General and rare bacterial taxa demonstrating different temporal dynamic patterns in an activated sludge bioreactor

Microbial community structure and water quality performance in local scrubber reclaim system for water reclamation of the semiconductor industry: A case study of a semiconductor plant in Beijing

The local scrubber reclaim (LSR) system plays a critical role in water reclamation and in reducing environmental pollution emissions in semiconductor factories. This study monitored the changes in water quality and assessed the key stages of pollutant removal, with a primary focus on evaluating microbial growth and the shifts in microbial community structure and function in the LSR system. The results showed that activated carbon filtration (ACF) effectively removed total organic carbon (TOC) with a removal rate of 59.35%, while ion exchange (IEX) was essential for reducing conductivity, with a removal rate of 87.33%. Furthermore, severe bacterial growth was observed (more than 1000 CFU/ml) in the system. Bacteria numbers in the MMF and ACF stages grew dramatically, at least four times higher than that in the influent tank. After chlorination in the storage tank, microbial numbers sharply dropped, yet microbial diversity increased. The dominant microbial group in the LSR system was Patescibacteria (average relative abundance was 32.37%), considered part of the "microbial dark matter" and also known as Candidate Phyla Radiation (CPR). Following the effluent from the storage tank, the biofilm-forming potential of bacteria significantly increased (relative abundance rose from 7.19% to 15.20%), along with a varying increase in the abundance of genes related to metabolism. Measures should be implemented to prevent pipeline blockage and improve water reclamation efficiency.

DNA and RNA sequencing reveal the role of rare bacterial taxa in constructed wetlands: Insights into community activities, ecological functions, and assembly processes

Microorganisms are essential for the functioning of constructed wetlands (CWs), yet the role of rare bacterial taxa in CWs remains poorly understood. In this study, the community structure, metabolic activities, ecological functions, and assembly processes of abundant and rare bacterial taxa in CWs were examined using DNA and RNA high-throughput sequencing. Our results revealed that Gammaproteobacteria, Alphaproteobacteria, Bacteroidia, and Actinobacteria exhibited high diversity and sequence abundance. Retention in CWs generally reduced the metabolic activities of bacterial communities, with intermediate and rare taxa showing significantly lower activity compared to those in the influent. Despite their low abundance, functional groups involved in nitrogen and phosphorus removal exhibited high metabolic activities, highlighting their crucial role in these processes. Co-occurrence network analysis showed that non-rare taxa interacted more frequently with rare taxa than with conspecifics, and that keystone species included comparable numbers of both abundant and rare species. These highlight the importance of rare taxa in ecological functions and maintaining the stability of bacterial community structure in CWs. The assembly of bacterial communities was driven by both deterministic and stochastic processes, with stochastic processes predominantly shaping the rare taxa and deterministic processes primarily influencing the abundant taxa. Overall, this study provides novel insights into bacterial community structure, metabolic activity, and assembly processes in CWs, particularly the ecological roles of rare taxa.

Candidatus Thiothrix phosphatis SCUT-1: A novel polyphosphate-accumulating organism abundant in the enhanced biological phosphorus removal system

A novel coccus Thiothrix-related polyphosphate-accumulating organism (PAO) was enriched in an acetate-fed enhanced biological phosphorus removal (EBPR) system. High EBPR performance was achieved for an extended period (>100 days). A high-quality draft genome (completeness 97.2 %, contamination 3.26 %) was retrieved, representing a novel Thiothrix species (with similarity<93.2 % to known Thiothrix species), and was denoted as 'Candidatus Thiothrix phosphatis SCUT-1'. Its acetate uptake rate (6.20 mmol C/g VSS/h) surpassed most Ca. Accumulibacter and known glycogen-accumulating organisms (GAOs), conferring their predominance in the acetate-fed system. Metatranscriptomic analysis suggested that Ca. Thiothrix phosphatis SCUT-1 employed both low- and high-affinity pathways for acetate activation, and both the conventional (PhaABC) pathway and the fatty acid β-oxidation pathway for PHA synthesis; additionally, a much more efficient FAD-dependent malate: quinone oxidoreductase (MQO) were encoded and employed than the traditional malate dehydrogenase (MDH) to oxidize malate to oxaloacetate in the TCA and glyoxylate cycle, collectively contributing to a higher acetate utilization and processing rate of this microorganism. Batch tests further demonstrated the versatile ability of this PAO in using VFA (acetate, propionate, and butyrate), lactate, amino acids (aspartate and glutamate), and glucose as carbon sources for EBPR, showing a partially overlapped but unique ecological niche of this microorganism comparing to Ca. Accumulibacter and known GAOs. A metabolic model was built for Ca. Thiothrix phosphatis SCUT-1 using the above-mentioned carbon sources for EBPR. Overall, this study represents the first comprehensive characterization of the physiology and metabolic characteristics of representative coccus Thiothrix-related PAOs, which are expected to provide new insights into PAO microbiology in EBPR systems.

Impact of Temperature Elevation on Microbial Communities and Antibiotic Degradation in Cold Region Soils of Northeast China

This study systematically investigated the effects of temperature changes on the degradation of antibiotics in soil, as well as the alterations in microbial community structure and aggregation, through a field warming experiment in a greenhouse. Compared to non-warming soil, the warming treatment significantly accelerated the degradation rate of tetracyclines during soil freezing and mitigated the impact of environmental fluctuations on soil microbial communities. The greenhouse environment promoted the growth and reproduction of a wide range of microbial taxa, but the abundance of Myxococcota was positively correlated with antibiotic concentrations in both treatments, suggesting a potential specific association with antibiotic degradation processes. Long-term warming in the greenhouse led to a shift in the assembly process of soil microbial communities, with a decrease in dispersal limitation and an increase in the drift process. Furthermore, co-occurrence network analysis revealed a more loosely structured microbial community in the greenhouse soil, along with the emergence of new characteristic taxa. Notably, more than 60% of the key taxa that connected the co-occurrence networks in both groups belonged to rare taxa, indicating that rare taxa play a crucial role in maintaining community structure and function.

The roles of rare and abundant microbial species in the primary succession of biological soil crusts are differentiated in metal tailings ponds with different states

Tailings ponds formed by long-term accumulation of mineral processing waste have become a global environmental problem. Even worse, tailings ponds are often simply abandoned or landfilled after they cease to be used. This allows pollution to persist and continue to spread in the environment. The significance of primary succession mediated by biological soil crusts for tailings pond remediation has been illustrated by previous studies. However, the process of primary succession may not be the same at different stages during the lifetime of tailings ponds. Therefore, we investigated the environmental differences and the successional characteristics of microbial communities in the primary successional stage of tailings ponds at three different states. The results showed that the primary succession process positively changed the environment of tailings ponds in any state of tailings ponds. The primary successional stage determined the environmental quality more than the state of the tailings pond. In the recently abandoned tailings ponds, abundant species were more subjected to heavy metal stress, while rare species were mainly limited by nutrient content. We found that as the succession progressed, rare species gradually acquired their own community space and became more responsive to environmental stresses. Rare species played an important role in microbial keystone species groups.

Stochastic processes shape microbial community assembly in biofilters: Hidden role of rare taxa

Stochastic and deterministic processes are the major themes governing microbial community assembly; however, their roles in bioreactors are poorly understood. Herein, the mechanisms underlying microbial assembly and the effect of rare taxa were studied in biofilters. Phylogenetic tree analysis revealed differences in microbial communities at various stages. Null model analysis showed that stochastic processes shaped the community assembly, and deterministic processes emerged only in the inoculated activated sludge after domestication. This finding indicates the dominant role of stochastic factors (biofilm formation, accumulation, and aging). The Sloan neutral model corroborated the advantages of stochastic processes and mainly attributed these advantages to rare taxa. Cooccurrence networks revealed the importance of rare taxa, which accounted for more than 85% of the keystones. Overall, these results provide good foundations for understanding community assembly, especially the role of rare taxa, and offer theoretical support for future community design and reactor regulation.

