Culture-Independent Analyses Reveal Novel Anaerolineaceae as Abundant Primary Fermenters in Anaerobic Digesters Treating Waste Activated Sludge

Analyzing performance and microbial mechanisms in an incineration leachate treatment after waste separation: Integrated metagenomic and metaproteomic analyses

The absence of food waste after separation poses a significant challenge to incineration leachate treatment, as it decreases the C/N ratio and COD of leachate, greatly impacting the biological treatment process. A one-year in-situ study was systematically conducted in an incineration leachate treatment plant that experienced waste separation, focusing on the variations in carbon and nitrogen removal performance as well as the involved microbial mechanism of the "anaerobic digestion (AD) + two-stage A/O" process. Results indicated that the biodegradability of leachate significantly decreased over time, with COD concentration decreasing by 10 times and the average C/N ratio decreasing from 12.3 to 1.4. The AD process was maintained stable, achieving a COD removal efficiency exceeding 92 %. The nitrification process also remained stable; while the denitrification process was significantly affected, and a nine-fold increase in external glucose addition was required to achieve a nitrogen removal efficiency of 85 %. Metagenomic analysis indicated that comammox Nitrospira (contributing 90 % to ammonia monooxygenase) occupied the dominant position over Nitrosomonas for nitrification due to the low NH4+-N concentration in A/O tanks (<35 mg/L), and Methanothrix was substituted by Methanosarcina for methanogenesis in AD unit. Metaproteomic results further elucidated that the expression of enzymes responsible for denitrification process, i.e., Nir, Nor, Nos (convert NO2- to N2), was decreased significantly, although the expression of enzymes related to glycolysis and TCA cycle were stimulated by glucose addition. The expression of Nar (convert NO3--N to NO2--N) remained stable, while the imbalance expression within denitrifying enzymes might have facilitated occurrence of partial denitrification, attributed to the low C/N ratio. The results prove that the function robustness and metabolic versatility were achieved in leachate treatment plant after waste separation but at the cost of the high external carbon resource addition, highlighting the urgent requirement for low-carbon nitrogen removal technologies.

De novo anaerobic granulation with varying organic substrates: granule growth and microbial community responses

Anaerobic granulation from dispersed inoculum is recognized as a slow process. However, studies under saline conditions have shown that adding complex proteinaceous substrates can accelerate this process. To explore whether this holds true also under non-saline conditions, we conducted a 262-days experiment with four lab-scale upflow anaerobic sludge blanket reactors inoculated with digested sewage sludge. Each reactor received a synthetic feed containing varying amount of carbohydrate/protein substrate: glucose (RGlu), acetate/tryptone (RAc+Try), glucose/tryptone (RGlu+Try), and glucose/starch (RGlu+Sta). Development of granules with different influent composition was monitored with macroscopy, analysis of the extracellular polymeric substances, and microbial diversity. Granulation was faster in reactors RGlu+Try and RGlu+Sta. Increasing granule diameters positively correlated with the occurrence of bacteria from Muribaculaceae and Lachnospiraceae families, suggesting their involvement in de novo granulation. Granules of RGlu+Try also had high relative abundances of both fermenting bacteria (e.g. Lactococcus, Streptococcus, Trichococcus) and bacteria involved in the oxidation of volatile fatty acids (Smithella, Acetobacteroides). The results of this study provide a basis for strategies to enhance the sludge granulation rate in practice when granular inoculum is not available. Specifically, supplementing small amounts of waste protein during reactor start-up can be effective.

Feasibility assessment and underlying mechanisms of metabisulfite pretreatment for enhanced volatile fatty acids production from anaerobic sludge fermentation

Employing chemical pretreatment for waste activated sludge (WAS) fermentation is crucial to achieving sustainable sludge management. This study investigated the feasibility of metabisulfite (MS) pretreatment for enhancing volatile fatty acids (VFAs) production from WAS. The results show that after 24-h MS pretreatment, the content of soluble organic matter and loosely bound extracellular polymeric substances (LB-EPS), especially proteins, increased significantly. During the fermentation, MS pretreatment under alkaline conditions was more efficient, with VFA peaking on the fifth day, showing a 140 % increase compared to the alkaline control group. Correlation analysis suggests that the dosage of MS, rather than pH, is closely related to the levels of soluble protein, polysaccharides, LB-EPS, and subsequential VFAs production, while alkaline conditions facilitate the dissolution of total organic carbon. Furthermore, sulfite radicals (SO3•-) are attributed to cell inactivation and lysis, while alkaline conditions initially reduce the size of the flocs, further promoting MS for attacking flocs, thereby improving the performance of fermentation. The study also found that MS pretreatment reduced microbial community diversity, enriched hydrolytic and fermentation bacteria (Actinobacteriota and Firmicutes), and suppressed methanogens (Methanobacteriaceae and Methanosaetaceae), making it a safe, viable, and cost-effective chemical agent for sustainable sludge management.

