Community dynamics of prokaryotic and eukaryotic microbes in an estuary reservoir

On-Site Inactivation for Disinfection of Antibiotic-Resistant Bacteria in Hospital Effluent by UV and UV-LED

The problem of antimicrobial resistance (AMR) is not limited to the medical field but is also becoming prevalent on a global scale in the environmental field. Environmental water pollution caused by the discharge of wastewater into aquatic environments has caused concern in the context of the sustainable development of modern society. However, there have been few studies focused on the treatment of hospital wastewater, and the potential consequences of this remain unknown. This study evaluated the efficacy of the inactivation of antimicrobial-resistant bacteria (AMRB) and antimicrobial resistance genes (AMRGs) in model wastewater treatment plant (WWTP) wastewater and hospital effluent based on direct ultraviolet (UV) light irradiation provided by a conventional mercury lamp with a peak wavelength of 254 nm and an ultraviolet light-emitting diode (UV-LED) with a peak emission of 280 nm under test conditions in which the irradiance of both was adjusted to the same intensity. The overall results indicated that both UV- and UV-LED-mediated disinfection effectively inactivated the AMRB in both wastewater types (>99.9% after 1-3 min of UV and 3 min of UV-LED treatment). Additionally, AMRGs were also removed (0.2-1.4 log10 for UV 254 nm and 0.1-1.3 log10 for UV 280 nm), and notably, there was no statistically significant decrease (p < 0.05) in the AMRGs between the UV and UV-LED treatments. The results of this study highlight the importance of utilizing a local inactivation treatment directly for wastewater generated by a hospital prior to its flow into a WWTP as sewage. Although additional disinfection treatment at the WWTP is likely necessary to remove the entire quantity of AMRB and AMRGs, the present study contributes to a significant reduction in the loads of WWTP and urgent prevention of the spread of infectious diseases, thus alleviating the potential threat to the environment and human health risks associated with AMR problems.

Differentiated cognition of the effects of human activities on typical persistent organic pollutants and bacterioplankton community in drinking water source

Accelerated urbanization in developing countries led to a typical gradient of human activities (low, moderate and high human activities), which affected the pollution characteristics and ecological functions of aquatic environment. However, the occurrence characteristics of typical persistent organic pollutants, including organochlorine pesticides (OCPs) and polycyclic aromatic hydrocarbons (PAHs), and bacterioplankton associated with the gradient of human activities in drinking water sources is still lacking. Our study focused on a representative case - the upper reaches of the Dongjiang River (Pearl River Basin, China), a drinking water source characterized by a gradient of human activities. A comprehensive analysis of PAHs, OCPs and bacterioplankton in the water phase was performed using gas chromatography-mass spectrometry (GC-MS) and the Illumina platform. Moderate human activity could increase the pollution of OCPs and PAHs due to local agricultural activities. The gradient of human activities obviously influenced the bacterioplankton community composition and interaction dynamics, and low human activity resulted in low bacterioplankton diversity. Co-occurrence network analysis indicated that moderate human activity could promote a more modular organization of the bacterioplankton community. Structural equation models showed that nutrients could exert a negative influence on the composition of bacterioplankton, and this phenomenon did not change with the gradient of human activities. OCPs played a negative role in shaping bacterioplankton composition under the low and high human activities, but had a positive effect under the moderate human activity. In contrast, PAHs showed a strong positive effect on bacterioplankton composition under low and high human activities and a weak negative effect under moderate human activity. Overall, these results shed light on the occurrence characteristics of OCPs, PAHs and their ecological effects on bacterioplankton in drinking water sources along the gradient of human activities.

Diversity and distribution analysis of eukaryotic communities in the Xiangshan Bay, East China sea by metabarcoding approach

Eukaryotic communities play an important role in the coastal ecosystem of Xiangshan Bay, a narrow semi-closed bay famous for fisheries and marine farming. However, information on the diversity and composition of eukaryotic communities in Xiangshan Bay remains unclear. In this study, the metabarcoding approach was utilized to comprehensively investigate the eukaryotic plankton community structure and dominant taxa, particularly eukaryotic microalgae, in the Xiangshan Bay over a period of four months in 2018. The results showed that the three major phyla were Arthropoda, Chlorophyta, and Bacillariophyta. The richness indices revealed that species richness peaked in February and was at its lowest in May. Diversity indices showed that the samples collected in May had the lowest diversity. Centropages was detected in the samples of all months, however, its highest dominance was observed in the samples collected in February. In addition, compared to other months, a greater proportion of eukaryotic microalgae was witnessed in March. The three eukaryotic algae with highest abundances in March were Cyclotella, Prorocentrum, and Thalassiosira. Moreover, high diversity of pico-sized (0.2-2.0 μm) phytoplankton (which are often easily missed by microscopy) was discovered in this study by using metabarcoding approach. This study highlights the strength and significance of the metabarcoding approach to uncover a large number of eukaryotic species which remains undetectable during application of conventional approaches. The findings of this study reveals that the eukaryotic community structure varies noticeably in both time and space throughout sampling period, with temperature being the most important environmental factor influencing these changes. This study lays a solid foundation to understand eukaryotic plankton composition, temporal and spatial dynamics and the distribution mechanism of eukaryotic plankton community in Xiangshan Bay, providing theoretical reference for further studies related to marine ecology.

Transplanting human infant gut microbiome species into Galleria mellonella

OBJECTIVE

Study of the human infant gut microbiome requires the use of surrogate mammalian species such as mice. We sought to investigate the usefulness of the greater wax moth larva, Galleria mellonella, as an alternative.

RESULTS

We have analysed the native gut microbiome of Galleria and developed methods for clearing the native microbiome and introducing species from human infant faecal samples. We find that some species, e.g. enterococci, are more successful at recolonisation, but that others, e.g. Bifidobacterium, are less so. The work paves the way for using Galleria rather than mice in this and similar work.

Effects of Fishery Utilization on the Physicochemical Index and Microbial Community Composition in Saline-Alkaline Water

Fishery utilization of idle saline-alkaline water resources offers various benefits including reducing surrounding soil salinity, improving the ecological environment, increasing arable land area, and providing economic advantages to the fishery industry. However, for decades, the characteristics and regulatory mechanisms of microbial communities that affect fishery utilization have not been clear, which restricts their application. In this study, high-throughput 16S rRNA amplicon sequencing was employed to analyze the bacterial community in these water resources. The sequencing yielded high-quality sequences (2,765,063), resulting in the identification of 18,761 bacterial operational taxonomic units (OTUs). Analysis revealed that the type of saline-alkaline water had a more significant influence on the bacterial community compared to seasonal variations within the aquaculture period. The Chao index for saline-alkaline ponds (ASW) was significantly lower (P < 0.05) than for still saline-alkaline water (SSW) and flowing saline-alkaline water (FSW), while the Shannon index for ASW was also significantly lower (P < 0.05) compared to FSW. When comparing ASW to nonaquaculture saline-alkaline water, a decrease in Proteobacteria to 26.87% was noted, particularly α-proteobacteria and γ-proteobacteria, accompanied by a rapid increase in Actinobacteria and Cyanobacteria to 28.60%. Networkx analysis further revealed that ASW significantly increased competition and amensalism from secondary saline-alkaline water microorganisms, resulting in a more solitary bacterial community composition as an adaptive strategy to cope with intense environmental pressures. Key bacterial species such as Pseudomonas, Hydrogenophaga, and Flavobacterium were found to be involved in hydrogen-cycling, nitrogen-cycling, and carbon-cycling, respectively, with all three exhibiting high abundance in FSW. Consequently, FSW demonstrates significant advantages in biogeochemical cycling, pollutant degradation, and the utilization of indigenous probiotic bacteria. Although the surface of abandoned secondary saline-alkaline land was covered with white salt particles, the fishery utilization of saline-alkaline water with low salinity levels (4.0-5.5), and the presence of nitrate and phosphate were identified as primary determinants of bacterial community composition. Nevertheless, a comparison of coastal high-salinity ponds indicated that salinity still selectively affects bacterial communities to some extent. Overall, our study provides valuable insights into the microbial regulation of nitrite during saline-alkaline water aquaculture, thereby aiding in the efficient utilization of secondary saline-alkaline water resources for fisheries.

