Archaeal diversity in biofilm technologies applied to treat urban and industrial wastewater: recent advances and future prospects

Archaea communities in aerobic granular sludge: A mini-review

Recent research on the archaea community in aerobic granular sludge (AGS) has attracted considerable attention. This review summarizes the existing literature on composition, distribution, and related functions of archaea community in AGS. Furthermore, the effects of granulation, substrate, temperature, process types, and aeration models on the archaea community were discussed. Significantly, the layered structure of AGS facilitates the enrichment of archaea, including methanogenic archaea and ammonia-oxidizing archaea. Archaea engage in metabolic interactions with other microorganisms, enhancing the ecological functionalities of AGS and its tolerance to adverse conditions. Future investigations should focus on minimizing greenhouse gas emissions and exploring the roles and interactive mechanisms of archaea and other microorganisms within AGS.

Perspective on the use of methanogens in lithium recovery from brines

Methanogenic archaea stand out as multipurpose biocatalysts for different applications in wide-ranging industrial sectors due to their crucial role in the methane (CH4) cycle and ubiquity in natural environments. The increasing demand for raw materials required by the manufacturing sector (i.e., metals-, concrete-, chemicals-, plastic- and lubricants-based industries) represents a milestone for the global economy and one of the main sources of CO2 emissions. Recovery of critical raw materials (CRMs) from byproducts generated along their supply chain, rather than massive mining operations for mineral extraction and metal smelting, represents a sustainable choice. Demand for lithium (Li), included among CRMs in 2023, grew by 17.1% in the last decades, mostly due to its application in rechargeable lithium-ion batteries. In addition to mineral deposits, the natural resources of Li comprise water, ranging from low Li concentrations (seawater and freshwater) to higher ones (salt lakes and artificial brines). Brines from water desalination can be high in Li content which can be recovered. However, biological brine treatment is not a popular methodology. The methanogenic community has already demonstrated its ability to recover several CRMs which are not essential to their metabolism. Here, we attempt to interconnect the well-established biomethanation process with Li recovery from brines, by analyzing the methanogenic species which may be suitable to grow in brine-like environments and the corresponding mechanism of recovery. Moreover, key factors which should be considered to establish the techno-economic feasibility of this process are here discussed.

Metatranscriptional characterization of metabolic dynamics in anaerobic membrane bioreactor producing methane from low-strength wastewater

An anaerobic membrane bioreactor (AnMBR) with media is an emerging carbon-neutral biotechnology for low-strength wastewater (LSWW) treatment and methane recovery. Understanding metabolic dynamics among methanogens and syntrophic bacteria is important in optimizing the design and operation of AnMBR. However, little is known about it, especially in media-attached microbial communities. This study explored metabolic dynamics to compare media-attached and suspended conditions. Accordingly, metagenomes and metatranscriptomes from AnMBRs with polymeric media and fed with different influent concentrations (350 and 700 mg-COD/L) were analyzed. Metabolic dynamics were profoundly influenced by the different growth habitats and influent conditions, although the applied influent concentrations are within the range of typical LSWW. Metabolic dynamics prediction results suggest that media-attached-growth habitats may have provided a more favorable microenvironment for methanogens to grow and produce methane, especially under low influent conditions. These findings provide significant implications for optimizing floating media design and operation of AnMBR-producing methane from LSWW.

Addition of Trichocladium canadense to an anaerobic membrane bioreactor: evaluation of the microbial composition and reactor performance

Membrane bioreactors are powerful systems for wastewater treatment and the removal of toxic compounds. However, membrane biofouling stands in the way of their widespread usage. In this study, the saprophytic fungus Trichocladium canadense was used as the bioaugmentor in an anaerobic membrane bioreactor (AnMBR) and its impact on membrane biofouling, biogas production, the microbial communities of the reactor and removal of the common antibiotics erythromycin (ERY), sulfamethoxazole (SMX) and tetracycline (TET) from synthetic wastewater was investigated. The results indicated that through bioaugmentation with 20% T. canadense, membrane biofouling was slowed by 25%, the chemical oxygen demand removal increased by 16% and a higher efficiency removal of ERY and SMX was achieved. The presence of T. canadense significantly increased the abundance and diversity of the biofilm archaeal community and the bacterial phylum Firmicutes, a known bio-foulant.