Genome-resolved metagenomics reveals the nitrifiers enrichment and species succession in activated sludge under extremely low dissolved oxygen

Nitrification, a process carried out by aerobic microorganisms that oxidizes ammonia to nitrate via nitrite, is an indispensable step in wastewater nitrogen removal. To facilitate energy and carbon savings, applying low dissolved oxygen (DO) is suggested to shortcut the conventional biological nitrogen removal pathway, however, the impact of low DO on nitrifying communities within activated sludge is not fully understood. This study used genome-resolved metagenomics to compare nitrifying communities under extremely low- and high-DO. Two bioreactors were parallelly operated to perform nitrification and DO was respectively provided by limited gas-liquid mass transfer from the atmosphere (AN reactor, DO < 0.1 mg/L) and by sufficient aeration (AE reactor, DO > 5.0 mg/L). Low DO was thought to limit nitrifiers growth; however, we demonstrated that complete nitrification could still be achieved under the extremely low-DO conditions, but with no nitrite accumulation observed. Kinetic analysis showed that after long-term exposure to low DO, nitrifiers had a higher oxygen affinity constant and could maintain a relatively high nitrification rate, particularly at low levels of DO (<0.2 mg/L). Community-level gene analysis indicated that low DO promoted enrichment of nitrifiers (the genera Nitrosomonas and Nitrospira, increased by 2.3- to 4.3-fold), and also harbored with 2.3 to 5.3 times higher of nitrification functional genes. Moreover, 46 high-quality (>90 % completeness and <5 % contamination) with 3 most abundant medium-quality metagenome-assembled genomes (MAGs) were retrieved using binning methods. Genome-level phylogenetic analysis revealed the species succession within nitrifying populations. Surprisingly, compared to DO-rich conditions, low-DO conditions were found to efficiently suppressed the ordinary heterotrophic microorganisms (e.g., the families Anaerolineales, Phycisphaerales, and Chitinophagales), but selected for the specific candidate denitrifiers (within phylum Bacteroidota). This study provides new microbial insights to demonstrate that low-DO favors the enrichment of autotrophic nitrifiers over heterotrophs with species-level successions, which would facilitate the optimization of energy and carbon management in wastewater treatment.

Carbon dioxide and weak magnetic field enhance iron-carbon micro-electrolysis combined autotrophic denitrification

Combining iron-carbon micro-electrolysis and autotrophic denitrification is promising for nitrate removal from wastewater. In this study, four continuous reactors were constructed using CO2 and weak magnetic field (WMF) to address challenges like iron passivation and pH stability. In the reactors with CO2 + WMF (10 and 35 mT), the increase in total nitrogen removal efficiency was significantly higher (96.2 ± 1.6 % and 94.1 ± 2.7 %, respectively) than that of the control (51.6 ± 2.7 %), and Fe3O4 converted to low-density FeO(OH) and FeCO3, preventing passivation film formation. The WMF application decreased the N2O emissions flux by 8.7 % and 20.5 %, respectively. With CO2 + WMF, the relative enzyme activity and abundance of denitrifying bacteria, especially unclassified_Rhodocyclaceae and Denitratisoma, increased. Thus, this study demonstrates that CO2 and WMF optimize the nitrate removal process, significantly enhancing removal efficiency, reducing greenhouse gas emissions, and improving process stability.

Evolutionary plasticity and functional repurposing of the essential metabolic enzyme MoeA

MoeA, or gephyrin in higher eukaryotes, is crucial for molybdenum cofactor biosynthesis required in redox reactions. Gephyrin is a moonlighting protein also involved in postsynaptic receptor clustering, a feature thought to be a recent evolutionary trait. We showed previously that a repurposed copy of MoeA (Glp) is involved in bacterial cell division. To investigate how MoeA acquired multifunctionality, we used phylogenetic inference and protein structure analyses to understand the diversity and evolutionary history of MoeA. Glp-expressing Bacteria have at least two copies of the gene, and our analysis suggests that Glp has lost its enzymatic role. In Archaea we identified an ancestral duplication where one of the paralogs might bind tungsten instead of molybdenum. In eukaryotes, the acquisition of the moonlighting activity of gephyrin comprised three major events: first, MoeA was obtained from Bacteria by early eukaryotes, second, MogA was fused to the N-terminus of MoeA in the ancestor of opisthokonts, and finally, it acquired the function of anchoring GlyR receptors in neurons. Our results support the functional versatility and adaptive nature of the MoeA scaffold, which has been repurposed independently both in eukaryotes and bacteria to carry out analogous functions in network organization at the cell membrane.

