The divergence between fungal and bacterial communities in seasonal and spatial variations of wastewater treatment plants

Ecological and functional differences of abundant and rare sub-communities in wastewater treatment plants across China

The microbial community in activated sludge is composed of a small number of abundant sub-community with high abundance and a large number of rare sub-community with limited abundance. Our knowledge regarding the ecological properties of both abundant and rare sub-communities in activated sludge is limited. This article presented an analysis of functional prediction, assembly mechanisms, and biogeographic distribution characteristics of abundant and rare sub-communities in 211 activated sludge samples from 60 wastewater treatment plants across China. Moreover, this study investigated the dominant factors influencing the community structure of these two microbial groups. The results showed that the functions associated with carbon and nitrogen cycling were primarily detected in abundant sub-community, while rare sub-community were primarily involved in sulfur cycling. Both microbial groups were mainly influenced by dispersal limitation, which, to some extent, resulted in a distance-decay relationship in their biogeographic distribution. Moreover, a higher spatial turnover rate of rare sub-communities (0.0887) suggested that spatial differences in microbial community structure among different WWTPs may mainly result from rare sub-community. Moreover, SEM showed that geographic locations affected rare sub-communities greatly, which agreed with their higher dispersal limitation and turnover rate. In contrast, influent characteristics showed stronger correlations with abundant sub-communities, suggesting that abundant sub-community may contribute more to the removal of pollutants. This study enhanced our understanding of abundant and rare microorganisms in activated sludge especially the role of rare species and provided scientific evidence for precise regulation and control of wastewater treatment plants.

Machine learning modeling for the prediction of phosphorus and nitrogen removal efficiency and screening of crucial microorganisms in wastewater treatment plants

The effectiveness of wastewater treatment plants (WWTPs) is largely determined by the microbial community structure in their activated sludge (AS). Interactions among microbial communities in AS systems and their indirect effects on water quality changes are crucial for WWTP performance. However, there is currently no quantitative method to evaluate the contribution of microorganisms to the operating efficiency of WWTPs. Traditional assessments of WWTP performance are limited by experimental conditions, methods, and other factors, resulting in increased costs and experimental pollutants. Therefore, an effective method is needed to predict WWTP efficiency based on AS community structure and quantitatively evaluate the contribution of microorganisms in the AS system. This study evaluated and compared microbial communities and water quality changes from WWTPs worldwide by meta-analysis of published high-throughput sequencing data. Six machine learning (ML) models were utilized to predict the efficiency of phosphorus and nitrogen removal in WWTPs; among them, XGBoost showed the highest prediction accuracy. Cross-entropy was used to screen the crucial microorganisms related to phosphorus and nitrogen removal efficiency, and the modeling confirmed the reasonableness of the results. Thirteen genera with nitrogen and phosphorus cycling pathways obtained from the screening were considered highly appropriate for the simultaneous removal of phosphorus and nitrogen. The results showed that the microbes Haliangium, Vicinamibacteraceae, Tolumonas, and SWB02 are potentially crucial for phosphorus and nitrogen removal, as they may be involved in the process of phosphorus and nitrogen removal in sewage treatment plants. Overall, these findings have deepened our understanding of the relationship between microbial community structure and performance of WWTPs, indicating that microbial data should play a critical role in the future design of sewage treatment plants. The ML model of this study can efficiently screen crucial microbes associated with WWTP system performance, and it is promising for the discovery of potential microbial metabolic pathways.

Application of rhizobacteria to improve microbial community structure and maize (Zea mays L.) growth in saline soil

The utilization of plant growth-promoting rhizobacteria (PGPR) has emerged as a prominent focus in contemporary research on soil microbiology, microecology, and plant stress tolerance. However, how PGPR influence the soil bacterial community and related ecological functions remains unclear. The aim of this study was to investigate the effects of three natural PGPR inoculations (YL07, Planococcus soli WZYH02; YL10, Bacillus atrophaeus WZYH01; YL0710, Planococcus soli WZYH02 and Bacillus atrophaeus WZYH01) on maize (Zea mays L.) growth under two salt stress conditions (S1, ECe = 2.1 ~ 2.5 dS/m; S2, ECe = 5.5 ~ 5.9 dS/m). The results revealed that compared to the control (CK), the average plant height of maize seedlings significantly increased by 27%, 23%, and 29% with YL07, YL10, and YL0710 inoculation under S1 conditions, respectively, and increased by 30%, 20%, and 18% under S2 conditions, respectively. Moreover, PGPR inoculation positively influenced the content of superoxide dismutase, catalase, soluble sugar, and proline in maize under salt stress. Subsequent analysis of alpha diversity indices, relative microbial abundance, principal coordinate analysis, cladograms, and linear discriminant analysis effect size histograms indicated significant alterations in the rhizosphere microbial community due to PGPR inoculation. FAPROTAX analysis demonstrated that YL10 inoculation in S2 rhizosphere soil had a notable impact on carbon cycle functions, specifically chemoheterotrophy, fermentation, and phototrophy. Thus, this study provides evidence that PGPR inoculation improves soil microbial communities and plant indices under salt stress. These findings shed light on the potential of PGPR as a viable approach for enhancing plant stress tolerance and fostering sustainable agricultural practices.

Formation characteristics of bacteria and fungi in sewers: In terms of signal molecule generation

Bio-metabolism of diverse communities is the main reason of water quality variation in sewers, and the signal molecule generation of communities is dementated to be the key regulation procedure for community metabolism. To reveal the mechanism of pollutant biotransformation in complex sewer environment, this study explored the formation of bacteria and fungi and the signal molecule transduction characteristics in a pilot sewer. In this study, several kinds of signal molecules that produced by bacteria and fungi (C4-HSL, C6-HSL, C8-HSL, farnesol and tyrosol) were detected along the formation process of sewer biofilms. The results showed that, in the early stage, bacterial AHLs signaling molecules are beneficial to the synthesis of EPS, providing a good material basis for the growth of bacterial flora. In addition, tyrosol stimulates the formation of embryonic tubes in yeast cells, further promoting the growth of hyphae. At the later stage, AHLs signaling molecules and tyrosol jointly promoted the growth of biofilms. In conclusion, it is precisely because of the coexistence of bacteria and fungi in the sewer system that the generated signal molecules can jointly promote the synthesis and growth of biofilms through different pathways, and have positive feedback on the biodegradation of various pollutants. Based on the exploration, the ecological patterns of bacterial-fungal communities in urban sewer system were proposed and it could improve the understanding on the pollutant transformation behaviors in sewers.

Sustainable formulation polymers for home, beauty and personal care: challenges and opportunities

As society moves towards a net-zero future, the need to adopt more sustainable polymers is well understood, and as well as plastics, less visible formulation polymers should also be included within this shift. As researchers, industries and consumers move towards more sustainable products there is a clear need to define what sustainability means in fast moving consumer goods and how it can be considered at the design stage. In this perspective key challenges in achieving sustainable formulation polymers are highlighted, and opportunities to overcome them are presented.

Spatio-temporal variation of bacterial community structure in two intertidal sediment types of Jiaozhou Bay

The intertidal sediment environment is dynamic and the biofilm bacterial community within it must constantly adapt, but an understanding of the differences in the biofilm bacterial community within sediments of different types is still relatively limited. The semi-enclosed Jiaozhou Bay has a temperate monsoon climate, with strong currents at the mouth of the bay. In this study, the structure of the bacterial community in Jiaozhou Bay sediment biofilms are described using high-throughput 16 S rRNA gene sequencing and the effects of temporal change and different sediment environment types are discussed. Alpha diversity was significantly higher in sandy samples than in muddy samples. Sandy sediments with increased heterogeneity promote bacterial aggregation. Beta diversity analysis showed significant differences between sediment types and between stations. Proteobacteria and Acidobacteria were significantly more abundant at ZQ, while Campilobacterota was significantly more abundant at LC. The relative abundances of Bacteroidetes, Campilobacterota, Firmicutes, and Chloroflexi were significantly higher in the muddy samples, while Actinobacteria and Proteobacteria were higher in the sandy samples. There were different phylum-level biomarkers between sediment types at different stations. There were also different patterns of functional enrichment in biogeochemical cycles between sediment types and stations with the former having more gene families that differed significantly, highlighting their greater role in determining bacterial function. Bacterial amplicon sequence variant variation between months was less than KEGG ortholog variation between months, presumably the temporal change had an impact on shaping the intertidal sediment bacterial community, although this was less clear at the gene family level. Random forest prediction yielded a combination of 43 family-level features that responded well to temporal change, reflecting the influence of temporal change on sediment biofilm bacteria.