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.

Effects of deterministic assembly of communities caused by global warming on coexistence patterns and ecosystem functions

Seasonal rhythms in biological and ecological dynamics are fundamental in regulating the structuring of microbial communities. Evaluating the seasonal rhythms of microorganisms in response to climate change could provide information on their variability and stability over longer timescales (>20-year). However, information on temporal variability in microorganism responses to medium- and long-term global warming is limited. In this study, we aimed to elucidate the temporal dynamics of microbial communities in response to global warming; to this end, we integrated data on the maintenance of species diversity, community composition, temporal turnover rates (v), and community assembly process in two typical ecosystems (meadows and shrub habitat) on the Qinghai-Tibet Plateau. Our results showed that 21 years of global warming would increase the importance of the deterministic process for microorganisms in both ecosystems across all seasons (R2 of grassland (GL) control: 0.524, R2 of GL warming: 0.467; R2 of shrubland (SL) control: 0.556, R2 of SL warming: 0.543), reducing species diversity and altering community composition. Due to environmental filtration pressure from 21 years of warming, the low turnover rate (v of warming: -3.13/-2.00, v of control: -2.44/-1.48) of soil microorganisms reduces the resistance and resilience of ecological communities, which could lead to higher community similarity and more clustered taxonomic assemblages occurring across years. Changes to temperature might increase selection pressure on specialist taxa, which directly causes dominant species (v of warming: -1.63, v of control: -2.49) primarily comprising these taxa to be more strongly impacted by changing temperature than conditionally (v of warming: -1.47, v of control: -1.75) or always rare taxa (v of warming: -0.57, v of control: -1.33). Evaluation of the seasonal rhythms of microorganisms in response to global warming revealed that the variability and stability of different microbial communities in different habitats had dissimilar biological and ecological performances when challenged with an external disturbance. The balance of competition and cooperation, because of environmental selection, also influenced ecosystem function in complex terrestrial ecosystems. Overall, our study enriches the limited information on the temporal variability in microorganism responses to 21 years of global warming, and provides a scientific basis for evaluating the impact of climate warming on the temporal stability of soil ecosystems.

Microeukaryotic predators shape the wastewater microbiome

The physicochemical parameters that shape the prokaryotic community composition in wastewater have been extensively studied. In contrast, it is poorly understood whether and how biotic interactions affect the prokaryotic community composition in wastewater. We used metatranscriptomics data from a bioreactor sampled weekly over 14 months to investigate the wastewater microbiome, including often neglected microeukaryotes. Our analysis revealed that while prokaryotes are unaffected by seasonal changes in water temperature, they are impacted by a seasonal, temperature-induced change in the microeukaryotic community. Our findings suggest that selective predation pressure exerted by microeukaryotes is a significant factor shaping the prokaryotic community in wastewater. This study underscores the importance of investigating the entire wastewater microbiome to develop a comprehensive understanding of wastewater treatment.

Global warming readiness: Feasibility of enhanced biological phosphorus removal at 35 °C

Recent research has shown enhanced biological phosphorus removal (EBPR) from municipal wastewater at warmer temperatures around 30 °C to be achievable in both laboratory-scale reactors and full-scale treatment plants. In the context of a changing climate, the feasibility of EBPR at even higher temperatures is of interest. We operated two lab-scale EBPR sequencing batch reactors for > 300 days at 30 °C and 35 °C, respectively, and followed the dynamics of the communities of polyphosphate accumulating organisms (PAOs) and competing glycogen accumulating organisms (GAOs) using a combination of 16S rRNA gene metabarcoding, quantitative PCR and fluorescence in situ hybridization analyses. Stable and nearly complete phosphorus (P) removal was achieved at 30 °C; similarly, long term P removal was stable at 35 °C with effluent PO₄^3-_P concentrations < 0.5 mg/L on half of all monitored days. Diverse and abundant Candidatus Accumulibacter amplicon sequence variants were closely related to those found in temperate environments, suggesting that EBPR at this temperature does not require a highly specialized PAO community. A slow-feeding strategy effectively limited the carbon uptake rates of GAOs, allowing PAOs to outcompete GAOs at both temperatures. Candidatus Competibacter was the main GAO, along with cluster III Defluviicoccus members. These organisms withstood the slow-feeding regime, suggesting that their bioenergetic characteristics of carbon uptake differ from those of their tetrad-forming relatives. Comparative cycle studies revealed higher carbon and P cycling activity of Ca. Accumulibacter when the temperature was increased from 30 °C to 35 °C, implying that the lowered P removal performance at 35 °C was not a direct effect of temperature, but a result of higher metabolic rates of carbon (and/or P) utilization of PAOs and GAOs, the resultant carbon deficiency, and escalated community competition. An increase in the TOC-to-PO₄^3--P ratio (from 25:1 to 40:1) effectively eased the carbon deficiency and benefited PAOs. In general, a slow-feeding strategy and sufficiently high carbon input benefited a high and stable EBPR at 35 °C, representing basic conditions suitable for full-scale treatment plants experiencing higher water temperatures.

Successions of rare and abundant microbial subcommunities during fish carcass decomposition in a microcosm under the influence of variable factors

Animal carcasses are hotspots of ecological activity. The study of the role of microbes in carcass decomposition has been exclusively focused on microbes with higher abundance. The comparative study of abundant and rare subcommunities associated with decomposition needs in-depth exploration. The current experiment has been conducted on the decomposition of a fish carcass in a microcosm. We conducted 16S rRNA gene sequencing of the microbial communities. The correlation of the physicochemical properties of tap and Yellow river water with the microbial communities was evaluated. Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria were found to be the dominant phyla in both abundant and rare subcommunities. Among bacteria, the Acidobacteria, Planctomycetes, and Cyanobacteria were found only in the rare subcommunity. In both subcommunities, the abundance of Proteobacteria was found to increase over time, and that of Firmicutes to decrease. The rare subcommunity shows higher alpha diversity than the abundant one. The variation in the abundant subcommunity was influenced by time and water type, and that in the rare subcommunity was influenced by pH and water type. These results have implications for future research on the ecological role of rare and abundant subcommunities in the decomposition of carcasses in the aquatic ecosystem.

Similar geographic patterns but distinct assembly processes of abundant and rare bacterioplankton communities in river networks of the Taihu Basin

Bacterioplankton play an important role in the biogeochemical cycling in rivers. The dynamics of hydrologic conditions in rivers were believed to affect geographic pattern and assembly process of these microorganisms, which have not been widely investigated. In this study, the geographic pattern and assembly process of bacterioplankton community in river networks of the Taihu Basin were systematically explored using amplicon sequencing of the 16S rRNA gene. The results showed that the diversity, structure,  and taxonomic composition of bacterioplankton community all exhibited significant temporal variation during wet, normal, and dry seasons (p<0.01). The neutral community model and null model were applied to reveal the assembly process of bacterioplankton community. The stochastic process and deterministic process both shaped the bacterioplankton community with greater influence of deterministic process. In addition, the abundant and rare bacterioplankton communities were comparatively analyzed. The abundant and rare bacterioplankton communities exhibited similar temporal dynamics (principal coordinates analysis) and spatial variations (distance-decay relationship), indicating similar geographic patterns. Meanwhile, distinct assembly processes were observed for the abundant and rare bacterioplankton communities. Stochastic process (dispersal limitation) shaped the abundant bacterioplankton community while deterministic process (heterogeneous selection) dominated the assembly process of rare bacterioplankton community. Mantel test, redundancy analysis, and correlation analysis together indicated that pH and dissolved oxygen were the major environmental attributes that affected thestructure and assembly process of bacterioplankton community. These results expanded our understanding of the geographic pattern, assembly process, and driving factors of bacterioplankton community in river networks and provided clues for the underlying mechanisms.