Inactivation of antibiotic-resistant bacteria in hospital wastewater by ozone-based advanced water treatment processes

The emergence and spread of antimicrobial resistance (AMR) continue on a global scale. The impacts of wastewater on the environment and human health have been identified, and understanding the environmental impacts of hospital wastewater and exploring appropriate forms of treatment are major societal challenges. In the present research, we evaluated the efficacy of ozone (O3)-based advanced wastewater treatment systems (O3, O3/H2O2, O3/UV, and O3/UV/H2O2) for the treatment of antimicrobials, antimicrobial-resistant bacteria (AMRB), and antimicrobial resistance genes (AMRGs) in wastewater from medical facilities. Our results indicated that the O3-based advanced wastewater treatment inactivated multiple antimicrobials (>99.9%) and AMRB after 10-30 min of treatment. Additionally, AMRGs were effectively removed (1.4-6.6 log10) during hospital wastewater treatment. The inactivation and/or removal performances of these pollutants through the O3/UV and O3/UV/H2O2 treatments were significantly (P < 0.05) better than those in the O3 and O3/H2O2 treatments. Altered taxonomic diversity of microorganisms based on 16S rRNA gene sequencing following the O3-based treatment showed that advanced wastewater treatments not only removed viable bacteria but also removed genes constituting microorganisms in the wastewater. Consequently, the objective of this study was to apply advanced wastewater treatments to treat wastewater, mitigate environmental pollution, and alleviate potential threats to environmental and human health associated with AMR. Our findings will contribute to enhancing the effectiveness of advanced wastewater treatment systems through on-site application, not only in wastewater treatment plants (WWTPs) but also in medical facilities. Moreover, our results will help reduce the discharge of AMRB and AMRGs into rivers and maintain the safety of aquatic environments.

Isolation and Identification of Growth-Promoting Bacteria from Plants Growing Under Abiotic Stresses

Identification and isolation of plant growth-promoting bacteria (PGPB) are critical steps toward understanding the role of these bacteria in stress tolerance in plants. This procedure also provides essential knowledge about the microbes needed to formulate effective biofertilizers. This chapter describes culture-dependent and culture-independent strategies to identify and isolate PGPB. The culture-dependent strategy commonly involves growing PGPB on general and selective media. However, the culture-independent strategy involves next-generation sequencing technologies. A combination of both strategies would identify the structure of the bacterial communities and isolate bacteria from their environments. Therefore, this chapter describes a comprehensive strategy where the methods are sequentially applied to identify and isolate epiphytic and endophytic PGPB from a particular environmental sample. However, a single procedure can also be employed to identify and isolate a specific type of PGPB.

Microbial community structure and its driving mechanisms in the Hangbu estuary of Chaohu Lake under different sedimentary areas

Estuaries are known for their high ecological diversity and biological productivity. Sediment microorganisms, as crucial components of estuarine ecosystems, play a pivotal role in reflecting the intricate and dynamic ecological niches. However, our research on microbial community characteristics in estuarine ecosystems under different sedimentary types remains limited. In this study, we collected a total of 27 samples from three sampling sites at Hangbu estuary in Chaohu Lake, and three sedimentary areas were classified based on the overlying water flow conditions and sediment particle properties to elucidate their microbial community structure, environmental drivers, assembly processes, and co-occurrence network characteristics. Our results showed significant differences in microbial community composition and diversity among three sedimentary areas. Redundancy analysis indicated that the differences in microbial community composition at the OTU level among the three sedimentary areas were mainly determined by nitrate-nitrogen, temperature, and water content. Phylogenetic bin-based null model analysis revealed that temperature was a key factor influencing deterministic processes among the three sedimentary areas, while stochastic processes predominantly governed the assembly of microbial communities. In addition, co-occurrence network analysis demonstrated that the network in the hydraulically driven sedimentary area of the lake, consisting mainly of medium and fine silt, had the highest complexity, stability, and cohesion, but was missing potential keystone taxa. The remaining two sedimentary areas had 5 and 8 potential keystone taxa, respectively. Overall, our study proposes the delineation of sedimentary types and comprehensively elucidates the microbial community characteristics under different sedimentary areas, providing a new perspective for studying sediment microbial community structure and helping future scholars systematically study ecological dynamics in estuaries.

Microbial Communities Are Shaped by Different Ecological Processes in Subtropical Reservoirs of Different Trophic States

Understanding microbial community structure and the underlying control mechanisms are fundamental purposes of aquatic ecology. However, little is known about the seasonality and how trophic conditions regulate plankton community in subtropical reservoirs. In this study, we study the prokaryotic and picoeukaryotic communities and their interactions during wet and dry seasons in two subtropical reservoirs: one at oligotrophic state and another at mesotrophic state. Distinct microbial community compositions (prokaryotes and picoeukaryotes) and seasonal variation pattern were detected in the oligotrophic and mesotrophic reservoirs. The interactions between prokaryotic and picoeukaryotic communities were more prevalent in the oligotrophic reservoir, suggesting enhanced top-down control of small eukaryotic grazers on the prokaryotic communities. On the other hand, the microbial community in the mesotrophic reservoir was more influenced by physico-chemical parameters and showed a stronger seasonal variation, which may be the result of distinct nutrient levels in wet and dry seasons, indicating the importance of bottom-up control. Our study contributes to new understandings of the environmental and biological processes that shape the structure and dynamics of the planktonic microbial communities in reservoirs of different trophic states.

Spatiotemporal distributions of sulfonamide and tetracycline resistance genes and microbial communities in the coastal areas of the Yangtze River Estuary

In this paper, water and sediments were sampled at eight monitoring stations in the coastal areas of the Yangtze River Estuary in summer and autumn 2021. Two sulfonamide resistance genes (sul1 and sul2), six tetracycline resistance genes (tetM, tetC, tetX, tetA, tetO, and tetQ), one integrase gene (intI1), 16 S rRNA genes, and microbial communities were examined and analyzed. Most resistance genes showed relatively higher abundance in summer and lower abundance in autumn. One-way analysis of variance (ANOVA) showed significant seasonal variation of some ARGs (7 ARGs in water and 6 ARGs in sediment). River runoff and WWTPs are proven to be the major sources of resistance genes along the Yangtze River Estuary. Significant and positive correlations between intI1 and other ARGs were found in water samples (P < 0.05), implying that intI1 may influence the spread and propagation of resistance genes in aquatic environments. Proteobacteria was the dominant phylum along the Yangtze River Estuary, with an average proportion of 41.7%. Redundancy analysis indicated that the ARGs were greatly affected by temperature, dissolved oxygen, and pH in estuarine environments. Network analysis showed that Proteobacteria and Cyanobacteria were the potential host phyla for ARGs in the coastal areas of the Yangtze River Estuary.

Pro- and eukaryotic keystone taxa as potential bio-indicators for the water quality of subtropical Lake Dongqian

The microbial community plays an important role in the biogeochemical cycles in water aquatic ecosystems, and it is regulated by environmental variables. However, the relationships between microbial keystone taxa and water variables, which play a pivotal role in aquatic ecosystems, has not been clarified in detail. We analyzed the seasonal variation in microbial communities and co-occurrence network in the representative areas taking Lake Dongqian as an example. Both pro- and eukaryotic community compositions were more affected by seasons than by sites, and the prokaryotes were more strongly impacted by seasons than the eukaryotes. Total nitrogen, pH, temperature, chemical oxygen demand, dissolved oxygen and chlorophyll a significantly affected the prokaryotic community, while the eukaryotic community was significantly influenced by total nitrogen, ammonia, pH, temperature and dissolved oxygen. The eukaryotic network was more complex than that of prokaryotes, whereas the number of eukaryotic keystone taxa was less than that of prokaryotes. The prokaryotic keystone taxa belonged mainly to Alphaproteobacteria, Betaproteobacteria, Actinobacteria and Bacteroidetes. It is noteworthy that some of the keystone taxa involved in nitrogen cycling are significantly related to total nitrogen, ammonia, temperature and chlorophyll a, including Polaromonas, Albidiferax, SM1A02 and Leptolyngbya so on. And the eukaryotic keystone taxa were found in Ascomycota, Choanoflagellida and Heterophryidae. The mutualistic pattern between pro- and eukaryotes was more evident than the competitive pattern. Therefore, it suggests that keystone taxa could be as bio-indicators of aquatic ecosystems.

Insight into the dynamics of drinking water resistome in China

Antibiotic resistance (AR) is a serious environmental hazard of the current age. Antibiotic resistance genes (ARGs) are the fundamental entities that spread AR in the environment. ARGs are likely to be transferred from the non-pathogenic to pathogenic microbes that might ultimately be responsible for the AR in humans and other organisms. Drinking water (DW) is the primary interaction route between ARGs and humans. Being the highest producer and consumer of antibiotics China poses a potential threat to developing superbugs and ARGs dissemination. Herein, we comprehensively seek to review the ARGs from dominant DW sources in China. Furthermore, the origin and influencing factors of the ARGs to the DW in China have been evaluated. Commonly used methods, both classical and modern, are being compiled. In addition, the risk posed and mitigation strategies of DW ARGs in China have been outlined. Overall, we believe this review would contribute to the assessment of ARGs in DW of China and their dissemination to humans and other animals and ultimately help the policymakers and scientists in the field to counteract this problem on an emergency basis.