Predicting microbial community compositions in wastewater treatment plants using artificial neural networks

BACKGROUND

Activated sludge (AS) of wastewater treatment plants (WWTPs) is one of the world's largest artificial microbial ecosystems and the microbial community of the AS system is closely related to WWTPs' performance. However, how to predict its community structure is still unclear.

RESULTS

Here, we used artificial neural networks (ANN) to predict the microbial compositions of AS systems collected from WWTPs located worldwide. The predictive accuracy R²_1:1 of the Shannon-Wiener index reached 60.42%, and the average R²_1:1 of amplicon sequence variants (ASVs) appearing in at least 10% of samples and core taxa were 35.09% and 42.99%, respectively. We also found that the predictability of ASVs was significantly positively correlated with their relative abundance and occurrence frequency, but significantly negatively correlated with potential migration rate. The typical functional groups such as nitrifiers, denitrifiers, polyphosphate-accumulating organisms (PAOs), glycogen-accumulating organisms (GAOs), and filamentous organisms in AS systems could also be well recovered using ANN models, with R²_1:1 ranging from 32.62% to 56.81%. Furthermore, we found that whether industry wastewater source contained in inflow (IndConInf) had good predictive abilities, although its correlation with ASVs in the Mantel test analysis was weak, which suggested important factors that cannot be identified using traditional methods may be highlighted by the ANN model.

CONCLUSIONS

We demonstrated that the microbial compositions and major functional groups of AS systems are predictable using our approach, and IndConInf has a significant impact on the prediction. Our results provide a better understanding of the factors affecting AS communities through the prediction of the microbial community of AS systems, which could lead to insights for improved operating parameters and control of community structure. Video Abstract.

The Roles of Microbes in Stream Restorations

The goods and services provided by riverine systems are critical to humanity, and our reliance increases with our growing population and demands. As our activities expand, these systems continue to degrade throughout the world even as we try to restore them, and many efforts have not met expectations. One way to increase restoration effectiveness could be to explicitly design restorations to promote microbial communities, which are responsible for much of the organic matter breakdown, nutrient removal or transformation, pollutant removal, and biomass production in river ecosystems. In this paper, we discuss several design concepts that purposefully create conditions for these various microbial goods and services, and allow microbes to act as ecological restoration engineers. Focusing on microbial diversity and function could improve restoration effectiveness and overall ecosystem resilience to the stressors that caused the need for the restoration. Advances in next-generation sequencing now allow the use of microbial 'omics techniques (e.g., metagenomics, metatranscriptomics) to assess stream ecological conditions in similar fashion to fish and benthic macroinvertebrates. Using representative microbial communities from stream sediments, biofilms, and the water column may greatly advance assessment capabilities. Microbes can assess restorations and ecosystem function where animals may not currently be present, and thus may serve as diagnostics for the suitability of animal reintroductions. Emerging applications such as ecological metatranscriptomics may further advance our understanding of the roles of specific restoration designs towards ecological services as well as assess restoration effectiveness.

Pollutants removal, microbial community shift and oleic acid production in symbiotic microalgae-bacteria system

The functional interaction between microorganisms is key in symbiotic microalga-bacteria systems; however, evaluations of fungi and pathogenic microorganisms are not clear. In this study, the roles of three groups (i.e., microalgae-activated sludge (MAS), Microalgae, and activated sludge) in pollutant removal and biomass recovery were comparatively studied. The data implied that microalgal assimilation and bacterial heterotrophic degradation were the major approaches for degradation of nutrients and organic matter, respectively. According to 16S rRNA and internal transcribed spacer sequencing, the relative abundance of Rhodotorula increased remarkably, favoring nutrient exchange between the microalgae and bacteria. The abundances of two types of pathogenic genes (human pathogens and animal parasites) were reduced in the MAS system. The oleic acid content in the MAS system (51.2 mg/g) was 1.7 times higher than that in the Microalgae system. The results can provide a basis for practical application and resource utilization of symbiotic microalgae-bacteria systems.

Factors influencing carrion communities are only partially consistent with those of deadwood necromass

Research on decomposer communities has traditionally focused on plant litter or deadwood. Even though carrion forms highly nutrient-rich necromass that enhance ecosystem heterogeneity, the factors influencing saprophytic communities remain largely unknown. For deadwood, experiments have shown that different drivers determine beetles (i.e., decay stage, microclimate, and space), fungi (i.e., decay stage and tree species) and bacteria (decay stage only) assemblages. To test the hypothesis that similar factors also structure carrion communities, we sampled 29 carcasses exposed for 30 days that included Cervus elaphus (N = 6), Capreolus capreolus (N = 18), and Vulpes vulpes (N = 5) in a mountain forest throughout decomposition. Beetles were collected with pitfall traps, while microbial communities were characterized using amplicon sequencing. Assemblages were determined with a focus from rare to dominant species using Hill numbers. With increasing focus on dominant species, the relative importance of carcass identity on beetles and space on bacteria increased, while only succession and microclimate remained relevant for fungi. For beetle and bacteria with focus on dominant species, host identity was more important than microclimate, which is in marked contrast to deadwood. We conclude that factors influencing carrion saprophytic assemblages show some consistency, but also differences from those of deadwood assemblages, suggesting that short-lived carrion and long-lasting deadwood both provide a resource pulse with different adaptions in insects and microbes. As with deadwood, a high diversity of carcass species under multiple decay stages and different microclimates support a diverse decomposer community.

Combined metagenomic and metabolomic analyses reveal that Bt rice planting alters soil C-N metabolism

The environmental impacts of genetically modified (GM) plants remain a controversial global issue. To address these issues, comprehensive environmental risk assessments of GM plants is critical for the sustainable development and application of transgenic technology. In this paper, significant differences were not observed between microbial metagenomic and metabolomic profiles in surface waters of the Bt rice (T1C-1, the transgenic line) and non-Bt cultivars (Minghui 63 (the isogenic line) and Zhonghua 11 (the conventional japonica cultivar)). In contrast, differences in these profiles were apparent in the rhizospheres. T1C-1 planting increased soil microbiome diversity and network stability, but did not significantly alter the abundances of potential probiotic or phytopathogenic microorganisms compared with Minghui 63 and Zhonghua 11, which revealed no adverse effects of T1C-1 on soil microbial communities. T1C-1 planting could significantly alter soil C and N, probably via the regulation of the abundances of enzymes related to soil C and N cycling. In addition, integrated multi-omic analysis of root exudate metabolomes and soil microbiomes showed that the abundances of various metabolites released as root exudates were significantly correlated with subsets of microbial populations including the Acidobacteria, Actinobacteria, Chloroflexi, and Gemmatimonadetes that were differentially abundant in T1C-1 and Mnghui 63 soils. Finally, the potential for T1C-1-associated root metabolites to exert growth effects on T1C-1-associated species was experimentally validated by analysis of bacterial cultures, revealing that Bt rice planting could selectively modulate specific root microbiota. Overall, this study indicate that Bt rice can directly modulate rhizosphere microbiome assemblages by altering the metabolic compositions of root exudates that then alters soil metabolite profiles and physiochemical properties. This study unveils the mechanistic associations of Bt plant-microorganism-environment, which provides comprehensive insights into the potential ecological impacts of GM plants.

Structure of fungal communities in sequencing batch reactors operated at different salinities for the selection of triacylglyceride-producers from a fish-canning lipid-rich waste stream

Oleaginous fungi natively accumulate large amounts of triacylglycerides (TAG), widely used as precursors for sustainable biodiesel production. However, little attention has been paid to the diversity and roles of fungal mixed microbial cultures (MMCs) in sequencing batch reactors (SBR). In this study, a lipid-rich stream produced in the fish-canning industry was used as a substrate in two laboratory-scale SBRs operated under the feast/famine (F/F) regime to enrich microorganisms with high TAG-storage ability, under two different concentrations of NaCl (SBR-N: 0.5g/L; SBR-S: 10g/L). The size of the fungal community in the enriched activated sludge (EAS) was analyzed using 18S rRNA-based qPCR, and the fungal community structure was determined by Illumina sequencing. The different selective pressures (feeding strategy and control of pH) implemented in the enrichment SBRs throughout operation increased the abundance of total fungi. In general, there was an enrichment of genera previously identified as TAG-accumulating fungi (Apiotrichum, Candida, Cutaneotrichosporon, Geotrichum, Haglerozyma, Metarhizium, Mortierella, Saccharomycopsis, and Yarrowia) in both SBRs. However, the observed increase of their relative abundances throughout operation was not significantly linked to a higher TAG accumulation.