Metagenomic community composition and resistome analysis in a full-scale cold climate wastewater treatment plant

BACKGROUND

Wastewater treatment plants are an essential part of maintaining the health and safety of the general public. However, they are also an anthropogenic source of antibiotic resistance genes. In this study, we characterized the resistome, the distribution of classes 1-3 integron-integrase genes (intI1, intI2, and intI3) as mobile genetic element biomarkers, and the bacterial and phage community compositions in the North End Sewage Treatment Plant in Winnipeg, Manitoba. Samples were collected from raw sewage, returned activated sludge, final effluent, and dewatered sludge. A total of 28 bacterial and viral metagenomes were sequenced over two seasons, fall and winter. Integron-integrase genes, the 16S rRNA gene, and the coliform beta-glucuronidase gene were also quantified during this time period.

RESULTS

Bacterial classes observed above 1% relative abundance in all treatments were Actinobacteria (39.24% ± 0.25%), Beta-proteobacteria (23.99% ± 0.16%), Gamma-proteobacteria (11.06% ± 0.09%), and Alpha-proteobacteria (9.18 ± 0.04%). Families within the Caudovirales order: Siphoviridae (48.69% ± 0.10%), Podoviridae (23.99% ± 0.07%), and Myoviridae (19.94% ± 0.09%) were the dominant phage observed throughout the NESTP. The most abundant bacterial genera (in terms of average percent relative abundance) in influent, returned activated sludge, final effluent, and sludge, respectively, includes Mycobacterium (37.4%, 18.3%, 46.1%, and 7.7%), Acidovorax (8.9%, 10.8%, 5.4%, and 1.3%), and Polaromonas (2.5%, 3.3%, 1.4%, and 0.4%). The most abundant class of antibiotic resistance in bacterial samples was tetracycline resistance (17.86% ± 0.03%) followed by peptide antibiotics (14.24% ± 0.03%), and macrolides (10.63% ± 0.02%). Similarly, the phage samples contained a higher prevalence of macrolide (30.12% ± 0.30%), peptide antibiotic (10.78% ± 0.13%), and tetracycline (8.69% ± 0.11%) resistance. In addition, intI1 was the most abundant integron-integrase gene throughout treatment (1.14 × 104 gene copies/mL) followed by intI3 (4.97 × 103 gene copies/mL) while intI2 abundance remained low (6.4 × 101 gene copies/mL).

CONCLUSIONS

Wastewater treatment successfully reduced the abundance of bacteria, DNA phage and antibiotic resistance genes although many antibiotic resistance genes remained in effluent and biosolids. The presence of integron-integrase genes throughout treatment and in effluent suggests that antibiotic resistance genes could be actively disseminating resistance between both environmental and pathogenic bacteria.

Microbial Community Composition in Municipal Wastewater Treatment Bioreactors Follows a Distance Decay Pattern Primarily Controlled by Environmental Heterogeneity

Understanding spatiotemporal patterns in microbial community composition is a central goal of microbial ecology. The objective of this study was to better understand the biogeography of activated sludge microbial communities, which are important for the protection of surface water quality. Monthly samples were collected from 20 facilities (25 bioreactors) within 442 km of each other for 1 year. Microbial community composition was characterized by sequencing of PCR-amplified 16S rRNA gene fragments. Statistically significant distance decay of community similarity was observed in these bioreactors independent of clustering method (operational taxonomic units [OTUs] at 97% similarity, genus-level phylotypes) and community dissimilarity metric (Sørensen, Bray-Curtis, and weighted Unifrac). Universal colonizers (i.e., detected in all samples) and ubiquitous genus-level phylotypes (i.e., detected in every facility at least once) also exhibited a significant distance decay relationship. Variation partitioning analysis of community composition showed that environmental characteristics (temperature, influent characteristics, etc.) explained more of the variance in community composition than geographic distance did, suggesting that environmental heterogeneity is more important than dispersal limitation as a mechanism for determining microbial community composition. Distance decay relationships also became stronger with increasing distance between facilities. Seasonal variation in community composition was also observed from selected bioreactors, but there was no clear seasonal pattern in the distance decay relationships.

IMPORTANCE Understanding the spatiotemporal patterns of biodiversity is a central goal of ecology. The distance decay of community similarity is one of the spatial scaling patterns observed in many forms of life, including plants, animals, and microbial communities. Municipal wastewater treatment relies on microorganisms to prevent the release of excessive quantities of nutrients and other pollutants, but relatively few studies have explored distance decay relationships in wastewater treatment bioreactors. Our results demonstrate a strong distance decay pattern in wastewater treatment bioreactors, regardless of the sequence clustering method or the community dissimilarity metric. Our results suggest that microbial communities in wastewater treatment bioreactors are not randomly assembled but rather exhibit a statistically significant spatial pattern.

High salinity gradients and intermediate spatial scales shaped similar biogeographical and co-occurrence patterns of microeukaryotes in a tropical freshwater-saltwater ecosystem

Microeukaryotes play key ecological roles in the microbial web of aquatic ecosystems. However, large knowledge gaps urgently need to be filled regarding the biogeography with associated shaping mechanisms and co-occurrence patterns of microeukaryotes under freshwater-saltwater gradients, especially true in tropical regions. Here, we investigated microeukaryotes of six mixed freshwater-saltwater regions in the Pearl River Estuary and surrounding coasts in southern China, with salinity ranging 0.1-32.0% and distances spanned up to 500 km, using molecular ecological methods. Results indicate that the biogeography of abundant and rare microeukaryotic communities was similar, both their co-occurrence patterns and biogeographical patterns were driven by deterministic and stochastic processes. The environmental factors with higher selective pressure than dispersal limitation meant that the role of deterministic process in structuring communities was more significant than that of stochastic process, and salinity played important role in structuring both microeukaryotic communities and networks. The abundant communities had stronger influence on entire microeukaryotic communities and seemed to be more sensitive to environmental changes than their rare counterparts, while rare ones had stronger interspecific relationships. Finally, the geographic scale and environmental gradients of study regions should firstly be clarified in future research on the ecological processes of microeukaryotes before conclusions are drawn.

Transient-rare Bacterial Taxa Are Assembled Neutrally across Temporal Scales

Despite the importance of microbial communities in ecosystem functions, the mechanisms underlying the assembly of rare taxa over time are poorly understood. It remains largely unknown whether rare taxa exhibit similar assembly processes to common taxa in local communities. We herein retrieved the 16S rRNA sequences of bacteria collected bimonthly for 2 years from the Pohang wastewater treatment plant. The transient-rare taxa showed different abundance distributions from the common taxa. Transient-rare taxon assemblages also exhibited higher temporal variations than common taxon assemblages, suggesting the distinct ecological patterns of the two assemblages. A multivariate analysis revealed that environmental parameters accounted for 25.3 and 61.6% of temporal variations in the transient-rare and common taxon assemblages, respectively. The fitting of all observed taxa to a neutral community model revealed that 96.4% of the transient-rare taxa (relative abundance, 71.4%) and 73.3% of the common taxa (relative abundance, 45.6%) followed the model, suggesting that stochastic mechanisms were more important than deterministic ones in the assembly of the transient-rare taxa. Collectively, the present results indicate that the transient-rare bacterial taxa at the Pohang wastewater treatment plant differed from the common taxa in ecological patterns, suggesting that dispersal is a key process in their assembly.

