In bioaugmented wastewater treatment systems, it is essential for recalcitrant pollutant-degrading bacteria to form biofilms. Inducing biofilm formation in these bacteria, however, is challenging as it involves multiple inter-related regulating pathways and environmental factors. Herein, we report the remarkable promoting effect of Ca2+ on biofilm formation of two novel pyridine-degrading bacteria with poor innate biofilm-forming capabilities, Pseudomonas sp. ZX01 and Arthrobacter sp. ZX07. The roles of Ca2+ in different biofilm development stages were investigated. Our data showed strong influences of Ca2+ on the initial attachment of the two strains onto positively charged glass surfaces by altering cell surface charge as well as the cation bridging effect. Contrary to many other biofilm promoting mechanisms, Ca2+ downregulated the extracellular polymeric substances (EPS) production per cell in both Pseudomonas sp. ZX01 and Arthrobacter sp. ZX07, while increasing biofilm biomass. This is attributed to the strong cationic bridging between Ca2+ and EPS which can elevate the efficiency of the extracellular products in binding bacterial cells. Furthermore, Ca2+ increased the protein-to-polysaccharide (PN/PS) ratio in biofilm EPS of both strains, which favored cell aggregation, and biofilm establishment by increasing the hydrophobicity of cell surfaces. More intriguingly, the intracellular c-di-GMP, which can drive the switch of bacterial lifestyle from planktonic state to biofilm state, was also elevated markedly by exogenous Ca2+. Taken together, these results would be of guidance for applying the two strains into bioaugmented biofilm reactors where Ca2+ supplement strategy can be employed to facilitate their biofilm formation on the surfaces of engineering carriers.

Nutrient scarcity is pervasive for natural microbial communities, affecting species reproduction and co-existence. However, it remains unclear whether there are general rules of how microbial species abundances are shaped by biotic and abiotic factors. Here we show that the ribosomal RNA gene operon (rrn) copy number, a genomic trait related to bacterial growth rate and nutrient demand, decreases from the abundant to the rare biosphere in the nutrient-rich coastal sediment but exhibits the opposite pattern in the nutrient-scarce pelagic zone of the global ocean. Both patterns are underlain by positive correlations between community-level rrn copy number and nutrients. Furthermore, inter-species co-exclusion inferred by negative network associations is observed more in coastal sediment than in ocean water samples. Nutrient manipulation experiments yield effects of nutrient availability on rrn copy numbers and network associations that are consistent with our field observations. Based on these results, we propose a “hunger games” hypothesis to define microbial species abundance rules using the rrn copy number, ecological interaction, and nutrient availability.

Microplastics have become global emerging issue and received widespread attention in recent years. Due to their chemical persistence, plastic particles can be broken into smaller items but accumulated for long time in the environment like sediment. However, limited by current detection technologies, the distribution and characteristics of small-sized microplastics in coastal sediment remain uncertain. In this study, we established a new method based on micro-Raman spectroscopy for detecting small-sized microplastics, namely multipoint confocal micro-Raman spectrum scanning (MCmRSS). The MCmRSS was first applied in detecting microplastics in the sediment samples collected from three bays of the East China Sea. The minimum size of microplastics was 4 μm and average microplastics concentration was 91 ± 55 items /g dry weight sediment, with fragment and polyethylene as the most common shape and polymer type, respectively. The spatial variation of microplastics was in accordance with the strength of coastal human activities and marine dynamics. In all the microplastic items, the small-sized ones (<10 μm) accounted for 67%; and the relationship between microplastic concentration and its size followed a power-exponential equation. Compared with previous studies, the number of microplastics in coastal sediments detected by the MCmRSS increased by 2 orders of magnitude, which was benefited from the advantages of multipoint scanning in the fixed identification areas and high resolution of micro-Raman spectrum. Our findings would summon the re-evaluation of the potential risks of small-sized microplastics in the coastal environment.