Encapsulation of bacteria in different stratified extracellular polymeric substances and its implications for performance enhancement and resource recovery

Simultaneous recovery of biopolymers and enhanced bio-reactor performance are promising options for sustainable wastewater treatment, and the bioactivity of sludge after biopolymer extraction is thus critical for the performance of the system. To this end, stratified extracellular polymeric substances (EPS), including slime, loosely bound EPS (LB-EPS), and tightly bound EPS (TB-EPS), were extracted, and the bioactivities of the consequent extraction residues were assessed using aerobic respirogram, kinetic, and flow cytometry (FCM). After the initial weak extraction of slime, the particle size distribution of the sludge significantly decreased, and subsequent extractions of LB-EPS and TB-EPS produced an equivalent size distribution. In contrast, the fractal dimension decreased after each extraction, suggesting that LB-EPS and TB-EPS affected the compactness of flocs rather than the size. The aerobic bacteria distribution estimated using respirogram shows that slime mainly encapsulated heterotrophs while LB-EPS mainly encapsulated nitrifiers. In addition, the ammonia-nitrogen affinity coefficient decreased from 1.79 to 0.28 mg/L when slime was removed, thereby encouraging the activities of autotrophic nitrifiers. Further removal of LB-EPS induced high energy dispersion as the maintenance coefficient m and the metabolic dispersion index μ/m increased from 0.11 to 0.22 and 0.44 to 0.63, respectively. Meanwhile, the yield rate decreased from 0.77 to 0.66. Although pellets that resulted from TB-EPS extraction were not aerobically active as described by respirogram and growth curves, they were still metabolically active as measured by live/dead cell counting and redox sensor green signal. These pellets used more energy for maintenance as indicated by the high maintenance coefficient than those residual after either slime or LB-EPS extraction. In addition, the variation in bacteria community distribution across flocs was related to the variation in temperatures, suggesting that the inner part of a floc might be hotter than the outer side. Therefore, compared to bacteria in the raw sludge, the viable bacteria bounded in LB-EPS and TB-EPS convert more energy to heat rather than growth. These results indicate that energy was dispersed as metabolic heat for the LB-EPS extracted sludge, and removal of LB-EPS favored thermogenesis and sludge reduction. Based on the above findings, a simultaneously EPS-recovery and performance enhancement configuration is thus proposed, which holds great promise for the integration of next-generation wastewater treatment plants.

Fungal Diversity in Two Wastewater Treatment Plants in North Italy

In urban wastewater treatment plants, bacteria lead the biological component of the depuration process, but the microbial community is also rich in fungi (mainly molds, yeasts and pseudo-yeasts), whose taxonomical diversity and relative frequency depend on several factors, e.g., quality of wastewater input, climate, seasonality, and depuration stage. By joining morphological and molecular identification, we investigated the fungal diversity in two different plants for the urban wastewater treatment in the suburbs of the two major cities in Lombardia, the core of industrial and commercial activities in Italy. This study presents a comparison of the fungal diversity across the depuration stages by applying the concepts of α-, β- and ζ-diversity. Eurotiales (mainly with Aspergillus and Penicillium), Trichosporonales (Trichosporon sensu lato), Saccharomycetales (mainly with Geotrichum) and Hypocreales (mainly with Fusarium and Trichoderma) are the most represented fungal orders and genera in all the stages and both the plants. The two plants show different trends in α-, β- and ζ-diversity, despite the fact that they all share a crash during the secondary sedimentation and turnover across the depuration stages. This study provides an insight on which taxa potentially contribute to each depuration stage and/or keep viable propagules in sludges after the collection from the external environment.

Characterization of carbapenem resistance in environmental samples and Acinetobacter spp. isolates from wastewater and river water in Poland

The aim of this study was to analyze the prevalence of carbapenem resistance genes in Acinetobacter spp. isolated from wastewater in a municipal WWTP and to determine their spread from treated wastewater to river water with the use of conventional and molecular microbiology methods (qualitative and quantitative PCR and metagenomic analysis). Samples of untreated and treated wastewater and samples of river water obtained upstream and downstream from the wastewater discharge point were collected in 3 seasons (February, June, and September) of 2019. Acinetobacter spp. isolates were obtained by the culture method on the CHROMagar™ Acinetobacter medium. Additionally, environmental DNA was extracted from the samples for metagenomic and qPCR analyses. The presence of beta-lactam resistance genes (Ambler class B and D), insertion sequence ISAba1, and class I, II, and III integron-integrase genes was determined, and the bacterial taxonomic structure and wastewater and river samples was analyzed. Out of the 301 isolates obtained on the CHROMagar™ Acinetobacter medium, 258 belonged to the genus Acinetobacter, including 21 isolates that were identified as Acinetobacter baumannii. The highest number of Acinetobacter spp. and A. baumannii isolates were obtained from wastewater and river water samples collected in June and September. The ISAba1/bla_OXA-51 complex was identified in 13 isolates, which confirms the occurrence of carbapenem-resistance isolates in the analyzed samples. The number of Acinetobacter isolates carrying antibiotic resistance genes (ARGs) increased in river water samples collected downstream from the wastewater discharge point (48 out of 258 isolates - 18.6%) compared to river water samples collected upstream from the wastewater discharge point (34 out of 258 isolates - 13.2%), which suggests that WWTP is a source of pollution in the natural environment. The conducted research provides evidence that bacteria of the genus Acinetobacter may spread alarming beta-lactam resistance in the environment and, therefore, pose a serious epidemiological threat.

The Coupling Response between Different Bacterial Metabolic Functions in Water and Sediment Improve the Ability to Mitigate Climate Change

Extreme climatic events, such as heat wave and large temperature fluctuations, are predicted to increase in frequency and intensity during the next hundred years, which may rapidly alter the composition and function of lake bacterial communities. Here, we conducted a year-long experiment to explore the effect of warming on bacterial metabolic function of lake water and sediment. Predictions of the metabolic capabilities of these communities were performed with FAPROTAX using 16S rRNA sequencing data. The results indicated that the increase in temperature changed the structure of bacterial metabolic functional groups in water and sediment. During periods of low temperature, the carbon degradation pathway decreased, and the synthesis pathway increased, under the stimulation of warming, especially under the conditions temperature fluctuation. We also observed that nitrogen fixation ability was especially important in the warming treatments during the summer season. However, an elevated temperature significantly led to reduced nitrogen fixation abilities in winter. Compared with the water column, the most predominant functional groups of nitrogen cycle in sediment were nitrite oxidation and nitrification. Variable warming significantly promoted nitrite oxidation and nitrification function in winter, and constant warming was significantly inhibited in spring, with control in sediments. Co-occurrence network results showed that warming, especially variable warming, made microbial co-occurrence networks larger, more connected and less modular, and eventually functional groups in the water column and sediment cooperated to resist warming. We concluded that warming changed bacterial functional potentials important to the biogeochemical cycling in the experimental mesocosms in winter and spring with low temperature. The effect of different bacteria metabolism functions in water column and sediment may change the carbon and nitrogen fluxes in aquatic ecosystems. In conclusion, the coupling response between different bacterial metabolic functions in water and sediment may improve the ability to mitigate climate change.

Effects of influent immigration and environmental factors on bacterial assembly of activated sludge microbial communities

The functional mechanism of microbial assembly of activated sludge (AS) in urban wastewater treatment plants (UWTPs) remains unclear. A comprehensive quantitative evaluation of the contribution of influent immigration and environmental factors to AS community composition requires investigation. In this study, the microbial characteristics of six full-scale UWTPs with different influent compositions and environmental factors (altitude, temperature, dissolved oxygen (DO), pH, chemical oxygen demand (COD), total nitrogen (TN), ammonia nitrogen (NH₄⁺-N), and total phosphorus (TP)) were analyzed to determine the main forces affecting the bacterial assembly of AS microbial communities. Abundant and core taxa were screened out based on the abundance and frequency of operational taxonomic units (OTUs) occurrence in all samples. Abundant OTUs (18.7% occurrence) accounted for 87.7% of the total 16S rRNA sequences, while rare OTUs (71.7% occurrence) accounted for only 7.8% of the total 16S rRNA sequences. A total of 135 OTUs were identified as core taxa, accounting for 14.6-26.2% of the total reads, of which 83 OTUs belonged to abundant taxa. The richness and uniformity of the influent community were significantly lower than those of the AS system. The community composition in influent varied from that in AS. Moreover, about 89.7% (86.5% of 16S rRNA sequences) OTUs in AS samples showed positive growth rates, indicating that immigration of influent communities had a limited effect on the microbial composition of AS. Redundancy analysis (RDA) combined with co-occurrence network showed that the bacterial assembly of microbial communities was significantly correlated with altitude, pH, and TN (P < 0.05), and these three parameters could explain 23.3%, 21.1%, and 17.7% of the bacterial assembly of AS microbial communities in UWTPs, respectively.