Identifying the Biogeographic Patterns of Rare and Abundant Bacterial Communities Using Different Primer Sets on the Loess Plateau

High-throughput sequencing is commonly used to study soil microbial communities. However, different primers targeting different 16S rRNA hypervariable regions often generate different microbial communities and result in different values of diversity and community structure. This study determined the consequences of using two bacterial primers (338f/806r, targeting the V3-V4 region, and 520f/802r, targeting the V4 region) to assess bacterial communities in the soils of different land uses along a latitudinal gradient. The results showed that the variations in the soil bacterial diversity in different land uses were more evident based on the former pair. The statistical results showed that land use had no significant impact on soil bacterial diversity when primer pair 520f/802r was used. In contrast, when primer pair 338f/806r was used, the cropland and orchard soils had significantly higher operational taxonomic units (OTUs) and Shannon diversity index values than those of the shrubland and grassland soils. Similarly, the soil bacterial diversity generated by primer pair 338f/806r was significantly impacted by mean annual precipitation, soil total phosphorus (TP), soil total nitrogen (TN), and soil available phosphorus (AVP), while the soil bacterial diversity generated by primer pair 520f/802r showed no significant correlations with most of these environmental factors. Multiple regression models indicated that soil pH and soil organic carbon (SOC) shaped the soil bacterial community structure on the Loess Plateau regardless of what primer pair was used. Climatic conditions mainly affected the diversity of rare bacteria. Abundant bacteria are more sensitive than rare bacteria to environmental changes. Very little of the variation in the rare bacterial community was explained by environmental factors or geographic distance, suggesting that the communities of rare bacteria are unpredictable. The distributions of the abundant taxa were mainly determined by variations in environmental factors.

Pilot study of thermal alkaline pretreatment of waste activated sludge: Seasonal effects on anaerobic digestion and impact on dewaterability and refractory COD

Thermal alkaline pretreatment (TAP) of waste activate sludge (WAS) was carried out in pilot-scale over a year to investigate its seasonal effects on anaerobic digestion and its impact on dewaterability, sludge liquor quality and formation of soluble refractory COD (sCOD_ref). Temperature of TAP was set at 65-70 °C and pH was increased by initial dosing of sodium hydroxide [NaOH] (50% w/w, 1-2.5 mL/L sludge) as alkali agent following 2-2.5 h reaction time. Pilot digesters were fed with primary sludge (PS) and hydrolyzed WAS (HWAS) and compared to a reference digester fed with PS and untreated WAS. Biogas yield increase due to TAP of WAS showed a sinusoidal trend throughout the year with maximum in summer (+42%), minimum in winter (+3%) and average of +20%, indicating a strong seasonal effect on TAP efficiency. Ammonium [NH₄⁺-N], orthophosphate [PO₄^3--P] and sulphate [SO₄^2-] in sludge liquor increased by 34.6%, 17.0% and 21.6% with TAP, respectively. Centrifugation tests showed no significant difference in dewaterability of both digestates with respect to total solids of sludge cake. Normalized capillary suction time of digestate increased due to TAP, indicating a lower capability for water release. Furthermore, detected sCOD_ref after batch aerobic biodegradation tests showed an increase of 30.3% with TAP. Hence, implementation of TAP of WAS in full-scale will potentially lead to an increase of 0.8-1.1 mg/L of sCOD_ref in effluent of six wastewater treatment plants (WWTP) in Berlin. In conclusion, TAP of WAS leads to increase in biogas production with a slighter negative impact on effluent COD quality than high-temperature thermal hydrolysis.

Press Disturbance Alters Community Structure and Assembly Mechanisms of Bacterial Taxa and Functional Genes in Mesocosm-Scale Bioreactors

Press disturbances are of interest in microbial ecology, as they can drive microbial communities to alternative stable states. However, the effect of press disturbances in community assembly mechanisms, particularly with regard to taxa and functional genes at different levels of abundance (i.e., common and rare), remains largely unknown. Here, we tested the effect of a continuous alteration in substrate feeding scheme on the structure, function, and assembly of bacterial communities. Two sets of replicate 5-liter sequencing batch reactors were operated at two different organic carbon loads for a period of 74 days, following 53 days of acclimation after inoculation with sludge from a full-scale treatment plant. Temporal dynamics of community taxonomic and functional gene structure were derived from metagenomics and 16S rRNA gene metabarcoding data. Disturbed reactors exhibited different community function, structure, and assembly compared to undisturbed reactors. Bacterial taxa and functional genes showed dissimilar α-diversity and community assembly patterns. Deterministic assembly mechanisms were generally stronger in disturbed reactors and in common fractions compared to rare ones. Function quickly recovered after the disturbance was removed, but community structure did not. Our results highlight that functional gene data from metagenomics can indicate patterns of community assembly that differ from those obtained from taxon data. This study reveals how a joint evaluation of assembly mechanisms and community structure of bacterial taxa and functional genes as well as ecosystem function can unravel the response of complex microbial systems to a press disturbance.IMPORTANCE Ecosystem management must be viewed in the context of increasing frequencies and magnitudes of various disturbances that occur at different scales. This work provides a glimpse of the changes in assembly mechanisms found in microbial communities exposed to sustained changes in their environment. These mechanisms, deterministic or stochastic, can cause communities to reach a similar or variable composition and function. For a comprehensive view, we use a joint evaluation of temporal dynamics in assembly mechanisms and community structure for both bacterial taxa and their functional genes at different abundance levels, in both disturbed and undisturbed states. We further reverted the disturbance state to contrast recovery of function with community structure. Our findings are relevant, as very few studies have employed such an approach, while there is a need to assess the relative importance of assembly mechanisms for microbial communities across different spatial and temporal scales, environmental gradients, and types of disturbance.

Biogeographic patterns of abundant and rare bacterial and microeukaryotic subcommunities in connected freshwater lake zones subjected to different levels of nutrient loading

AIMS

To reveal whether the patterns of abundant and rare subcommunity composition of both bacteria and microeukaryotes vary between connected regions with different levels of nutrient loading in freshwater lakes.

METHODS AND RESULTS

We investigated the abundant and rare subcommunity composition of both bacteria and microeukaryotes in two connected zones (Meiliang Bay (MLB) and Xukou Bay (XKB)) of a large shallow freshwater Lake Taihu via the high-throughput sequencing of bacterial 16S rRNA and microeukaryotic 18S rRNA genes. Even though these two lake zones are connected and share a species bank, they diverge in community composition. Significantly higher alpha diversity was observed for the abundant bacterial subcommunity in the MLB. However, no significant difference in alpha diversity between the rare bacterial subcommunities, as well as both rare and abundant microeukaryotic subcommunities were observed between MLB and XKB. It is demonstrated that both environmental factors and geographic distance play central roles in controlling the rare and abundant microbial subcommunities in the two connected lake zones.

CONCLUSIONS

The abundant subcommunity composition of bacteria and microeukaryotes vary between connected regions with different levels of nutrient loading. Dispersal limitation plays a vital role in shaping microbial communities even in connected zones of freshwater lakes.

SIGNIFICANCE AND IMPACT OF THE STUDY

Leading to a comprehensive understanding of the characteristics of microbial community in connected lake regions with different levels of nutrient loading.

Stochastic Dispersal Rather Than Deterministic Selection Explains the Spatio-Temporal Distribution of Soil Bacteria in a Temperate Grassland

Spatial and temporal processes shaping microbial communities are inseparably linked but rarely studied together. By Illumina 16S rRNA sequencing, we monitored soil bacteria in 360 stations on a 100 square meter plot distributed across six intra-annual samplings in a rarely managed, temperate grassland. Using a multi-tiered approach, we tested the extent to which stochastic or deterministic processes influenced the composition of local communities. A combination of phylogenetic turnover analysis and null modeling demonstrated that either homogenization by unlimited stochastic dispersal or scenarios, in which neither stochastic processes nor deterministic forces dominated, explained local assembly processes. Thus, the majority of all sampled communities (82%) was rather homogeneous with no significant changes in abundance-weighted composition. However, we detected strong and uniform taxonomic shifts within just nine samples in early summer. Thus, community snapshots sampled from single points in time or space do not necessarily reflect a representative community state. The potential for change despite the overall homogeneity was further demonstrated when the focus shifted to the rare biosphere. Rare OTU turnover, rather than nestedness, characterized abundance-independent β-diversity. Accordingly, boosted generalized additive models encompassing spatial, temporal and environmental variables revealed strong and highly diverse effects of space on OTU abundance, even within the same genus. This pure spatial effect increased with decreasing OTU abundance and frequency, whereas soil moisture – the most important environmental variable – had an opposite effect by impacting abundant OTUs more than the rare ones. These results indicate that – despite considerable oscillation in space and time – the abundant and resident OTUs provide a community backbone that supports much higher β-diversity of a dynamic rare biosphere. Our findings reveal complex interactions among space, time, and environmental filters within bacterial communities in a long-established temperate grassland.

