Quantifying community dynamics of nitrifiers in functionally stable reactors

Resistance of aerobic granular sludge microbiomes to periodic loss of biomass

Granular sludge is a biofilm process used for wastewater treatment which is currently being implemented worldwide. It is important to understand how disturbances affect the microbial community and performance of reactors. Here, two acetate-fed replicate reactors were inoculated with acclimatized sludge and the reactor performance, and the granular sludge microbial community succession were studied for 149 days. During this time, the microbial community was challenged by periodically removing half of the reactor biomass, subsequently increasing the food-to-microorganism (F/M) ratio. Diversity analysis together with null models show that overall, the microbial communities were resistant to the disturbances, observing some minor effects on polyphosphate-accumulating and denitrifying microbial communities and their associated reactor functions. Community turnover was driven by drift and random granule loss, and stochasticity was the governing ecological process for community assembly. These results evidence the aerobic granular sludge process as a robust system for wastewater treatment.

Functional guilds and drivers of diversity in seaweed-associated bacteria

Comparisons of functional and taxonomic profiles from bacterial communities in different habitats have suggested the existence of functional guilds composed of taxonomically or phylogenetically distinct members. Such guild membership is, however, rarely defined and the factors that drive functional diversity in bacteria remain poorly understood. We used seaweed-associated bacteria as a model to shed light on these important aspects of community ecology. Using a large dataset of over 1300 metagenome-assembled genomes from 13 seaweed species we found substantial overlap in the functionality of bacteria coming from distinct taxa, thus supporting the existence of functional guilds. This functional equivalence between different taxa was particularly pronounced when only functions involved in carbohydrate degradation were considered. We further found that bacterial taxonomy is the dominant driver of functional differences between bacteria and that seaweed species or seaweed type (i.e. brown, red and green) had relatively stronger impacts on genome functionality for carbohydrate-degradation functions when compared to all other cellular functions. This study provides new insight into the factors underpinning the functional diversity of bacteria and contributes to our understanding how community function is generated from individual members.

Dietary Effects of a Short-Term Administration of Microalgae Blend on Growth Performance, Tissue Fatty Acids, and Predominant Intestinal Microbiota in Sparus aurata

Given the potential of microalgae as new aquafeed ingredients, this study focuses on using a blend of microalgae, Tisochrysis lutea, Nannochloropsis gaditana, and Scenedesmus almeriensis, as a dietary ingredient for feeding Sparus aurata juveniles. The growth performance, carcass composition, tissue fatty acid profile, and intestinal microbiota were evaluated after a 30 day-feeding period. A microalgae-free diet was used as control, and three experimental diets were formulated containing 5%, 15%, and 25% of the microalgae blend (MB-5%, MB-15%, and MB-25%, respectively). After 7, 15, and 30 days of feeding experimental diets, biological samples were taken. Growth performance and nutrient utilization were not significantly modified at the end of the experiment. Microalgae inclusion tended to decrease body lipids and affected the fatty acid profile, especially MB-25 diet increased DHA levels. Diet MB-25 promoted appropriate microbial diversity, favoring the presence of probiotic bacteria, such as Lactobacillus, and significantly influencing the fatty acid composition and lipid metabolism in fish. In conclusion, using a short pulse of dietary administration of 25% microalgal blend in S. aurata modulates the intestinal microbiota and lipid composition while maintaining growth performance.

Comparison of prokaryotes between Mount Everest and the Mariana Trench

BACKGROUND

Mount Everest and the Mariana Trench represent the highest and deepest places on Earth, respectively. They are geographically separated, with distinct extreme environmental parameters that provide unique habitats for prokaryotes. Comparison of prokaryotes between Mount Everest and the Mariana Trench will provide a unique perspective to understanding the composition and distribution of environmental microbiomes on Earth.

RESULTS

Here, we compared prokaryotic communities between Mount Everest and the Mariana Trench based on shotgun metagenomic analysis. Analyzing 25 metagenomes and 1176 metagenome-assembled genomes showed distinct taxonomic compositions between Mount Everest and the Mariana Trench, with little taxa overlap, and significant differences in genome size, GC content, and predicted optimal growth temperature. However, community metabolic capabilities exhibited striking commonality, with > 90% of metabolic modules overlapping among samples of Mount Everest and the Mariana Trench, with the only exception for CO₂ fixations (photoautotrophy in Mount Everest but chemoautotrophy in the Mariana Trench). Most metabolic pathways were common but performed by distinct taxa in the two extreme habitats, even including some specialized metabolic pathways, such as the versatile degradation of various refractory organic matters, heavy metal metabolism (e.g., As and Se), stress resistance, and antioxidation. The metabolic commonality indicated the overall consistent roles of prokaryotes in elemental cycling and common adaptation strategies to overcome the distinct stress conditions despite the intuitively huge differences in Mount Everest and the Mariana Trench.

CONCLUSION

Our results, the first comparison between prokaryotes in the highest and the deepest habitats on Earth, may highlight the principles of prokaryotic diversity: although taxa are habitat-specific, primary metabolic functions could be always conserved. Video abstract.

Mathematical modelling of an intermittent anoxic/aerobic MBBR: Estimation of nitrification rates and energy savings

This study aimed at modelling the performance of a novel MBBR configuration, named A/O-MBBR, comprised of a pre-anoxic reactor, with an HRT of 4.5 h, coupled with an intermittent anoxic/aerobic MBBR (HRT = 6.8 h). The lab-scale system was fed with municipal wastewater with an average influent Total Ammonia Nitrogen (TAN) and total COD (TCOD) concentrations of 46 mg of TAN-N L^-1 and 310 mg TCOD L^-1. During the whole experimental period, TAN removal efficiency was always higher than 96%; denitrification was also very effective, achieving nitrate and nitrite concentrations in the effluent both lower than 5 mg NO_x-N L^-1 on average. Moreover, TCOD average removal efficiency was equal to 85%. Modelling was performed to investigate the nitrification efficacy enhancement; to this aim, a biofilm model was developed, adopting the equations for mixed-culture biofilms and the Activated Model Sludge n°1 (ASM1) for the biological processes rates. The model allowed to determine the maximum uptake rate for autotrophic growth (μ_A was 2.5 d^-1) and the semisaturation constant (K_OA was 0.2 mg O₂ L^-1), suggesting that the nitrification process was 3-fold faster than average and very effective at low oxygen concentrations. The model estimated that about 85% of TAN was removed by the biofilm and only the remaining part by suspended biomass in the bulk liquid. Finally, it was assessed that the A/O-MBBR configuration allowed for a 45-60% savings of the energy requirement compared to a Benchmark WWTP layout.