Composting effect and antibiotic removal under a new temperature control strategy

The main objective of this study was to investigate the feasibility of a new temperature control strategy in the co-composting process to accelerate operation cycle and remove antibiotics from mixed organic wastes. The evaluation of the composting process showed that composting with temperature control (TC) was completed within 14 days. The final compost of TC exhibited a 10% higher degradation of organic matters, more humus formation and 11.25% lower heavy metals concentration than conventional composting (CC), which fully met the Chinese National Agricultural Organic Fertilizer Standard requirements. The degradation extent and kinetic of macrolides, tetracyclines, sulfonamides and fluoroquinolones showed that the removal efficiency of total antibiotics in TC was 23.58% higher than CC, with less half-life, which was significantly correlated with higher temperature. Particularly, the highest removal was observed for sulfonamides (87.45%) in TC, the half-life of which was reduced by 75.95% compared with CC. The higher degradation rate was attributed to enhanced decomposition of unstable antibiotics and degrading activity of microbes at high temperature. The microbiological analysis showed that the external heating led to a distinct composition and succession of bacterial community in TC. Firmicutes, Proteobacteria, Actinobacteriota and Bacteroidota were dominant and the emergence of Patescibacteria and Chloroflexi at cooling period in TC proved that the later composting environment was in an oligotrophic state. Current research provided a promising rapid composting approach for high-quality fertilizer production and antibiotic management in organic waste disposal.

The effect of graphene photocatalysis on microbial communities in Lake Xingyun, southwestern China

Graphene photocatalysis is a new method for harmful algae and water pollution control. However, microbial communities undergoing graphene photocatalysis treatment in freshwater lakes have been poorly studied. Here, using 16S rRNA and 18S rRNA gene high-throughput sequencing, the responses of microbial communities to graphene photocatalysis were analyzed in the eutrophic lake, Lake Xinyun, southwestern China. For microeukaryotes, we found that Arthropoda was dominant in summer, while its abundant level declined in spring under natural conditions. The evident reduction of Arthropods was observed after graphene photocatalysis treatment in summer and then reached a relatively stable level. For bacteria, Cyanobacteria decreased in summer due to the graphene photocatalysis-mediated inactivation. However, Cyanobacteria was higher in the treated group in spring with a genera group-shift. Functional analysis revealed that microeukaryotes showed higher potential for fatty acid oxidation and TCA cycle in the treated group in summer, but they were more abundant in control in spring. Pathways of starch and sucrose metabolism and galactose metabolism were more abundant in control in summer, while they were enriched in the treated group in spring for bacteria. This study offers insights into the effects of graphene photocatalysis on microbial communities and their functional potential in eutrophic lake.

Microbial Richness of Marine Biofilms Revealed by Sequencing Full-Length 16S rRNA Genes

Marine biofilms are a collective of microbes that can grow on many different surfaces immersed in marine environments. Estimating the microbial richness and specificity of a marine biofilm community is a challenging task due to the high complexity in comparison with seawater. Here, we compared the resolution of full-length 16S rRNA gene sequencing technique of a PacBio platform for microbe identification in marine biofilms with the results of partial 16S rRNA gene sequencing of traditional Illumina PE250 platform. At the same time, the microbial richness, diversity, and composition of adjacent seawater communities in the same batch of samples were analyzed. Both techniques revealed higher species richness, as reflected by the Chao1 index, in the biofilms than that in the seawater communities. Moreover, compared with Illumina sequencing, PacBio sequencing detected more specific species for biofilms and less specific species for seawater. Members of Vibrio, Arcobacter, Photobacterium, Pseudoalteromonas, and Thalassomonas were significantly enriched in the biofilms, which is consistent with the previous understanding of species adapted to a surface-associated lifestyle and validates the taxonomic analyses in the current study. To conclude, the full-length sequencing of 16S rRNA genes has probably a stronger ability to analyze more complex microbial communities, such as marine biofilms, the species richness of which has probably been under-estimated in previous studies.

Phycocyanin-rich Synechococcus dominates the blooms in a tropical estuary lake

Cyanobacterial blooms challenge the safe water supply in estuary reservoirs. Yet, data are limited for the variation of phytoplankton dynamics during an algal bloom event at refined scales, which is essential for interpreting the formation and cessation of blooms. The present study investigated the biweekly abundances and dynamics of pico- and nano-phytoplankton in a tropical estuary lake following a prolonged bloom event. Flow cytometry analysis resolved eight phenotypically distinct groups of phytoplankton assigned to nano-eukaryotes (nano-EU), pico/nano-eukaryotes (PicoNano-EU), cryptophyte-like cells (CRPTO), Microcystis-like cells (MIC), pico-eukaryotes (Pico-EU) and three groups of Synechococcus-like cells. Total phytoplankton abundance ranged widely from 2.4 × 104 to 2.8 × 106 cells cm-3. The phytoplankton community was dominated by Synechococcus-like cells with high phycocyanin content (SYN-PC). Temporal dynamics of the phytoplankton community was phytoplankton- and site-specific. Peak values were observed for SYN-PC, SYN-PE2 (Synechococcus-like cells with low levels of phycoerythrin) and Pico-EU, while the temporal dynamics of other groups were less pronounced. Redundancy analysis (RDA) showed the importance of turbidity as an abiotic factor in the formation of the current SYN-PC induced blooms, and Spearman correlation analysis suggested a competitive relationship between SYN-PC and Pico-EU.

Inactivation of Antibiotic-Resistant Bacteria in Wastewater by Ozone-Based Advanced Water Treatment Processes

The inactivating effect of ozone (O₃)-based advanced oxidation processes (AOPs) (O₃/H₂O₂, O₃/UV, and O₃/UV/H₂O₂ systems) on antimicrobial-resistant bacteria (AMRB) and antimicrobial-susceptible bacteria (AMSB) in sewage treatment plant (STP) wastewater was investigated. The AMRB were grouped into six classes: carbapenem-resistant Enterobacteriaceae (CRE), extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae (ESBL-E), multidrug-resistant Acinetobacter (MDRA), multidrug-resistant Pseudomonas aeruginosa (MDRP), methicillin-resistant Staphylococcus aureus (MRSA), and vancomycin-resistant Enterococcus (VRE); these classes constituted the World Health Organization (WHO) global priority list of AMRB. The results indicate that O₃-based advanced wastewater treatment inactivated all AMRB and AMSB (>99.9%) after 10 min of treatment, and significant differences (p < 0.5) were not observed in the disinfection of AMRB and AMSB by each treatment. Altered taxonomic diversity of micro-organisms based on 16S rRNA gene sequencing via O₃/UV and O₃/UV/H₂O₂ treatment showed that advanced wastewater treatments not only inactivated AMRB but also removed antimicrobial resistance genes (AMRGs) in the wastewater. Consequently, this study recommends the use of advanced wastewater treatments for treating the STP effluent, reducing environmental pollution, and alleviating the potential hazard to human health caused by AMRB, AMSB, and infectious diseases. Overall, this study provides a new method for assessing environmental risks associated with the spread of AMRB and AMSB in aquatic environments, while keeping the water environment safe and maintaining human health.

eDNA revealed in situ microbial community changes in response to Trapa japonica in Lake Qionghai and Lake Erhai, southwestern China

Trapa japonica was observed to have inhibiting effects and could be used as a potential environment-friendly control strategy for cyanobacterial blooms in freshwater. However, the changes and effecting mechanisms in eukaryotic and prokaryotic communities by T. japonica are not yet clear. In this study, the effects of T. japonica on microbial communities were assessed in Lake Qionghai and Lake Erhai by 18S rRNA and 16S rRNA amplicon sequencing, respectively. The results showed that T. japonica can improve biodiversity and change the microbial community structures to varying degrees in both lakes. The alpha diversity indexes of microbial communities (e.g., Shannon, Sobs, Ace and Chao 1) were higher in the water inhabited by T. japonica (TJ group) than the water uninhabited by T. japonica (control) (P < 0.05). The PCoA results suggested that the microbial community compositions differed between the two groups (PERMANOVA P = 0.001). In Lake Qionghai, the relative abundances of dominant taxa and nutrients level showed little differences between the two groups. These may result from the homogenous water condition in Lake Qionghai. While the genera Cyanobium_PCC-6307, the majority of Cyanobacteria, decreased significantly in TJ group than control according to 16S rRNA gene sequencing. In Lake Erhai, environmental variables were distinctly affected by T. japonica, which was found to drive Cryptophyceae to become the main taxa through taxonomic analysis of 18S rRNA. Based on 16S rRNA gene sequencing, T. japonica reduced the relative abundance of Cyanobacteria, such as Planktothrix_NIVA-CYA_15 and Cyanobium_PCC-6307, by enriching cyanobactericidal bacteria and growth-inhibiting bacteria (e.g., Limnohabitans and Flavobacterium) and changing environmental parameters. Our results revealed that T. japonica acts in shaping microbial communities in lakes on the community level, shedding new lights on eutrophication mitigation, one of the most serious global ecological problems we are facing.

