Micron-scale biogeography reveals conservative intra anammox bacteria spatial co-associations

Deciphering the adaptation mechanism of anammox consortia under sulfamethoxazole stress: A model coupling resistance accumulation and interspecies-cooperation

Sulfamethoxazole (SMX) is frequently detected in wastewater where anammox applications are promising. While it has been demonstrated that anammox consortia can adapt to SMX stress, the underlying community adaptation strategy has not yet been fully addressed. Therefore, in this study, we initially ascertained anammox consortia's ability to co-metabolize SMX in batch tests. Then, a 200-day domestication process of anammox consortia under SMX stress was carried out with community variations and transcriptional activities monitored by metagenomic and metatranscriptomic sequencing techniques. Despite the initial drop to 41.88 %, the nitrogen removal efficiency of the anammox consortia rebounded to 84.64 % post-domestication under 5 mg/L SMX. Meanwhile, a 4.85-fold accumulation of antibiotic resistance genes (ARGs) under SMX stress was observed as compared to the control group. Interestingly, the anammox consortia may unlock the SMX-inhibited folate synthesis pathway through a novel interspecies cooperation triangle among Nitrospira (NAA), Desulfobacillus denitrificans (DSS1), and the core anammox population Candidatus Brocadia sinica (AMX1), in which the modified dihydropteroate synthase (encoded by sul1) of NAA reconnected the symbiotic cooperation between AMX1 and DSS1. Overall, this study provides a new model for the adaptation strategies of anammox consortia to SMX stress.

Distribution characteristics and microbial synergistic degradation potential of polyethylene and polypropylene in freshwater estuarine sediments

The microbial degradation of polyethylene (PE) and polypropylene (PP) resins in rivers and lakes has emerged as a crucial issue in the management of microplastics. This study revealed that as the flow rate decreased longitudinally, ammonia nitrogen (NH4+-N), heavy fraction of organic carbon (HFOC), and small-size microplastics (< 1 mm) gradually accumulated in the deep and downstream estuarine sediments. Based on their surface morphology and carbonyl index, these sediments were identified as the potential hot zone for PE/PP degradation. Within the identified hot zone, concentrations of PE/PP-degrading genes, enzymes, and bacteria were significantly elevated compared to other zones, exhibiting strong intercorrelations. Analysis of niche differences revealed that the accumulation of NH4+-N and HFOC in the hot zone facilitated the synergistic coexistence of key bacteria responsible for PE/PP degradation within biofilms. The findings of this study offer a novel insight and comprehensive understanding of the distribution characteristics and synergistic degradation potential of PE/PP in natural freshwater environments.

Management of biofilm by an innovative layer-structured membrane for membrane biofilm reactor (MBfR) to efficient methane oxidation coupled to denitrification (AME-D)

Aerobic methane oxidation coupled with denitrification (AME-D) has garnered significant attention as a promising technology for nitrogen removal from water. Effective biofilm management on the membrane surface is essential to enhance the efficiency of nitrate removal in AME-D systems. In this study, we introduce a novel and scalable layer-structured membrane (LSM) developed using a meticulously designed polyurethane sponge. The application of the LSM in advanced biofilm management for AME-D resulted in a substantial enhancement of denitrification performance. Our experimental results demonstrated remarkable improvements in nitrate-removal flux (92.8 mmol-N m-2 d-1) and methane-oxidation rate (325.6 mmol m-2 d-1) when using an LSM in a membrane biofilm reactor (L-MBfR) compared with a conventional membrane reactor (C-MBfR). The l-MBfR exhibited 12.4-, 6.8- and 3.4-fold increases in nitrate-removal rate, biomass-retention capacity, and methane-oxidation rate, respectively, relative to the control C-MBfR. Notably, the l-MBfR demonstrated a 3.5-fold higher abundance of denitrifying bacteria, including Xanthomonadaceae, Rhodocyclaceae, and Methylophilaceae. In addition, the denitrification-related enzyme activity was twice as high in the l-MBfR than in the C-MBfR. These findings underscore the LSM's ability to create anoxic/anaerobic microenvironments conducive to biofilm formation and denitrification. Furthermore, the LSM exhibited a unique advantage in shaping microbial community structures and facilitating cross-feeding interactions between denitrifying bacteria and aerobic methanotrophs. The results of this study hold great promise for advancing the application of MBfRs in achieving efficient and reliable nitrate removal through the AME-D pathway, facilitated by effective biofilm management.