Dynamics and response of microbial diversity to nutritional conditions in denitrifying bioreactor for linear alkylbenzene sulfonate removal

The aim of this study was to evaluate the microbial structure and phylogenetic diversity under the influence of nutritional conditions and hydraulic retention time (HRT) in fluidized bed reactors (FBR), operated in short HRT (8 h - FBR8; 12 h - FBR12) for linear alkylbenzene sulfonate (LAS) removal from laundry wastewater. After each phase, biofilm samples from FBR8 and FBR12 were submitted to microbial sequencing by Mi-Seq Illumina®. Higher LAS removal rates were observed after 313 days, achieving 99 ± 3% in FBR12 (22.5 ± 5.9 mg LAS/L affluent) and 93 ± 12% in FBR8 (20.6 ± 4.4 mg LAS/L affluent). Different modifications involving genera of bacteria were observed throughout the reactors operation. The identified microorganisms were, mostly, related to LAS degradation and nitrogen conversion such as Dechloromonas, Flavobacterium, Pseudomonas, and Zoogloea.

Distinct Assembly Mechanisms Underlie Similar Biogeographic Patterns of Rare and Abundant Bacterioplankton in Cascade Reservoirs of a Large River

Bacterioplankton communities commonly consist of few highly abundant species and a large number of rare species that play key roles in biogeochemical cycles of aquatic ecosystems. However, little is known about the biogeographic assemblies of these communities, especially in large rivers suffering from cascade dam regulation. Here, we used a 16S rRNA gene amplicon sequencing approach to investigate the biogeographic patterns and underlying assembly mechanisms of abundant and rare bacterioplankton taxa in cascade reservoirs of the Jinsha River in China. The results revealed species loss of bacterioplankton due to dam construction, which was more significant for rare taxa than for abundant ones. The distributions of abundant and rare taxa exhibited similar spatial and temporal patterns, which were significantly distinct between winter and summer and between upstream and downstream reservoirs. Both spatial (dispersal-related process) and environmental (selection process) factors seemed to together govern the assembly and biogeography of abundant and rare taxa, although both factors explained only a small fraction of variation in the rare taxa. More importantly, environmental factors explained more community variation in abundant sub-community than that in rare sub-community. Co-occurrence network analysis revealed that abundant species with closer interactions were more often located in a central position of the network compared with rare species. Nevertheless, half of the keystone species were rare species and may play important roles in maintaining the network stability. Overall, these findings indicate that distinct assembly mechanisms underlie the similar biogeography of rare and abundant bacteria in cascade reservoirs of a large river.

Stochastic processes shape microeukaryotic community assembly in a subtropical river across wet and dry seasons

BACKGROUND

The deep mechanisms (deterministic and/or stochastic processes) underlying community assembly are a central challenge in microbial ecology. However, the relative importance of these processes in shaping riverine microeukaryotic biogeography is still poorly understood. Here, we compared the spatiotemporal and biogeographical patterns of microeukaryotic community using high-throughput sequencing of 18S rRNA gene and multivariate statistical analyses from a subtropical river during wet and dry seasons.

RESULTS

Our results provide the first description of biogeographical patterns of microeukaryotic communities in the Tingjiang River, the largest river in the west of Fujian province, southeastern China. The results showed that microeukaryotes from both wet and dry seasons exhibited contrasting community compositions, which might be owing to planktonic microeukaryotes having seasonal succession patterns. Further, all components of the microeukaryotic communities (including total, dominant, always rare, and conditionally rare taxa) exhibited a significant distance-decay pattern in both seasons, and these communities had a stronger distance-decay relationship during the dry season, especially for the conditionally rare taxa. Although several variables had a significant influence on the microeukaryotic communities, the environmental and spatial factors showed minor roles in shaping the communities. Importantly, these microeukaryotic communities were strongly driven by stochastic processes, with 89.9%, 88.5%, and 89.6% of the community variation explained by neutral community model during wet, dry, and both seasons, respectively. The neutral community model also explained a large fraction of the community variation across different taxonomic groups and levels. Additionally, the microeukaryotic taxa, which were above and below the neutral prediction, were ecologically and taxonomically distinct groups, which might be interactively structured by deterministic and stochastic processes.

CONCLUSIONS

This study demonstrated that stochastic processes are sufficient in shaping substantial variation in river microeukaryotic metacommunity across different hydrographic regimes, thereby providing a better understanding of spatiotemporal patterns, processes, and mechanisms of microeukaryotic community in waters.

Importance of Species Sorting and Immigration on the Bacterial Assembly of Different-Sized Aggregates in a Full-Scale Aerobic Granular Sludge Plant

In aerobic granular sludge (AGS) systems, different-sized microbial aggregates having different solids retention time (SRT) coexist in the same reactor compartment and are subjected to the same influent wastewater. Thus, the AGS system provides a unique ecosystem to study the importance of local (species sorting) and regional (immigration) processes in bacterial community assembly. The microbial communities of different-sized aggregates (flocs <0.2 mm, small granules (0.2-1.0 mm) and large granules >1.0 mm), influent wastewater, excess sludge and effluent of a full-scale AGS plant were characterized over a steady-state operation period of 6 months. Amplicon sequencing was integrated with mass balance to determine the SRT and net growth rate of operational taxonomic units (OTUs). We found strong evidence of species sorting as opposed to immigration, which was significantly higher at short SRT (i.e., flocs and small granules) than that at long SRT (large granules). Rare OTUs in wastewater belonging to putative functional groups responsible for nitrogen and phosphorus removal were progressively enriched with an increase in microbial aggregates size. In contrast, fecal- and sewage infrastructure-derived microbes progressively decreased in relative abundance with increase in microbial aggregate size. These findings highlight the importance of AGS as a unique model ecosystem to study fundamental microbial ecology concepts.

The Composition and Assembly of Bacterial Communities across the Rhizosphere and Phyllosphere Compartments of Phragmites Australis

The rhizosphere and the phyllosphere represent two different epiphytic compartments of host plant, which are closely related to plant growth, health, and productivity. However, the understanding of the diversity, composition, and assembly of the bacterial communities in different epiphytic microenvironments of large emerged macrophytes has remained elusive, especially the abundant and rare taxa across rhizosphere and phyllosphere communities. In this study, we collected samples of two different epiphytic compartments (rhizosphere and phyllosphere) of Phragmites australis. Both 16S rRNA gene-based high-throughput sequencing and null-model analysis were employed to determine the difference in the composition and assembly of above-mentioned epiphytic bacterial communities. Our results indicated that bacterial communities of rhizosphere exhibited higher diversity and richness than those of phyllosphere. Deterministic processes dominated the assembly of bacterial community in both compartments, and stochastic processes contributed a certain proportion (30.30%) in the assembly of phyllosphere bacterial community. We also found that rare taxa contributed more significantly to the alpha- and beta-diversity of bacterial community than those of abundant taxa. The obtained data are useful for better understanding the bacterial community of different epiphytic compartments of P. australis.