Succession of diversity, functions, and interactions of the fungal community in activated sludge under aromatic hydrocarbon stress

Although fungi are regarded as the important degraders of aromatic hydrocarbons (AHs) in various environments, the dynamic succession and interaction of their community under aromatic hydrocarbon stress has been rarely reported. In this study, we systematically investigated the responses of the fungal community and the associations among fungal species when facing the continuous stress of two typical AHs, benzene and naphthalene. Using high-throughput sequencing technology, we demonstrated that fungal diversity displayed a significant downward trend during six weeks of continuous aromatic hydrocarbon treatment. Community succession was observed during the operational period, and the relative abundance of some typical degraders, such as Exophiala sp. and Candida sp., increased during the later period of operation. Meanwhile, by predicting the functions of the fungal community through PICRUSt2, we found that some relevant enzymes, such as peroxidase, dioxygenase, and monooxygenase, may play an important role in the degradation process and maintaining overall community multifunctionality. Furthermore, the measurement of modified normalized stochasticity ratio (MST) indicated that continuous aromatic hydrocarbon stress resulted in a stronger deterministic process in community assembly over time, suggesting environmental selection dominated succession of the fungal community in activated sludge. Finally, molecular ecological network analysis (MENA) demonstrated that, the cooperative behaviors among members, the network keystone genera related to biodegradation, such as Exophiala sp. and Haglerozyma sp., and a well-organized topological structure, together, maintained the structural stability of the fungal community under AH stress. Our study provides new insights for understanding the stability of fungal communities during the degradation of contaminants in activated sludge.

C12-HSL is an across-boundary signal molecule that could alleviate fungi Galactomyces's filamentation: A new mechanism on activated sludge bulking

Fungal bulking is caused by fungi excessive growth and morphological changes, resulting from the evolution toward fungi dominant activated sludge. Communication across fungi and bacteria boundary that mediated by bacterial signal molecules (SMs) probably is the central induce caused fungal bulking occurrence. In this work, it intended to identify the bacterial SM that affected fungal bulking, and verified its roles in regulate the spore germination and hyphal growth. We found C12-HSL concentration decreased significantly from 12.36 to 3.38 ng/g-VSS (P < 0.05) when fungal sludge bulking happened, and filamentous Galactomyces's relatively abundant was correlatively enriched. To test the effects of this SM, trace commercial C12-HSL was added to pure cultured Galactomyces, in which spore germination rates decreased by 20 % and hyphal extension inhibited by 15 %. Ras1-cAMP-PKA and mitogen-activated protein kinase (MAPK) pathways of Galactomyces were responsible for signal C12-HSL transduction, which inhibited peroxisome biosynthesis, suppressed the biological activity of the actin cytoskeleton, and disrupted intercellular organelle transport. All these results showed C12-HSL was the functional SM that could suppress the development of fungal filamentous. This study provided a new insight into the sludge bulking mechanism from view of cross-kingdom communication.

Homogeneous Selection and Dispersal Limitation Dominate the Effect of Soil Strata Under Warming Condition

Global warming is likely to affect the underground microbial communities in various ecosystems, but the response of soil microbial communities along a vertical depth profile to global warming has been elusive. Herein, we leveraged a warming field experiment in Qinghai-Tibet Plateau grassland and investigated the community structure of prokaryotes and fungi from the upper (0-15 cm) and lower (15-30 cm) strata under ambient and elevated temperature treatments. Three-years continual warming only significantly shifted the prokaryotic community within the upper strata and there was no significant effect observed for the fungal community. Additionally, under ambient temperature, there were significant differences between the two strata in both the prokaryotic and fungal communities, but under warming, this effect was alleviated. Next, the prokaryotic and fungal community assembly processes were measured by a phylogenetic-bin-based null approach (iCAMP). Though deterministic and stochastic processes dominated the assembly of prokaryotic and fungal communities, respectively, the deterministic processes were strengthened under warming for both communities. Specifically, the increased portion of homogeneous selection, contributing to a homogenous state, led to a smaller difference between prokaryotic communities of the two soil strata under warming. The smaller difference in the stochastic process component, i.e., dispersal limitation, contributed to the similar fungal community structures between the two strata under warming. This study deepens our understanding of warming effects on grassland microbial communities and gives greater insights on the underlying mechanisms for microbial assembly between upper and lower soil strata under warming scenarios.

Characterization and phylogeny of fungi isolated from industrial wastewater using multiple genes

The aim of this study was the isolation and molecular characterization of fungi from untreated refinery effluent by using multiple conserved genes. The Fungi isolated were characterized based on PCR amplification and genomic sequencing of the internal transcribed spacer region (ITS), partial β-tubulin (BenA), calmodulin (CaM), and RNA polymerase second large subunit (RPB2) genes, along with morphological characterization. The obtained sequences were subjected to BLAST analysis and the corresponding fungal isolates were assigned species names after comparison with representative sequences available in GenBank. Fifteen (15) Fungi species belonging to four genera of Aspergillus, Penicillium, Fusarium, and Trichoderma with Aspergillus as the predominant genus were identified. Therefore these genes should be used as molecular markers for species level identification of fungi (especially Aspergillus and Penicillium as proven in this study.

A comprehensive assessment of fungi in urban sewer biofilms: Community structure, environmental factors, and symbiosis patterns

Sewers are important parts of wastewater treatment facilities and the fungal microbial communities therein make large contributions to the biotransformation of wastewater. Therefore, this experiment constructed an experimental sewer system and characterized the fungal microbial communities using ITS high-throughput sequencing technology in combination with network structure analysis and statistical correlation analysis methods. The results demonstrated that the overall diversity of the fungal communities gradually increased as growth phases progressed, but the dominant groups differed significantly among phases. In the early growth phase (RS1) the dominant genera were Apiotrichum and Inocybe, with abundances of 34% and 14%, respectively, while the middle and late growth phases (RS2 and RS3) were dominated by Candida, with a relative abundance of 47%-66%. CCA and correlation analysis showed that the fungal communities diversity from the artificial sewers had significant positive correlations with COD (r² = 0.44, p < 0.05) and NH₄⁺ (r² = 0.64, p < 0.05) and that environmental factors significantly influenced the abundances of Fusarium and Aspergillus. Network analysis revealed differences in the fungal groups representing key nodes during different periods. Candida, Trichosporon, Fusarium, and Aspergillus played important roles in the microbial ecosystem of the simulated sewer systems. This study provides data-supported insight into the bacterial-fungal interaction mechanisms and associated pollutant biodegradation technologies in sewers.

Arthrobacter is a universal responder to di-n-butyl phthalate (DBP) contamination in soils from various geographical locations

Plasticizer phthalic acid esters (PAEs) are commonly found as contaminants in various soils. Previous studies indicated that their natural degradation can substantially differ among soil types; however, potential implications of the soil microbiome remained largely unexplored. Here, we have collected ten soil types from nine different geographical regions of China to investigate the degradation of DBP therein and role of bacteria in this process. Results showed that the degradation rate of DBP was lowest in nutrient-poor red soils from Jiangxi Province, while it was highest in fluvo-aquatic soil from Hebei Province. Bacterial community responses to DBP substantially differed in each of the analyzed soils. Arthrobacter is known for its broad-spectrum activity in terms of DBP degradation in soil and was therefore implemented as bioremediating inoculant in many polluted environments. In the present study, network analyses indicated that synergism between soil bacteria increased following exposure to DBP. Arthrobacter and Sphingomonas were found to expand their positive interactions with other members of the microbiome in DBP-contaminated soils. The overall findings of our study provide a basis for biomarker development for detection of DBP contaminations and an extended basis for future bioremediation approaches based on beneficial bacteria.