Background Mangrove ecosystems are vulnerable due to the exotic Spartina alterniflora (S. alterniflora) invasion in China. However, little is known about mangrove sediment microbial community assembly processes and interactions under S. alterniflora invasion. Here, we investigated the assembly processes and co-occurrence networks of the archaeal and bacterial communities under S. alterniflora invasion along the coastlines of Fujian province, southeast China. Results Assembly of overall archaeal and bacterial communities was driven predominantly by stochastic processes, and the relative role of stochasticity was stronger for bacteria than archaea. Co-occurrence network analyses showed that the network structure of bacteria was more complex than that of the archaea. The keystone taxa often had low relative abundances (conditionally rare taxa), suggesting low abundance taxa may significantly contribute to network stability. Moreover, S. alterniflora invasion increased bacterial and archaeal drift process (part of stochastic processes), and improved archaeal network complexity and stability, but decreased the network complexity and stability of bacteria. This could be attributed to S. alterniflora invasion influenced microbial communities diversity and dispersal ability, as well as soil environmental conditions. Conclusions This study fills a gap in the community assembly and co-occurrence patterns of both archaea and bacteria in mangrove ecosystem under S. alterniflora invasion. Thereby provides new insights of the plant invasion on mangrove microbial biogeographic distribution and co-occurrence network patterns.

Widespread antibiotic resistance across Earth's habitats has become a critical health concern. However, large-scale investigation on the distribution of antibiotic resistance genes (ARGs) in the microbiomes from most types of ecosystem is still lacking. In this study, we provide a comprehensive characterization of ARGs for 52,515 microbial genomes covering various Earth's ecosystems, and conduct the risk assessment for ARG-carrying species based on further identification of mobile genetic elements (MGEs) and virulence factor genes (VFGs). We identify a total of 6159 ARG-carrying metagenome-assembled genomes (ACMs), and most of them are recovered from human gut and city subway. Our results show that efflux pump is the most common mechanism for bacteria to acquire multidrug resistance genes in Earth's microbiomes. Enterobacteriaceae species are the largest hosts of ARGs, accounting for 14% of total ACMs with 64% of the total ARG hits. Most of ARG-carrying species are unique in the different ecosystem categories, while 33 potential background ARGs are commonly shared by all ecosystem categories. We then detect 36 high-risk ARGs that likely threat public health in all ACMs. Based on ranking the importance of ARG-carrying species in the different ecosystem categories, several bacterial taxa such as Escherichia coli, Enterococcus faecalis, and Pseudomonas_A stutzeri are recognized as priority species for surveillance and control. Overall, our study gives a broad view of ARG-host associations in the environments.

The occurrence of man-made antibiotics in natural environment has aroused attentions from both scientists and publics. However, few studies tracked antibiotics from their production site to the end of disposal environment. Taking the coastal region of Hangzhou Bay as the study area, the fate of 77 antibiotics from 6 categories in two-step wastewater treatment plants (WTPs, i.e. pharmaceutical WTP and integrated WTP) was focused; and the antibiotics in both dissolved and adsorbed phases were investigated simultaneously in this study. The ubiquitous occurrence of antibiotics was observed in the two-step WTPs, with antibiotic concentrations following the order of PWTP (LOQ - 1.0 × 105 ng·L−1) > IWTPi (for industrial wastewater treatment, LOQ - 3.7 × 103 ng·L−1) > IWTPd (for domestic sewage treatment, LOQ - 1.3 × 103 ng·L−1). And the types of antibiotics detected in excess sludge and suspended particles were in accordance with those in wastewater. Quinolones were invariably dominant in both dissolved and adsorbed fractions. High removal efficiencies (median values >50.0%) were acquired for the dissolved quinolones (except for DFX), tetracyclines, β-lactams, and lincosamides. Anaerobic/anoxic/oxic achieved the highest aqueous removal of antibiotics among the investigated treatment technologies in the three WTPs. PWTP and IWTP removed 9797 and 487 g·d−1 of antibiotics, respectively; and a final effluent with 126.4 g·d−1 of antibiotics was discharged into the effluent-receiving area (ERA) of Hangzhou Bay. Source apportionment analysis demonstrated that the effluents of IWTPd and IWTPd contributed respectively 39.3% and 8.9% to the total antibiotics in the ERA. The results illustrate quantitatively the antibiotic flows from engineered wastewater systems to natural water environment, on the basis of which the improvements of wastewater treatment technologies and discharge management would be put forward.