Insights into the microbial diversity and structure in a full-scale municipal wastewater treatment plant with particular regard to Archaea

Due to limited description of the role and diversity of archaea in WWTPs, the aim of the study was to analyze microbial community structures and diversities with particular regard to Archaea in the samples taken from different stages of the full-scale municipal wastewater treatment plant and effluent receiving water (upstream and downstream discharge point). Our study was focused on showing how the treatment processes influenced the Eubacteria and Archaea composition. Alpha and Beta diversity were used to evaluate the microbial diversity changes in the collected samples. Proteobacteria was the largest fraction ranging from 28% to 67% with 56% relative abundance across all samples. Archaea were present in all stages of WWTP ranged from 1 to 8%. Among the Archaea, two groups of methanogens, acetoclastic (Methanosarcina, Methanosaeta) and hydrogenotrophic methanogens (Methanospirillium, Methanoculleus, Methanobrevibacter) were dominant in the technological stages. The obtained results indicate that the treated wastewater did not significantly affect eubacterial and archaeal composition in receiving water. However, differences in richness, diversity and microbial composition of Eubacteria and Archaea between the wastewater samples taken from the primary and secondary treatment were observed.

Carbon Nanomaterials: Application and Prospects of Urban and Industrial Wastewater Pollution Treatment Based on Abrasion and Corrosion Resistance

Environmental pollution as a result of urban and industrial wastewater has become an increasingly prominent issue. Rivers, lakes, and oceans that have become eutrophicated or polluted by suspended solids and hazardous substances in wastewater have endangered the environment. A root cause of this is the discharge of untreated urban and industrial wastewater into the ecosystem. As a solution to the pollution, wastewater treatment facilities have seen increasingly rapid development. Sewage pumps are designed to transport urban and industrial wastewater containing solid particles or hazardous substances to water treatment centers for purification and treatment. Sewage pumps are of great importance in the entire wastewater treatment system. Sewage in the environment where sewage pumps work usually contains sands, suspended particles, and plenty of saline ions. Flow passage components and sealing elements of the pump become vulnerable to abrasion and chemical corrosion, which further challenges operational stability of the pump. Research has remained focused on how to improve reliability of sewage pumps under severe conditions. Because of advances in materials science, the application of an increasing number of new materials has been witnessed, such as carbon-based composite materials and carbon nanomaterials, thanks to their fine self-lubrication performance, heat resistance, thermal and electrical conductivity, chemical stability, heat and seismic resistance, as well as plasticity. These properties contribute to enormous potential that new carbon-based composite materials and carbon nanomaterials have to offer in terms of corrosion resistance. This paper outlines application scenarios, research progress, and the prospect of new materials in sewage pumps.

A novel universal primer pair for prokaryotes with improved performances for anammox containing communities

Abundance profiling via 16S rRNA targeted next generation sequencing (NGS) is a common procedure to characterize mixtures of prokaryotic populations inhabiting an environment. Depending on the variable region/s addressed, different maps can be obtained due to their different information content. In this work, we focussed on wastewater microbial communities and we compared several recently developed universal primers that addressed regions V1-V3, V3-V4 and V4. They all proved to have good performance over a wide range of microbial phyla, but the phylum Planctomycetes was not optimally covered, especially for members of the Brocadiales family. Such bacteria are at the basis of the novel nitrogen removal strategy based on anammox process. To overcome this limitation we performed an extensive bioinformatic analysis that allowed the design of a primer (Pro341FB) that shows increased sensitivity for this specific phylum with respect to the previously proposed Pro341F primer. Upon validation using a 16S NGS survey on microbial communities from different wastewater treatment plant (activated sludge systems, anaerobic digesters, aerobic and anaerobic granules) we demonstrated that Pro341FB is able to reveal up to 5 times more members of the Candidatus Brocadiales family (plus many other previously under-covered prokaryotes) than Pro341F, without affecting its excellent previous coverage.