Structural and functional changes in the fungal community of plant detritus in an invaded Atlantic Forest

BACKGROUND

Changes in the fungal community in the litter decomposition by invasive plants can negatively impact nutrient cycling in natural ecosystems. One still does not know the dimension of this hypothesis, but apparently, it is not despicable. This study evaluated the assemblage composition of fungi during litter decomposition in areas of Atlantic Forest invaded or not invaded by Tradescantia zebrina using Illumina MiSeq and metabarcoding analysis.

RESULTS

The invaded sample showed significantly higher richness and a difference in the species dominance than the invaded litter. Ascomycota was the first most abundant phylum in both areas. Even so, the dissimilarity between areas can be evidenced. The fungal from Basidiomycota were very representative in the non-invaded areas (ranged from an abundance of 43.29% in the non-invaded to 2.35% in the invaded sample). The genus Lepiota can indicate the primary functional group related to biomass degradation and showed the might difference about the invaded areas due to its essential reduction by the invader. In the invaded sample, there was a total absence of the endophyte-undefined saprotroph guild. Also, some genera not taxonomically characterized were eliminated in the invaded sample, revealing that the fungal biodiversity of areas has not yet been thoroughly characterized.

CONCLUSIONS

Hence, makes impossible the real interpretation of the invasive plant impact, showing the importance of continuing research on fungal biodiversity. It is important to emphasize that the replacement of the native species by T. zebrina may be responsible for the elimination of fungal groups that have not yet been identified.

Structural and functional changes in the fungal community of plant detritus in an invaded Atlantic Forest

BACKGROUND

Changes in the fungal community in the litter decomposition by invasive plants can negatively impact nutrient cycling in natural ecosystems. One still does not know the dimension of this hypothesis, but apparently, it is not despicable. This study evaluated the assemblage composition of fungi during litter decomposition in areas of Atlantic Forest invaded or not invaded by Tradescantia zebrina using Illumina MiSeq and metabarcoding analysis.

RESULTS

The invaded sample showed significantly higher richness and a difference in the species dominance than the invaded litter. Ascomycota was the first most abundant phylum in both areas. Even so, the dissimilarity between areas can be evidenced. The fungal from Basidiomycota were very representative in the non-invaded areas (ranged from an abundance of 43.29% in the non-invaded to 2.35% in the invaded sample). The genus Lepiota can indicate the primary functional group related to biomass degradation and showed the might difference about the invaded areas due to its essential reduction by the invader. In the invaded sample, there was a total absence of the endophyte-undefined saprotroph guild. Also, some genera not taxonomically characterized were eliminated in the invaded sample, revealing that the fungal biodiversity of areas has not yet been thoroughly characterized.

CONCLUSIONS

Hence, makes impossible the real interpretation of the invasive plant impact, showing the importance of continuing research on fungal biodiversity. It is important to emphasize that the replacement of the native species by T. zebrina may be responsible for the elimination of fungal groups that have not yet been identified.

Candidatus Kaistella beijingensis sp. nov., Isolated from a Municipal Wastewater Treatment Plant, Is Involved in Sludge Foaming

Biological foaming (or biofoaming) is a frequently occurring problem in wastewater treatment plants (WWTPs) and is attributed to the overwhelming growth of filamentous bulking and foaming bacteria (BFB). Biological foaming has been intensively investigated, with BFB like Microthrix and Skermania having been identified from WWTPs and implicated in foaming. Nevertheless, studies are still needed to improve our understanding of the microbial diversity of WWTP biofoams and how microbial activities contribute to foaming. In this study, sludge foaming at the Qinghe WWTP of China was monitored, and sludge foams were investigated using culture-dependent and culture-independent microbiological methods. The foam microbiomes exhibited high abundances of Skermania, Mycobacterium, Flavobacteriales, and Kaistella. A previously unknown bacterium, Candidatus Kaistella beijingensis, was cultivated from foams, its genome was sequenced, and it was phenotypically characterized. Ca. K. beijingensis exhibits hydrophobic cell surfaces, produces extracellular polymeric substances (EPS), and metabolizes lipids. Ca. K. beijingensis abundances were proportional to EPS levels in foams. Several proteins encoded by the Ca. K. beijingensis genome were identified from EPS that was extracted from sludge foams. Ca. K. beijingensis populations accounted for 4 to 6% of the total bacterial populations in sludge foam samples within the Qinghe WWTP, although their abundances were higher in spring than in other seasons. Cooccurrence analysis indicated that Ca. K. beijingensis was not a core node among the WWTP community network, but its abundances were negatively correlated with those of the well-studied BFB Skermania piniformis among cross-season Qinghe WWTP communities. IMPORTANCE Biological foaming, also known as scumming, is a sludge separation problem that has become the subject of major concern for long-term stable activated sludge operation in decades. Biological foaming was considered induced by foaming bacteria. However, the occurrence and deterioration of foaming in many WWTPs are still not completely understood. Cultivation and characterization of the enriched bacteria in foaming are critical to understand their genetic, physiological, phylogenetic, and ecological traits, as well as to improve the understanding of their relationships with foaming and performance of WWTPs.

Community Structure and Function of Epiphytic Bacteria Associated With Myriophyllum spicatum in Baiyangdian Lake, China

Epiphytic bacteria on the surfaces of submerged macrophytes play important roles in the growth of the host plant, nutrient cycling, and the conversion of pollutants in aquatic systems. A knowledge of the epiphytic bacterial community structure could help us to understand these roles. In this study, the abundance, diversity, and functions of the epiphytic bacterial community of Myriophyllum spicatum collected from Baiyangdian Lake in June, August, and October 2019 were studied using quantitative PCR (qPCR), high-throughput sequencing, and the prediction of functions. An analysis using qPCR showed that the epiphytic bacteria were the most abundant in October and the least abundant in August. High-throughput sequencing revealed that Proteobacteria, Gammaproteobacteria, and Aeromonas were the dominant phylum, class, and genus in all the samples. The common analyses of operational taxonomic units (OTUs), NMDS, and LDA showed that the epiphytic bacterial communities were clustered together based on the seasons. The results of a canonical correlation analysis (CCA) showed that the key water quality index that affected the changes of epiphytic bacterial community of M. spicatum was the total phosphorus (TP). The changes in abundance of Gammaproteobacteria negatively correlated with the TP. Predictive results from FAPROTAX showed that the predominant biogeochemical cycle functions of the epiphytic bacterial community were chemoheterotrophy, nitrate reduction, and fermentation. These results suggest that the epiphytic bacterial community of M. spicatum from Baiyangdian Lake varies substantially with the seasons and environmental conditions.

Eukaryotic communities in coastal water from Shenzhen in South China

Eukaryotic microorganisms are ubiquitous in the marine environment, and have a wide variety of ecosystem functions. Shenzhen is one of the most developed cities in South China, but the eukaryotic communities in the water along its coastlines remain poorly understood. The study applied 18S rRNA gene ITS (internal transcribed spacer) sequencing to identify the eukaryotic community from twenty sites of Shenzhen coast water. The alpha-diversity of the samples between these sites were significantly different, and the seawater of eastern coast had higher alpha-diversity compared to that of the western coast. The abundance of Chlorophyta was notably higher in the seawater of western coast, but Picozoa was relatively depleted. Specifically, Cryptocaryon, Pseudovorticella, and Cyclotella were significantly higher in the water of western coast, while Guinardia, Minutocellus, and Amoebophrya were increased in eastern samples. The spatially variations of eukaryotic microorganism community in the seawater of Shenzhen coast were associated with the water quality. The results have important significance for the understanding of coastal eukaryotic community, their interaction network, and build a foundation for future management and protection of coastal water quality.

High-Throughput Single-Cell Technology Reveals the Contribution of Horizontal Gene Transfer to Typical Antibiotic Resistance Gene Dissemination in Wastewater Treatment Plants

The spread of antibiotic resistance genes (ARGs) has gained much attention worldwide, while the contribution of vertical gene transfer (VGT) and horizontal gene transfer (HGT) is still elusive. Here, we improved an emerging high-throughput single-cell-based technology, emulsion, paired isolation, and concatenation polymerase chain reaction (epicPCR), by lengthening the sequence of ARG in the fused ARG-16S rRNA fragments to cover the variance of both ARG and its hosts. The improved epicPCR was applied to track the hosts of a widely detected ARG, sul1 gene, in five urban wastewater treatment plants (UWTPs) during two seasons. The sul1 host bacteria were highly diverse and mostly classified as Proteobacteria and Bacteroidetes. Clear seasonal divergence of α-diversity and interaction networks were present in the host community. The consensus phylogenetic trees of the sul1 gene and their host demonstrated incorrespondence on the whole and regularity on abundant groups, suggesting the important role of both HGT and VGT, respectively. The relative importance of these two ways was further measured; HGT (54%) generally played an equal or even more important role as VGT (46%) in UWTPs. The application of the improved epicPCR technology provides a feasible approach to quantify the relative contributions of VGT and HGT in environmental dissemination of ARGs.