Seasonal and spatial patterns of eukaryotic phytoplankton communities in an urban river based on marker gene

The seasonal and spatial eukaryotic phytoplankton composition in the Fenhe River was investigated based on the 18S rDNA V4 region. The relationship between phytoplankton functional groups and environmental factors was explored to effectively capture the responses of these taxa to environmental gradients and their effects on ecosystem function. Our results indicated that the Chlorophyta and Bacillariophyta had higher relative abundance than other taxa, and their diversity and richness indices in spring were higher than those in other seasons. The linear discriminant analysis effect size (LEfSe) analyses detected that the potential seasonal biomarkers included Desmodesmus, Cyclotella, Pseudoschroederia, Discostella, Scenedesmus, Monoraphidium, and Nannochloropsis; the spatial biomarkers included Amphora, Neochloris, Hindakia, Pseudomuriella, Coccomyxa, Chloroidium, Scherffelia, Chromochloris, and Scotinosphaera. The systemic evolution and distribution characteristics of the first 50 representative sequences showed that the dominant genus included Desmodesmus in spring, Pseudopediastrum in summer, Mychonastes in autumn, and Monoraphidium in winter. Main seasonal variation of phytoplankton functional groups was as follows: spring (J + F + C + X1) → summer (J + F + X1 + X2) → autumn (J + F + X1 + C) → winter (X1 + J + B + X2). Pearson correlation, redundancy analysis, and variance partitioning analysis showed temperature and phosphate were the determining factors causing the changes of phytoplankton functional groups and community composition in the Fenhe River.

Microbiome of juvenile corals in the outer reef slope and lagoon of the South China Sea: insight into coral acclimatization to extreme thermal environments

Environmental conditions between the outer reef slope (ORS) and lagoon in tropical atolls are significantly different, but the variations of juvenile coral-microbiomes in the two environments and their relationship with coral thermal acclimatization are poorly understood. We explored this issue based on local water conditions and the microbiome of juvenile corals in the ORS and lagoon in the central South China Sea. Coral-symbiotic Symbiodiniaceae showed significant differences among coral species; Pocillopora verrucosa and Pachyseris rugosa in the ORS, and Acropora formosa in the lagoon were dominated by Durusdinium, but other corals were dominated by Cladocopium. Although A. formosa in the ORS were dominated by Cladocopium (C3u), they were dominated by Durusdinium (D1/D1a) and Cladocopium (C50) in the lagoon. Other coral species were both dominated by Cladocopium in the lagoon and ORS. The relative abundance of bacteria in the Deinococcus-Thermus was generally higher in the lagoon corals than in the ORS corals. Our study indicates that P. verrucosa, P. rugosa and Porites lutea may have high thermal tolerance based on the relatively high abundance of heat-tolerant Durusdinium and Thermus scotoductus. Likewise, A. formosa in the lagoon may acclimatize to the thermal environment based on a high relative abundance of heat-tolerant Durusdinium.

Effects of natural sunlight on antimicrobial-resistant bacteria (AMRB) and antimicrobial-susceptible bacteria (AMSB) in wastewater and river water

The effects of natural sunlight on antimicrobial-resistant bacteria (AMRB) and antimicrobial-susceptible bacteria (AMSB) were investigated in three types of water: sewage treatment plant (STP) influent, STP secondary effluent, and river water in an urban area of Japan. The AMRB were grouped into six classes: carbapenem-resistant Enterobacteriaceae (CRE), extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae (ESBL-E), multi-drug-resistant Acinetobacter (MDRA), multi-drug-resistant Pseudomonas aeruginosa (MDRP), methicillin-resistant Staphylococcus aureus (MRSA), and vancomycin-resistant Enterococcus (VRE). The amount of each group of bacteria present was estimated using specific chromogenic agar formulations. AMRB were detected in all water samples, with 13-2,407 colony-forming units (CFU)/mL in the STP influent, N.D. to 202 CFU/mL in the secondary STP effluent, and N.D. to 207 CFU/mL in the river water. The distribution profiles of the AMSB in water samples were similar to those of AMRB. The degree to which AMRB and AMSB present in the river water were inactivated by natural sunlight was tested as the main aim of this study. Irradiation by natural sunlight was found to inactivate almost 100% of all the target AMRB after 5 h of exposure, with no significant differences (P < 0.05) observed in the effects that sunlight had on AMSB and AMRB. Analysis of the bacterial community structure based on 16S rRNA gene sequencing showed that the structure of the bacterial community was apparently not affected by the exposure to sunlight. In addition, the taxonomic diversity in the STP secondary effluent did not change as a result of additional disinfection with chlorine. The results of this study suggest that it is possible that exposure to sunlight could be used as an alternative to disinfection via chlorine. To our knowledge, this is the first report to demonstrate the mitigation of AMSB and AMRB pollution in a river environment via the exposure to natural sunlight.

Comparative responses of cell growth and related extracellular polymeric substances in Tetraselmis sp. to nonylphenol, bisphenol A and 17α-ethinylestradiol

Estuarine ecosystems near mega-cities are sinks of anthropogenic endocrine disrupting chemicals (EDCs). As the most important primary producer, indigenous microalgae and their secreted extracellular polymeric substances (EPSs) might interact with EDCs and contribute to their fate and risk. Tetraselmis sp. is a representative model of estuarine microalga, for which EDC toxicity and its effects on EPS synthesis have rarely been studied. Through microalgal isolation, algal cell growth tests, EDC removal and the characterization of related EPS profiles, the present work intends to clarify the comparative responses of Tetraselmis sp. to nonylphenol (NP), bisphenol A (BPA) and 17α-ethinylestradiol (EE₂). The results showed that the half inhibitory concentration on cell growth was 0.190-0.313 mg/dm³ for NP, which was one order of magnitude lower than the comparable values for BPA and EE₂ at 2.072-3.254 mg/dm³. Regarding chlorophyll, NP induced its degradation, EE₂ led to its decreased production, and BPA had no obvious effect. Under EDC stress, only the concentrations of colloidal polysaccharides and proteins responded dose-dependently to EE₂. Except for the colloidal fraction in the EE₂ treatment group, the increase in neutral monosaccharides, especially glucose and galactose, was a common response to EDCs. Compared to the recalcitrant BPA, NP underwent abiotic degradation in alga-free water, and EE₂ could be biodegraded in water containing this microalga. The chemical-specific responses of cell growth, chlorophyll and related EPS profiles were driven by the different fates of EDCs, and the underlying mechanism was further discussed. The results obtained in the present work are of critical importance for understanding the fate and effects of different EDCs mediated by microalgae and their related EPSs.

Change of dominant phytoplankton groups in the eutrophic coastal sea due to atmospheric deposition

Nutrient stoichiometry and input of trace metals may profoundly affect the growth and community structure of phytoplankton. A bioassay experiment was designed to explore the key components in atmospheric deposition that affect marine phytoplankton growth by adding aerosols and analogues nutrients and Cu to the surface water of the coastal East China Sea (ECS). Our results showed that atmospheric deposition along with the input of phosphate could largely enhance the chlorophyll a (Chl a) concentrations in this eutrophic water. Phosphorus addition lifted the proportions of T. oceanica in Diatoms and B. brevisulcata in Dinoflagellates. T. oceanica replaced S. costatum and became the dominant diatom species after the Chl a peak, probably associated with the N/P ratio approaching to 16. Atmospheric aerosols containing affluent N and little P showed limited promotion to Chl a, and the positive effect was very likely due to the soluble Cu and other trace metals supplied by the aerosol. Moreover, soluble aerosol Cu was found to be conducive to the relative abundance of most dominant class Coscinodiscophyceae, and both soluble aerosol Fe and Cu seemed to be very important for increasing the proportion of S. costatum. Soluble metals could be the key components in aerosols controlling the phytoplankton composition in the eutrophic sea and such impact might exceed affluent P provided by other exogenous sources.