Interactions between Bacterial Inoculants and Native Soil Bacterial Community: the Case of Spore-forming Bacillus spp

Microbial diversity can restrict the invasion and impact of alien microbes into soils via resource competition. However, this theory has not been tested on various microbial invaders with different ecological traits, particularly spore-forming bacteria. Here we investigated the survival capacity of two introduced spore-forming bacteria, Bacillus mycoides (BM) and B. pumillus (BP) and their impact on the soil microbiome niches with low and high diversity. We hypothesized that higher soil bacterial diversity would better restrict Bacillus survival via resource competition, and the invasion would alter the resident bacterial communities' niches only if inoculants do not escape competition with the soil community (e.g. through sporulation). Our findings showed that BP could not survive as viable propagules and transiently impacted the bacterial communities' niche structure. This may be linked to its poor resource usage and low growth rate. Having better resource use capacities, BM better survived in soil, though its survival was weakly related to the remaining resources left for them by the soil community. BM strongly affected the community niche structure, ultimately in less diverse communities. These findings show that the inverse diversity-invasibility relationship can be valid for some spore-forming bacteria, but only when they have sufficient resource use capacity.

Composition of dissolved organic matter (DOM) in lakes responds to the trophic state and phytoplankton community succession

Dissolved organic matter (DOM), a heterogeneous mixture of diverse compounds with different molecular weights, is crucial for the lake carbon cycle. The properties and concentration of DOM in lakes are closely related to anthropogenic activities, terrigenous input, and phytoplankton growth. Thus, the lake's trophic state, along with the above factors, has an important effect on DOM. We determined the DOM sources and molecular composition in six lakes along a trophic gradient during and after phytoplankton bloom by combining optical techniques and the Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS). CDOM pools in eutrophic lakes may be more biologically refractory than in oligotrophic and mesotrophic lakes. Molecular formulas of DOM were positively correlated with the TSI (trophic state index) value (R² = 0.73), with the nitrogen-containing compounds (CHON) being the most abundant formulas in all studied lakes. Eutrophication modified the molecular formulas of DOM to have less CHO% and more heteroatom S-containing compounds (CHOS% and CHNOS%), and this was the synactic result of the anthropogenic perturbation and phytoplankton proliferation. In eutrophic lakes, summer DOM showed higher molecular lability than in autumn, which was related to the seasonal phytoplankton community succession. Although the phytoplankton-derived DOM is highly bioavailable, we detected a simpler and more fragile phytoplankton community ecosystem in autumn, which may be accompanied by a lower phytoplankton production and metabolic activity. Therefore, we concluded that the lake eutrophication increased the allochthonous DOM accumulation along with sewage and nutrient input, and subsequently increased its release with phytoplankton bloom. Eutrophication and phytoplankton growth are accompanied by more highly unsaturated compounds, O₃S+O₅S compounds, and carboxylic-rich alicyclic compounds (CRAMs), which are the biotransformation product of phytoplankton-derived DOM. Eutrophication may be a potential source of refractory DOM compounds for biodegradation and photodegradation. Our results can clarify the potential role of water organic matter in the future global carbon cycle processes, considering the increasing worldwide eutrophication of inland waters.

Performances and enhanced mechanisms of nitrogen removal in a submerged membrane bioreactor coupled sponge iron system

Sponge iron is a potential material for nitrogen removal, but lack of a study about nitrogen removal in a membrane bioreactor (MBR) coupled with sponge iron. The performances and mechanisms of nitrogen removal of SI-MBR were investigated and compared it with that in GAC-MBR. The results showed that the average rate of organic matter removal in the SI-MBR was 92.74%, which was higher than that in the GAC-MBR (87.48%). And the average effluent NO₂^--N and NO₃^--N concentration in the SI-MBR (0.02 mg/L and 3.73 mg/L) was lower than that in the GAC-MBR (0.05 mg/L and 7.51 mg/L). Meanwhile, the highest nitrification rate and denitrification rate was respectively 3.544 ± 0.25 mg/(g VSS·h) and 6.643 ± 0.2 mg/(g VSS·h) in the SI-MBR, which was higher than that (3.094 ± 0.25 mg/(g VSS·h) and (6.376 ± 0.2 mg/(g VSS·h)) in the GAC-MBR. Additionally, the bacterial activities (e.g., DHA activity and respiratory activity) were obviously enhanced through the iron ion from sponge iron. The bacterial community in the SI-MBR system was more richness and diverse than that in the GAC-MBR. Ultimately, the mechanisms of enhanced biological nitrogen removal with sponge iron in MBR were analyzed. On the surface of sponge iron, the DIRB and FOB could use the iron ion from sponge iron as the electron transfer to improve the nitrogen and organic removal. With sponge iron, there is not only the nitrification bacteria and heterotrophic denitrifying microorganism enriched, but also the autotrophic denitrifying bacteria abounded obviously. The autotrophic denitrifying bacteria could use Fe(II) as an electron donor to achieve denitrification and enhance the nitrogen removal.

Functional and Taxonomic Effects of Organic Amendments on the Restoration of Semiarid Quarry Soils

The application of organic amendments to mining soils has been shown to be a successful method of restoration, improving key physicochemical soil properties. However, there is a lack of a clear understanding of the soil bacterial community taxonomic and functional changes that are brought about by these treatments. We present further metagenomic sequencing (MGS) profiling of the effects of different restoration treatments applied to degraded, arid quarry soils in southern Spain which had previously been profiled only with 16S rRNA gene (16S) and physicochemical analyses. Both taxonomic and functional MGS profiles showed clear separation of organic treatment amendments from control samples, and although taxonomic differences were quite clear, functional redundancy was higher than expected and the majority of the latter signal came from the aggregation of minor (<0.1%) community differences. Significant taxonomic differences were seen with the presumably less-biased MGS-for example, the phylum Actinobacteria and the two genera Chloracidobacterium (Acidobacteria) and Paenibacillus (Firmicutes) were determined to be major players by the MGS and this was consistent with their potential functional roles. The former phylum was much less present, and the latter two genera were either minor components or not detected in the 16S data. Mapping of reads to MetaCyc/BioCyc categories showed overall slightly higher biosynthesis and degradation capabilities in all treatments versus control soils, with sewage amendments showing highest values and vegetable-based amendments being at intermediate levels, matching higher nutrient levels, respiration rates, enzyme activities, and bacterial biomass previously observed in the treated soils. IMPORTANCE The restoration of soils impacted by human activities poses specific challenges regarding the reestablishment of functional microbial communities which will further support the reintroduction of plant species. Organic fertilizers, originating from either treated sewage or vegetable wastes, have shown promise in restoration experiments; however, we still do not have a clear understanding of the functional and taxonomic changes that occur during these treatments. We used metagenomics to profile restoration treatments applied to degraded, arid quarry soils in southern Spain. We found that the assortments of individual functions and taxa within each soil could clearly identify treatments, while at the same time they demonstrated high functional redundancy. Functions grouped into higher pathways tended to match physicochemical measurements made on the same soils. In contrast, significant taxonomic differences were seen when the treatments were previously studied with a single marker gene, highlighting the advantage of metagenomic analysis for complex soil communities.