Long-term dynamics of the bacterial community in a Swedish full-scale wastewater treatment plant

The operational efficiency of activated sludge wastewater treatment plants depends to a large extent on the microbial community structure of the activated sludge. The aims of this paper are to describe the composition of the bacterial community in a Swedish full-scale activated sludge wastewater treatment plant, to describe the dynamics of the community and to elucidate possible causes for bacterial community composition changes. The bacterial community composition in the activated sludge was described using 16S rRNA gene libraries and monitored for 15 months by a terminal restriction fragment (T-RF) length polymorphism (T-RFLP) analysis of the 16S rRNA gene. Despite variable environmental conditions, a large fraction of the observed T-RFs were present at all times, making up at least 50% in all samples, possibly representing a relatively stable core fraction of the bacterial community. However, the proportions of the different T-RFs in this fraction as well as the T-RFs in the more variable fraction showed a significant variation over time and temperature. The difference in community composition between summer and winter coincided with observed differences in floc structure. These observations suggest a relationship between floc properties and bacterial community composition, although additional experiments are required to determine causality.

Abundant and rare microbial sub-communities in anammox granules present contrasting assemblage patterns and metabolic functions in response to inorganic carbon stresses

Nitrogen-transforming microorganisms play pivotal roles for the microbial nitrogen-cycling network in the anammox granular system. However, little is known about the effects of inorganic carbon (IC) stresses on the assemblage patterns and functional profiles of abundant and rare taxa. Herein, the community assemblage and functional traits of abundant and rare sub-communities were investigated. Results revealed that insufficient IC had adverse influences on the process performance, while anammox activity could be recovered by IC addition. Co-occurrence network analysis indicated that abundant and rare sub-communities present divergent co-occurrence patterns. Additionally, environmental filtering had different influences on the ecological adaptability of bacterial sub-communities. Furthermore, qPCR results illustrated that NH₄⁺-N and NO₂^--N consumption were regulated by abundant sub-community, while their accumulation was mediated by rare sub-community. Collectively, these findings suggest that abundant and rare sub-communities present contrasting assemblage patterns and metabolic pathways, and functional profiles dominated selection of bacterial sub-communities under IC stresses.

Abundant and Rare Bacterioplankton in Freshwater Lakes Subjected to Different Levels of Tourism Disturbances

Anthropogenic disturbances have a negative impact on lake ecosystems, such as water environmental degradation. Bacterioplankton communities are essential components in lakes and consist of a few abundant species and several rare taxa. However, little is known about the community diversity and composition of abundant and rare bacterioplankton subjected to different levels of anthropogenic disturbances. In this study, water samples were collected from twelve freshwater lakes located around the city of Nanjing, China. Both Illumina MiSeq sequencing and multivariate statistical analysis were employed to determine the bacterioplankton community composition and its relation to environmental variables. The results indicated that tourism disturbances (mostly sewage discharge and tourist activities) altered the community structure of both abundant and rare bacterioplankton by changing water physicochemical characteristics. Alpha diversity of both abundant and rare taxa did not differ among different anthropogenic disturbance lakes (p > 0.05). Rare bacterial taxa possessed higher alpha diversity than abundant taxa, though rare taxa occupied a tiny portion of abundance (4.5%). Redundancy analysis demonstrated that dissolved organic carbon (DOC) was the most significant correlation variable for constraining the variation of abundant taxa, whereas total phosphorus (TP), ammonium nitrogen (NH4+-N), and chlorophyll-a (Chl-a) were the most dominant environmental factors constraining the rare taxa, indicating abundant and rare taxa may have different ecological niches.

Temporal dynamics of activated sludge bacterial communities in two diversity variant full-scale sewage treatment plants

Bacterial community in activated sludge (AS) is diverse and highly dynamic. Little is known about the mechanism shaping bacterial community composition and dynamics of AS and no study had quantitatively compared the contribution of abiotic environmental factors and biotic associations to the temporal dynamics of AS microbial communities with significantly different diversity. In this study, two full-scale sewage treatment plants (STPs) with distinct operational parameters and influent composition were sampled biweekly over 1 year to reveal the correlating factors to whole and sub-groups of AS bacterial community diversity and dynamics. The results show that the bacterial communities of the two STPs were entirely different and correlated with the influent composition and operating configurations. Bacterial associations represented by cohesion metrics and the environmental factor temperature were the primary correlated factors to the temporal bacterial community dynamics within each STP. The STP with high diversity and evenness could treat influent with higher suspended solid and a shorter sludge retention time, and was less correlated with environmental factors, implying the importance of diversity for AS system.

Biodegradation tests of mercaptocarboxylic acids, their esters, related divalent sulfur compounds and mercaptans

Mercaptocarboxylic acids and their esters, a class of difunctional compounds bearing both a mercapto and a carboxylic acid or ester functional group, are industrial chemicals of potential environmental concern. Biodegradation of such compounds was systematically investigated here, both by literature search and by experiments (Closed Bottle Test OECD 301D and Manometric Respirometry Test OECD 301F). These compounds were found either readily biodegradable or at least biodegradable to a significant extent. Some related compounds of divalent sulfur were tested for comparison (mercaptans, sulfides, disulfides). For the two relevant monofunctional compound classes, carboxylic acids/esters and mercaptans, literature data were compiled, and by comparison with structurally similar compounds without these functional groups, the influence of COOH/COOR' and SH groups on biodegradability was evaluated. Thereby, an existing rule of thumb for biodegradation of carboxylic acids/esters was supported by experimental data, and a rule of thumb could be formulated for mercaptans. Concurrent to biodegradation, abiotic processes were observed in the experiments, rapid oxidative formation of disulfides (dimerisation of monomercaptans and cyclisation of dimercaptans) and hydrolysis of esters. Some problems that compromise the reproducibility of biodegradation test results were discussed.

Linking nitrous oxide emissions to population dynamics of nitrifying and denitrifying prokaryotes in four full-scale wastewater treatment plants

Ammonia-oxidizing bacteria (AOB), ammonia oxidizing archaea (AOA) and N₂O-reducing denitrifiers were measured by quantitative real-time PCR (qPCR) in activated sludge samples from four full-scale wastewater treatment plants (WWTPs) in South Spain, and their abundances were linked to the generation of N₂O in the samples using multivariate analysis (Non-metric multidimensional scaling, MDS, and BIO-ENV). The average abundances of AOA remained in similar orders of magnitude in all WWTPs (10⁶ copies amoA/L activated sludge mixed liquor), while significant differences were detected for AOB (10⁵-10⁹copies amoA/L) and N₂O-reducers (10⁷-10¹⁰copies nosZ/L). Average N₂O emissions measured in activated sludge samples ranged from 0.10 ± 0.05 to 6.49 ± 8.89 mg N₂O-N/h/L activated sludge, and were strongly correlated with increased abundances of AOB and lower counts of N₂O-reducers. A significant contribution of AOA to N₂O generation was unlikely, since their abundance correlated negatively to N₂O emissions. AOB abundance was favoured by higher NO₃^- and NO₂^-concentrations in the activated sludge.

Community structures and population dynamics of "Candidatus Accumulibacter" in activated sludges of wastewater treatment plants using ppk1 as phylogenetic marker

Candidatus Accumulibacter has been identified as dominant polyphosphate-accumulating organisms (PAOs) in enhanced biological phosphorus (P) removal (EBPR) from wastewater. This study revealed the relevance of community structure, abundance and seasonal population dynamics of Candidatus Accumulibacter to process operation of wastewater treatment plants (WWTPs) in China using ppk1 gene as phylogenetic marker. All sludge samples had properties of denitrifying P removal using nitrate as an electron acceptor. Accumulibacter abundance in the anaerobic-anoxic-oxic (A²O) process was the highest (26% of total bacteria), and higher in winter than in summer with a better EBPR performance. Type-II was the dominant Accumulibacter in all processes, and type-I accounted for a small proportion of total Accumulibacter. The abundance of Clade-IIC as the most dominant clade reached 2.59×10⁹ cells/g MLSS and accounted for 87.3% of total Accumulibacter. Clade IIC mainly contributed to denitrifying P removal. Clades IIA, IIC and IID were found in all processes, while clade-IIF was only found in oxidation ditch process through phylogenetic analysis. High proportion of clade IID to total Accumulibacter led to poor performance of aerobic P-uptake in inverted A²O process. Therefore, Accumulibacter clades in WWTPs were diverse, and EBPR performance was closely related to the clade-level community structures and abundances of Accumulibacter.