Changes in planktonic and sediment bacterial communities under the highly regulated dam in the mid-part of the Three Gorges Reservoir

Bacterial communities play an important role in the biogeochemical cycle in reservoir ecosystems. However, the dynamic changes in both planktonic and sediment bacterial communities in a highly regulated dam reservoir remain unclear. This study investigated the temporal distribution patterns of bacterial communities in a transition section of the Three Gorges Reservoir (TGR) using Illumina MiSeq sequencing. Results suggested that in comparison to the planktonic bacteria, sediment bacteria contributed more to the reservoir microbial communities, accounting for 97% of the 7434 OTUs. The Shannon diversity index in the water (3.22~5.68) was generally lower than that in the sediment (6.72~7.56). In the high water level period (January and March), Proteobacteria, Actinobacteria, Cyanobacteria, and Firmicutes were the most abundant phyla, whereas in the low water level period (May, July, and September), the dominant phyla were Proteobacteria, Actinobacteria, and Bacteroidetes. Sediment samples were dominated by Proteobacteria, Chloroflexi, and Acidobacteria. Principal coordinate analysis of the bacterioplankton communities showed greater sensitivity to monthly changes than that of the sediment bacterial communities. Network analysis suggested that in comparison to planktonic bacterial communities, sediment bacterial communities were more complex and stable. The linear relationship between the CH₄/CO₂ ratio, water level, and relative abundance of methanotrophs highlighted the potential methane-oxidizing process in the mid-part of the TGR. Moreover, the potential impact of dam regulation on the bacterial communities was revealed by the significant relationship between abundant phyla and the inflow of the TGR. KEY POINTS: • Bacterioplankton communities showed great sensitivity to monthly changes. • Potential methane-oxidizing process was revealed in this representative area. • Water inflow regulated by dam has significant effects on dominant bacterioplankton.

Structural Characteristics and Driving Factors of the Planktonic Eukaryotic Community in the Danjiangkou Reservoir, China

Planktonic eukaryotes are widespread in aquatic ecosystems, and the study of their community composition and driving factors is of great significance to protecting and maintaining the balance of these ecosystems. This study evaluates five typical ecological sites in the Danjiangkou Reservoir—the water source for the project. This was done to comprehensively understand the composition of Danjiangkou Reservoir planktonic eukaryotes, and ensure the ecological balance of the water source for the South-to-North Water Diversion Project. The diversity of the planktonic eukaryotes in surface water and the factors driving changes in their abundance are analyzed with an 18S ribosomal DNA sequencing approach. Monitoring shows that the Danjiangkou Reservoir has good water quality. The Danjiangkou Reservoir planktonic eukaryote community is mainly composed of 11 phyla, of which Cryptomonadales is dominant, accounting for an average percentage of 65.19% of the community (47.2–84.90%). LEFSe analysis shows significant differences among samples in the abundances of 13 phyla, 20 classes, 23 orders, 26 families, and 27 genera, and there are also significant differences in the diversity of planktonic eukaryotes at different temporal and spatial scales. Redundancy analysis (RDA) show that water temperature, DO, SD, TN, and Chla are significant factors that affect the composition of the planktonic eukaryote community. Spearman rank correlation analysis combined with taxonomic difference analysis shows that Kathablepharidae and Choanoflagellida are not sensitive to environmental or physicochemical factors and that the interannual variations in their abundance are not significant. Network analysis shows that Protalveolata, Basidiomycota, P1-31, Bicosoecida, and Ochrophyta represent important nodes in the single-factor network, while Chytridiomycota, P1-31, Cryptomycota, Ochrophyta, Ichthyosporea, Bicosoecida, Protalveolata, and physicochemical factors (ORP, TN, WT, DO, SD, NH3-N, and NO3-N) represent important nodes in the two-factor network.

Reservoir water stratification and mixing affects microbial community structure and functional community composition in a stratified drinking reservoir

To investigate how the aquatic bacterial community of a stratified reservoir drives the evolution of water parameters, the microbial community structure and network characteristics of bacteria in a stratified reservoir were investigated using Illumina MiSeq sequencing technology. A total of 42 phyla and 689 distinct genera were identified, which showed significant seasonal variation. Additionally, stratified variations in the bacterial community strongly reflected the vertical gradient and seasonal changes in water temperature, dissolved oxygen, and nutrition concentration. Furthermore, principal coordinate analysis indicated that most microorganisms were likely influenced by changes in water stratification conditions, exhibiting significant differences during the stratification period and mixing period based on Adonis, MRPP, and Anosim. Compared to the stratification period, 123 enhanced operational taxonomic units (OTUs; 29%) and 226 depleted OTUs (52%) were identified during the mixing period. Linear discriminant analysis effect size results showed that 15 major genera were enriched in the mixing period and 10 major genera were enriched in the stratification period. Importantly, network analysis revealed that the keystone species belonged to hgcI_clade, CL500-29, Acidibacter, Paucimonas, Flavobacterium, Prochlorothrix, Xanthomonadales, Chloroflexia, Burkholderiales, OPB56, KI89A_clade, Synechococcus, Caulobacter or were unclassified. Redundancy analysis showed that temperature, dissolved oxygen, pH, chlorophyll-α, total phosphorus, nitrate, and ammonia were important factors influencing the water bacterial community and function composition, which were consistent with the results of the Mantel test analysis. Furthermore, random forest analysis showed that temperature, dissolved oxygen, ammonia, and total dissolved phosphorous were the most important variables predicting water bacterial community and function community α- and β-diversity (P < 0.05). Overall, these results provide insight into the interactions between the microbial community and water quality evolution mechanism in Zhoucun reservoir.

Diazotroph Diversity Associated With Scleractinian Corals and Its Relationships With Environmental Variables in the South China Sea

Coral reef ecosystems cannot operate normally without an effective nitrogen cycle. For oligotrophic coral reef areas, coral-associated diazotrophs are indispensable participants in the nitrogen cycle. However, the distribution of these diazotrophs and the correlation with the physical and chemical variables of the surrounding seawater remain unclear. To this end, 68 scleractinian coral colonies were sampled from 6 coral reef areas with different environmental variables in the South China Sea to investigate the composition of associated diazotrophs based on nifH gene amplification using high-throughput sequencing. The six coral reefs can be clearly divided into two types (fringing reefs and island reefs), are affected by varying degrees of human activities and are located at different latitudes from 9°20’06”N to 22°34’55”N with different seawater temperatures. Alpha- and beta-diversity analyses showed that the distribution of diazotrophs among coral reefs exhibited significant geographical fluctuations (p ≤ 0.05) and non-significant interspecific fluctuations (p > 0.05). The predominant bacterial phyla included Proteobacteria, Chlorobi, Cyanobacteria, and two unclassified phyla. Chlorobi exhibited a relative abundance of 47–96% in coral samples from the high-latitude Daya Bay fringing reef affected by eutrophication. Unclassified bacteria II, with a relative abundance of 28–87%, was found in all coral samples from the midlatitude Luhuitou fringing reef affected by eutrophication. However, unclassified bacteria I and Proteobacteria dominated (>80% relative abundance) in most of the coral samples from the Weizhou Island fringing reef, which is far from land, and three island reefs (Huangyan Island, Xinyi Reef, and Sanjiao Reef) at relatively low latitudes. At the genus level, some core diazotrophs were found in different coral sample groups. In addition, correlation analysis with various environmental variables revealed that the variables were positively or negatively correlated with different diazotrophic genera. Coral-associated diazotrophs were common among coral individuals. However, their composition was closely related to the different environmental variables. These results provide insights into the geographical distribution characteristics of coral-associated diazotrophs and their evolutionary trends in response to environmental change in the South China Sea.

Harmful algal blooms significantly reduce the resource use efficiency in a coastal plankton community

Harmful algal blooms (HABs) have been investigated for their catastrophic effects on public health and aquaculture intensively, but the research about HABs effects on the diversity patterns and intrinsic functions of the plankton community based on a species identification with high resolution and accuracy has been scarce. We therefore investigated the shifts of plankton diversity via pyrosequencing during and around a natural dinoflagellate (Prorocentrum donghaiense) bloom and analyzed the effect of P. donghaiense abundance on the operationally-defined resource use efficiency (RUE) of plankton community to test our hypothesis that outbreaks of HABs will reduce RUE of the plankton community via shifting the plankton community structure, species composition in particular. We found that the species diversity of eukaryotic plankton community was significantly decreased during the bloom, as reflected in OTU (operational taxonomic unit) richness, and Pielou's evenness index. Principal coordinates analysis indicated significant difference in plankton community structure between blooming and non-blooming periods. As hypothesized, the species richness was positively correlated to RUE (defined as the ratio of phytoplankton biomass to total phosphorus), and more importantly, the cell density of P. donghaiense exhibited significant negative correlation with RUE. Our results explicitly demonstrated HABs reduce RUE via reducing species richness (corresponding to a less occupancy of the trophic niches), which supports the previously documented notion that niche partitioning enhances RUE (a key ecosystem function). Also, our work provides striking evidence for the relationship between plankton species richness (or diversity) and community function (resource use efficiency) via studying on HABs, a natural but exceptional phenomenon, in addition to revealing a profound consequence of HABs.

