Co-occurrence network analysis reveals thermodynamics-driven microbial interactions in methanogenic bioreactors

Microbial community assembly in engineered bioreactors

Microbial community assembly (MCA) processes that shape microbial communities in environments are being used to analyze engineered bioreactors such as activated sludge systems and anaerobic digesters. The goal of studying MCA is to be able to understand and predict the effect of design and operation procedures on bioreactor microbial composition and function. Ultimately, this can lead to bioreactors that are more efficient, resilient, or resistant to perturbations. This review summarizes the ecological theories underpinning MCA, evaluates MCA analysis methods, analyzes how these MCA-based methods are applied to engineered bioreactors, and extracts lessons from case studies. Furthermore, we suggest future directions in MCA research in engineered bioreactor systems. The review aims to provide insights and guidance to the growing number of environmental engineers who wish to design and understand bioreactors through the lens of MCA.

Microbiological insights into anaerobic phenol degradation mechanisms and bulking phenomenon in a mesophilic upflow anaerobic sludge blanket reactor in long-term operation

In this study, a long-term operation of 2,747 days was conducted to evaluate the performance of the upflow anaerobic sludge blanket (UASB) reactor and investigated the degradation mechanisms of high-organic loading phenol wastewater. During the reactor operation, the maximum chemical oxygen demand (COD) removal rate of 6.1 ± 0.6 kg/m3/day under 1,680 mg/L phenol concentration was achieved in the mesophilic UASB reactor. After a significant change in the operating temperature from 24.0 ± 4.1 °C to 35.9 ± 0.6 °C, frequent observations of floating and washout of the bloated granular sludge (novel types of the bulking phenomenon) were made in the UASB reactor, suggesting that the change in operating temperature could be a trigger for the bulking phenomenon. Through the metagenomic analysis, phenol degradation mechanisms were predicted that phenol was converted to 4-hydroxybenzoate via two possible routes by Syntrophorhabdaceae and Pelotomaculaceae bacteria. Furthermore, the degradation of 4-hydroxybenzoate to benzoyl-CoA was carried out by members of Syntrophorhabdaceae and Smithellaceae. In the bulking sludge, a predominant presence of Nanobdellota, belonging to DPANN archaea, was detected. The metagenome-assembled genome of the Nanobdellota lacks many biosynthetic pathways and has several genes for the symbiotic lifestyle such as trimeric autotransporter adhesin-related protein. Furthermore, the Nanobdellota have significant correlations with several methanogenic archaea that are predominantly present in the UASB reactor. Considering the results of this study, the predominant Nanobdellota may negatively affect the growth of the methanogens through the parasitic lifestyle and change the balance of microbial interactions in the granular sludge ecosystem.

Electric-Inducive Microbial Interactions in a Thermophilic Anaerobic Digester Revealed by High-Throughput Sequencing of Micron-Scale Single Flocs

Although conductive materials have been shown to improve efficiency in anaerobic digestion (AD) by modifying microbial interactions, the interacting network under thermophilic conditions has not been examined. To identify the true taxon-taxon associations within thermophilic anaerobic digestion (TAD) microbiome and reveal the influence of carbon cloth (CC) addition, we sampled micron-scale single flocs (40-70 μm) randomly isolated from lab-scale thermophilic digesters. Results revealed that CC addition not only significantly boosted methane yield by 25.3% but also increased the spatial heterogeneity of the community in the sludge medium. After CC addition, an evident translocation of Pseudomonas from the medium to the biofilm was observed, showing their remarkable capacity for biofilm formation. Additionally, Clostridium and Thermotogaceae tightly aggregated and steadily co-occurred in the medium and biofilm of the TAD microbiome, which might be associated with their unique extracellular sugar metabolizing style. Finally, CC induced syntrophic interaction between Syntrophomonas and denitrifiers of Rhodocyclaceae. The upregulated respiration-associated electron transferring genes (Cyst-c, complex III) on the cellular membranes of these collaborating partners indicated a potential coupling of the denitrification pathway with syntrophic acetate oxidation via direct interspecies electron transfer (DIET). These findings provide an insight into how conductive materials promote thermophilic digestion performance and open the path for improved community monitoring of biotreatment systems.