Invasion by Cordgrass Increases Microbial Diversity and Alters Community Composition in a Mangrove Nature Reserve

Invasion by exotic plant species can alter ecosystem function and reduce native plant diversity, but relatively little is known about their effects on belowground microbial communities. Here we investigated the effects of exotic cordgrass (Spartina alterniflora) invasion on the distribution of soil bacterial communities in a mangrove nature reserve of the Jiulong River Estuary, southeast China using high-throughput sequencing of 16S rRNA gene and multivariate statistical analysis. Our results showed that S. alterniflora invasion altered soil properties, and significantly increased soil bacterial taxa richness, primarily by stimulating an increase in conditionally rare or rare taxa, and changes in community composition and function. Abundant, conditionally rare and rare subcommunities exhibited similar response patterns to environment changes, with both conditionally rare and rare taxa showing a stronger response than abundant ones. Habitat generalists were detected among abundant, conditionally rare and rare taxa, whereas habitat specialists were only identified among conditionally rare taxa and rare taxa. In addition, we found that vegetation was the key factor driving these patterns. However, our comparative analysis indicated that both environmental selection, and neutral process, significantly contributed to soil bacterial community assembly. These results could improve the understanding of the microbial processes and mechanisms of cordgrass invasion, and offer empirical data of use in the restoration and management of the mangrove wetlands.

Microbial Communities Shaped by Treatment Processes in a Drinking Water Treatment Plant and Their Contribution and Threat to Drinking Water Safety

Bacteria play an important role in water purification in drinking water treatment systems. On one hand, bacteria present in the untreated water may help in its purification through biodegradation of the contaminants. On the other hand, some bacteria may be human pathogens and pose a threat to consumers. The present study investigated bacterial communities using Illumina MiSeq sequencing of 16S rRNA genes and their functions were predicted using PICRUSt in a treatment system, including the biofilms on sand filters and biological activated carbon (BAC) filters, in 4 months. In addition, quantitative analyses of specific bacterial populations were performed by real-time quantitative polymerase chain reaction (qPCR). The bacterial community composition of post-ozonation effluent, BAC effluent and disinfected water varied with sampling time. However, the bacterial community structures at other treatment steps were relatively stable, despite great variations of source water quality, resulting in stable treatment performance. Illumina MiSeq sequencing illustrated that Proteobacteria was dominant bacterial phylum. Chlorine disinfection significantly influenced the microbial community structure, while other treatment processes were synergetic. Bacterial communities in water and biofilms were distinct, and distinctions of bacterial communities also existed between different biofilms. By contrast, the functional composition of biofilms on different filters were similar. Some functional genes related to pollutant degradation were found widely distributed throughout the treatment processes. The distributions of Mycobacterium spp. and Legionella spp. in water and biofilms were revealed by real-time quantitative polymerase chain reaction (qPCR). Most bacteria, including potential pathogens, could be effectively removed by chlorine disinfection. However, some bacteria presented great resistance to chlorine. qPCRs showed that Mycobacterium spp. could not be effectively removed by chlorine. These resistant bacteria and, especially potential pathogens should receive more attention. Redundancy analysis (RDA) showed that turbidity, ammonia nitrogen and total organic carbon (TOC) exerted significant effects on community profiles. Overall, this study provides insight into variations of microbial communities in the treatment processes and aids the optimization of drinking water treatment plant design and operation for public health.

Effects of an applied voltage on direct interspecies electron transfer via conductive materials for methane production

Direct interspecies electron transfer (DIET) between exoelectrogenic bacteria and methanogenic archaea via conductive materials is reported as an efficient method to produce methane in anaerobic organic waste digestion. A voltage can be applied to the conductive materials to accelerate the DIET between two groups of microorganisms to produce methane. To evaluate this hypothesis, two sets of anaerobic serum bottles with and without applied voltage were used with a pair of graphite rods as conductive materials to facilitate DIET. Initially, the methane production rate was similar between the two sets of serum bottles, and later the serum bottles with an applied voltage of 0.39V showed a 168% higher methane production rate than serum bottles without an applied voltage. In cyclic voltammograms, the characteristic redox peaks for hydrogen and acetate oxidation were identified in the serum bottles with an applied voltage. In the microbial community analyses, hydrogenotrophic methanogens (e.g. Methanobacterium) were observed to be abundant in serum bottles with an applied voltage, while methanogens utilizing carbon dioxide (e.g., Methanosaeta and Methanosarcina) were dominant in serum bottles without an applied voltage. Taken together, the applied voltage on conductive materials might not be effective to promote DIET in methane production. Instead, it appeared to generate a condition for hydrogenotrophic methanogenesis.

Taxonomic variability and functional stability in microbial communities infected by phages

Microbial communities can display large variation in taxonomic composition, yet this variation can coincide with stable metabolic functional structure and performance. The mechanisms driving the taxonomic variation within functional groups remain largely unknown. Biotic interactions, such as predation by phages, have been suggested as potential cause of taxonomic turnover, but the conditions for this scenario have not been rigorously examined. Further, it is unknown how predation by phages affects community function, and how these effects are modulated by functional redundancy in the communities. Here, we address these questions using a model for a methanogenic microbial community that includes several interacting metabolic functional groups. Each functional group comprises multiple competing clades, and each clade is attacked by a specialist lytic phage. Our model predicts that phages induce intense taxonomic turnover, resembling the variability observed in previous experiments. The functional structure and performance of the community are also disturbed by phage predation, but they become more stable as the functional redundancy in the community increases. The extent of this stabilization depends on the particular functions considered. Our model suggests mechanisms by which functional redundancy stabilizes community function and supports the interpretation that biotic interactions promote taxonomic turnover within microbial functional groups.

Microbial Population Dynamics and Ecosystem Functions of Anoxic/Aerobic Granular Sludge in Sequencing Batch Reactors Operated at Different Organic Loading Rates

The granular sludge process is an effective, low-footprint alternative to conventional activated sludge wastewater treatment. The architecture of the microbial granules allows the co-existence of different functional groups, e.g., nitrifying and denitrifying communities, which permits compact reactor design. However, little is known about the factors influencing community assembly in granular sludge, such as the effects of reactor operation strategies and influent wastewater composition. Here, we analyze the development of the microbiomes in parallel laboratory-scale anoxic/aerobic granular sludge reactors operated at low (0.9 kg m^-3d^-1), moderate (1.9 kg m^-3d^-1) and high (3.7 kg m^-3d^-1) organic loading rates (OLRs) and the same ammonium loading rate (0.2 kg NH₄-N m^-3d^-1) for 84 days. Complete removal of organic carbon and ammonium was achieved in all three reactors after start-up, while the nitrogen removal (denitrification) efficiency increased with the OLR: 0% at low, 38% at moderate, and 66% at high loading rate. The bacterial communities at different loading rates diverged rapidly after start-up and showed less than 50% similarity after 6 days, and below 40% similarity after 84 days. The three reactor microbiomes were dominated by different genera (mainly Meganema, Thauera, Paracoccus, and Zoogloea), but these genera have similar ecosystem functions of EPS production, denitrification and polyhydroxyalkanoate (PHA) storage. Many less abundant but persistent taxa were also detected within these functional groups. The bacterial communities were functionally redundant irrespective of the loading rate applied. At steady-state reactor operation, the identity of the core community members was rather stable, but their relative abundances changed considerably over time. Furthermore, nitrifying bacteria were low in relative abundance and diversity in all reactors, despite their large contribution to nitrogen turnover. The results suggest that the OLR has considerable impact on the composition of the granular sludge communities, but also that the granule communities can be dynamic even at steady-state reactor operation due to high functional redundancy of several key guilds. Knowledge about microbial diversity with specific functional guilds under different operating conditions can be important for engineers to predict the stability of reactor functions during the start-up and continued reactor operation.