Linkage of community composition and function over short response time in anaerobic digestion systems with food fermentation wastewater

We investigated the short-term dynamics of microbial composition and function in bioreactors with inocula collected from full-scale and laboratory-based anaerobic digestion (AD) systems. The Bray-Curtis dissimilarity of both inocula was approximately 10% of the predicted Kyoto Encyclopedia of Genes and Genomes pathway and 40% of the taxonomic composition and yet resulted in a similar performance in methane production, implying that the variation of community composition may be decoupled from performance. However, the significant correlation of volatile fatty acids with taxonomic variation suggested that the pathways of AD could be different because of the varying genus. The predicted function of the significantly varying genus was mostly related to fermentation, which strengthened the conclusion that most microbial variation occurred within the fermentative species and led to alternative routes to result in similar methane production in methanogenic bioreactors. This finding sheds some light on the understanding of AD community regulation, which depends on the aims to recover intermediates or methane.

Lake microbial communities are not resistant or resilient to repeated large-scale natural pulse disturbances

Opportunities to study community level responses to extreme natural pulse disturbances in unaltered ecosystems are rare. Lake sediment records that span thousands of years can contain well resolved sediment pulses, triggered by earthquakes. These paleo-records provide a means to study repeated pulse disturbance and processes of resistance (insensitivity to disturbance) and ecological resilience (capacity to regain structure, function and process). In this study, sedimentary DNA was extracted from a sediment core from Lake Paringa (New Zealand) that is situated in a near natural catchment. Metabarcoding and inferred functions were used to assess the lake microbial community over the past 1,100 years - a period that included four major earthquakes. Microbial community composition and function differed significantly between highly perturbed (postseismic, c. 50 yrs) phases directly after the earthquakes and more stable (interseismic, c. 250 yr) phases, indicating a lack of community resistance. Although community structure differed significantly in successive postseismic phases, function did not, suggesting potential functional redundancy. Significant differences in composition and function in successive interseismic phases demonstrates communities are not resilient to large-scale natural pulse disturbances. The clear difference in structure and function, and high number of indicator taxa (responsible for driving differences in communities between phases) in the fourth interseismic phase likely represents a regime shift, possibly due to the two-fold increase in sediment and terrestrial biospheric organic carbon fluxes recorded following the fourth earthquake. Large pulse disturbances that enhance sediment inputs into lake systems may produce an underappreciated mechanism that destabilises lake ecosystem processes.

DNA metabarcoding of the leachate microbiota from sanitary landfill: potential for bioremediation process

Leachate generation contains a variety of toxic compounds, and is a major problem for municipal solid waste (MSW). Microbial profile knowledge is essential to new alternatives and improvements in current treatments of these effluents. In this respect, the microbial community in the leachate from the sanitary landfill of the city of Foz do Iguaçu was analyzed. The 16S rDNA metabarcoding suggested the dominance of fermenting bacteria belonging to Firmicutes phylum, followed by Proteobacteria, Bacteroidetes, and Synergistetes. The most abundant genera were Sedimentibacter, Vulcanibacillus, and Anaerovorax. However, 60% of amplicon sequence variants (ASVs) were not classified taxonomically. In addition, an expressive abundance was attributed to the superphylum known as PVC group, little studied and with unknown scientific potential. The leachate acidogenic phase was masked in the chemical and physical analyzes. Nevertheless, it was evidenced in the metabarcoding methodology. No specifically methanogenic group was detected in significant abundance. Therefore, from bacterial community identification, a bioremediation process can be designed. Enriched culture media can be developed and targeted to the recovery of specific groups which may be involved in leachate biodegradation. What is more, the results expand the knowledge of bacterial diversity, especially from the presence of unknown genera in this habitat.

Dietary tryptophan depletion alters the faecal bacterial community structure of compulsive drinker rats in schedule-induced polydipsia

RATIONALE

Compulsive behaviour, present in different psychiatric disorders such as obsessive-compulsive disorder, schizophrenia and drug abuse, is associated with altered levels of serotonin (5-hydroxytryptamine, 5-HT). The gut microbiota regulates tryptophan (TRP) metabolism and may affect global 5-H synthesis in the enteric and central nervous systems, suggesting a possible involvement of gut microbiota in compulsive spectrum disorders.

OBJECTIVES

The present study investigated whether chronic TRP depletion by diet alters the faecal bacterial community profiles of compulsive versus non-compulsive rats in schedule-induced polydipsia (SIP). Peripheral plasma 5-HT and brain-derived neurotrophic factor (BDNF) levels were evaluated.

METHODS

Wistar rats were selected as High Drinkers (HD) or Low Drinkers (LD) according to their SIP behaviour and were fed for 14 days with either a TRP-free diet (T-) or a TRP-supplemented diet (T+). The faecal bacterial community structure was investigated with 16S rRNA gene-targeted denaturing gradient gel electrophoresis (DGGE) fingerprinting analysis.

RESULTS

Compulsive HD rats showed a lower bacterial diversity than LD rats, irrespectively of the diet. The TRP-depleted HD rats, the only group increasing compulsive licking in SIP, showed a reduction of bacterial evenness and a highly functionally organized community compared with the other groups, indicating that this bacterial community is more fragile to external changes due to the dominance of a low number of species. The chronic TRP depletion by diet effectively reduced peripheral plasma 5-HT levels in both HD and LD rats, while plasma BDNF levels were not altered.

CONCLUSIONS

These results highlight the possible implication of reduced microbial diversity in compulsive behaviour and the involvement of the serotonergic system in modulating the gut brain-axis in compulsive spectrum disorders.

Probiotic Shewanella putrefaciens (SpPdp11) as a Fish Health Modulator: A Review

Aquaculture is considered one of the largest food production sectors in the world. Probiotics have long been considered as a beneficial tool in this industry since these microorganisms improve the welfare of different fish species by modulating several physiological functions, such as metabolism, digestion, immune response, stress tolerance, and disease resistance, among others. SpPdp11, a probiotic isolated from the skin of healthy gilthead seabream, has been the center of attention in a good number of studies since its discovery. The purpose of this paper is to summarize, comment, and discuss the current knowledge related to the effects of SpPdp11 in two commercially important fish species in aquaculture (gilthead seabream and Senegalese sole). Furthermore, some considerations for future studies are also indicated.

Multistability and Reversibility of Aerobic Granular Sludge Microbial Communities Upon Changes From Simple to Complex Synthetic Wastewater and Back

Aerobic granular sludge (AGS) is a promising alternative wastewater treatment to the conventional activated sludge system allowing space and energy saving. Basic understanding of AGS has mainly been obtained using simple wastewater containing acetate and propionate as carbon source. Yet, the aspect and performances of AGS grown in such model systems are different from those obtained in reactor treating real wastewater. The impact of fermentable and hydrolyzable compounds on already formed AGS was assessed separately by changing the composition of the influent from simple wastewater containing volatile fatty acids to complex monomeric wastewater containing amino acids and glucose, and then to complex polymeric wastewater containing also starch and peptone. The reversibility of the observed changes was assessed by changing the composition of the wastewater from complex monomeric back to simple. The introduction of fermentable compounds in the influent left the settling properties and nutrient removal performance unchanged, but had a significant impact on the bacterial community. The proportion of Gammaproteobacteria diminished to the benefit of Actinobacteria and the Saccharibateria phylum. On the other hand, the introduction of polymeric compounds altered the settling properties and denitrification efficiency, but induced smaller changes in the bacterial community. The changes induced by the wastewater transition were only partly reversed. Seven distinct stables states of the bacterial community were detected during the 921 days of experiment, four of them observed with the complex monomeric wastewater. The transitions between these states were not only caused by wastewater changes but also by operation failures and other incidences. However, the nutrient removal performance and settling properties of the AGS were globally maintained due to the functional redundancy of its bacterial community.