A Critical Review on Nitrous Oxide Production by Ammonia-Oxidizing Archaea

The continuous increase of nitrous oxide (N₂O) in the atmosphere has become a global concern because of its property as a potent greenhouse gas. Given the important role of ammonia-oxidizing archaea (AOA) in ammonia oxidation and their involvement in N₂O production, a clear understanding of the knowledge on archaeal N₂O production is necessary for global N₂O mitigation. Compared to bacterial N₂O production by ammonia-oxidizing bacteria (AOB), AOA-driven N₂O production pathways are less-well elucidated. In this Critical Review, we synthesized the currently proposed AOA-driven N₂O production pathways in combination with enzymology distinction, analyzed the role of AOA species involved in N₂O production pathways, discussed the relative contribution of AOA to N₂O production in both natural and anthropogenic environments, summarized the factors affecting archaeal N₂O yield, and compared the distinctions among approaches used to differentiate ammonia oxidizer-associated N₂O production. We, then, put forward perspectives for archaeal N₂O production and future challenges to further improve our understanding of the production pathways, putative enzymes involved and potential approaches for identification in order to potentially achieve effective N₂O mitigations.

Archaeal biofilm formation

Biofilms are structured and organized communities of microorganisms that represent one of the most successful forms of life on Earth. Bacterial biofilms have been studied in great detail, and many molecular details are known about the processes that govern bacterial biofilm formation, however, archaea are ubiquitous in almost all habitats on Earth and can also form biofilms. In recent years, insights have been gained into the development of archaeal biofilms, how archaea communicate to form biofilms and how the switch from a free-living lifestyle to a sessile lifestyle is regulated. In this Review, we explore the different stages of archaeal biofilm development and highlight similarities and differences between archaea and bacteria on a molecular level. We also consider the role of archaeal biofilms in industry and their use in different industrial processes.

Comparative analysis of deep sequenced methanogenic communities: identification of microorganisms responsible for methane production

BACKGROUND

Although interactions between microorganisms involved in biogas production are largely uncharted, it is commonly accepted that methanogenic Archaea are essential for the process. Methanogens thrive in various environments, but the most extensively studied communities come from biogas plants. In this study, we employed a metagenomic analysis of deeply sequenced methanogenic communities, which allowed for comparison of taxonomic and functional diversity as well as identification of microorganisms directly involved in various stages of methanogenesis pathways.

RESULTS

A comprehensive metagenomic approach was used to compare seven environmental communities, originating from an agricultural biogas plant, cattle-associated samples, a lowland bog, sewage sludge from a wastewater treatment plant and sediments from an ancient gold mine. In addition to the native consortia, two laboratory communities cultivated on maize silage as the sole substrate were also analyzed. Results showed that all anaerobic communities harbored genes of all known methanogenesis pathways, but their abundance varied greatly between environments and that genes were encoded by different methanogens. Identification of microorganisms directly involved in different stages of methane production revealed that hydrogenotrophic methanogens, such as Methanoculleus, Methanobacterium, Methanobrevibacter, Methanocorpusculum or Methanoregula, predominated in most native communities, whereas acetoclastic Methanosaeta seemed to be the key methanogen in the wastewater treatment plant. Furthermore, in many environments, the methylotrophic pathway carried out by representatives of Methanomassiliicoccales, such as Candidatus Methanomethylophilus and Candidatus Methanoplasma, seemed to play an important role in methane production. In contrast, in stable laboratory reactors substrate versatile Methanosarcina predominated.

CONCLUSIONS

The metagenomic approach presented in this study allowed for deep exploration and comparison of nine environments in which methane production occurs. Different abundance of methanogenesis-related functions was observed and the functions were analyzed in the phylogenetic context in order to identify microbes directly involved in methane production. In addition, a comparison of two metagenomic analytical tools, MG-RAST and MetAnnotate, revealed that combination of both allows for a precise characterization of methanogenic communities.

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

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

Efficacy of methanogenic biomass acclimation in mesophilic anaerobic digestion of ultrasound pretreated sludge

Methanogenic biomass plays a key role with regard to methane production during anaerobic bioconversion of organic substrates. In this study, the effect of two different acclimated inocula on digestion performances was investigated by means of anaerobic batch tests on untreated and sonicated waste-activated sludge. Organics solubilization and removal kinetics, the abundance and physiological conditions of archaeal cells on ultimate methane yield were evaluated. The simultaneous presence of Methanosarcina and Methanosaeta in the archaeal biomass, the higher initial archaeal cells relative abundance and their occurrence in the aggregated forms were the main factors positively affecting the conversion into methane. The presence of the acclimated inoculum at the start-up influenced positively the methane improvement due to sonication, and the methane-specific production increased from 0.335 ± 0.03 to 0.420 ± 0.05 Nm³/kg VS_fed. Moreover, the better physiological state of methanogens permitted to appreciate the effect of hydrolysis improvement by ultrasound pretreatment.