Evidence of Potential Anammox Activities from Rice Paddy Soils in Microaerobic and Anaerobic Conditions

Anammox, a reaction in which microorganisms oxidize ammonia under anaerobic conditions, is used in the industry to remove ammonium from wastewater in an environmentally friendly manner. This process does not produce intermediate products such as nitrite or nitrate, which can act as secondary pollutants in soil and water environments. For industrial applications, anammox bacteria should be obtained from the environment and cultivated. Anammox bacteria generally exhibit a slow growth rate and may not produce a large number of cells due to their anaerobic metabolism. Additionally, their habitats appear to be limited to specific environments, such as oxidation-reduction transition zones. Consequently, most of the anammox bacteria that are used or studied originate from marine environments. In this study, anammox bacterial evidence was found in rice paddy soil and cultured under various conditions of aerobic, microaerobic, and anaerobic batch incubations to determine whether enrichment was possible. The anammox-specific gene (hzsA) and microbial community analyses were performed on the incubated soils. Although it was not easy to enrich anammox bacteria due to co-occurrence of denitrification and nitrification based on the chemistry data, potential existence of anammox bacteria was assumed in the terrestrial paddy soil environment. For potential industrial uses, anammox bacteria could be searched for in rice paddy soils by applying optimal enrichment conditions.

MiDAS 5: Global diversity of bacteria and archaea in anaerobic digesters

Anaerobic digestion of organic waste into methane and carbon dioxide (biogas) is carried out by complex microbial communities. Here, we use full-length 16S rRNA gene sequencing of 285 full-scale anaerobic digesters (ADs) to expand our knowledge about diversity and function of the bacteria and archaea in ADs worldwide. The sequences are processed into full-length 16S rRNA amplicon sequence variants (FL-ASVs) and are used to expand the MiDAS 4 database for bacteria and archaea in wastewater treatment systems, creating MiDAS 5. The expansion of the MiDAS database increases the coverage for bacteria and archaea in ADs worldwide, leading to improved genus- and species-level classification. Using MiDAS 5, we carry out an amplicon-based, global-scale microbial community profiling of the sampled ADs using three common sets of primers targeting different regions of the 16S rRNA gene in bacteria and/or archaea. We reveal how environmental conditions and biogeography shape the AD microbiota. We also identify core and conditionally rare or abundant taxa, encompassing 692 genera and 1013 species. These represent 84-99% and 18-61% of the accumulated read abundance, respectively, across samples depending on the amplicon primers used. Finally, we examine the global diversity of functional groups with known importance for the anaerobic digestion process.

Metagenome reveals the possible mechanism that microbial strains promote methanogenesis during anaerobic digestion of food waste

For better understanding the mechanism of microbial strains promoting methane production, four strains Hungatella xylanolytica A5, Bacillus licheniformis B1, Paraclostridium benzoelyticum C2 and Advenella faeciporci E1 were inoculated into anaerobic digestion systems. After bioaugmentation, the cumulative methane production of A5, B1, C2 and E1 groups elevated by 11.68%, 8.20%, 18.21% and 15.67% compared to CK group, respectively. The metagenomic analysis revealed that the species diversity and uniformity of the experimental groups was improved, and hydrolytic acidifying bacteria, represented by Clostridiaceae, Anaerolineaceae and Oscillospiraceae, and methanogens, such as Methanotrichaceae and Methanobacteriaceae, were enriched. Meanwhile, the abundance of key genes in carbohydrate, pyruvate and methane metabolism was increased in the inoculated groups, providing reasonable reasons for more methane production. The strengthening mechanism of microbial strains in this study offered a theoretical foundation for selecting a suitable bioaugmentation strategy to solve the problems of slow start-up and low methane production in anaerobic digestion.