Time-course relationship between environmental factors and microbial diversity in tobacco soil

Soil physicochemical properties and microbial diversity both play equally important roles in tobacco cultivation. However, the relationship between these factors remains unclear. In this study, we investigated their correlations through the whole tobacco growth period, including the pretransplanting (YX-p), root extending (R), flourishing (F), and mature (M) stages in the Yuxi region of the Yunnan-Guizhou Plateau by measuring physicochemical properties and conducting 16S/18S rRNA analysis. The analysis demonstrated that the microbial community richness and diversity continuously changed along with the growth course of the tobacco. Multiple environmental factors showed a certain correlation with the diversity of microbial communities. Some bacteria could accumulate nitrogen during the growth stages, and the diversity of the bacterial community also increased when the content of organic matter rose. In addition, the water content and available K also influenced the diversity of the microbial community. The dynamic changes in soil physicochemical properties and enzyme activities gave rise to differences in the microbial community composition and structure, all of which affected the growth of tobacco. This study revealed the time-course relationship between environmental factors and microbial diversity in tobacco soil. An understanding of this relationship provides guidance for research on the interaction system of plants, soil and microbes and on improving plant yield and quality.

Diversity of Symbiodiniaceae in 15 Coral Species From the Southern South China Sea: Potential Relationship With Coral Thermal Adaptability

It is well-known that the adaptability of coral-Symbiodiniaceae symbiosis to thermal stress varies among coral species, but the cause and/or mechanism behind it are not well-understood. In this study, we aimed to explore this issue based on zooxanthellae density (ZD) and Symbiodiniaceae genus/subclade. Hemocytometry and next-generation sequencing of the internal transcribed spacer region 2 (ITS2) marker gene were used to observe ZDs and Symbiodiniaceae genera/subclades associated with 15 typical coral species in the southern South China Sea (SCS). Average ZDs of all corals were in low levels, ranging from 0.84 to 1.22 × 10⁶ cells cm⁻², with a total of five Symbiodiniaceae genera, Symbiodinium, Cladocopium, Durusdinium, Fugacium, and Gerakladium, as well as 24 dominant subclades, were detected and varied among these coral species. Pocillopora verrucosa was dominated by Durusdinium (subclade D1/D1a), and other colonial corals were dominated by Cladocopium, but the subclades were varied among these species. Porites lutea and Montipora efflorescens were dominated by C15, and Echinopora lamellosa, Hydnophora exesa, and Coscinaraea exesa were dominated by C40. Acropora corymbosa, Merulina ampliata, and five species of Faviidae were mainly associated with Cladocopium types of C3u and Cspc. In contrast to other colonial corals, the dominant subclade of solitary Fungia fungites was C27, with high host specificity. Our study indicates that coral thermal stress adaptability is mainly affected by dominant Symbiodiniaceae type instead of ZD in the southern SCS. Some heat-sensitive corals, such as P. verrucosa corals, have acquired a high abundance of heat-tolerant Durusdinium to adapt to thermal stress. This could be the main reason for these corals becoming the dominant corals in this reef region. Background subclades analyses showed significant differences among coral species in subclade quantity and diversity. These suggest that numbers of coral species may have adapted to high environmental temperature by adopting various symbionts and/or associating with heat-tolerant Symbiodiniaceae.

Environmental media exert a bottleneck in driving the dynamics of antibiotic resistance genes in modern aquatic environment

With the rapid construction of dams worldwide, reservoir system has become a representation of modern aquatic environment. However, the profiles of antibiotic resistance genes (ARGs) and associated factor influencing their dynamics in modern aquatic environment (e.g., water phase, sediment phase, and soil phase) are largely unknown. Here, we comprehensively characterized the diversity, abundance, distribution of ARGs in a large drinking water reservoir using high-throughput quantitative PCR, as well as ranked the factors (e.g., mobile genetic elements (MGEs), bacteria community, bacterial biomass, antibiotics, and basic properties) influencing the profiles of ARGs on the basis of structural equation models (SEMs). Water phase was prone to harbor more diverse ARGs as compared to sediment phase and soil phase, and soil phase in drawdown area was a potential reservoir and hotspot for ARGs. Environmental media partially affected the ARG diversity in modern aquatic environment, while it observably influenced the distributions of ARGs and MGEs and their co-occurrence patterns. The pathways for the proliferation and spread of ARGs in water phase were both the horizontal gene transfer (HGT) and vertical gene transfer (VGT), while the dominant pathways in sediment phase and soil phase were the HGT and VGT, respectively. The SEMs demonstrated that MGEs contributed the most to drive the ARG dynamics in both water phase and sediment phase, while the most dominant factor for this in soil phase was bacterial community. Overall, environmental media exerted a bottleneck in driving the dynamics of ARGs in modern aquatic environment probably via diversifying the MGEs, bacterial community, bacterial biomass, antibiotics and basic properties.

Driving Factors and Dynamics of Phytoplankton Community and Functional Groups in an Estuary Reservoir in the Yangtze River, China

Qingcaosha Reservoir, an estuary reservoir on the Yangtze River and a drinking water source, is facing phytoplankton blooms and the factors driving changes in phytoplankton composition and distribution have not been well understood so far. To facilitate the understanding of this problem, we collected surface water samples from January to December 2014 monthly at 12 sampling sites. A total of 205 taxa classified into eight major taxonomic groups were identified. Cyclotella meneghiniana, Melosira varians, Melosira granulata, Cryptomonas ovata and Chlorella vulgaris were the species dominating at least one season. The long stratification period and high nutrient concentration resulted in high chlorophyll a concentration (36.1 ± 18.5 μg L−1) in the midstream and downstream during summer, and mass phytoplankton growth and sedimentation process led to nutrients decrease. In the reservoir, neither P or N limitation was observed in the study period. We observed that water temperature, nutrient concentrations and light availability (Zeu/Zmix) are critical in selecting functional groups. These results highlight that the functional groups characterized the water body well and showed a good ecological status based on the assemblage index (Q average = 4.0). This work also highlights that mixing regime, water temperature and light availability were the driving factors that determine phytoplankton dynamics.

Microbial Community Structure in the Sediments and Its Relation to Environmental Factors in Eutrophicated Sancha Lake

To study the microbial community structure in sediments and its relation to eutrophication environment factors, the sediments and the overlying water of Sancha Lake were collected in the four seasons. MiSeq high-throughput sequencing was conducted for the V3–V4 hypervariable regions of the 16S rRNA gene and was used to analyze the microbial community structure in sediments. Pearson correlation and redundancy analysis (RDA) were conducted to determine the relation between microbial populations and eutrophic factors. The results demonstrated four main patterns: (1) in the 36 samples that were collected, the classification annotation suggested 64 phyla, 259 classes, 476 orders, 759 families, and 9325 OTUs; (2) The diversity indices were ordered according to their values as with summer > winter > autumn > spring; (3) The microbial populations in the four seasons belonged to two distinct characteristic groups; (4) pH, dissolved oxygen (DO), total phosphorus (TP), and total nitrogen (TN) had significant effects on the community composition and structure, which further affected the dissolved total phosphorus (DTP) significantly. The present study demonstrates that the microbial communities in Sancha Lake sediments are highly diverse, their compositions and distributions are significantly different between spring and non-spring, and Actinobacteria and Cyanobacteria may be the key populations or indicator organisms for eutrophication.

The Composition, Diversity and Predictive Metabolic Profiles of Bacteria Associated With the Gut Digesta of Five Sea Urchins in Luhuitou Fringing Reef (Northern South China Sea)

Sea urchins strongly affect reef ecology, and the bacteria associated with their gut digesta have not been well studied in coral reefs. In the current study, we analyze the bacterial composition of five sea urchin species collected from Luhuitou fringing reef, namely Stomopneustes variolaris, Diadema setosum, Echinothrix calamaris, Diadema savignyi, and Tripneustes gratilla, using high-throughput 16S rRNA gene-based pyrosequencing. Propionigenium, Prolixibacter, and Photobacterium were found to be the dominant bacterial genera in all five species. Interestingly, four sea urchin species, including S. variolaris, D. setosum, E. calamaris, and D. savignyi, displayed a higher mean total abundance of the three bacterial genera (69.72 ± 6.49%) than T. gratilla (43.37 ± 13.47%). Diversity analysis indicated that the gut digesta of sea urchin T. gratilla displayed a higher bacterial α-diversity compared with the other four species. PCoA showed that the four groups representing D. setosum, D. savignyi, E. calamaris, and S. variolaris were overlapping, but distant from the group representing T. gratilla. Predictive metagenomics performed by PICRUSt revealed that the abundances of genes involved in amino acid metabolism and metabolism of terpenoid and polyketide were higher in T. gratilla, while those involved in carbohydrate metabolism were higher in the other four sea urchin species. Therefore, our results indicated that the composition, diversity and predictive metabolic profiles of bacteria associated with the gut digesta of T. gratilla were significantly different from those of the other four sea urchin species in Luhuitou fringing reef.