Bacterial community structure in simultaneous nitrification, denitrification and organic matter removal process treating saline mustard tuber wastewater as revealed by 16S rRNA sequencing

A simultaneous nitrification, denitrification and organic matter removal (SNDOR) process in sequencing batch biofilm reactor (SBBR) was established to treat saline mustard tuber wastewater (MTWW) in this study. An average COD removal efficiency of 86.48% and total nitrogen removal efficiency of 86.48% were achieved at 30gNaClL^-1 during 100days' operation. The underlying mechanisms were investigated by PacBio SMRT DNA sequencing (V1-V9) to analyze the microbial community structures and its variation from low salinity at 10gNaClL^-1 to high salinity at 30gNaClL^-1. Results showed elevated salinity did not affect biological performance but reduced microbial diversity in SBBR, and halophilic bacteria gradually predominated by succession. Despite of high C/N, autotrophic ammonia-oxidizing bacteria (AOB) Nitrosomonas and ammonia-oxidizing archaea (AOA) Candidatus Nitrososphaera both contributed to ammonium oxidation. As salinity increasing, nitrite-oxidizing bacteria (NOB) were significantly inhibited, partial nitrification and denitrification (PND) process gradually contributed to nitrogen removal.

Development of Anaerobic High-Rate Reactors, Focusing on Sludge Bed Technology

In the last 40 years, anaerobic sludge bed reactor technology has evolved from localized laboratory-scale trials to worldwide successful implementations in a variety of industries. High-rate sludge bed reactors are characterized by a very small footprint and high applicable volumetric loading rates. Best performances are obtained when the sludge bed consists of highly active and well settleable granular sludge. Sludge granulation provides a rich microbial diversity, high biomass concentration, high solids retention time, good settling characteristics, reduction in both operation costs and reactor volume, and high tolerance to inhibitors and temperature changes. However, sludge granulation cannot be guaranteed on every type of industrial wastewater. Especially in the last two decades, various types of high-rate anaerobic reactor configurations have been developed that are less dependent on the presence of granular sludge, and many of them are currently successfully used for the treatment of various kinds of industrial wastewaters worldwide. This study discusses the evolution of anaerobic sludge bed technology for the treatment of industrial wastewaters in the last four decades, focusing on granular sludge bed systems.

Fungal β-1,3-glucan increases ofloxacin tolerance of Escherichia coli in a polymicrobial E. coli/Candida albicans biofilm

In the past, biofilm-related research has focused mainly on axenic biofilms. However, in nature, biofilms are often composed of multiple species, and the resulting polymicrobial interactions influence industrially and clinically relevant outcomes such as performance and drug resistance. In this study, we show that Escherichia coli does not affect Candida albicans tolerance to amphotericin or caspofungin in an E. coli/C. albicans biofilm. In contrast, ofloxacin tolerance of E. coli is significantly increased in a polymicrobial E. coli/C. albicans biofilm compared to its tolerance in an axenic E. coli biofilm. The increased ofloxacin tolerance of E. coli is mainly biofilm specific, as ofloxacin tolerance of E. coli is less pronounced in polymicrobial E. coli/C. albicans planktonic cultures. Moreover, we found that ofloxacin tolerance of E. coli decreased significantly when E. coli/C. albicans biofilms were treated with matrix-degrading enzymes such as the β-1,3-glucan-degrading enzyme lyticase. In line with a role for β-1,3-glucan in mediating ofloxacin tolerance of E. coli in a biofilm, we found that ofloxacin tolerance of E. coli increased even more in E. coli/C. albicans biofilms consisting of a high-β-1,3-glucan-producing C. albicans mutant. In addition, exogenous addition of laminarin, a polysaccharide composed mainly of poly-β-1,3-glucan, to an E. coli biofilm also resulted in increased ofloxacin tolerance. All these data indicate that β-1,3-glucan from C. albicans increases ofloxacin tolerance of E. coli in an E. coli/C. albicans biofilm.