Comprehensive understanding of DOM reactivity in anaerobic fermentation of persulfate-pretreated sewage sludge via FT-ICR mass spectrometry and reactomics analysis

Understanding the composition and reactivity of dissolved organic matter (DOM) at molecular level is vital for deciphering potential regulators or indicators relating to anaerobic process performance, though it was hardly achieved by traditional analyses. Here, the DOM composition, molecular reactivity and transformation in the enhanced sludge fermentation process were comprehensively elucidated using high-resolution mass spectrometry measurement, and data mining with machine learning and paired mass distance (PMD)-based reactomics. In the fermentation process for dewatered sludge, persulfate (PDS) pretreatment presented its highest performance in improving volatile fatty acids (VFAs) production with the increase from 2,711 mg/L to 3,869 mg/L, whereas its activation in the presence of Fe (as well as the hybrid of Fe and activated carbon) led to the decreased VFAs production performance. In addition to the conventional view of improved decomposition and solubilization of N-containing structures from sludge under the sole PDS pretreatment, the improved VFAs production was associated with the alternation of DOM molecular compositions such as humification generating molecules with high O/C, N/C, S/C and aromatic index (AI_mod). Machine learning was capable of predicting the DOM reactivity classes with 74-76 % accuracy and found that these molecular parameters in addition to nominal oxidation state of carbon (NOSC) were among the most important variables determining the generation or disappearance of bio-resistant molecules in the PDS pretreatment. The constructed PMD-based network suggested that highly connected molecular network with long path length and high diameter was in favor of VFAs production. Especially, -NH related transformation was found to be active under the enhanced fermentation process. Moreover, network topology analysis revealed that CHONS compounds (e.g., C₁₃H₂₇O₈N₁S₁) can be the keystone molecules, suggesting that the presence of sulfur related molecules (e.g., cysteine-like compounds) should be paid more attention as potential regulators or indicators for controlling sludge fermentation performance. This study also proposed the non-targeted DOM molecular analysis and downstream data mining for extending our understanding of DOM transformation at molecular level.

Electron acceptors determine the BTEX degradation capacity of anaerobic microbiota via regulating the microbial community

Anaerobic degradation is the major pathway for microbial degradation of benzene, toluene, ethylbenzene, and xylenes (BTEX) under electron acceptor lacking conditions. However, how exogenous electron acceptors modulate BTEX degradation through shaping the microbial community structure remains poorly understood. Here, we investigated the effect of various exogenous electron acceptors on BTEX degradation as well as methane production in anaerobic microbiota, which were enriched from the same contaminated soil. It was found that the BTEX degradation capacities of the anaerobic microbiota gradually increased along with the increasing redox potentials of the exogenous electron acceptors supplemented (WE: Without exogenous electron acceptors < SS: Sulfate supplement < FS: Ferric iron supplement < NS: Nitrate supplement), while the complexity of the co-occurring networks (e.g., avgK and links) of the microbiota gradually decreased, showing that microbiota supplemented with higher redox potential electron acceptors were less dependent on the formation of complex microbial interactions to perform BTEX degradation. Microbiota NS showed the highest degrading capacity and the broadest substrate-spectrum for BTEX, and it could metabolize BTEX through multiple modules which not only contained fewer species but also different key microbial taxa (eg. Petrimonas, Achromobacter and Comamonas). Microbiota WE and FS, with the highest methanogenic capacities, shared common core species such as Sedimentibacter, Acetobacterium, Methanobacterium and Smithella/Syntrophus, which cooperated with Geobacter (microbiota WE) or Desulfoprunum (microbiota FS) to perform BTEX degradation and methane production. This study demonstrates that electron acceptors may alter microbial function by reshaping microbial community structure and regulating microbial interactions and provides guidelines for electron acceptor selection for bioremediation of aromatic pollutant-contaminated anaerobic sites.

Symbiosis between Candidatus Patescibacteria and Archaea Discovered in Wastewater-Treating Bioreactors