Periphytic Biofilm Formation on Natural and Artificial Substrates: Comparison of Microbial Compositions, Interactions, and Functions

Periphytic biofilms have been widely used in wastewater purification and water ecological restoration, and artificial substrates have been progressively used for periphyton immobilisation to substitute natural substrates. However, there is insufficient knowledge regarding the interaction network structure and microbial functions in biofilm communities on artificial substrates, which are essential attribute affecting their applications in biofilm immobilisation. This study compared the community structure, co-occurrence network, and metabolic functions of bacterial and microeukaryotic periphytic biofilms during a 35-day indoor cultivation on artificial substrates, such as artificial carbon fibre (ACF) and polyvinyl chloride (PVC), and natural substrates, such as pebble and wood. Results demonstrated that different types of artificial substrates could affect the community composition and functional diversity of bacterial and microeukaryotic biofilms. The bacterial and microeukaryotic community on ACF and PVC showed significantly higher Simpson index compared to those on wood. Bacterial networks on artificial substrates were more complex than those on natural substrates, while the keystone species on natural substrates were more abundant, indicating that the bacterial communities on artificial substrates had stronger stability and resistance to external interference. Furthermore, the functional metabolic profiles predicted showed the abilities of bacterial communities to metabolise nitrogen and carbon sources colonised on artificial substrates were stronger than those on natural substrates. These findings demonstrated that artificial substrates could be special niches for microbial colonisation, possibly altering microbial compositions, interactions, and functions. Therefore, this study provides a powerful theoretical basis for choosing suitable artificial substrates for microbial aggregation and immobilisation technology.

Relative Weight of Organic Waste Origin on Compost and Digestate 16S rRNA Gene Bacterial Profilings and Related Functional Inferences

Even though organic waste (OW) recycling via anaerobic digestion (AD) and composting are increasingly used, little is known about the impact of OW origin (fecal matters and food and vegetable wastes) on the end products' bacterial contents. The hypothesis of a predictable bacterial community structure in the end products according to the OW origin was tested. Nine OW treatment plants were selected to assess the genetic structure of bacterial communities found in raw OW according to their content in agricultural and urban wastes and to estimate their modifications through AD and composting. Two main bacterial community structures among raw OWs were observed and matched a differentiation according to the occurrences of urban chemical pollutants. Composting led to similar 16S rRNA gene OTU profiles whatever the OW origin. With a significant shift of about 140 genera (representing 50% of the bacteria), composting was confirmed to largely shape bacterial communities toward similar structures. The enriched taxa were found to be involved in detoxification and bioremediation activities. This process was found to be highly selective and favorable for bacterial specialists. Digestates showed that OTU profiles differentiated into two groups according to their relative content in agricultural (manure) and urban wastes (mainly activated sludge). About one third of the bacterial taxa was significantly affected by AD. In digestates of urban OW, this sorting led to an enrichment of 32 out of the 50 impacted genera, while for those produced from agricultural or mixed urban/agricultural OW (called central OW), a decay of 54 genera over 60 was observed. Bacteria from activated sludge appeared more fit for AD than those of other origins. Functional inferences showed AD enriched genera from all origins to share similar functional traits, e.g., chemoheterotrophy and fermentation, while being often taxonomically distinct. The main functional traits among the dominant genera in activated sludge supported a role in AD. Raw OW content in activated sludge was found to be a critical factor for predicting digestate bacterial contents. Composting generated highly predictable and specialized community patterns whatever the OW origin. AD and composting bacterial changes were driven by functional traits selected by physicochemical factors such as temperature and chemical pollutants.

Carbon availability shifts the nitrogen removal pathway and microbial community in biofilm airlift reactor

This study investigated the response of nitrogen removal performance and microbial community to different carbon composites in biofilm airlift reactors for wastewater treatment. Three reactors were filled with poly (butylene succinate) and bamboo powder composite at the blending ratio of 9:1, 1:1 and 1:9. Increasing the component of bamboo powder in the carrier reduced the carbon availability and had an adverse effect on nitrate removal efficiency. However, bamboo powder improved the ammonia removal rate which mainly through autotrophic nitrification. Three reactors exhibited distinct microbial compositions in both bacterial and fungal diversity. High inclusion of bamboo power decreased the relative abundance of denitrifiers Denitromonas and increased the relative abundance of nitrifiers, including Nitromonas, Nitrospina and Nitrospira. Moreover, correlation network revealed a competitive interaction between the taxa responsible for ammonia removal and nitrate removal processes. Those results indicated the feasibility of steering nitrogen removal pathway through carrier formulation in wastewater treatment.

Exploration of Intrinsic Microbial Community Modulators in the Rice Endosphere Indicates a Key Role of Distinct Bacterial Taxa Across Different Cultivars

Microbial communities associated with the plant phyllosphere and endosphere can have both beneficial as well as detrimental effects on their hosts. There is an ongoing debate to which extend the phyllosphere and endosphere microbiome assembly is controlled by the host plant how pronounced cultivar effects are. We investigated the bacterial and fungal communities from the phyllosphere and endosphere of 10 different rice cultivars grown under identical environmental conditions in the frame of a targeted approach to identify drivers of community assembly. The results indicated that the endophytic bacterial communities were clearly separated into two groups. The α-diversity and microbial network complexity within Group I were significantly lower than in Group II. Moreover, the genera Nocardioides, Microvirga, and Gaiella were significantly more abundant in Group II and only present in the interaction networks of this group. These three genera were significantly correlated with α- and β-diversity of the endophytic bacterial community and thus identified as major drivers of the endosphere community. We have identified keystone taxa that shape endophytic bacterial communities of different rice cultivars. Our overall findings provide new insights into plant-microbe interactions, and may contribute to targeted improvements of rice varieties in the future.

Disentangling Responses of the Subsurface Microbiome to Wetland Status and Implications for Indicating Ecosystem Functions

In this study, we analyzed microbial community composition and the functional capacities of degraded sites and restored/natural sites in two typical wetlands of Northeast China-the Phragmites marsh and the Carex marsh, respectively. The degradation of these wetlands, caused by grazing or land drainage for irrigation, alters microbial community components and functional structures, in addition to changing the aboveground vegetation and soil geochemical properties. Bacterial and fungal diversity at the degraded sites were significantly lower than those at restored/natural sites, indicating that soil microbial groups were sensitive to disturbances in wetland ecosystems. Further, a combined analysis using high-throughput sequencing and GeoChip arrays showed that the abundance of carbon fixation and degradation, and ~95% genes involved in nitrogen cycling were increased in abundance at grazed Phragmites sites, likely due to the stimulating impact of urine and dung deposition. In contrast, the abundance of genes involved in methane cycling was significantly increased in restored wetlands. Particularly, we found that microbial composition and activity gradually shifts according to the hierarchical marsh sites. Altogether, this study demonstrated that microbial communities as a whole could respond to wetland changes and revealed the functional potential of microbes in regulating biogeochemical cycles.

Tropical and temperate wastewater treatment plants assemble different and diverse microbiomes

The diversity and assembly of activated sludge microbiomes play a key role in the performances of municipal wastewater treatment plants (WWTPs), which are the most widely applied biotechnological process systems. In this study, we investigated the microbiomes of municipal WWTPs in Bangkok, Wuhan, and Beijing that respectively represent tropical, subtropical, and temperate climate regions, and also explored how microbiomes assembled in these municipal WWTPs. Our results showed that the microbiomes from these municipal WWTPs were significantly different. The assembly of microbiomes in municipal WWTPs followed deterministic and stochastic processes governed by geographical location, temperature, and nutrients. We found that both taxonomic and phylogenetic α-diversities of tropical Bangkok municipal WWTPs were the highest and were rich in yet-to-be-identified microbial taxa. Nitrospirae and β-Proteobacteria were more abundant in tropical municipal WWTPs, but did not result in better removal efficiencies of ammonium and total nitrogen. Overall, these results suggest that tropical and temperate municipal WWTPs harbored diverse and unique microbial resources, and the municipal WWTP microbiomes were assembled with different processes. Implications of these findings for designing and running tropical municipal WWTPs were discussed. KEY POINTS: • Six WWTPs of tropical Thailand and subtropical and temperate China were investigated. • Tropical Bangkok WWTPs had more diverse and yet-to-be-identified microbial taxa. • Microbiome assembly processes were associated with geographical location.