Achieving advanced nitrogen removal from mature landfill leachate in continuous flow system involving partial nitrification-anammox and denitrification

Considering the challenges associated with nitrogen removal from mature landfill leachate, a novel combined continuous-flow process integrating denitrification and partial nitrification-Anammox (PN/A) was developed using an internal circulation (IC) system and a biological aerated filter (BAF) biofilm reactor (IBBR). In this study, IBBR successfully operated for 343 days, and when influent NH4+-N concentration of mature landfill leachate reached 1258.1 mg/L, an impressive total nitrogen removal efficiency (TNRE) of 93.3 % was achieved, along with a nitrogen removal rate (NRR) of 1.13 kg N/(m3·d). The analysis of the microbial community revealed that Candidatus Kuenenia, the dominant genus responsible for anammox, accounted for 1.7 % (day 265). Additionally, Nitrosomonas, Thauera and Truepera were identified as key contributors to the efficient removal of nitrogen from mature landfill. As a novel nitrogen removal strategy, the practical application of the IBBR system offers novel perspectives on addressing mature landfill leachate.

Dead in the water - Role of relic DNA and primer choice for targeted sequencing surveys of anaerobic sewage sludge intended for biological monitoring

DNA-based monitoring of microbial communities that are responsible for the performance of anaerobic digestion of sewage wastes has the potential to improve resource recoveries for wastewater treatment facilities. By treating sludge with propidium monoazide (PMA) prior to amplicon sequencing, this study explored how the presence of DNA from dead microbial biomass carried over with feed sludge may mislead process-relevant biomarkers, and whether primer choice impacts such assessments. Four common primers were selected for amplicon preparation, also to determine if universal primers have sufficient taxonomic or functional coverage for monitoring ecological performance; or whether two domain-specific primers for Bacteria and Archaea are necessary. Anaerobic sludges of three municipal continuously stirred-tank reactors in Victoria, Australia, were sampled at one time-point. A total of 240 amplicon libraries were sequenced on a Miseq using two universal and two domain-specific primer pairs. Untargeted metabolomics was chosen to complement biological interpretation of amplicon gene-based functional predictions. Diversity, taxonomy, phylogeny and functional potentials were systematically assessed using PICRUSt2, which can predict community wide pathway abundance. The two chosen universal primers provided similar diversity profiles of abundant Bacteria and Archaea, compared to the domain-specific primers. About 16 % of all detected prokaryotic genera covering 30 % of total abundances and 6 % of PICRUSt2-estimated pathway abundances were affected by PMA. This showed that dead biomass in the anaerobic digesters impacted DNA-based assessments, with implications for predicting active processes, such as methanogenesis, denitrification or the identification of organisms associated with biological foams. Hence, instead of running two sequencing runs with two different domain-specific primers, we propose conducting PMA-seq with universal primer pairs for routine performance monitoring. However, dead sludge biomass may have some predictive value. In principal component analysis the compositional variation of 239 sludge metabolites resembled that of 'dead-plus-alive' biomass, suggesting that dead organisms contributed to the potentially process-relevant sludge metabolome.

Low-temperature thermal hydrolysis for enhancing sludge anaerobic digestion and antibiotic resistance management: Significance of digester solids retention time

Recently, there has been a growing inclination towards utilizing primary sludge (PS) fermentation prior to anaerobic digestion (AD) in water resource recovery facilities (WRRFs), where sludge liquor containing volatile fatty acids is used for biological nutrient removal. Nevertheless, using a low-temperature thermal hydrolysis process (THP) to improve AD in WRRFs adopting PS fermentation remains an area that has received limited research attention. Here, we studied the impact of THP (90 °C, 90 min) on anaerobic co-digestion of thickened waste activated sludge (TWAS) and fermented primary sludge (FPS) under varying solids retention times (SRTs) in semi-continuous mode. The study involved two THP schemes: scheme 1, where THP was done for both TWAS and FPS, and scheme 2, where THP was applied to TWAS only. The results demonstrated that reducing SRT from 20 to 15 and 10 d leads to decreased methane yield in both schemes. However, THP significantly enhances methane production, showing improvements of up to 37.9 % (scheme 1) and 31.2 % (scheme 2) under a 15-d SRT. Furthermore, while decreasing SRT increased the proliferation of antibiotic resistance genes (ARGs), thermal hydrolysis could effectively reduce most ARGs, indicating its potential to mitigate antibiotic resistance in the AD process. Overall, these results provide useful perceptions regarding the potential adoption of low-temperature THP in WRRFs with PS fermentation.