Functional redundancy imparts process stability to acidic Fe(II)-oxidizing microbial reactors

In previous work, lab-scale reactors designed to study microbial Fe(II) oxidation rates at low pH were found to have stable rates under a wide range of pH and Fe(II) concentrations. Since the stirred reactor environment eliminates many of the temporal and spatial variations that promote high diversity among microbial populations in nature, we were surprised that the reactors supported multiple taxa presumed to be autotrophic Fe(II) oxidizers based on their phylogeny. Metagenomic analyses of the reactor communities revealed differences in the metabolic potential of these taxa with respect to Fe(II) oxidation and carbon fixation pathways, acquisition of potentially growth-limiting substrates and the ability to form biofilms. Our findings support the hypothesis that the long-term co-existence of multiple autotrophic Fe(II)-oxidizing populations in the reactors are due to distinct metabolic potential that supports differential growth in response to limiting resources such as nitrogen, phosphorus and oxygen. Our data also highlight the role of biofilms in creating spatially distinct geochemical niches that enable the co-existence of multiple taxa that occupy the same apparent metabolic niche when the system is viewed in bulk. The distribution of key metabolic functions across different co-existing taxa supported functional redundancy and imparted process stability to these reactors.

Stochasticity in microbiology: managing unpredictability to reach the Sustainable Development Goals

Pure (single) cultures of microorganisms and mixed microbial communities (microbiomes) have been important for centuries in providing renewable energy, clean water and food products to human society and will continue to play a crucial role to pursue the Sustainable Development Goals. To use microorganisms effectively, microbial engineered processes require adequate control. Microbial communities are shaped by manageable deterministic processes, but also by stochastic processes, which can promote unforeseeable variations and adaptations. Here, we highlight the impact of stochasticity in single culture and microbiome engineering. First, we discuss the concepts and mechanisms of stochasticity in relation to microbial ecology of single cultures and microbiomes. Second, we discuss the consequences of stochasticity in relation to process performance and human health, which are reflected in key disadvantages and important opportunities. Third, we propose a suitable decision tool to deal with stochasticity in which monitoring of stochasticity and setting the boundaries of stochasticity by regulators are central aspects. Stochasticity may give rise to some risks, such as the presence of pathogens in microbiomes. We argue here that by taking the necessary precautions and through clever monitoring and interpretation, these risks can be mitigated.

Identifying the link between MBRs' key operating parameters and bacterial community: A step towards optimized leachate treatment

A MBR treating compost leachate was studied in order to link the operating parameters (solid and hydraulic retention time) to contaminant's specific bacterial catabolic activity. In this context, a lab-scale aerobic membrane bioreactor was operated for 200 days, at solid retention times (SRT) of 30 and 45 days and four different contaminant load rates. Results showed that increasing the food to microorganism ratio (F/M) by increasing the contaminant load rates lessened the selectivity pressure, which allowed the proliferation of subdominant operational taxonomic units (OTU) (relative abundance >3%) that were otherwise inhibited by highly adapted dominant OTUs (relative abundance >10%). Subsequently, increasing the SRT resulted in a lower species richness and the selection of two dominant types of bacteria: 1) genera with low growth rates that feed on non-limiting substrates or substrates with few competitors, and 2) genera with metabolisms that are highly specific to the available substrates and that can outcompete the other genera by using the substrate more efficiently. The bacterial population evolution observed during this study suggests that the mixed liquor population diversity and structure can be modulated with the operating conditions for the bioenhancement of contaminant specific catabolic activity. Identified dominant and subdominant genera were linked to the MBR's NH₄⁺ and COD removal performances. Interestingly, nitrification performances were unaffected by the organic load rate and the Nitrosomonas relative abundance.

Unraveling interactive characteristics of microbial community associated with bioelectric energy production in sludge fermentation fluid-fed microbial fuel cells

This first-attempt study deciphered the interactive characteristics of anodophilic microbial community-associated bioelectricity production in waste activated sludge (WAS) fermentation fluid-fed microbial fuel cells (MFCs). A novel schematic elucidation for illustrating synergistic interactions in anodic microbial consortia towards electrogenesis was proposed. Moreover, the specific genera of Pseudomonas, Desulfovibrio, Phyllobacterium, Desulfuromonas, Chelatococcus and Aminivibrio were dominant in anodic biofilms, leading to an electrogenesis efficiency of 1.254 kWh/kg COD and peak power density of 0.182 W/m² (at feeding level of 1.20 g COD/L). It was apparently higher than those MFCs fed with glucose/acetate. The fermentative species contributed positively in reorganizing microbial community structure in anodic biofilms, positively relating to electrogenesis via interactions with exoeletrogens in MFCs. Finally, a more electrogenesis was positively associated to larger anodic microbial diversity, relatively medium anodic community evenness, together with higher abundance of functional genes related to electrogenesis in functional species in MFCs fed with WAS fermentation fluid.

Insights into microbial community profiles associated with electric energy production in microbial fuel cells fed with food waste hydrolysate

Insights of microbial community profiles associated with electric energy production in microbial fuel cells (MFCs) fed with food waste hydrolysate (FWH) were investigated in this study. High power density of 0.173 W/m² was obtained from FWH which was produced from food waste after the pretreatment with fungal mash at an influent COD concentration of 1.2 g/L. The main genera in the MFCs fed with FWH were found to be Rummeliibacillus, Burkholderia, Enterococcus and Clostridium in anodic biofilms, leading to an electrogenesis efficiency of 0.977 kWh/kg COD higher than those obtained in MFCs with single carbon source feed. The key members in the anodic community responsible for electrogenesis were conceptually identified with their metabolic interactions in MFCs fed with FWH. It appeared that the syntrophic cooperation of fermentative species with exoelectrogens played an essential role in the generation of electric energy via specific microbes in anodic biofilm. The power produced from FWH was positively associated with microbial diversity, intermediate community evenness and abundance of functional genes for bioelectrogenesis.