Given that long-term treated wastewater discharge may alter the microbial community of the recipient coast, it is important to evaluate whether and how the community's stability is impacted. We constructed microcosms using coastal sediments with (near-coast) and without (far-coast) a wastewater disposal history and compared the communities’ responses to p-chloroaniline (PCAN, a typical organic pollutant) in low (10 mg/L) and high (100 mg/L) concentrations. Compared to the far-coast community, the near-coast community drove faster PCAN attenuation and nitrate generation. More significant negative correlations were observed between the alpha-diversity indices and PCAN concentrations in the far-coast communities than the near-coast ones. The community turnover rate, represented by the slopes of the time–decay curves, was slower for the near-coast community (−0.187) than that for the far-coast community (−0.233), but only when the PCAN was added in low concentration. Our study revealed that the long-term wastewater disposal may cause the sediment bacterial community to be less sensitive and more stable in response to a future disturbance, demonstrating a significant historical effect of environmental context on the coastal microbial community's stability.

In order to obtain in-depth insight of the behavioral fate and ecological risks of antibiotics in coastal environment, this study investigated the distribution, partitioning and primary influencing factors of antibiotics in water and sediment in the East China Sea. After quantification of 77 target antibiotics in 6 categories, ten antibiotics were detected simultaneously with a detection frequency >50.0% in water and sediment; the concentrations of these ten antibiotics were 0.1–1508.0 ng L−1 and 0.01–9.4 ng g−1 in water and dry sediment, respectively. Sulfadiazine and Azithromycin (Pseudo partitioning coefficient were 28–3814 L kg−1 and 21–2405 L kg−1, respectively.) had the largest partitioning coefficient between sediment and water. In addition, pseudo partitioning coefficient of Sulfadiazine and Clindamycin were higher than the values of corresponding equilibrium partitioning constant (Kd), which would likely cause them to re-release from sediment to water. Compared to the physiochemical properties of the sediment, water quality has a greater impact on antibiotic partitioning. We found that the partitioning of antibiotics was significantly positively correlated with salinity, suspended solids, pH, NH4+-N and Zn; and negatively correlated with temperature, dissolved oxygen, PO43−, chemical oxygen demand, NO3−-N, oil, Cu and Cd. The ecological risks of antibiotics in water and sediment were also evaluated for revealing their relationship with the concentration partitioning of antibiotics. Results showed that the target antibiotics mainly pose ecological risks to Daphnia with low and median chronic toxicity risk rather than fish and green algae. The antibiotics in sediment were more chronically toxic to Daphnia than that in water. The risk quotient ratio of sediment and water (RQs/RQw) ranged from 0 to 1154.0, which were exactly opposite of the values of organic carbon normalized partition coefficient (Koc), suggesting that the physical properties of antibiotics drove the ecological risk allocation of antibiotics in sediment and water.

Microbial densities, functional genes, and their responses to environment factors have been studied for years, but still a lot remains unknown about their interactions with each other. In this study, the abundances of 7 nitrogen cycling genes in the sediments from Hangzhou Bay were analyzed along with bacterial and archaeal 16S rRNA abundances as the biomarkers of their densities. The amount of organic matter (OM) and total nitrogen (TN) strongly positively correlated with each other and microbial densities, while total phosphate (TP) and ammonia-nitrogen (NH3–N) did not. Most studied genes were density suppressed, while nirS was density stable, and nosZ and hzo were density irrelevant. This suggests eutrophication could limit inorganic nitrogen cycle pathways and the removal of nitrogen in the sediment and emit more greenhouse gases. This study provides a new insight of microbial community structures, functions and their interactions in the sediments of eutrophic bays.