Evaluation of the Abundance of Fungi in Wastewater Treatment Plants Using Quantitative PCR (qPCR)

Assessment of the abundance of fungi in environmental samples by quantitative PCR (qPCR) of community DNA is often a difficult task due to biases introduced during PCR amplification, resulting from the differences associated with length polymorphism and the varying number of copies of the rRNA operon among fungal species, the lack of specificity of the primers targeting the different regions of the rRNA operon, or their insufficient coverage of the fungal lineages. To overcome those limitations, it is crucial to test and select the specific primers sets which provide the more accurate approximation to the quantification of the targeted fungal populations in a given set of samples. Fungi are a significant fraction of the microbiota in wastewater treatment plants (WWTPs), but the activated sludge microbial communities comprise many other eukaryotic microorganisms whose molecular markers are often coamplified by primers initially designed as fungal-specific. Here, the use of the FungiQuant primer set is recommended for the quantification of fungal molecular markers (18S rRNA genes) by qPCR in activated sludge samples and the full protocol is described.

Seasonal dynamics of lotic bacterial communities assessed by 16S rRNA gene amplicon deep sequencing

Aquatic microbial diversity, composition, and dynamics play vital roles in sustaining water ecosystem functionality. Yet, there is still limited knowledge on bacterial seasonal dynamics in lotic environments. This study explores a temporal pattern of bacterial community structures in lotic freshwater over a 2-year period. The aquatic bacterial communities were assessed using Illumina MiSeq sequencing of 16S rRNA genes. Overall, the communities were dominated by α-, β-, and γ-Proteobacteria, Bacteroidetes, Flavobacteriia, and Sphingobacteriia. The bacterial compositions varied substantially in response to seasonal changes (cold vs. warm), but they were rather stable within the same season. Furthermore, higher diversity was observed in cold seasons compared to warm periods. The combined seasonal-environmental impact of different physico-chemical parameters was assessed statistically, and temperature, suspended solids, and nitrogen were determined to be the primary abiotic factors shaping the temporal bacterial assemblages. This study enriches particular knowledge on the seasonal succession of the lotic freshwater bacteria.

Seasonality and Community Separation of Fungi in a Municipal Wastewater Treatment Plant

Fungi are known to play important roles in pollutant transformation in activated sludge-based wastewater treatment plants (WWTPs). However, the seasonality and distributions of fungal populations in different-sized flocs have still remained largely unknown. In this study, seasonal population dynamics and community separation of fungi in a municipal WWTP across a 1-year period were investigated. We classified all taxa into six categories based on abundances to assess their roles and contributions to the whole community. The results showed that the rare taxa (<0.01%) contributed greatly to species richness (95.27%). Conversely, although low in species diversity, abundant taxa (≥1%) accounted for the majority (89.45%) of the total relative abundance, which suggested that a few core abundant fungi existed in the activated sludge ecosystem. The abundant, conditionally rare, and rare taxa contributed 30.14%, 31.11%, and 38.75%, respectively, to temporal shifts in community structure, and their abundances responded differently to environmental variables, suggesting that these three subcommunities exhibited a large difference in environmental sensitivity. Importantly, the results revealed seasonal dynamics of the whole fungal community and the subcommunities of all the microbial taxon categories, resulting in significant differences in community structures between warm and cold seasons. Furthermore, fungal diversity and the compositions of the whole community and subcommunities differed significantly among flocs of different sizes, which underlined the size-based fungal community separation in activated sludge of WWTPs. The findings of this work improved our understanding of fungal population dynamics and community separation in WWTPs.IMPORTANCE Fungi are important contributors to the various functions of activated sludge in wastewater treatment plants (WWTPs). Unlike previous studies, this work demonstrated the seasonality of the fungal community over a longer time span while it also systematically assessed the contributions of abundant, conditionally rare, and rare taxa to the whole community. Importantly, in the present study, we considered sludge flocs of a certain size range rather than the whole sludge flocs as a community. Our results revealed significant differences in fungal community structure among different-sized flocs, which supported the idea that size-based fungal community segregation is occurring in activated sludge ecosystems. The findings provide new insights into the dynamic changes or distribution of fungi in the bioaggregates of sludge flocs in WWTPs.

Structure, Function, Diversity, and Composition of Fungal Communities in Rhizospheric Soil of Coptis chinensis Franch under a Successive Cropping System

Soil types and cropping systems influence the diversity and composition of the rhizospheric microbial communities. Coptis chinensis Franch is one of the most important medicinal plants in China. In the current study, we provide detailed information regarding the diversity and composition of rhizospheric fungal communities of the C. chinensis plants in continuous cropping fields and fallow fields in two seasons (winter and summer), using next-generation sequencing. Alpha diversity was higher in the five-year C. chinensis field and lower in fallow fields. Significant differences analysis confirmed more fungi in the cultivated field soil than in fallow fields. Additionally, PCoA of beta diversity indices revealed that samples associated with the cultivated fields and fallow fields in different seasons were separated. Five fungal phyla (Ascomycota, Basidiomycota, Chytridiomycota, Glomeromycota and Mucoromycota) were identified from the soil samples in addition to the unclassified fungal taxa and Cryptomycota, and among these phyla, Ascomycota was predominantly found. FUNGuild fungal functional prediction revealed that saprotroph was the dominant trophic type in all two time-series soil samples. Redundancy analysis (RDA) of the dominant phyla data and soil physiochemical properties revealed the variations in fungal community structure in the soil samples. Knowledge from the present study could provide a valuable reference for solving the continuous cropping problems and promote the sustainable development of the C. chinensis industry.

Casimicrobium huifangae gen. nov., sp. nov., a Ubiquitous "Most-Wanted" Core Bacterial Taxon from Municipal Wastewater Treatment Plants

Microorganisms in wastewater treatment plants (WWTPs) play a key role in the removal of pollutants from municipal and industrial wastewaters. A recent study estimated that activated sludge from global municipal WWTPs harbors 1 × 10⁹ to 2 × 10⁹ microbial species, the majority of which have not yet been cultivated, and 28 core taxa were identified as "most-wanted" ones (L. Wu, D. Ning, B. Zhang, Y. Li, et al., Nat Microbiol 4:1183-1195, 2019, https://doi.org/10.1038/s41564-019-0426-5). Cultivation and characterization of the "most-wanted" core bacteria are critical to understand their genetic, physiological, phylogenetic, and ecological traits, as well as to improve the performance of WWTPs. In this study, we isolated a bacterial strain, designated SJ-1, that represents a novel cluster within Betaproteobacteria and corresponds to OTU_16 within the 28 core taxa in the "most-wanted" list. Strain SJ-1 was identified and nominated as Casimicrobium huifangae gen. nov., sp. nov., of a novel family, Casimicrobiaceae. C. huifangae is ubiquitously distributed and is metabolically versatile. In addition to mineralizing various carbon sources (including carbohydrates, aromatic compounds, and short-chain fatty acids), C. huifangae is capable of nitrate reduction and phosphorus accumulation. The population of C. huifangae accounted for more than 1% of the bacterial population of the activated sludge microbiome from the Qinghe WWTP, which showed seasonal dynamic changes. Cooccurrence analysis suggested that C. huifangae was an important module hub in the bacterial network of Qinghe WWTP.IMPORTANCE The activated sludge process is the most widely applied biotechnology and is one of the best ecosystems to address microbial ecological principles. Yet, the cultivation of core bacteria and the exploration of their physiology and ecology are limited. In this study, the core and novel bacterial taxon C. huifangae was cultivated and characterized. This study revealed that C. huifangae functioned as an important module hub in the activated sludge microbiome, and it potentially plays an important role in municipal wastewater treatment plants.