Comparative study on pilots between ANAMMOX favored conditions in a partially saturated vertical flow constructed wetland and a hybrid system for rural wastewater treatment

The objective of this research was to evaluate the nitrogen removal in a single stage rural wastewater treatment system. It was a modified subsurface vertical flow (SSVF) constructed wetland. The so-called Anaerobic Ammonium Oxidation(ANAMMOX) process is favored by imposing a saturated zone at the bottom of the basin. The nitrogen removal performances of this modified SSVF were compared to those of a conventional hybrid system where the well-known nitrification-denitrification process is performed. This study was carried out using three lab-scale pilots of constructed wetlands during four months: (1) a hybrid constructed wetlands with a reed-Phragmites australis SSVF bed in serial with a cattail-Typha angustofolia SSHF bed (SSVF_p + SSHF). (2) A reed-Phragmites australis SSVF bed partially saturated at 40% of its depth (SSVF_PS); (3) A cattail-Typha angustofolia SSVF bed partially saturated at 40% of its depth (SSVF_TS). The results showed that the three configurations used in this study were efficient for most of the pollutants reduction. In fact, single-stage reactors have achieved similar chemical oxygen demand (COD) removal in comparison to the two-stage reactor independently of the macrophytes species. However, for Total Kjeldahl Nitrogen (TKN), a slightly higher nitrogen removal efficiency was recorded for (SSVF _p + SSHF) with an average removal rate of 53% versus 48% and 51% for SSVF _PS and SSVF_TS respectively. These findings were highlighted with fluorescent in situ hybridization (FISH) analysis, which demonstrated the presence of major differences in the community composition and abundance of the bacteria involved with denitrification and nitrification in the three systems. In fact, SSVF_P of the hybrid system was characterized by highest relative abundance of nitrifying bacteria (13% Nitrosomonas, 11% Nitrosospira, 14% Nitrospira and 10% Nitrobacter). While, the SSHF of hybrid system had larger number of denitrifying species than SSVF, with relative abundances of pseudomonas (3%), Paracoccus (9%), Zoogloea (6%), Thauera (4%), Thiobacillus (2%) and Aeromonas (1%). Interestingly, in the SSVF_ST (planted with Thypha angustofolia) where the relative abundance of nitrifying bacteria was very low (4% Nitrosomonas, 4% Nitrosospira, 4% Nitrospira and 1% Nitrobacter), we have detected the presence of ANAMMOX bacteria (3%). Accordingly SSVF_ST in the presence of Thypha angustofolia have favored the development of ANAMMOX activity in comparison to the other configurations.

Denitrification performance and microbial versatility in response to different selection pressures

This study investigated functional dynamics of microbial community in response to different selection pressures, with a focus on denitrification. Suspended-biomass experiments demonstrated limited aerobic and relatively higher anoxic nitrate and nitrite reduction capabilities; the highest NO₂-N and NO₃-N removal rates were 1.3 ± 0.1 and 0.74 ± 0.01 in aerobic and 1.4 ± 0.05 and 3.4 ± 0.1 mg/L.h in anoxic media, respectively. Key potential denitrifiers were identified as: (i) complete aerobic denitrifiers: Dokdonella, Flavobacterium, and Ca. Accumulibacter; (ii) complete anoxic denitrifiers: Acinetobacter, Pseudomonas, Arcobacter, and Comamonas; (iii) incomplete nitrite denitrifier: Diaphorobacter (aerobic/anoxic), (iv): incomplete nitrate denitrifiers: Thauera (aerobic/anoxic) and Zoogloea (strictly-aerobic). Granular biomass removed 72 mg/L NH₄-N with no NO_x^- accumulation. Heterotrophic nitrification and aerobic denitrification were proposed as the principal nitrogen removal pathway in granular reactors, potentially performed by two key organisms Thuaera and Flavobacterium. Biodiversity analysis suggested that the selection pressure of nourishment condition was the decisive factor for microbial selection and nitrogen removal mechanism.

Deterministic mechanisms define the long-term anaerobic digestion microbiome and its functionality regardless of the initial microbial community

The impact of the starting inoculum on long-term anaerobic digestion performance, process functionality and microbial community composition remains unclear. To understand the impact of starting inoculum, active microbial communities from four different full-scale anaerobic digesters were each used to inoculate four continuous lab-scale anaerobic digesters, which were operated identically for 295 days. Digesters were operated at 15 days solid retention time, an organic loading rate of 1 g COD L_r^-1 d^-1 (75:25 - cellulose:casein) and 37 °C. Results showed that long-term process performance, metabolic rates (hydrolytic, acetogenic, and methanogenic) and microbial community are independent of the inoculum source. Digesters process performance converged after 80 days, while metabolic rates and microbial communities converged after 120-145 days. The convergence of the different microbial communities towards a core-community proves that the deterministic factors (process operational conditions) were a stronger driver than the initial microbial community composition. Indeed, the core-community represented 72% of the relative abundance among the four digesters. Moreover, a number of positive correlations were observed between higher metabolic rates and the relative abundance of specific microbial groups. These correlations showed that both substrate consumers and suppliers trigger higher metabolic rates, expanding the knowledge of the nexus between microorganisms and functionality. Overall, these results support that deterministic factors control microbial communities in bioreactors independently of the inoculum source. Hence, it seems plausible that a desired microbial composition and functionality can be achieved by tuning process operational conditions.

Investigating the bacterial community and amoebae population in rural domestic wastewater reclamation for irrigation

Reclamation of domestic wastewater for agricultural irrigation is viewed as a sustainable option to create an alternative water source and address water scarcity. Free-living amoebae (FLA), which are amphizoic protozoa, are widely distributed in various environmental sources. The FLA could cause considerable environmental and health risks. However, little information is available on the risk of these protozoa. In this study, we evaluated the feasibility using rural domestic wastewater for agricultural irrigation, and analyzed dynamic changes of the microbial community structure and FLA populations in raw and treated wastewater, as well as the phyllosphere and rhizosphere of lettuce production sites that were irrigated with different water sources. The bacterial community dynamics were analyzed by terminal restriction fragment length polymorphism (T-RFLP). The bacterial community structures in the influent were similar to that in the effluent, while in some cases relative abundances varied significantly. The populations of Acanthamoeba spp. and Hartmannella vermiformis in the anaerobically treated wastewater were significantly higher than in the raw wastewater. The vegetables could harbor diverse amoebae, and the abundances of Acanthamoeba spp. and H. vermiformis in the rhizosphere were significantly higher than in the phyllosphere. Accordingly, our studies show insight into the distribution and dissemination of amoebae in wastewater treatment and irrigation practices.

Trends in bacterial and fungal communities in ant nests observed with Terminal-Restriction Fragment Length Polymorphism (T-RFLP) and Next Generation Sequencing (NGS) techniques-validity and compatibility in ecological studies

Microbes are ubiquitous and often occur in functionally and taxonomically complex communities. Unveiling these community dynamics is one of the main challenges of microbial research. Combining a robust, cost effective and widely used method such as Terminal Restriction Fragment Length Polymorphism (T-RFLP) with a Next Generation Sequencing (NGS) method (Illumina MiSeq), offers a solid alternative for comprehensive assessment of microbial communities. Here, these two methods were combined in a study of complex bacterial and fungal communities in the nest mounds of the ant Formica exsecta, with the aim to assess the degree to which these methods can be used to complement each other. The results show that these methodologies capture similar spatiotemporal variations, as well as corresponding functional and taxonomical detail, of the microbial communities in a challenging medium consisting of soil, decomposing plant litter and an insect inhabitant. Both methods are suitable for the analysis of complex environmental microbial communities, but when combined, they complement each other well and can provide even more robust results. T-RFLP can be trusted to show similar general community patterns as Illumina MiSeq and remains a good option if resources for NGS methods are lacking.