Regional synchrony in full-scale activated sludge bioreactors due to deterministic microbial community assembly

Seasonal community structure and regionally synchronous population dynamics have been observed in natural microbial ecosystems, but have not been well documented in wastewater treatment bioreactors. Few studies of community dynamics in full-scale activated sludge systems facing similar meteorological conditions have been done to compare the importance of deterministic and neutral community assembly mechanisms. We subjected weekly activated sludge samples from six regional full-scale bioreactors at four wastewater treatment plants obtained over 1 year to Illumina sequencing of 16S ribosomal RNA genes, resulting in a library of over 17 million sequences. All samples derived from reactors treating primarily municipal wastewater. Despite variation in operational characteristics and location, communities displayed temporal synchrony at the individual operational taxonomic unit (OTU), broad phylogenetic affiliation and community-wide scale. Bioreactor communities were dominated by 134 abundant and highly regionally synchronized OTU populations that accounted for over 50% of the total reads. Non-core OTUs displayed abundance-dependent population synchrony. Alpha diversity varied by reactor, but showed a highly reproducible and synchronous seasonal fluctuation. Community similarity was dominated by seasonal changes, but individual reactors maintained minor stable differences after 1 year. Finally, the impacts of mass migration driven by direct biomass transfers between reactors was investigated, but had no significant effect on community similarity or diversity in the sink community. Our results show that population dynamics in activated sludge bioreactors are consistent with niche-driven assembly guided by seasonal temperature fluctuations.

Temporal dynamics of bacterioplankton communities in response to excessive nitrate loading in oligotrophic coastal water

Coastal ecosystems are receiving elevated loads of nitrogen (N) from anthropogenic sources. Understanding how excessive N loading affects bacterioplankton communities is critical to predict the biodiversity of marine ecosystems under conditions of eutrophic disturbance. In this study, oligotrophic coastal water microcosms were perturbed with nitrate in two loading modes: 1) one-off loading at the beginning of the incubation period; and 2) periodic loading every two days for 16days. Turnover in the bacterioplankton community was investigated by 16S rDNA gene amplicon sequencing. The alpha diversity of the bacterioplankton community showed great temporal variability and similar responses to the different treatments. Bacterioplankton community composition was influenced remarkably by time and N loading mode. The effects of N loading on bacterioplankton community structure showed obvious temporal variation, probably because of the great temporal variation in environmental parameters. This study provides insights into the effects of N pollution in anthropogenically perturbed marine environments.

Insights in Waste Management Bioprocesses Using Genomic Tools

Microbial capacities drive waste stabilization and resource recovery in environmental friendly processes. Depending on the composition of waste, a stress-mediated selection process ensures a scenario that generates a specific enrichment of microbial community. These communities dynamically change over a period of time while keeping the performance through the required utilization capacities. Depending on the environmental conditions, these communities select the appropriate partners so as to maintain the desired functional capacities. However, the complexities of these organizations are difficult to study. Individual member ratios and sharing of genetic intelligence collectively decide the enrichment and survival of these communities. The next-generation sequencing options with the depth of structure and function analysis have emerged as a tool that could provide the finer details of the underlying bioprocesses associated and shared in environmental niches. These tools can help in identification of the key biochemical events and monitoring of expression of associated phenotypes that will support the operation and maintenance of waste management systems. In this chapter, we link genomic tools with process optimization and/or management, which could be applied for decision making and/or upscaling. This review describes both, the aerobic and anaerobic, options of waste utilization process with the microbial community functioning as flocs, granules, or biofilms. There are a number of challenges involved in harnessing the microbial community intelligence with associated functional plasticity for efficient extension of microbial capacities for resource recycling and waste management. Mismanaged wastes could lead to undesired genotypes such as antibiotic/multidrug-resistant microbes.

High-rate activated sludge communities have a distinctly different structure compared to low-rate sludge communities, and are less sensitive towards environmental and operational variables

High-rate activated sludge processes allow for the recovery of organics and energy from wastewaters. These systems are operated at a short sludge retention time and high sludge-specific loading rates, which results in a higher sludge yield and better digestibility than conventional, low-rate activated sludge. Little is known about the microbial ecology of high-rate systems. In this work, we address the need for a fundamental understanding of how high-rate microbial communities differ from low-rate communities. We investigated the high-rate and low-rate communities in a sewage treatment plant in relation to environmental and operational variables over a period of ten months. We demonstrated that (1) high-rate and low-rate communities are distinctly different in terms of richness, evenness and composition, (2) high-rate community dynamics are more variable and less shaped by deterministic factors compared to low-rate communities, (3) sub-communities of continuously core and transitional members are more shaped by deterministic factors than the continuously rare members, both in high-rate and low-rate communities, and (4) high-rate community members showed a co-occurrence pattern similar to that of low-rate community members, but were less likely to be correlated to environmental and operational variables. These findings provide a basis for further optimization of high-rate systems, in order to facilitate resource recovery from wastewater.

Summer holidays as break-point in shaping a tannery sludge microbial community around a stable core microbiota

Recently, several investigations focused on the discovery of a bacterial consortium shared among different wastewater treatment plants (WWTPs). Nevertheless, the definition of a core microbiota over time represents the necessary counterpart in order to unravel the dynamics of bacterial communities in these environments. Here we performed a monthly survey on the bacterial community of a consortial industrial plant. Objectives of this study were: (1) to identify a core microbiota constant over time; (2) to evaluate the temporal dynamics of the community during one year. A conspicuous and diversified core microbiota is constituted by operational taxonomic units which are present throughout the year in the plant. Community composition data confirm that the presence and abundance of bacteria in WWTPs is highly consistent at high taxonomic level. Our results indicate however a difference in microbial community structure between two groups of samples, identifying the summer holiday period as the break-point. Changes in the structure of the microbial community occur otherwise gradually, one month after another. Further studies will clarify how the size and diversity of the core microbiota could affect the observed dynamics.

Performance Assessment of Full-Scale Wastewater Treatment Plants Based on Seasonal Variability of Microbial Communities via High-Throughput Sequencing

Microbial communities of activated sludge (AS) play a key role in the performance of wastewater treatment processes. However, seasonal variability of microbial population in varying AS-based processes has been poorly correlated with operation of full-scale wastewater treatment systems (WWTSs). In this paper, significant seasonal variability of AS microbial communities in eight WWTSs located in the city of Guangzhou were revealed in terms of 16S rRNA-based Miseq sequencing. Furthermore, variation redundancy analysis (RDA) demonstrated that the microbial community compositions closely correlated with WWTS operation parameters such as temperature, BOD, NH₄⁺-N and TN. Consequently, support vector regression models which reasonably predicted effluent BOD, SS and TN in WWTSs were established based on microbial community compositions. This work provided an alternative tool for rapid assessment on performance of full-scale wastewater treatment plants.

Enrichment of specific electro-active microorganisms and enhancement of methane production by adding granular activated carbon in anaerobic reactors

Direct interspecies electron transfer (DIET) via conductive materials can provide significant benefits to anaerobic methane formation in terms of production amount and rate. Although granular activated carbon (GAC) demonstrated its applicability in facilitating DIET in methanogenesis, DIET in continuous flow anaerobic reactors has not been verified. Here, evidences of DIET via GAC were explored. The reactor supplemented with GAC showed 1.8-fold higher methane production rate than that without GAC (35.7 versus 20.1±7.1mL-CH4/d). Around 34% of methane formation was attributed to the biomass attached to GAC. Pyrosequencing of 16S rRNA gene demonstrated the enrichment of exoelectrogens (e.g. Geobacter) and hydrogenotrophic methanogens (e.g. Methanospirillum and Methanolinea) from the biomass attached to GAC. Furthermore, anodic and cathodic currents generation was observed in an electrochemical cell containing GAC biomass. Taken together, GAC supplementation created an environment for enriching the microorganisms involved in DIET, which increased the methane production rate.