Enhancing start-up strategies for anammox granular sludge systems: A review

The anaerobic ammonium oxidation (anammox) process has been developed as one of the optimal alternatives to the conventional biological nitrogen removal process because of its high nitrogen removal capacity and low energy consumption. However, the slow growth rate of anammox bacteria and its high sensitivity to environmental changes have resulted in fewer anammox sludge sources for process start-up and a lengthy start-up period. Given that anammox microorganisms tend to aggregate, granular-anammox sludge is a frequent byproduct of the anammox process. In this study, we review state-of-the-art strategies for promoting the formation of anammox granules and the start-up of the anammox process based on the literature of the past decade. These strategies are categorized as the transformation of alternative sludge, the addition of accelerators, the introduction of functional carriers, and the implementation of other physical methods. In addition, the formation mechanism of anammox granules, the operational performance of various strategies, and their promotion mechanisms are introduced. Finally, prospects are presented to indicate the gaps in contemporary research and the potential future research directions. This review functions as a summary guideline and theoretical reference for the cultivation of granular-anammox sludge, the start-up of the anammox process, and its practical application.

Distinct spatiotemporal succession of bacterial generalists and specialists in the lacustrine plastisphere

The assembly processes of generalists and specialists and their driving mechanisms during spatiotemporal succession is a central issue in microbial ecology but a poorly researched subject in the plastisphere. We investigated the composition variation, spatiotemporal succession, and assembly processes of bacterial generalists and specialists in the plastisphere, including non-biodegradable (NBMPs) and biodegradable microplastics (BMPs). Although the composition of generalists and specialists on NBMPs differed from that of BMPs, colonization time mainly mediated the composition variation. The relative abundance of generalists and the relative contribution of species replacement were initially increased and then decreased with colonization time, while the specialists initially decreased and then increased. Besides, the richness differences also affected the composition variation of generalists and specialists in the plastisphere, and the generalists were more susceptible to richness differences than corresponding specialists. Furthermore, the assembly of generalists in the plastisphere was dominated by deterministic processes, while stochastic processes dominated the assembly of specialists. The network stability test showed that the community stability of generalists on NBMPs and BMPs was lower than corresponding specialists. Our results suggested that different ecological assembly processes shaped the spatiotemporal succession of bacterial generalists and specialists in the plastisphere, but were less influenced by polymer types.

Insights into the composition and assembly mechanism of microbial communities on intertidal microsand grains

Introduction

Marine microorganisms are essential in marine ecosystems and have always been of interest. Currently, most marine microbial communities are studied at the bulk scale (millimeters to centimeters), and the composition, function and underlying assembly mechanism of microbial communities at the microscale (sub-100 micrometers) are unclear.

Methods

The microbial communities on microsand grains (40-100 µm, n = 150) from marine sediment were investigated and compared with those on macrosand grains (400-1000 µm, n = 60) and bulk sediments (n = 5) using amplicon sequencing technology.

Results

The results revealed a significant difference between microsand grains and macrosand grains. Microsand grains had lower numbers of operational taxonomic units (OTUs(97%)) and predicted functional genes than macrosand grains and bulk-scale samples. Microsand grains also showed greater intersample differences in the community composition and predicted functional genes than macrosand grains, suggesting a high level of heterogeneity of microbial communities at the microscale. Analyses based on ecological models indicated that stochastic processes dominated the assembly of microbial communities on sand grains. Consistently, cooccurrence network analyses showed that most microbial cooccurrence associations on sand grains were highly unstable. Metagenomic sequencing and further genome-scale metabolic modeling revealed that only a small number (1.3%) of microbe pairs showed high cooperative potential.

Discussion

This study explored the microbial community of marine sediments at the sub-100 µm scale, broadening the knowledge of the structure and assembly mechanism of marine microbial communities.

Directed regulation of anammox communities based on exogenous siderophores for highly efficient nitrogen removal

It is expected that the quicker domestication of anaerobic ammonia oxidation (anammox) communities and the enhancement of their nitrogen transformation capability can be achieved through targeted regulation of anammox communities. Iron cast a vital role in the growth and metabolism of anammox bacteria. Specific siderophores offer promising prospects for the targeted regulation of anammox communities by facilitating the efficient utilization of iron. Two siderophores-enterobactin and putrebactin-exclusively for Ca. Brocadia and Ca. Kuenenia were developed to specifically regulate anammox communities towards different directions, respectively. Anammox communities in the reactors evoluted targetedly towards Ca. Brocadia-dominated communities and Ca. Kuenenia-dominated communities, respectively, leading to a maximum increase in community nitrogen removal capacity by 84.64±0.55% and 210.26±0.57%, respectively, under different nitrogen concentrations. It was indicated that siderophores could regulate anammox communities by redistributing iron resources in a targeted manner based on the analyses of transcriptome and proteome. This study provides novel insights into the rational selection and utilization of exogenous siderophores as an effective implement to manipulate anammox communities and create communities with high nitrogen removal ability fleetly.