Influence of polyphenol rich seabuckthorn berries juice on release of polyphenols and colonic microbiota on exposure to simulated human digestion model

The present study investigated the effect of polyphenol rich Sea buckthorn berries juice (SBJ) on colonic microbial composition and diversity using in vitro simulated gut model. The release of polyphenols, their antioxidant activity and impact on microbial diversity was evaluated under long term fermentation for 21 days. The treatment of colonic reactors with basal feed supplemented with SBJ resulted in an increase in population and diversity of beneficial bacteria as revealed by viable cell count and PCR-DGGE. A higher release of phenolics was observed, which resulted in higher antioxidant activity in the colonic reactors throughout the treatment period (p < 0.05). Higher content of resveratrol, rutin and chlorogenic acid were observed in ascendens colon whereas quercetin, ferulic and caeffic acid level were higher in descendens colon due to biotransformation of polyphenols in the later part of colon. The Principal Component Analysis also indicated the stimulatory effect of SBJ on the beneficial microbial population of Lactobacilli, Bacteroides/Prevotella and Bifidobacteria in all the three reactors. It also confirmed higher release of polyphenolic compounds and associated antioxidant activities in descendens colon.

Function and functional redundancy in microbial systems

Microbial communities often exhibit incredible taxonomic diversity, raising questions regarding the mechanisms enabling species coexistence and the role of this diversity in community functioning. On the one hand, many coexisting but taxonomically distinct microorganisms can encode the same energy-yielding metabolic functions, and this functional redundancy contrasts with the expectation that species should occupy distinct metabolic niches. On the other hand, the identity of taxa encoding each function can vary substantially across space or time with little effect on the function, and this taxonomic variability is frequently thought to result from ecological drift between equivalent organisms. Here, we synthesize the powerful paradigm emerging from these two patterns, connecting the roles of function, functional redundancy and taxonomy in microbial systems. We conclude that both patterns are unlikely to be the result of ecological drift, but are inevitable emergent properties of open microbial systems resulting mainly from biotic interactions and environmental and spatial processes.

Insights into Feast-Famine polyhydroxyalkanoate (PHA)-producer selection: Microbial community succession, relationships with system function and underlying driving forces

The Feast-Famine (FF) process has been frequently used to select polyhydroxyalkanoate (PHA)-accumulating mixed cultures (MCs), but there has been little insight into the ecophysiology of the microbial community during the selection process. In three FF systems with well-defined conditions, synchronized variations in higher-order properties of MCs and complicate microbial community succession mainly including enrichment and elimination of non-top competitors and unexpected turnover of top competitors, were observed. Quantification of PHA-accumulating function genes (phaC) revealed that the top competitors maintained the PHA synthesis by playing consecutive roles when the highly dynamic turnover occurred. Due to its specific physiological characteristics during the PHA-accumulating process, Thauera strain OTU 7 was found to be responsible for the fluctuating SVI, which threatened the robustness of the FF system. This trait was also responsible for its later competitive exclusion by the other PHA-producer, Paracoccus strain OTU 1. Deterministic processes dominated the entire FF system, resulting in the inevitable microbial community succession in the acclimation phase and maintenance of the stable PHA-accumulating function in the maturation phase. However, neutral processes, likely caused by predation from bacterial phages, also occurred, which led to the unpredictable temporal dynamics of the top competitors.

Volatile fatty acid augmentation and microbial community responses in anaerobic co-fermentation process of waste-activated sludge mixed with corn stalk and livestock manure

This study investigated the acidogenic and microbiological perspectives in the anaerobic co-fermentation of waste-activated sludge (WAS) mixed with corn stalk (CS) and pig manure (PM). The volatile fatty acids (VFAs) increased dramatically to over 5000 mg COD/L accumulation just within 4-5 days with the feedstock carbon to nitrogen (C/N) ratio regulation of 20/1. The CS and PM addition enhanced the compressibility of fermentation residuals by increasing the particle distribution spread index (DSI). Moreover, the external carbon addition conduced to bacterial consortia diversity rising and uneven population distribution in the co-fermentation, which contributed to VFAs accumulation potentially. The organic loading rate (OLR) correlated with bacterial community closely at the early stage (days 1-5), while the oxidation-reduction potential (ORP) and pH played more important roles on bacterial consortia at the terminal stage (days 6-10). The C/N ratio adjustment by CS and PM and proper optimizations of OLR, pH, and ORP at various running stages facilitated VFA accumulation during the co-fermentation operation.

Enzymes catalyzing pre-hydrolysis facilitated the anaerobic fermentation of waste activated sludge with acidogenic and microbiological perspectives

This study investigated acidogenic and microbiological perspectives in the anaerobic fermentation (AF) of waste activated sludge (WAS) pre-hydrolyzed by enzymes catalysis. The enzymes catalysis boosted WAS biodegradability dramatically with nearly 8500 mg/L soluble chemical oxygen demand (SCOD) increase just within 4 h. The volatile fatty acids (VFAs) in the acidogenesis were accumulated effectively with over 3200 mg COD/L in 12 d, which reached 0.687 kWh/kg VSS electricity conversion efficiency (2.5 times higher than the control test). The fermentation process favored the compression of fermentative sludge with the distribution spread index (DSI) rising. The core populations of bacteria and archaea shifting enlarged the dissimilarity of communities at different fermentation stages. Increase of community diversity contributed to VFAs accumulation stability. Moreover, the intermediate bacterial community evenness favored VFAs accumulation potentially. The enzymes catalysis might be a promising solution for strengthening VFAs accumulation in the WAS fermentation with boosting the electricity conversion potential.

A year of monitoring 20 mesophilic full-scale bioreactors reveals the existence of stable but different core microbiomes in bio-waste and wastewater anaerobic digestion systems

BACKGROUND

Anaerobic digestion (AD) is a microbe-driven process of biomass decomposition to CH₄ and CO₂. In addition to renewable and cost-effective energy production, AD has emerged in the European Union as an environmentally friendly model of bio-waste valorisation and nutrient recycling. Nevertheless, due to the high diversity of uncharacterised microbes, a typical AD microbiome is still considered as "dark matter".

RESULTS

Using the high-throughput sequencing of small rRNA gene, and a monthly monitoring of the physicochemical parameters for 20 different mesophilic full-scale bioreactors over 1 year, we generated a detailed view of AD microbial ecology towards a better understanding of factors that influence and shape these communities. By studying the broadly distributed OTUs present in over 80% of analysed samples, we identified putatively important core bacteria and archaea to the AD process that accounted for over 70% of the whole microbial community relative abundances. AD reactors localised at the wastewater treatment plants were shown to operate with distinct core microbiomes than the agricultural and bio-waste treating biogas units. We also showed that both the core microbiomes were composed of low (with average community abundance ≤ 1%) and highly abundant microbial populations; the vast majority of which remains yet uncharacterised, e.g. abundant candidate Cloacimonetes. Using non-metric multidimensional scaling, we observed microorganisms grouping into clusters that well reflected the origin of the samples, e.g. wastewater versus agricultural and bio-waste treating biogas units. The calculated diversity patterns differed markedly between the different community clusters, mainly due to the presence of highly diverse and dynamic transient species. Core microbial communities appeared relatively stable over the monitoring period.