Characterization of the archaeal community fouling a membrane bioreactor

Biofilm formation, one of the primary causes of biofouling, results in reduced membrane flux or increased transmembrane pressure and thus represents a major impediment to the wider implementation of membrane bioreactor (MBR) technologies for water purification. Most studies have focused on the role of bacteria in membrane fouling as they are the most dominant and best studied organisms present in the MBR. In contrast, there is limited information on the role of the archaeal community in biofilm formation in MBRs. This study investigated the composition of the archaeal community during the process of biofouling in an MBR. The archaeal community was observed to have lower richness and diversity in the biofilm than the sludge during the establishment of biofilms at low transmembrane pressure (TMP). Clustering of the communities based on the Bray-Curtis similarity matrix indicated that a subset of the sludge archaeal community formed the initial biofilms. The archaeal community in the biofilm was mainly composed of Thermoprotei, Thermoplasmata, Thermococci, Methanopyri, Methanomicrobia and Halobacteria. Among them, the Thermoprotei and Thermoplasmata were present at higher relative proportions in the biofilms than they were in the sludge. Additionally, the Thermoprotei, Thermoplasmata and Thermococci were the dominant organisms detected in the initial biofilms at low TMP, while as the TMP increased, the Methanopyri, Methanomicrobia, Aciduliprofundum and Halobacteria were present at higher abundances in the biofilms at high TMP.

Quantitative response of nitrifying and denitrifying communities to environmental variables in a full-scale membrane bioreactor

The abundance and transcription levels of specific gene markers of total bacteria, ammonia-oxidizing Betaproteobacteria, nitrite-oxidizing bacteria (Nitrospira-like) and denitrifiers (N2O-reducers) were analyzed using quantitative PCR (qPCR) and reverse-transcription qPCR during 9 months in a full-scale membrane bioreactor treating urban wastewater. A stable community of N-removal key players was developed; however, the abundance of active populations experienced sharper shifts, demonstrating their fast adaptation to changing conditions. Despite constituting a small percentage of the total bacterial community, the larger abundances of active populations of nitrifiers explained the high N-removal accomplished by the MBR. Multivariate analyses revealed that temperature, accumulation of volatile suspended solids in the sludge, BOD5, NH4(+) concentration and C/N ratio of the wastewater contributed significantly (23-38%) to explain changes in the abundance of nitrifiers and denitrifiers. However, each targeted group showed different responses to shifts in these parameters, evidencing the complexity of the balance among them for successful biological N-removal.

Conversion of crude oil to methane by a microbial consortium enriched from oil reservoir production waters

The methanogenic biodegradation of crude oil is an important process occurring in petroleum reservoirs and other oil-containing environments such as contaminated aquifers. In this process, syntrophic bacteria degrade hydrocarbon substrates to products such as acetate, and/or H2 and CO2 that are then used by methanogens to produce methane in a thermodynamically dependent manner. We enriched a methanogenic crude oil-degrading consortium from production waters sampled from a low temperature heavy oil reservoir. Alkylsuccinates indicative of fumarate addition to C5 and C6 n-alkanes were identified in the culture (above levels found in controls), corresponding to the detection of an alkyl succinate synthase encoding gene (assA/masA) in the culture. In addition, the enrichment culture was tested for its ability to produce methane from residual oil in a sandstone-packed column system simulating a mature field. Methane production rates of up to 5.8 μmol CH4/g of oil/day were measured in the column system. Amounts of produced methane were in relatively good agreement with hydrocarbon loss showing depletion of more than 50% of saturate and aromatic hydrocarbons. Microbial community analysis revealed that the enrichment culture was dominated by members of the genus Smithella, Methanosaeta, and Methanoculleus. However, a shift in microbial community occurred following incubation of the enrichment in the sandstone columns. Here, Methanobacterium sp. were most abundant, as were bacterial members of the genus Pseudomonas and other known biofilm forming organisms. Our findings show that microorganisms enriched from petroleum reservoir waters can bioconvert crude oil components to methane both planktonically and in sandstone-packed columns as test systems. Further, the results suggest that different organisms may contribute to oil biodegradation within different phases (e.g., planktonic vs. sessile) within a subsurface crude oil reservoir.