Research advances in application of mainstream anammox processes: Roles of quorum sensing and microbial metabolism

Anaerobic ammonium oxidation (anammox) is a low-carbon biological nitrogen removal process, that has been widely applied to treat high-strength wastewater. However, the practical application of mainstream anammox treatment is limited due to the slow growth rate of anammox bacteria (AnAOB). Therefore, it is important to provide a comprehensive summary of the potential impacts and regulatory strategies for system stability. This article systematically reviewed the effects of environmental fluctuations on anammox systems, summarizing the bacterial metabolisms and the relationship between metabolite and microbial functional effects. To address the shortcoming of mainstream anammox process, molecular strategies based on quorum sensing (QS) were proposed. Sludge granulation, gel encapsulation and carrier-based biofilm technologies were adopted to enhance the QS function in microbial aggregation and reduction of biomass loss. Furthermore, this article discussed the application and progress of anammox-coupled processes. Valuable insights were provided for the stable operation and development of mainstream anammox process from the perspectives of QS and microbial metabolism.

Insights into heavy metals shock on anammox systems: Cell structure-based mechanisms and new challenges

Anaerobic ammonium oxidation (anammox) as a low-carbon and energy-saving technology, has shown unique advantages in the treatment of high ammonia wastewater. However, wastewater usually contains complex heavy metals (HMs), which pose a potential risk to the stable operation of the anammox system. This review systematically re-evaluates the HMs toxicity level from the inhibition effects and the inhibition recovery process, which can provide a new reference for engineering. From the perspective of anammox cell structure (extracellular, anammoxosome membrane, anammoxosome), the mechanism of HMs effects on cellular substances and metabolism is expounded. Furthermore, the challenges and research gaps for HMs inhibition in anammox research are also discussed. The clarification of material flow, energy flow and community succession under HMs shock will help further reveal the inhibition mechanism. The development of new recovery strategies such as bio-accelerators and bio-augmentation is conductive to breaking through the engineered limitations of HMs on anammox. This review provides a new perspective on the recognition of toxicity and mechanism of HMs in the anammox process, as well as the promotion of engineering applicability.

A review of anammox metabolic response to environmental factors: Characteristics and mechanisms

Anaerobic ammonium oxidation (anammox) is a promising low carbon and economic biological nitrogen removal technology. Considering the anammox technology has been easily restricted by environmental factors in practical engineering applications, therefore, it is necessary to understand the metabolic response characteristics of anammox bacteria to different environmental factors, and then guide the application of the anammox process. This review presented the latest advances of the research progress of the effects of different environmental factors on the metabolic pathway of anammox bacteria. The effects as well as mechanisms of conventional environmental factors and emerging pollutants on the anammox metabolic processes were summarized. Also, the role of quorum sensing (QS) mediating the bacteria growth, gene expression and other metabolic process in the anammox system were also reviewed. Finally, interaction and cross-feeding mechanisms of microbial communities in the anammox system were discussed. This review systematically summarized the variations of metabolic mechanism response to the external environment and cross-feeding interactions in the anammox process, which would provide an in-depth understanding for the anammox metabolic process and a comprehensive guidance for future anammox-related metabolic studies and engineering applications.

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.

Nitrogen contribution and microbial community of size-fractionated anammox sludge in continuous stirred-tank reactors

In this study, the microbial diversity of size-fractionated anammox sludge in a well-mixed system and their contribution to nitrogen transformation were investigated. Results showed that small granules (0.2-1.0 mm) contributed to the major part of the nitrogen removal rate (56 %) due to its largest mixed liquor volatile suspended solids (1240 ± 80 mg·L^-1). However, large granules (>1.0 mm) possessed the highest relative abundances of Ca. Kuenenia stuttgartiensis and specific anammox activity, representing 49.34 % and 24.45 ± 0.01 mg-N·g^-1-mixed liquor volatile suspended solids·h^-1, respectively. The microbial diversity decreased as the increase of granular size, resulting in microbial community shifting to a simpler model. Metagenomic analysis showed that fine sludge might be the potential major for NO/N₂O production in the mature well-mixed system under inorganic conditions. This study provides guidance for the evaluation of nitrogen contribution by anammox size-fractionated sludge and the inhibition of the potential NO/N₂O emission in anammox processes.