Each prokaryotic domain, Bacteria and Archaea, contains a large and diverse group of organisms characterized by their ultrasmall cell size and symbiotic lifestyles (potentially commensal, mutualistic, and parasitic relationships), namely, Candidatus Patescibacteria (also known as the Candidate Phyla Radiation/CPR superphylum) and DPANN archaea, respectively. Cultivation-based approaches have revealed that Ca. Patescibacteria and DPANN symbiotically interact with bacterial and archaeal partners and hosts, respectively, but that cross-domain symbiosis and parasitism have never been observed. By amending wastewater treatment sludge samples with methanogenic archaea, we observed increased abundances of Ca. Patescibacteria (Ca. Yanofskybacteria/UBA5738) and, using fluorescence in situ hybridization (FISH), discovered that nearly all of the Ca. Yanofskybacteria/UBA5738 cells were attached to Methanothrix (95.7 ± 2.1%) and that none of the cells were attached to other lineages, implying high host dependency and specificity. Methanothrix filaments (multicellular) with Ca. Yanofskybacteria/UBA5738 attached had significantly more cells with no or low detectable ribosomal activity (based on FISH fluorescence) and often showed deformations at the sites of attachment (based on transmission electron microscopy), suggesting that the interaction is parasitic. Metagenome-assisted metabolic reconstruction showed that Ca. Yanofskybacteria/UBA5738 lacks most of the biosynthetic pathways necessary for cell growth and universally conserves three unique gene arrays that contain multiple genes with signal peptides in the metagenome-assembled genomes of the Ca. Yanofskybacteria/UBA5738 lineage. The results shed light on a novel cross-domain symbiosis and inspire potential strategies for culturing CPR and DPANN.

High-rate cotreatment of purified terephthalate and dimethyl terephthalate manufacturing wastewater by a mesophilic upflow anaerobic sludge blanket reactor and the microbial ecology relevant to aromatic compound degradation

Polyethylene terephthalate (PET) is produced worldwide, mainly as material for plastic drink bottles. PET is produced by polymerization of purified terephthalate (PTA) or dimethyl terephthalate (DMT) with ethylene glycol. During the synthetic manufacturing processes of PTA and DMT, high organic loading wastewater is produced, which is typically treated separately by anaerobic wastewater treatment technologies. Given the high demand for PET, manufacturing plants are expanding globally, which will result in an increase in the amounts of PTA and DMT wastewater in need of treatment. In terms of effective treatment, the cotreatment of PTA and DMT wastewater has several advantages, including lower area and energy requirements. In this study, we examined the performance of an upflow anaerobic sludge blanket (UASB) reactor in cotreating PTA and DMT wastewater with high organic loading, evaluating its removal characteristics after 518 days of continuous operation. In addition, we performed a microbiome analysis of the UASB granular sludge to uncover the microbial interactions and metabolic functions within the reactor. By continuous operation, we achieved an organic removal rate of 6.6 kg m^-3 day^-1. In addition, we confirmed that aromatic compounds in the complex wastewater from the PTA and DMT manufacturing processes are biodegradable in the following order: benzoate > orthophthalate > terephthalate > isophthalate > p-toluic acid. 16S rRNA gene-based network analysis shows that anaerobic Woesearchaeales belonging to phylum Nanoarchaeota has a positive correlation with Methanoregula, Candidatus Methanofastidiosum, and Methanosarcina, suggesting a symbiotic relationship with methanogens in granular sludge. Shotgun metagenomic analysis revealed that terephthalate, isophthalate/orthophthalate, and benzoate were degraded by different members of Pelotomaculaceae and Syntrophorhabdaceae. According to the genomic information, we propose two new possible routes for orthophthalate degradation by the Syntrophorhabdaceae organism.

Microbial co-occurrence network topological properties link with reactor parameters and reveal importance of low-abundance genera

Operational factors and microbial interactions affect the ecology in anaerobic digestion systems. From 12 lab-scale reactors operated under distinct engineering conditions, bacterial communities were found driven by temperature, while archaeal communities by both temperature and substrate properties. Combining the bacterial and archaeal community clustering patterns led to five sample groups (ambient, mesophilic low-solid-substrate, mesophilic, mesophilic co-digestion and thermophilic) for co-occurrence network analysis. Network topological properties were associated with substrate characteristics and hydrolysis-methanogenesis balance. The hydrolysis efficiency correlated (p < 0.05) with clustering coefficient positively and with normalized betweenness negatively. The influent particulate COD ratio and the relative differential hydrolysis-methanogenesis efficiency (D_efficiency) correlated negatively with the average path length (p < 0.05). Individual genera’s topological properties showed more connector genera in thermophilic network, representing stronger inter-module communication. Individual genera’s normalized degree and betweenness revealed that lower-abundance genera (as low as 0.1%) could perform central hub roles and communication roles, maintaining the stability and functionality of the microbial community.