Oxidation of sulfapyridine (SPY) by typical oxidant, hydrogen peroxide (H2O2) and/or potassium peroxydisulfate (PDS), was used as a pre-treatment for antibiotic wastewater. The degradation dynamics showed that SPY was successfully removed, and the trend was fitted to the first-order reaction kinetics. H2O2 removed SPY more efficiently in acid condition than in basic condition, while PDS was the opposite. Better performance was achieved by using PDS than using H2O2, but combined using of PDS and H2O2 got the best performance. Although SPY was oxidized by those oxidants and biodegradability was improved, the intermediates still exhibited antibacterial activity. The degradation pathways and mechanism of SPY were deduced through density functional theory (DFT) and evidenced by intermediates product detection. Nucleophilic attack and radical attack were determined to be the major attack pathways in H2O2 and PDS systems, respectively. The SPY degradation pathways proposed in the two systems were based on the cleavage of bonds and hydroxyl substitution. Additionally, intermediate ΔG value showed that stubborn molecules remained in the wastewater even after pre-oxidation, which is harmful for further bio-treatment. This study provides a new insight for the improvement of biodegradability and the efficient degradation of SPY in antibiotic wastewater.

The overuse of antibiotics has promoted the propagation and dissemination of antibiotic resistance genes (ARGs) in environment. Due to the dense human population and intensive activities in coastal areas, the health risk of ARGs in coastal environment is becoming a severe problem. To date, there still lacks of a quantitative method to assess properly the gross antibiotic resistance at microbial community level. Here, we collected sediment samples from Hangzhou Bay (HB), Taizhou Bay (TB), and Xiangshan Bay (XB) of the East China Sea for community-level ARGs analysis. Based on the 16S rRNA genes and predictive metagenomics, we predicted the composition of intrinsic ARGs (piARGs) and some related functional groups. Firstly, a total of 40 piARG subtypes, belonging to nine drug classes and five resistance mechanisms, were obtained, among which the piARGs encoding multidrug efflux pumps were the most dominant in the three bays. Secondly, XB had higher relative abundances of piARGs and pathogens than the other two bays, which posed higher potential health risk and implied the heavier impact of long-term maricultural activities in this bay. Thirdly, the co-occurrence network analysis identified that there were more connections between piARGs and some potential pathogenic bacteria. Several piARG subtypes (e.g., tetA, aacA, aacC, and aadK) distributed widely in the microbial communities. And finally, the microbial diversity correlated negatively with the relative abundance of piARGs. Oil, salinity, and arsenic had significant effects on the variations of piARGs and potential pathogenic bacteria. The abundance-weighted average ribosomal RNA operon (rrn) copy number of microbial communities could be regarded as an indicator to evaluate the antibiotic resistance status. In conclusion, this study provides a new insight on how to evaluate antibiotic resistance status and their potential risk in environment based on a quantitative analysis of microbial communities.

