutants in six habitats, and the content range was ND-104.94ng/g. Thereinto, aac (6') -IB, blaTEM-1, ermF, qnrA, qnrD, tetG, sul1, sul2 and tetM were detected in all the analyzed samples. The absolute abundance of sul1 was the highest (5.25 × 105 copies/g-6.21 × 107 copies/g) in most of the samples. In these different habitats, the abundance of antibiotics and ARGs in river estuary was the highest, and that in reed marshes was the lowest. There was a significant positive correlation between the abundance of heavy metals (Cu, Pb, Zn, Ni, Cd, Hg) and the absolute abundance of 11 ARGs (P < 0.01). Redundancy analysis showed that Cu, Zn, intI1, TP and macrolides were the important factors affecting the distribution of ARGs. Our finding provides a more likely driving and influencing factor for the transmission of ARGs in lakes with complex and diverse habitats.

Spatiotemporal distributions and relationships of phosphorus content, phosphomonoesterase activity, and bacterial phosphomonoesterase genes in sediments from a eutrophic brackish water lake in Chile

Phosphorus (P) cycling by microbial activity is highly relevant in the eutrophication of lakes. In this context, the contents of organic (Po) and inorganic (Pi) phosphorus, the activity of acid (ACP) and alkaline (ALP) phosphomonoesterase (Pase), and the abundances of bacterial Pase genes (phoD, phoC, and phoX) were studied in sediments from Budi Lake, a eutrophic coastal brackish water lake in Chile. Our results showed spatiotemporal variations in P fractions, Pase activities, and Pase gene abundances. In general, our results showed higher contents of Pi (110–144 mg kg−1), Po (512–576 mg kg−1), and total P (647–721 mg kg−1) in sediments from the more anthropogenized sampling sites in summer compared with those values of Pi (86–127 mg kg−1), Po (363–491 mg kg−1) and total P (449–618 mg kg−1) in less anthropogenized sampling sites in winter. In concordance, sediments showed higher Pase activities (μg nitrophenyl phosphate g−1 h−1) in sediments from the more anthropogenized sampling sites (9.7–22.7 for ACP and 5.9 to 9.6 for ALP) compared with those observed in less anthropogenized sampling sites in winter (4.2–12.9 for ACP and 0.3 to 6.7 for ALP). Higher abundances (gene copy g−1 sediment) of phoC (8.5–19 × 108), phoD (9.2–47 × 106), and phoX (8.5–26 × 106) genes were also found in sediments from the more anthropogenized sampling sites in summer compared with those values of phoC (0.1–1.1 × 108), phoD (1.4–2.4 × 106) and phoX (0.7–1.2 × 106) genes in the less anthropogenized sites in winter. Our results also showed a positive correlation between P contents, Pase activities, and abundances of bacterial Pase genes, independent of seasonality. The present study provided information on the microbial activity involved in P cycling in sediments of Budi Lake, which may be used in further research as indicators for the monitoring of eutrophication of lakes.

Metagenomic Characterization of Microbial Pollutants and Antibiotic- and Metal-Resistance Genes in Sediments from the Canals of Venice

The spread of fecal pollutants and antibiotic resistance in the aquatic environment represents a major public health concern and is predicted to increase in light of climate change consequences and the increasing human population pressure on the lagoon and coastal areas. The city of Venice (Italy) is affected by diverse microbial pollution sources, including domestic wastewaters that, due to the lack of modern sewage treatment infrastructure in the historical city center, are released into canals. The outflowing jets of its tidal inlets thus represent a source of contamination for the nearby beaches on the barrier island separating the lagoon from the sea. Metagenomic analyses of DNA extracted from sediment samples from six sites in the canals of the city’s historic center were undertaken to characterize the microbial community composition, the presence of fecal microbes as well as other non-enteric pathogens, and the content of genes related to antibiotic (AB) and heavy metal (HM) resistance, and virulence. The six sites hosted similar prokaryotic communities, although variations in community composition likely related to oxygen availability were observed. All sites displayed relatively high levels of fecal contamination, including the presence of Fecal Indicator Bacteria, sewage- and alternative feces-associated bacteria. Relatively high levels of other potential pathogens were also found. About 1 in 500 genes identified at these sites are related to AB and HM resistance; conversely, genes related to virulence were rare. Our data suggest the existence of widespread sediment microbial pollution in the canals of Venice, coupled with the prevalence of ARGs to antibiotics frequently used in humans as well as of HMRGs to toxic metals that still persists in the lagoon. All of this evidence raises concerns about the consequences on the water quality of the lagoon and adjacent marine areas and the potential risks for humans, deserving further studies.