Highly Distinct Microbial Communities in Elevated Strings and Submerged Flarks in the Boreal Aapa-Type Mire

Large areas in the northern hemisphere are covered by extensive wetlands, which represent a complex mosaic of raised bogs, eutrophic fens, and aapa mires all in proximity to each other. Aapa mires differ from other types of wetlands by their concave surface, heavily watered by the central part, as well as by the presence of large-patterned string-flark complexes. In this paper, we characterized microbial diversity patterns in the surface peat layers of the neighboring string and flark structures located within the mire site in the Vologda region of European North Russia, using 16S rRNA gene sequencing. The microbial communities in raised strings were clearly distinct from those in submerged flarks. Strings were dominated by the Alpha- and Gammaproteobacteria. Other abundant groups were the Acidobacteriota, Bacteroidota, Verrucomicrobiota, Actinobacteriota, and Planctomycetota. Archaea accounted for only 0.4% of 16S rRNA gene sequences retrieved from strings. By contrast, they comprised about 22% of all sequences in submerged flarks and mostly belonged to methanogenic lineages. Methanotrophs were nearly absent. Other flark-specific microorganisms included the phyla Chloroflexi, Spirochaetota, Desulfobacterota, Beijerinckiaceae- and Rhodomicrobiaceae-affiliated Alphaproteobacteria, and uncultivated groups env.OPS_17 and vadinHA17 of the Bacteroidota. Such pattern probably reflects local anaerobic conditions in the submerged peat layers in flarks.

Microbial Communities in Full-Scale Wastewater Treatment Systems Exhibit Deterministic Assembly Processes and Functional Dependency over Time

Microbial communities constitute the core component of biological wastewater treatment processes. We conducted a meta-analysis based on the 16S rRNA gene of temporal samples obtained from diverse full-scale activated sludge and anaerobic digestion systems treating municipal and industrial wastewater (collected in this study and published previously) to investigate their community assembly mechanism and functional traits over time, which are not currently well understood. The influent composition was found to be the main driver of the microbial community's composition, and relatively large proportions of specialist (26.1% and 18.6%) and transient taxa (67.2% and 68.1%) were estimated in both systems. Deterministic processes, especially homogeneous selection events (accounting for >53.8% of assembly events), were consistently identified as the dominant microbial community assembly mechanisms in both systems over time. Significant and strong correlations (Pearson's r = 0.51-0.92) were detected between the dynamics of the temporal community and the functional compositions in both systems, which suggests functional dependency. In contrast, the occurrence of sludge bulking and foaming in the activated sludge system led to an increase in stochastic assembly processes (i.e., limited dispersal and undominated events), a shift toward functional redundancy and less community diversity, a decreased community niche breadth index, and a more compact co-association network. This study illustrates that the mechanism of microbial community assembly and functional traits over time can be used to diagnose system performance and provide information on potential system malfunction.

Metagenomic and Metatranscriptomic Analyses Revealed Uncultured Bacteroidales Populations as the Dominant Proteolytic Amino Acid Degraders in Anaerobic Digesters

Current understanding of amino acid (AA) degraders in anaerobic digesters is mainly based on cultured species, whereas microorganisms that play important roles in a complex microbial community remain poorly characterized. This study investigated short-term enrichments degrading single AAs using metagenomics and metatranscriptomics. Metagenomic analysis revealed that populations related to cultured AA degraders had an abundance <2.5% of the sequences. In contrast, metagenomic-assembled bins related to uncultured Bacteroidales collectively accounted for >35% of the sequences. Phylogenetic analyses suggested that these Bacteroidales populations represented a yet-to-be characterized family lineage, i.e., Bacteroidetes vadinHA17. The bins possessed the genetic capacity related to protein degradation, including surface adhesion (3–7 genes), secreted peptidase (52–77 genes), and polypeptide-specific transporters (2–5 genes). Furthermore, metatranscriptomics revealed that these Bacteroidales populations expressed the complete metabolic pathways for degrading 16 to 17 types of AAs in enrichments fed with respective substrates. These characteristics were distinct from cultured AA degraders including Acidaminobacter and Peptoclostridium, suggesting the uncultured Bacteroidales were the major protein-hydrolyzing and AA-degrading populations. These uncultured Bacteroidales were further found to be dominant and active in full-scale anaerobic digesters, indicating their important ecological roles in the native habitats. “Candidatus Aminobacteroidaceae” was proposed to represent the previously uncharted family Bacteroidetes vadinHA17.