Forest Soil Fungal Community Elevational Distribution Pattern and Their Ecological Assembly Processes

Soil fungi play vital roles in natural ecosystems, however, their community distribution patterns along different environmental gradients and ecological assembly processes remain unclear. In this study, Illumina MiSeq sequencing was used to investigate the soil fungal community structures of five different forest types along an elevational gradient, and a framework based on a null model was adopted to quantify the relative contribution of deterministic and stochastic ecological assembly processes. The results showed that the majority of soil fungal OTUs were derived from Zygomycota, Basidiomycota, and Ascomycota. Soil fungal community structure differed significantly among the five sites (P < 0.01), and the fungal α-diversity decreased as elevation increased (P < 0.01). The null model showed that the relative contribution of stochastic processes (37.78-73.33%) was higher than that of deterministic processes (26.67-62.22%) within the same forest type, while that of deterministic processes (35.00-93.00%) was higher than stochastic processes (7.00-65.00%) between forest types. These results suggest that forest soil fungal diversity decreased significantly with increasing elevation, and that deterministic processes may be key factors influencing soil fungal community assemblies among forest types. The results of this study provide new insight into soil fungal distribution patterns and community assembly processes in natural forest ecosystems.

Diversity, Co-occurrence and Implications of Fungal Communities in Wastewater Treatment Plants

Three wastewater treatment plants (WWTPs) located in Gauteng province in South Africa were investigated to determine the diversity, co-occurrence and implications of their fungal communities using illumina sequencing platform and network analysis. Phylogenetic taxonomy revealed that members of the fungal communities were assigned to 6 phyla and 361 genera. Basidiomycota and Ascomycota were the most abundant phyla, dominated by the genera Naumovozyma, Pseudotomentella, Derxomyces, Ophiocordyceps, Pulchromyces and Paecilomyces. Phylogenetic analysis revealed the existence of fungal OTUs related to class lineages such as Agaricomycetes, Eurotiomycetes and Sordariomycetes indicating new fungal diversity in WWTPs. Dominant and rare fungal genera that can potentially be used in bioremediation such as Trichoderma, Acremonium, Talaromyces, Paecilomyces, cladophialophora and Saccharomyces were detected. Conversely, genera whose members are known to be pathogenic to human and plant such as Olpidium, Paecilomyces, Aspergillus, Rhodotorula, Penicillium, Candida, Synchytrium, Phyllosticta and Mucor were also detected in all WWTPs. Phylotype analysis confirmed that some fungal phylotypes were highly similar to the reported fungal pathogens of concern. Co-occurrence network analysis revealed that the fungal genera such as Minimedusa, Glomus, Circinella, Coltricia, Caloplaca, Phylosticta, Peziza, Candida, and Hydnobolites were the major networking hub in the WWTPs. The overall results in this study highlighted that WWTPs represent a potential source of beneficial fungi for bioremediation of pollutants in the ecosystem and the need to consider human and plant fungal pathogens during safety evaluation of treated wastewater for reuse.

Interdomain ecological networks between plants and microbes

While macroscopic interkingdom relationships have been intensively investigated in various ecosystems, the above-belowground ecology in natural ecosystems has been poorly understood, especially for the plant-microbe associations at a regional scale. In this study, we proposed a workflow to construct interdomain ecological networks (IDEN) between multiple plants and various microbes (bacteria and archaea in this study). Across 30 latitudinal forests in China, the regional IDEN showed particular topological features, including high connectance, nested structure, asymmetric specialization and modularity. Also, plant species exhibited strong preference to specific microbial groups, and the observed network was significantly different from randomly rewired networks. Network module analysis indicated that a majority of microbes associated with plants within modules rather than across modules, suggesting specialized associations between plants and microorganisms. Consistent plant-microbe associations were captured via IDENs constructed within individual forest locations, which reinforced the validity of IDEN analysis. In addition, the plant-forest link distribution showed the geographical distribution of plants had higher endemicity than that of microorganisms. With cautious experimental design and data processing, this study shows interdomain species associations between plants and microbes in natural forest ecosystems and provides new insights into our understanding of meta-communities across different domain species.

Temporal bacterial community succession during the start-up process of biofilters in a cold-freshwater recirculating aquaculture system

Start-up of biofilters plays crucial roles in the successful operation of recirculating aquaculture system, and the nature is bacterial community succession. We explored the pattern of bacterial temporal succession during the start-up process of biofilters in a commercial cold-freshwater recirculating aquaculture system (RAS). The whole succession process was divided into three distinct phases: incubation, growth and stability. Phylogenetic diversity and evenness of the bacterial community increased during the start-up process, whereas richness reached its peak at the growth phase. Seven biomarkers were identified, namely Cytophagales, Gemmatimonadales, Sphingomonadales, Sphingobacteriales, Rhizobiales, Clostridiales and Nitrospirales. The relative abundances of these functional bacteria increased, while those with a competitive growth advantage declined. The network interactions were dramatically altered from fairly simple to most complex, and then decreased in complexity during start-up. Positive relationships decreased, while competition increased. The shift in predicted function exhibited a trend from simple to diverse, and converged to idiosyncratic configuration.

Bioremediation of dibutyl phthalate in a simulated agricultural ecosystem by Gordonia sp. strain QH-11 and the microbial ecological effects in soil

Bioremediation of organic pollutants has been identified as an economically efficient and environmentally friendly method. Here, a pot experiment was conducted to evaluate the bioremediation efficiency of dibutyl phthalate (DBP) by Gordonia phthalatica sp. nov. QH-11 in agricultural soils, along with the effect of this exogenous organism on the native microbial community and ecosystem functions during the bioremediation process. The results showed that inoculation with strain QH-11 accelerated DBP degradation in the soil and decreased DBP accumulation in plants, thereby reducing the health risks associated with vegetables grown in those soils. High-throughput sequencing demonstrated that both DBP contamination and the bioremediation process significantly altered prokaryotic community composition, structure, and network interactions; however, these effects were greatly reduced after 30 d. Dibutyl phthalate affected the prokaryotic community by influencing soil properties rather than directly impacting on microorganisms. In addition, ecosystem functions, like the nitrogen cycle, were significantly altered. Contamination with DBP promoted nitrogen fixation and the denitrification processes while inhibiting nitrification. Bioremediation may mitigate some of the changes to nitrogen cycling, helping to maintain the balance of prokaryotic community function. According to this study, bioremediation through highly efficient degradation bacteria may be a safe and promising method for reducing PAEs contamination in soil-vegetable systems.

Euonymus japonicus phyllosphere microbiome is significantly changed by powdery mildew

Euonymus japonicus Thunb. is a woody and ornamental plant popular in China, Europe and North America. Powdery mildew is one of the most serious diseases that affect E. japonicus growth. In this study, the diseased and apparently healthy leaves were collected from E. japonicus planted in a greenbelt in Beijing, and the effect of powdery mildew on the epiphytic microbial community was investigated by using Illumina sequencing. The results showed that the healthy leaves (HL) harbored greater bacterial and fungal diversity than diseased leaves (DL). Furthermore, both bacterial and fungal communities in DL exhibited significantly different structures from those in HL. The relative abundance of several bacterial phyla (Proteobacteria and Firmicutes) and fungal phyla (Ascomycota and Basidiomycota) were altered by powdery mildew. At the genus level, most genera decreased as powdery mildew pathogen Erysiphe increased, while the genera Kocuria and Exiguobacterium markedly increased. Leaf properties, especially protein content was found to significantly affect beta-diversity of the bacterial and fungal community. Network analysis revealed that positive bacterial interactions in DL were stronger than those in HL samples. Insights into the underlying the indigenous microbial phyllosphere populations of E. japonicus response to powdery mildew will help in the development of methods for controlling plant diseases.

Dibutyl phthalate contamination remolded the fungal community in agro-environmental system

Dibutyl phthalate (DBP) is a typical soil contaminant that is widely used as plasticizer in modern agricultural production. In this study, an experiment was conducted to evaluate fungal community succession in a soil-vegetable ecosystem under different DBP concentrations. By using high-throughput sequencing of the ribosomal internal transcribed spacer (ITS) region, it was shown that DBP contamination caused significant changes to the soil fungal community, in terms of both α and β diversities. The largest changes in fungal α and β diversities were detected under 50 mg/kg DBP concentration at the first day of addition. The bulk soils, rhizosphere soils and the phyllosphere harbored different fungal communities, while the abundance of saprotrophs and plant pathogens in the phyllosphere have been increased under DBP contamination. From correlation analysis and partial Mantel test, the change in fungal community α diversity was the result of multiple factors (DBP concentration, bacterial community and soil properties) while the β diversity of fungal community was mainly co-varied with the bacterial community after DBP contamination. Moreover, molecular ecological network analysis demonstrated that DBP contamination was detrimental to mutualistic relationships among fungal species and destabilized the network structure. Overall, the fungal communities in soils and around vegetables were largely remolded by DBP contamination that provides new insight into DBP contamination impacts on agricultural ecosystems.