High-throughput profiling of antibiotic resistance gene dynamic in a drinking water river-reservoir system

The rapid construction of reservoir in river basin generates a river-reservoir system containing an environmental gradient from river system to reservoir system in modern aquatic environment worldwide. Profiles of antibiotic resistance genes (ARGs) in river-reservoir system is essential to better understand their dynamic mechanisms in aquatic eco-environment. In this study, we investigated the diversity, abundance, distribution of ARGs and mobile genetic elements (MGEs) in a representative river-reservoir system using high-throughput quantitative PCR, as well as ranked the factors (e.g. antibiotics, bacterial biomass, bacteria communities, and MGEs) influencing the patterns of ARGs based on structural equation models (SEMs). Seasonal variations in absolute abundance of ARGs and MGEs exhibited similar trends with local rainfall, suggesting that seasonal runoff induced by the rainfall potentially promote the absolute abundance of ARGs and MGEs. In contrast, environmental gradient played more important roles in the detected number, relative abundance, distribution pattern of ARGs and MGEs in the river-reservoir system. Moreover, environmental gradient also made the co-occurrence patterns associated with ARGs subtypes, MGEs and bacteria genera in river system different from those in reservoir system. The SEMs revealed that MGEs contributed the most to shape the ARG profiles. Overall, our findings provide novel insights into the mechanisms of environmental gradient on ARGs dynamics in river-reservoir system, probably via influencing the MGEs, antibiotics, pathogenic bacteria community and nonpathogenic bacteria community.

Characteristics of microbial community indicate anthropogenic impact on the sediments along the Yangtze Estuary and its coastal area, China

In the contaminated coastal sediments, variations of microbial community can reflect the impact of anthropogenic activities. The identification, evaluation and monitoring of the potential bio-indicator species and biomarker communities are vital for the ecological studies in sedimentary environments. Based on the high-throughput sequencing, the microbial communities were characterized in the sediments along the Yangtze Estuary and its coastal area. The results showed that the structure and composition of microbial communities varied greatly among different sampling sites at the phyla level, especially for Euryarchaeota. Metabolic pathway and quantitative PCR analyses suggested that the methane metabolism-related microbes were mainly included in the phylum of Euryarchaeota. Elevated abundances of methane metabolism-related microbes were found at Shidongkou (SDK) and Wusongkou (WSK), where microbes were seriously impacted by the wastewater treatment plant (WWTP) effluent and urban runoff. By comparing with the Euryarchaeota in WWTP sludge, the relatively high abundance of Euryarchaeota in sediment at SDK may be mainly related to the massive growth of indigenous species, promoted by anthropogenic nutrients. Moreover, redundancy discriminant analysis and correlation analysis revealed that methanogens and methanotrophs mainly respond to the nutrients and metals, such as total organic carbon, total phosphorus, total nitrogen, SO₄^2-, NO₂^-, NH₄⁺, Cr, and Zn, which were often related to human activities. Network analyses showed that the species related to the metabolism of methane may play a vital role in the interassociation among different microbial communities. Therefore, methanogens, methanotrophs and their community compositions could be considered as potential bio-indicator species and biomarker communities, indicating anthropogenic activities in the sediments along the Yangtze Estuary and its coastal area.

Assessment of 16S rRNA gene primers for studying bacterial community structure and function of aging flue-cured tobaccos

Selection of optimal primer pairs in 16S rRNA gene sequencing is a pivotal issue in microorganism diversity analysis. However, limited effort has been put into investigation of specific primer sets for analysis of the bacterial diversity of aging flue-cured tobaccos (AFTs), as well as prediction of the function of the bacterial community. In this study, the performance of four primer pairs in determining bacterial community structure based on 16S rRNA gene sequences in AFTs was assessed, and the functions of genes were predicted using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt). Results revealed that the primer set 799F-1193R covering the amplification region V5V6V7 gave a more accurate picture of the bacterial community structure of AFTs, with lower co-amplification levels of chloroplast and mitochondrial genes, and more genera covered than when using the other primers. In addition, functional gene prediction suggested that the microbiome of AFTs was involved in kinds of interested pathways. A high abundance of functional genes involved in nitrogen metabolism was detected in AFTs, reflecting a high level of bacteria involved in degrading harmful nitrogen compounds and generating nitrogenous nutrients for others. Additionally, the functional genes involved in biosynthesis of valuable metabolites and degradation of toxic compounds provided information that the AFTs possess a huge library of microorganisms and genes that could be applied to further studies. All of these findings provide a significance reference for researchers working on the bacterial diversity assessment of tobacco-related samples.

The Characteristics and Dynamics of Cyanobacteria-Heterotrophic Bacteria Between Two Estuarine Reservoirs - Tropical Versus Sub-Tropical Regions

In this study, Illumina MiSeq sequencing technique was employed to explore the characteristics and dynamics of cyanobacteria–heterotrophic bacteria between two estuarine reservoirs in sub-tropical (reservoir A in Shanghai) and tropical (reservoir B in Singapore) regions. The results indicated that significant differences in bacterial community composition were found between two estuarine reservoirs, which influenced by varied environmental variables. The environmental heterogeneity in reservoir A was much higher, which indicated that the composition of bacterial community in reservoir A was more complex. In contrast, reservoir B provided a suitable and temperate water environment conditions for bacterial growth, which resulted in higher community diversity and less co-exclusion correlations. The molecular ecological network indicated that the presence of dominant bacterial community in each of the reservoir were significant different. These differences mainly reflected the responses of bacterial community to the variations of environmental variables. Although Synechococcus was the dominant cyanobacterial species in both reservoirs, it exhibited co-occurrence patterns with different heterotrophic bacteria between reservoirs. In addition, the cyanobacteria–heterotrophic bacteria interaction exhibited highly dynamic variations, which was affected by nutrition and survive space. Also, the co-occurrence of Microcystis and Pseudanabaena found in reservoir B implied that the non-N-fixing Microcystis accompanied with N-fixing Pseudanabeana occurrence in freshwater lakes, so as to better meet the demand for nitrogen source.

Structural and functional shifts of bacterioplanktonic communities associated with spatiotemporal gradients in river outlets of the subtropical Pearl River Estuary, South China

In this study, we used high-throughput sequencing of 16S rRNA gene amplicons, to investigate the spatio-temporal variation in bacterial communities in surface-waters collected from eight major outlets of the Pearl River Estuary, South China. Betaproteobacteria were the most abundant class among the communities, followed by Gammaproteobacteria, Alphaproteobacteria, Actinobacteria, and Acidimicrobiia. Generally, alpha-diversity increased in winter communities and the taxonomic diversity of bacterial communities differed with seasonal and spatial differences. Temperature, conductivity, salinity, pH and nutrients were the crucial environmental factors associated with shifts in the bacterial community composition. Furthermore, inferred community functions that were associated with amino acid, carbohydrate and energy metabolisms were lower in winter, whereas the relative abundance of inferred functions associated with membrane transport, bacterial motility proteins, and xenobiotics biodegradation and metabolism, were enriched in winter. These results provide new insights into the dynamics of bacterial communities within estuarine ecosystems.

How bacterioplankton community can go with cascade damming in the highly regulated Lancang-Mekong River Basin

Rivers make vital contributions to the transport of water, sediment and nutrients from terrestrial to marine ecosystems. However, many large rivers worldwide are suffering from dam regulation. Increasing attention has been paid to bacterioplankton communities since they are highly responsive to river alterations and may influence biogeochemical processes. Here, a comprehensive study was conducted in the highly regulated Lancang-Mekong River Basin to address the question of how bacterioplankton communities respond to cascade damming. The results showed that dam constructions increased nutrient concentrations and threatened water quality in cascade reservoirs. Bacterioplankton cell abundance was reduced by damming, and α-diversity was inhibited in cascade reservoirs. Fortunately, however, river ecosystems were resilient after the remarkable disturbance caused by damming. Moreover, bacterioplankton community composition was significantly altered by cascade dams, including a shift in the dominant phylum from r-strategists to k-strategists. Meanwhile, according to GeoChip analysis, the functional composition of bacterioplankton was less affected than taxonomic composition. In addition, geographic and environmental features both followed a distance-decay relationship with community and functional composition, but the local environment condition was the dominant driver in the Lancang River. Therefore, the impoundments of cascade dams had significant impacts on bacterioplankton communities and more attention should be paid to the potential ecological consequences of river regulation.