Anaerobic digestion of aqueous phase from hydrothermal liquefaction of Spirulina using biostimulated sludge

Hydrothermal liquefaction is a process that converts wet biomass into biofuels, more specifically bio-crude oil. During the process, post hydrothermal liquefaction waste water (PHWW) is generated, rich in nutrient and organic matter, however potentially toxic. Anaerobic digestion of PHWW from Spirulina, was evaluated using biostimulated sludge as a strategy to optimize the process. The biostimulation was conducted in a sequential batch reactor fed with organic acids and methanol aiming at development of acetogenic and methanogenic microorganism. Anaerobic biodegradability batch assays were performed, with biostimulated sludge and with non-biostimulated sludge, using increasing PHWW concentrations. Biostimulated sludge were more favourable for reaching higher methane yields at higher organic matter concentrations in comparison to non-biostimulated sludge, presenting less inhibition at conditions tested. Biostimulation was a key process to select and favour potential microorganisms involved in specialized uptake of recalcitrant compounds, such as Mesotoga and Methanomethylovorans.

Unexpected diversity of acetate degraders in anaerobic membrane bioreactor treating organic solid waste revealed by high-sensitivity stable isotope probing

In anaerobic membrane bioreactor (AnMBR) treating organic solid waste, acetate is one of the most important precursors to CH₄. However, the identity and diversity of anaerobic acetate degraders are largely unknown, possibly due to their slow growth rates and low abundances. Here, we identified acetate-degrading microorganisms in the AnMBR sludges by high-sensitivity stable isotope probing. Degradation of the amended ¹³C-acetate coincided with production of ¹³CH₄ and ¹³CO₂ during the sludge incubation. High-throughput sequencing of RNA density fractions indicated that the aceticlastic and hydrogenotrophic methanogens, i.e., Methanosaeta sp. (acetate dissimilator) and Methanolinea sp. (acetate assimilator), incorporated ¹³C-acetate significantly. Remarkably, 22 bacterial species incorporating ¹³C-acetate were identified, whereas their majority was distantly related to the cultured representatives. Only two of them were the class Deltaproteobacteria-affiliated lineages with syntrophic volatile fatty acid oxidation activities. Phylogenetic tree analysis and population dynamics tracing revealed that novel species of the hydrolyzing and/or fermenting taxa, such as the phyla Bacteroidetes, Chloroflexi and Lentisphaerae, exhibited low relative abundances comparable to that of Methanolinea sp. (0.00011%) during the AnMBR operation, suggesting that these bacteria were involved in anaerobic acetate assimilation. Meanwhile, novel species of the phyla Firmicutes, Synergistetes and Caldiserica, the candidate phyla Aminicenantes and Atribacteria and the candidate division GOUTA4-related clade, as well as the known Deltaproteobacteria members, existed at relatively high abundances (0.00031%-0.31121%) in the reactor, suggesting that these bacterial species participated in anaerobic dissimilation of acetate, e.g., syntrophic acetate oxidation. The results of this study demonstrated the unexpected diversity and ecophysiological features of the anaerobic acetate degraders in the AnMBR treating organic solid waste.

Coupling growth kinetics modeling with machine learning reveals microbial immigration impacts and identifies key environmental parameters in a biological wastewater treatment process

BACKGROUND

Ubiquitous in natural and engineered ecosystems, microbial immigration is one of the mechanisms shaping community assemblage. However, quantifying immigration impact remains challenging especially at individual population level. The activities of immigrants in the receiving community are often inadequately considered, leading to potential bias in identifying the relationship between community composition and environmental parameters.

RESULTS

This study quantified microbial immigration from an upstream full-scale anaerobic reactor to downstream activated sludge reactors. A mass balance was applied to 16S rRNA gene amplicon sequencing data to calculate the net growth rates of individual populations in the activated sludge reactors. Among the 1178 observed operational taxonomic units (OTUs), 582 had a positive growth rate, including all the populations with abundance > 0.1%. These active populations collectively accounted for 99% of the total sequences in activated sludge. The remaining 596 OTUs with a growth rate ≤ 0 were classified as inactive populations. All the abundant populations in the upstream anaerobic reactor were inactive in the activated sludge process, indicating a negligible immigration impact. We used a supervised learning regressor to predict environmental parameters based on community composition and compared the prediction accuracy based on either the entire community or the active populations. Temperature was the most predictable parameter, and the prediction accuracy was improved when only active populations were used to train the regressor.

CONCLUSIONS

Calculating growth rate of individual microbial populations in the downstream system provides an effective approach to determine microbial activity and quantify immigration impact. For the studied biological process, a marginal immigration impact was observed, likely due to the significant differences in the growth environments between the upstream and downstream processes. Excluding inactive populations as a result of immigration further enhanced the prediction of key environmental parameters affecting process performance.