CONCLUSIONS

In this study, we characterised microbial communities in different AD systems that were monitored over a 1-year period. Evidences were shown to support the concept of a core community driving the AD process, whereas the vast majority of dominant microorganisms remain yet to be characterised.

Impact of multi-functional fermented goat milk beverage on gut microbiota in a dynamic colon model

The aim of this research was to evaluate the effect of grape probiotic fermented beverages made of goat milk, with or without added grape pomace on gut microbiota in a Simulator of Human Intestinal Microbial Ecosystem (SHIME®). SHIME® model was used to investigate to assess changes in microbial composition and fermentation metabolites (short- and branched-chain fatty acids and ammonium), as well as under the antioxidant capacity. The results demonstrated that the beverages formulated, with or without grape pomace extract, exhibited high dietary fiber, oleic acid, phenolic compounds content and antioxidant activity. Both beverages also kept L. rhamnosus and S. thermophilus viable during their passage through the intestinal tract and had a positive effect on gut microbiota metabolism, increasing the antioxidant capacity and the production of short-chain fatty acids, and decreasing the ammonium concentration. Therefore, the multifunctional beverages formulated in this study can offer a new perspective for the production of foods with positive potential effects on human health.

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.

Low temperature MBBR nitrification: Microbiome analysis

This study aims to investigate post carbon removal moving bed biofilm reactor (MBBR) nitrification through the transition from 20 °C to 1 °C and during through long term operation at 1 °C. Four pilot nitrifying MBBR reactors were operated at various ammonia loading rates to elucidate the temperature effects on ammonia removal rates, cell viability and bacterial communities. The transition from 20 °C to 1 °C and during long term operation at 1 °C were modeled using Arrhenius temperature correction coefficients. Specifically, the steady state removal rates at 1 °C on average were 22.8% of the maximum ammonia removal rate at 20 °C, which corresponds to an Arrhenius temperature correction of 1.086 during steady operation at 1 °C. The microbial communities of the nitrifying MBBR biofilm were shown to be significantly more diverse at 20 °C as compared to 1 °C operation. Although less diverse at 1 °C, 2000 species of bacteria were identified in the nitrifying biofilm during operation at this low temperature. Nitrosomonads were shown to be the dominant ammonia oxidizing bacteria (AOB) and Nitrospira was shown to be the dominant nitrite oxidizing bacteria (NOB) in all the pilot MBBR reactors at all temperatures. The performance of the post carbon removal nitrifying MBBR systems were shown to be enhanced at 1 °C by an increase in the viable embedded biomass as well as thicker biofilm. This effectively increases the number of viable cell present during low temperature operation, which partially compensates for the significant decrease in rate of ammonia removal per nitrifying cell. Operation at the highest loading conditions tested in this study at 1 °C were shown to reduce the ammonia removal rate compared to lower loading conditions at 1 °C. The lower performance at higher loading conditions at 1 °C demonstrated an enrichment in the stress response metagenomics pathways of the system.

Performance of a full-scale modified anaerobic/anoxic/oxic process: High-throughput sequence analysis of its microbial structures and their community functions

The average COD, TN, TP, and NH4(+)-N elimination rates in a new wastewater treatment plant (WWTP) based on a modified A2/O process were 83%, 72.4%, 93.5%, and 98.6%, respectively, even under conditions of a low C/N ratio and low temperature. Among the four potential denitrifying units, the post-anoxic unit was the least efficient with respect to the removal efficiency. However, the structures of the bacterial community among samples obtained from the treatment units were similar, as demonstrated using Illumina Miseq high-throughput sequencing. Genera with nitrifying, denitrifying, hydrolyzing, and glycogen-accumulating activities were identified in all units, indicating that functional groups were highly enriched in the active sludges and thus enabled nitrogen removal. The key functional microorganisms responsible for nitrification-denitrification in the WWTP were species belonging to the genera Nitrospira, Hydrogenophilaceae, Comamonas, Dechloromonas, Thauera, Haliangium, and Halomonas.

Dietary High Fluorine Alters Intestinal Microbiota in Broiler Chickens

This study investigated the effects of dietary high fluorine on ileal and cecal microbiota in broiler chickens. Two hundred eighty 1-day-old broiler chickens were randomly assigned to four groups and raised for 42 days. The control group was fed a corn-soybean basal diet (fluorine 22.6 mg/kg). The other three groups were fed the same basal diet, but supplemented with 400, 800, and 1200 mg/kg fluorine (high fluorine groups I, II, and III), administered in the form of sodium fluoride. The microbiota of ileal and cecal digesta was assessed with plate counts and polymerase chain reaction-based denaturing gradient gel electrophoresis (PCR-DGGE). It was found that, compared with those in the control group, the counts of Lactobacillus spp. and Bifidobacterium spp. were markedly decreased (P < 0.01 or P < 0.05), whereas the counts of Escherichia coli and Enterococcus spp. were significantly increased (P < 0.01 or P < 0.05) in the high fluorine groups II and III. PCR-DGGE analysis showed that the number of DGGE bands, similarity, and Shannon index of ileal and cecal bacteria were markedly reduced in the high fluorine groups II and III from 21 to 42 days. Sequencing analysis revealed that the composition of the intestinal microbiota was altered in the high fluorine groups. In conclusion, dietary fluorine in the range of 800-1200 mg/kg obviously altered the bacterial counts, and the diversity and composition of intestinal microbiota in broiler chickens, a finding which implies that dietary high fluorine can disrupt the natural balance and structure of the intestinal microbiota.

A Hardy Plant Facilitates Nitrogen Removal via Microbial Communities in Subsurface Flow Constructed Wetlands in Winter

The plants effect in subsurface flow constructed wetlands (SSF-CWs) is controversial, especially at low temperatures. Consequently, several SSF-CWs planted with Iris pseudacorus (CWI) or Typha orientalis Presl. (CWT) and several unplanted ones (CWC) were set up and fed with secondary effluent of sewage treatment plant during the winter in Eastern China. The 16S rDNA Illumina Miseq sequencing analysis indicated the positive effects of I. pseudacorus on the bacterial community richness and diversity in the substrate. Moreover, the community compositions of the bacteria involved with denitrification presented a significant difference in the three systems. Additionally, higher relative abundances of nitrifying bacteria (0.4140%, 0.2402% and 0.4318% for Nitrosomonas, Nitrosospira and Nitrospira, respectively) were recorded in CWI compared with CWT (0.2074%, 0.0648% and 0.0181%, respectively) and CWC (0.3013%, 0.1107% and 0.1185%, respectively). Meanwhile, the average removal rates of NH4(+)-N and TN in CWI showed a prominent advantage compared to CWC, but no distinct advantage was found in CWT. The hardy plant I. pseudacorus, which still had active root oxygen release in cold temperatures, positively affected the abundance of nitrifying bacteria in the substrate, and accordingly was supposed to contribute to a comparatively high nitrogen removal efficiency of the system during the winter.