Impact of biochar on persistence and diffusion of antibiotic resistance genes in sediment from an aquaculture pond.

Aquaculture sediments are a purported sizable pool of antibiotic resistance genes (ARGs). However, the pathways for transmission of ARGs from sediments to animals and humans remain unclear. We conducted an ARG survey in sediments from a bullfrog production facility located in Guangdong, China, and simulated zebrafish breeding systems were constructed, with or without biochar addition in sediments, to explore the effects of biochar on ARGs and their precursors of the sediment and zebrafish gut. After 60days, 6 subtypes of ARGs and intI1 were detected, with sediments harboring more ARGs than zebrafish gut. The addition of biochar reduced the abundance of ARGs in the sediment and zebrafish gut, as well as suppressed the horizontal transmission of ARGs from sediment to zebrafish gut. Network analysis and partial least squares path modeling revealed that ARG enrichment was mainly affected by bacterial groups dominated by Nitrospirae, Gemmatimonades, Chloroflexi, and Cyanobacteria and intI1. Our findings provide insights into the transmission of ARGs from sediment to animals and highlight the efficacy of biochar amendments to aquaculture sediments to reduce the transmission of ARGs.

Microbial Community Structure on Microplastic Surface in the Grus leucogeranus Reserve of Poyang Lake

As a new type of pollutant, microplastics have attracted increasing attention. Microplastics in aquatic ecosystems are accumulating at an unprecedented scale, causing significant environmental and economic impacts. In this study, sediments and different types of microplastic samples were collected from the Grus leucogeranus Reserve of Wuxing Reclamation Farm of Poyang Lake, which is the largest freshwater lake in China. The main types of microplastics were film (PE), debris (PP1), fiber (PP2), and foam (PS), and the polymers were identified as polyethylene, polypropylene, and polystyrene in the study area. The structures of microbial communities (fungi and bacteria) were identified using 16S high-throughput sequencing. The results showed that there was no significant difference in the Ace and Chao of bacteria between the surface of PE and PP1 and that of the surrounding sediments (P>0.05), whereas PP2 and PS were significantly lower than those in surrounding sediments (P<0.05). Ace and Chao of fungi showed that PE and PS had no significant differences with the sediment (P>0.05), and PP1 and PP2 were significantly lower than those in surrounding sediments (P<0.05). The species diversity Shannon and Simpson index of bacteria and fungi on different types of microplastic surfaces were lower than that of sediment. The bacterial communities on the sediment and microplastic surface mainly included Proteobacteria and Bacteroidetes. In the fungal community, Basidiomycota, Ascomycota, and Chytridiomycota were the dominant bacteria. Through KEGG functional prediction, it was found that most of the metabolic pathways with a significant difference between bacteria and sediments on the surface of microplastics and with an abundance ratio higher than 1% were related to metabolism. Compared with that of sediment, the metabolic pathways of PE and PP2 on microplastic surfaces were down-regulated mainly in cell motility, signal transduction, and carbohydrate metabolism, whereas the energy metabolism, general and global metabolism pathways, and cofactor metabolism were up-regulated. Compared with that of sediment, the bacterial metabolic pathways of PS and PP1 on microplastic surfaces were down-regulated, mainly including general and global metabolic pathways, translation, and exogenous biodegradation, and cell motility and signal transduction were up-regulated. However, the abundance of other functional genes in sediments and microplastic samples showed little difference. The results indicated that microplastics can change the structure of microbial communities, and the microbial community on the surface of microplastics could catalyze metabolic reactions and promote the decomposition of microplastics. The study of microplastic surface microbial structure in Poyang Lake can support management decisions to protect the ecological integrity of the lake.