Bioaugmentation is an effective technology for treating wastewater containing recalcitrant organic pollutants. However, it is restricted by several technical problems, including the difficult colonization and survival of the inoculated bacteria, and the time-consuming start-up process. Considering the important roles of quorum sensing (QS) in regulating microbial behaviors, this study investigated the effects of N-acyl-homoserine lactones (AHLs)-based manipulation on the start-up of biofilm reactors bioaugmented with a pyridine-degrading strain Paracoccus sp. BW001. The results showed that, in the presence of two specific exogenous AHLs (C6-HSL and 3OC6-HSL), the biofilm formation process on carriers was significantly accelerated, producing thick and structured biofilms. The protein and polysaccharide contents of the extracellular polymeric substances (EPS) and soluble microbial products (SMP) in sludge were also elevated, possibly due to the increased abundance of several EPS-producing bacterial genera. Specifically, the stability and complexity of protein structures were improved. Besides the reactor running time, the AHL-manipulation was proved to be the main factor that drove the shift of bacterial community structures in the reactors. The addition of exogenous AHLs significantly increased the succession rate of bacterial communities and decreased the bacterial alpha diversity. Most importantly, the final proportions of the inoculated strain BW001 were elevated by nearly 100% in both sludge and biofilm communities via the AHL-manipulation. These findings strongly elucidated that AHL-based QS was deeply involved in biofilm formation, sludge characteristics, and microbial community construction in bioaugmented reactors, providing a promising start-up strategy for bioaugmentation technology.

Crude oil could affect certain critical microbial processes of nitrogen cycling (N-cycling) in coastal sediments, and disturb the nitrogen balance. However, the understanding of the effects of crude oil on coastal sediments N-cycling under human disturbance was still limited. In this study, two sediments (named SY and HB with heavy and slight pollution, respectively) were sampled from Hangzhou Bay, China. After an incubation with exposure to different amounts of crude oil in above two sediments for 30 days, we found that crude oil affected microbial N-cycling in multiple levels. Potential rate measurements revealed that crude oil stimulated potential denitrification and N2O emissions in both sediments, which showed a higher influence on denitrification rates in higher concentration of oil. Quantitative PCR revealed that crude oil greatly increased abundances of bacterial and archaeal 16S rRNA genes and N-cycling genes (nirS, nosZ, nrfA, part of AOA and AOB amoA). On the other hand, only a few genes (16S rRNA and nrfA) showed higher transcriptional activities in oil-addition treatments. Results about relative changes of N-cycling genes revealed that the variations of N-cycling genes in oil-addition treatments were related to sediment types but not crude oil concentrations, and the genes in HB were more sensitive to crude oil than SY. Network analysis of N-cycling genes found that crude oil decreased the complexity of N-cycling gene networks in SY, while increased complexity in HB, and led to more competition among N-cycling microbes. Our findings help to look into the effects of crude oil on key N-cycling processes, and improve the understanding of the interactions among N-cycling under crude oil contamination.

【背景】 煤化工企业排放的废水中含有大量难降解、高毒性的有机污染物，采用以高效降解菌为基础的生物强化技术对其进行处理，是一种经济可行的策略；而促进高效降解菌在载体材料表面的生物膜形成，有助于提升生物膜法废水处理系统的效能。【目的】 探究一株吡啶高效降解菌 Pseudomonas sp.ZX08 的生物膜形成过程和特性，识别不同的环境因子如温度、 pH、 Na+、 K+、Ca2+、 Mg2+等对其生物膜形成的影响规律，为实现人工调控其在实际废水处理系统中的成膜过程提供理论依据。【方法】 采用改良的微孔板生物膜培养与定量方法，以单因子影响实验测定不同条件下菌株在 12 孔板内的生物膜形成量和浮游态细菌量；采用激光共聚焦显微镜(confocal laser scanning microscope，CLSM)观察和分析生物膜的结构特征。【结果】 Pseudomonas sp. ZX08 菌株具有良好的吡啶降解性能，且生物膜形成能力较强， CLSM 观察到其在载体表面形成的生物膜可达到 40-50 mm；生物膜外层的活细胞比例更高，分泌的胞外蛋白也更多。 ZX08 菌株的生物膜形成量具有明显的周期性变化特征， 12 h、48 h 的生物膜量是相对峰值。 ZX08 生物膜形成的最适温度是 25 °C，最适 pH范围是 7.0-9.0；较高浓度的 NaCl (>0.6 mol/L)和 KCl (>0.4 mol/L)均对 ZX08的生物膜形成有显著的抑制作用；一定范围内(0-16 mmol/L) Ca2+浓度的提高可以促进 ZX08 在 12 孔板底部固-液界面生物膜的形成，浓度更高时则显著抑制生物膜的形成；一定范围内(0-16 mmol/L) Mg2+浓度的提高对 ZX08 生物膜形成有促进作用，但促进幅度不大。【结论】 吡啶降解菌 Pseudomonas sp. ZX08 的生物膜形成能力较强，未来在实际废水处理系统中应用时需要综合考虑各种环境因子对其生物膜形成的影响。