Bacterial community structure in atmospheric particulate matters of different sizes during the haze days in Xi'an, China

Serious air pollution events have frequently occurred in China associated with the acceleration of urbanization and industrialization in recent years. Exposure to atmospheric particulate matter (PM) of high concentration can lead to adverse effects on human health. Airborne bacteria are important constituents of microbial aerosols and contain lots of pathogens. However, variations in bacterial community structure in atmospheric PM of different sizes (PM_2.5, PM₁₀ and TSP) have not yet been explored. In this study, PM samples of different sizes were collected during the hazy days from Jul.2016 to Apr.2017 to determine bacterial diversity and community structure. Samples from soils and leaf surfaces were also collected to determine potential sources of bacterial aerosols. High-throughput sequencing technology was used generate bacterial community profiles, where we determined their diversity and abundances in the samples. Results showed that the dominant bacterial community structures in PM_2.5, PM₁₀ and TSP were strongly similar. Compared with non-haze days, the relative abundances of most bacterial pathogens on the haze days did not increase. Meanwhile, temperature, O₃ and NO₂ had more significant effects on bacterial community than the other environmental factors. Source tracking analysis indicated that the airborne bacteria might be not from local environment. It may come from the entire city or other regions by long distance airflow transport. Results of this study improved our understanding of the influence of bioaerosols on human health and the potential sources of airborne microbes.

Variations of Bacterial Community Composition and Functions in an Estuary Reservoir during Spring and Summer Alternation

In this study, we focused on the dynamics of bacterial community composition in a large reservoir in the Yangtze estuary during spring and summer seasons, especially the variations of functional mechanisms of microbial community during the seasonal alternation between spring and summer. Both 16S rRNA gene sequencing and shotgun metagenomic sequencing technology were used for these purposes. The results indicated that obvious variations of bacterial community structures were found at different sites. Particle-associated bacterial taxa exhibited higher abundance at the inlet site, which was closer to the Yangtze River with a high level of turbidity. In other sites, Synechococcus, as the most dominant cyanobacterial species, revealed high abundance driven by increased temperature. Moreover, some heterotrophic bacterial taxa revealed high abundance following the increased Synechococcus in summer, which indicated potential correlations about carbon source utilization between these microorganisms. In addition, the shotgun metagenomic data indicated during the period of seasonal alternation between spring and summer, the carbohydrate transport and metabolism, energy production and conversion, translation/ribosomal biogenesis, and cell wall/membrane/envelope biogenesis were significantly enhanced at the exit site. However, the course of cell cycle control/division was more active at the internal site.

Seasonal variation in the bacterial community composition of a large estuarine reservoir and response to cyanobacterial proliferation

This study employed high-throughput sequencing (HTS) to understand the variations in microbial community in the largest estuary reservoir located at the Yangtze River for a year. Correlations between the heterotrophic bacterial and cyanobacterial communities in the estuarine ecosystem were also investigated. Significant spatial and temporal changes were observed in the microbial community composition at all sites. These differences were mainly reflected on the variations of bacterial relative abundance. The modularity analysis on the network indicate that bacterial community response to the variations of environmental factors in the form of co-occurrence/exclusion patterns. In warm season, Synechococcus spp. being the dominant Cyanobacteria taxa exhibited high relative abundance in the reservoir. Water temperature was the critical driver for the proliferation of Synechococcus. Moreover, heterotrophic bacteria belonging to Actinobacteria, Proteobacteria (α-, β-, and γ-Proteobacteria), Bacteroidetes and Chlorobi, exhibited positive correlations with Synechococcus. The co-occurrence of these bacterial OTUs suggests that specific taxa may benefit from the proliferation of Synechococcus. In cold season, bacterial OTUs belonging to Actinobacteria and Bacteroidetes shown co-occurrence pattern with salt ions (including K⁺, Na⁺, Mg²⁺, Ca²⁺, Cl^- and SO₄^2-) inside the reservoir. In conclusion, further research is required to investigate the ecological functions of these taxa in estuarine ecosystems.

Evaluation of different 16S rRNA gene V regions for exploring bacterial diversity in a eutrophic freshwater lake

Massive partial sequencing of 16S rRNA genes has become the predominant tool used for studying microbial ecology. However, determining which hypervariable regions and primer sets should be used for screening microbial communities requires extensive investigation if controversial results are to be avoided. Here, the performances of different variable regions of the 16S rRNA gene on bacterial diversity studies were evaluated in silico with respect to the SILVA non-redundant reference database (SILVA SSU Ref 123NR), and subsequently verified using samples from Lake Taihu in China, a eutrophic lake. We found that the bacterial community composition results were strongly impacted by the different V regions. The results show that V1-V2 and V1-V3 regions were the most reliable regions in the full-length 16S rRNA sequences, while most V3 to V6 regions (including V3, V4, V3-V4, V5, V4-V5, V6, V3-V6, V4-V6, and V5-V6) were more closely aligned with the SILVA SSU Ref 123NR database. Overall, V4 was the most prominent V region for achieving good domain specificity, higher coverage and a broader spectrum in the Bacteria domain, as confirmed by the validation experiments. S-D-Bact-0564-a-S-15/S-D-Bact-0785-b-A-18 is, therefore, a promising primer set for surveying bacterial diversity in eutrophic lakes.

Bacterial community structure in response to environmental impacts in the intertidal sediments along the Yangtze Estuary, China

This study was designed to investigate the characteristics of bacterial communities in intertidal sediments along the Yangtze Estuary and their responses to environmental factors. The results showed that bacterial abundance was significantly correlated with salinity, SO₄^2- and total organic carbon, while bacterial diversity was significantly correlated with SO₄^2- and total nitrogen. At different taxonomic levels, both the dominant taxa and their abundances varied among the eight samples, with Proteobacteria being the most dominant phylum in general. Cluster analysis revealed that the bacterial community structure was influenced by river runoff and sewerage discharge. Moreover, SO₄^2-, salinity and total phosphorus were the vital environmental factors that influenced the bacterial community structure. Quantitative PCR and sequencing of sulphate-reducing bacteria indicated that the sulphate reduction process occurs frequently in intertidal sediments. These findings are important to understand the microbial ecology and biogeochemical cycles in estuarine environments.

Environmental Factors Shape Water Microbial Community Structure and Function in Shrimp Cultural Enclosure Ecosystems

The effects of environmental factors on water microbial communities have been extensively studied, but little is known about the effects in shrimp cultural enclosure ecosystems. We analyzed 16S rRNA gene amplicons to determine the principal environmental factors that shape the structure and function of microbial communities in shrimp cultural enclosure ecosystems from Guangdong and Hainan provinces, in China. High quality sequences were clustered into operational taxonomic units (OTUs) at the 97% similarity level, generating 659-1,835 OTUs per sample. The 10 most abundant phyla were Proteobacteria, Bacteroidetes, Cyanobacteria, Planctomycetes, Actinobacteria, Verrucomicrobia, Firmicutes, Chlorobi, Chloroflexi, and Chlamydiae. The results of canonical correspondence analyses (CCA) indicated that salinity, total phosphate (TP), total nitrogen (TN), temperature, and pH were the most important factors shaping microbial community structure. Differences in microbial community structure between high and low salinity samples were explained by changes in the relative abundances of some OTUs (e.g., OTU5, OTU19, OTU21, OTU39, and OTU71). Moreover, the contribution of spatial distribution to the microbial community assembly was investigated via aggregated boosted tree (ABT) analyses, and the results indicated spatial isolation was not a major factor affecting the phylogenetic diversity and phylotypes of water microbial communities. Furthermore, we predicted water microbial community functional profiling using the PICRUSt program and principal component analyses (PCA) suggested that salinity was a major contributor to the structure and function of the microbial communities. Collectively, these results showed that environmental factors influenced the structure and function of water microbial communities, while salinity was the principal environmental factor instead of temperature, TP, TN, and pH in shrimp cultural enclosure ecosystems.

Bacterial community structure in the intertidal biofilm along the Yangtze Estuary, China

In this study, the 16S rRNA-based Illumina MiSeq sequencing was used to investigate the bacterial community structure and composition of intertidal biofilm taken along the Yangtze Estuary. The results showed that 680,721 valid sequences of seven samples were assigned to 147,239 operational taxonomic units, which belonged to 49 phyla, 246 family and 314 genera. Compared to other studies on water and sediments in the study area, biofilms showed highest index of bacterial diversity and abundances. At different taxonomic levels, both dominant taxa and their abundances varied among the seven samples, with Proteobacteria as the dominant phylum in general. Principal component analysis and cluster analysis revealed that bacterial communities at WSK differed from those at other sampling sites. Salinity, dissolved oxygen, pH and nutrients were the vital environmental factors to influence the bacterial community structure of biofilms. These results may provide a new insight into the microbial ecology in estuarine environments.