Microbial Communities Are Well Adapted to Disturbances in Energy Input

Although microbial systems are well suited for studying concepts in ecological theory, little is known about how microbial communities respond to long-term periodic perturbations beyond diel oscillations. Taking advantage of an ongoing microcosm experiment, we studied how methanotrophic microbial communities adapted to disturbances in energy input over a 20-day cycle period. Sequencing of bacterial 16S rRNA genes together with quantification of microbial abundance and ecosystem function were used to explore the long-term dynamics (510 days) of methanotrophic communities under continuous versus cyclic chemical energy supply. We observed that microbial communities appeared inherently well adapted to disturbances in energy input and that changes in community structure in both treatments were more dependent on internal dynamics than on external forcing. The results also showed that the rare biosphere was critical to seeding the internal community dynamics, perhaps due to cross-feeding or other strategies. We conclude that in our experimental system, internal feedbacks were more important than external drivers in shaping the community dynamics over time, suggesting that ecosystems can maintain their function despite inherently unstable community dynamics. IMPORTANCE Within the broader ecological context, biological communities are often viewed as stable and as only experiencing succession or replacement when subject to external perturbations, such as changes in food availability or the introduction of exotic species. Our findings indicate that microbial communities can exhibit strong internal dynamics that may be more important in shaping community succession than external drivers. Dynamic "unstable" communities may be important for ecosystem functional stability, with rare organisms playing an important role in community restructuring. Understanding the mechanisms responsible for internal community dynamics will certainly be required for understanding and manipulating microbiomes in both host-associated and natural ecosystems.

Novel nitrifiers and comammox in a full-scale hybrid biofilm and activated sludge reactor revealed by metagenomic approach

Biofilms are widely used in wastewater treatment for their particular enhancement of nitrogen removal and other significant advantages. In this study, the diversity and potential functions of nitrogen removal bacteria in suspended activated sludge (AS) and biofilm of a full-scale hybrid reactor were uncovered by metagenomes (∼34 Gb), coupled with PCR-based 454 reads (>33 K reads). The results indicated that the diversity and abundance of nitrifiers and denitrifiers in biofilm did not surpass that in AS, while more nitrification and denitrification genes were indeed found in biofilm than AS, suggesting that the increased nitrogen removal ability by applying biofilm might be attributed to the enhancement of removal efficiency, rather than the biomass accumulation of nitrogen removal bacteria. The gene annotation and phylogenetic analysis results revealed that AS and biofilm samples consisted of 6.0 % and 9.4 % of novel functional genes for nitrogen removal and 18 % and 30 % of new Nitrospira species for nitrite-oxidizing bacteria, respectively. Moreover, the identification of Nitrospira-like amoA genes provided metagenomic evidence for the presence of complete ammonia oxidizer (comammox) with the functional potential to perform the complete oxidation of ammonia to nitrate. These findings have significant implications in expanding our knowledge of the biological nitrogen transformations in wastewater treatment.

Nitrification at different salinities: Biofilm community composition and physiological plasticity

This paper describes an experimental study of microbial communities of three moving bed biofilm reactors (MBBR) inoculated with nitrifying cultures originated from environments with different salinity; freshwater, brackish (20‰) and seawater. All reactors were run until they operated at a conversion efficiency of >96%. The microbial communities were profiled using 454-pyrosequencing of 16S rRNA gene amplicons. Statistical analysis was used to investigate the differences in microbial community structure and distribution of the nitrifying populations with different salinity environments. Nonmetric multidimensional scaling analysis (NMDS) and the PERMANOVA test based on Bray-Curtis similarities revealed significantly different community structure in the three reactors. The brackish reactor showed lower diversity index than fresh and seawater reactors. Venn diagram showed that 60 and 78% of the total operational taxonomic units (OTUs) in the ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) guild, respectively, were unique OTUs for a given reactor. Similarity Percentages (SIMPER) analysis showed that two-thirds of the total difference in community structure between the reactors was explained by 10 OTUs, indicating that only a small number of OTUs play a numerically dominant role in the nitrification process. Acute toxicity of salt stress on ammonium and nitrite oxidizing activities showed distinctly different patterns, reaching 97% inhibition of the freshwater reactor for ammonium oxidation rate. In the brackish culture, inhibition was only observed at maximal level of salinity, 32‰. In the fully adapted seawater culture, higher activities were observed at 32‰ than at any of the lower salinities.

Process Recovery after CaO Addition Due to Granule Formation in a CSTR Co-Digester-A Tool to Influence the Composition of the Microbial Community and Stabilize the Process?

The composition, structure and function of granules formed during process recovery with calcium oxide in a laboratory-scale fermenter fed with sewage sludge and rapeseed oil were studied. In the course of over-acidification and successful process recovery, only minor changes were observed in the bacterial community of the digestate, while granules appeared during recovery. Fluorescence microscopic analysis of the granules showed a close spatial relationship between calcium and oil and/or long chain fatty acids. This finding further substantiated the hypothesis that calcium precipitated with carbon of organic origin and reduced the negative effects of overloading with oil. Furthermore, the enrichment of phosphate minerals in the granules was shown, and molecular biological analyses detected polyphosphate-accumulating organisms as well as methanogenic archaea in the core. Organisms related to Methanoculleus receptaculi were detected in the inner zones of a granule, whereas they were present in the digestate only after process recovery. This finding indicated more favorable microhabitats inside the granules that supported process recovery. Thus, the granule formation triggered by calcium oxide addition served as a tool to influence the composition of the microbial community and to stabilize the process after overloading with oil.

Effects of Cr(III) and Cr(VI) on nitrification inhibition as determined by SOUR, function-specific gene expression and 16S rRNA sequence analysis of wastewater nitrifying enrichments

The effect of Cr(III) and Cr(VI) on nitrification was examined with samples from nitrifying enrichment cultures using three different approaches: by measuring substrate (ammonia) specific oxygen uptake rates (SOUR), by using RT-qPCR to quantify the transcripts of functional genes involved in nitrification, and by analysis of 16S rRNA sequences to determine changes in structure and activity of the microbial communities. The nitrifying bioreactor was operated as a continuous reactor with a 24 h hydraulic retention time. The samples were exposed in batch vessels to Cr(III) (10-300 mg/L) and Cr(VI) (1-30 mg/L) for a period of 12 h. There was considerable decrease in SOUR with increasing dosages for both Cr(III) and Cr(VI), however Cr(VI) was more inhibitory than Cr(III). Based on the RT-qPCR data, there was reduction in the transcript levels of amoA and hao for increasing Cr(III) dosage, which corresponded well with the ammonia oxidation activity measured via SOUR. For Cr(VI) exposure, there was comparatively little reduction in amoA expression while hao expression decreased for 1-3 mg/L Cr(VI) and increased at 30 mg/L Cr(VI). While Nitrosomonas spp. were the dominant bacteria in the bioreactor, based on 16S rRNA sequencing, there was a considerable reduction in Nitrosomonas activity upon exposure to 300 mg/L Cr(III). In contrast, a relatively small reduction in activity was observed at 30 mg/L Cr(VI) loading. Our data that suggest that both Cr(III) and Cr(VI) were inhibitory to nitrification at concentrations near the high end of industrial effluent concentrations.