以吡啶为目标污染物,考察从焦化废水处理系统中分离的12株高效吡啶降解菌对吡啶的降解性能和生物膜形成特性,以期为在废水处理系统中构建降解型生物膜提供理论参考。结果表明:12株菌都具有较高的吡啶降解活性,其中代表性菌株Pseudomonas sp.ZX01和Arthrobacter sp.ZX07降解吡啶的最适温度是35°C,最适pH是7.0,在初始吡啶浓度为100～2000 mg/L的范围内,降解率均达到100%。不同菌株的生物膜形成能力差异明显,胞外蛋白分泌量、胞外多糖分泌量和由鞭毛参与的游动能力与各株菌的生物膜形成能力之间存在显著的正相关关系。 

Microbial community structure is affected by both natural processes and human activities. In coastal area, anthropegenetic activity can usually lead to the discharge of the effluent from wastewater treatment plant (WWTP) to sea, and thus the water quality chronically turns worse and marine ecosystem becomes unhealthy. Microorganisms play key roles in pollutants degradation and ecological restoration; however, there are few studies about how the WWTP effluent disposal influences coastal microbial communities. In this study, sediment samples were collected from two WWTP effluent-receiving areas (abbreviated as JX and SY) in Hangzhou Bay. First, based on the high-throughput sequencing of 16S rRNA gene, microbial community structure was analyzed. Secondly, several statistical analyses were conducted to reveal the microbial community characteristics in response to the effluent disposal. Using PCoA, the significant difference of in microbial community structure was determined between JX and SY; using RDA, water COD and temperature, and sediment available phosphate and ammonia nitrogen were identified as the key environmental factors for the community difference; using LDA effect size analysis, the most distinctive microbes were found and their correlations with environmental factors were investigated; and according to detrended beta-nearest-taxon-index, the sediment microbial communities were found to follow “niche theory”. An interesting and important finding was that in SY that received more and toxic COD, many distinctive microbes were related to the groups that were capable of degrading toxic organic pollutants. This study provides a clear illustration of eco-environmental deterioration under the long-term human pressure from the view of microbial ecology.

Current technologies could identify the abundance and functions of specific microbes, and evaluate their individual effects on microbial ecology. However, these microbes interact with each other, as well as environmental factors, in the form of complex network. Determination of their combined ecological influences remains a challenge. In this study, we developed a tripartite microbial-environment network (TMEN) analysis method that integrates microbial abundance, metabolic function, and environmental data as a tripartite network to investigate the combined ecological effects of microbes. Applying TMEN to analyzing the microbial-environment community structure in the sediments of Hangzhou Bay, one of the most seriously polluted coastal areas in China, we found that microbes were well-organized into 4 bacterial communities and 9 archaeal communities. The total organic carbon, sulfate, chemical oxygen demand, salinity, and nitrogen-related indexes were detected as crucial environmental factors in the microbial-environmental network. With close interactions with these environmental factors, Nitrospirales and Methanimicrococcu were identified as hub microbes with connection advantage. Our TMEN method could close the gap between lack of efficient statistical and computational approaches and the booming of large-scale microbial genomic and environmental data. Based on TMEN, we discovered a potential microbial ecological mechanism that crucial species with significant influence on the microbial community ecology would possess one or two of the community advantages for enhancing their ecological status and essentiality, including abundance advantage and connection advantage.