Distribution of Antibiotic Resistance Genes in Sediment of Erhai Lake, Yunnan-Kweichow Plateau, China: Their Relations with Non-Point Source Pollution Discharges from 26 Tributaries

Distribution of Antibiotic Resistance Genes in Sediment of Erhai Lake, Yunnan-Kweichow Plateau, China: Their Relations with Non-Point Source Pollution Discharges from 26 Tributaries

Pristine and sulfidized ZnO nanoparticles alter microbial community structure and nitrogen cycling in freshwater lakes

Zinc oxide nanoparticles (ZnO NPs) and its sulfidized form (ZnS NPs) are increasingly entering into freshwater systems through multiple pathways. However, their impacts on the composition and function of sedimentary microbial communities are still largely unknown. Here, two kinds of lake-derived microcosms were constructed and incubated with ZnO NPs, or ZnS NPs to investigate the short-term (7 days) and long-term (50 days) impacts on sedimentary microbial communities and nitrogen cycling. After 7 days, both ZnO NPs and ZnS NPs dosed microbial communities experienced distinct alterations as compared to the undosed controls. By day 50, the structural shifts of microbial communities caused by ZnO NPs were significantly enlarged, while the microbial shifts induced by ZnS NPs were largely resolved. Additionally, ZnO NPs and ZnS NPs could significantly alter nitrogen species and nitrogen cycling genes in sediments, revealing their non-negligible impacts on nitrogen cycling processes. Furthermore, our data clearly indicated that the impacts of ZnO NPs and ZnS NPs on nitrogen cycling differed distinctly in different lake-derived microcosms, and the impacts were significantly correlated with microbial community structure. Overall, this research suggests that the entrance of pristine or sulfidized ZnO NPs into freshwater systems may significantly impact the sedimentary microbial community structure and nitrogen cycling.

New Estimation of Antibiotic Resistance Genes in Sediment Along the Haihe River and Bohai Bay in China: A Comparison Between Single and Successive DNA Extraction Methods.

Sediment is thought to be a vital reservoir for antibiotic resistance genes (ARGs). Often, studies describing and comparing ARGs and their potential hosts in sediment are based on single DNA extractions. To date, however, no study has been conducted to assess the influence of DNA extraction efficiency on ARGs in sediment. To determine whether the abundance of ARGs is underestimated, we performed five successive extraction cycles with a widely used commercial kit in 10 sediment samples collected from the Haihe River and Bohai Bay. Our results showed that accumulated DNA yields after five extractions were 1.8–3.1 times higher than that by single DNA extractions. High-throughput sequencing showed that insufficient DNA extraction could generate PCR bias and skew community structure characterization in sediment. The relative abundances of some pathogenic bacteria, such as Enterobacteriales, Lactobacillales, and Streptomycetales, were significantly different between single and successive DNA extraction samples. In addition, real-time fluorescent quantitative PCR (qPCR) showed that ARGs, intI1, and 16S rRNA gene abundance strongly increased with increasing extraction cycles. Among the measured ARGs, sulfonamide resistance genes and multidrug resistance genes were dominant subtypes in the study region. Nevertheless, different subtypes of ARGs did not respond equally to the additional extraction cycles; some continued to have linear growth trends, and some tended to level off. Additionally, more correlations between ARGs and bacterial communities were observed in the successive DNA extraction samples than in the single DNA extraction samples. It is suggested that 3–4 additional extraction cycles are required in future studies when extracting DNA from sediment samples. Taken together, our results highlight that performing successive DNA extractions on sediment samples optimizes the extractable DNA yield and can lead to a better picture of the abundance of ARGs and their potential hosts in sediments.