Coupling extracellular glycan composition with metagenomic data in papermill and brewery anaerobic granular sludges

Glycans are crucial for the structure and function of anaerobic granular sludge in wastewater treatment. Yet, there is limited knowledge regarding the microorganisms and biosynthesis pathways responsible for glycan production. In this study, we analysed samples from anaerobic granular sludges treating papermill and brewery wastewater, examining glycans composition and using metagenome-assembled genomes (MAGs) to explore potential biochemical pathways associated with their production. Uronic acids were the predominant constituents of the glycans in extracellular polymeric substances (EPS) produced by the anaerobic granular sludges, comprising up to 60 % of the total polysaccharide content. MAGs affiliated with Anaerolineacae, Methanobacteriaceae and Methanosaetaceae represented the majority of the microbial community (30-50 % of total reads per MAG). Based on the analysis of MAGs, it appears that Anaerolinea sp. and members of the Methanobacteria class are involved in the production of exopolysaccharides within the analysed granular sludges. These findings shed light on the functional roles of microorganisms in glycan production in industrial anaerobic wastewater treatment systems.

Microbial community dynamics and functional potentials in the conversion of oil palm wastes into biomethane

Oil palm processing generates substantial waste materials rich in organic content, posing various environmental challenges. Anaerobic digestion (AD), particularly for palm oil mill effluent (POME), offers a sustainable solution, by converting waste into valuable biomethane for thermal energy or electricity generation. The synergistic activities of the AD microbiota directly affect the biomethane production, and the microbial community involved in biomethane production in POME anaerobic digestion has been reported. The composition of bacterial and archaeal communities varies under different substrate and physicochemical conditions. This review discusses the characteristics of POME, explores the microbial members engaged in each stage of AD, and elucidates the impacts of substrate and physicochemical conditions on the microbial community dynamics, with a specific focus on POME. Finally, the review outlines current research needs and provides future perspectives on optimizing the microbial communities for enhanced biomethane production from oil palm wastes.

Phylogenomic discernments into Anaerolineaceae thermal adaptations and the proposal of a candidate genus Mesolinea

This study delves into the evolutionary history of Anaerolineaceae, a diverse bacterial family within the Chloroflexota phylum. Employing a multi-faceted approach, including phylogenetic analyses, genomic comparisons, and exploration of adaptive features, the research unveils novel insights into the family's taxonomy and evolutionary dynamics. The investigation employs metagenome-assembled genomes (MAGs), emphasizing their prevalence in anaerobic environments. Notably, a novel mesophilic lineage, tentatively named Mesolinea, emerges within Anaerolineaceae, showcasing a distinctive genomic profile and apparent adaptation to a mesophilic lifestyle. The comprehensive genomic analyses shed light on the family's complex evolutionary patterns, including the conservation of key operons in thermophiles, providing a foundation for understanding the diverse ecological roles and adaptive strategies of Anaerolineaceae members.

Riboflavin-loaded carbon cloth aids the anaerobic digestion of cow dung by promoting direct interspecies electron transfer

Cow dung generates globally due to increased beef and milk consumption, but its treatment efficiency remains low. Previous studies have shown that riboflavin-loaded conductive materials can improve anaerobic digestion through enhance direct interspecies electron transfer (DIET). However, its effect on the practical anaerobic digestion of cow dung remained unclear. In this study, carbon cloth loaded with riboflavin (carbon cloth-riboflavin) was added into an anaerobic digester treating cow dung. The carbon cloth-riboflavin reactor showed a better performance than other two reactors. The metagenomic analysis revealed that Methanothrix on the surface of the carbon cloth predominantly utilized the CO2 reduction for methane production, further enhanced after riboflavin addition, while Methanothrix in bulk sludge were using the acetate decarboxylation pathway. Furthermore, the carbon cloth-riboflavin enriched various major methanogenic pathways and activated a large number of enzymes associated with DIET. Riboflavin's presence altered the microbial communities and the abundance of functional genes relate to DIET, ultimately leading to a better performance of anaerobic digestion for cow dung.

The faecal microbiome of Exmoor ponies shows step-wise compositional changes with increasing levels of management by humans

BACKGROUND

Horses can suffer from gastrointestinal (GI) disease in domestic environments, often precipitated by human-led changes in management. Understanding the consequences of these changes on equine gut microbiota is key to the prevention of such disease episodes.

OBJECTIVE

Profile the faecal microbiota of adult female Exmoor ponies under three management conditions, representing increasing levels of management by humans, encompassing different diets; whilst controlling for age, breed and sex.

STUDY DESIGN

Cross-sectional descriptive.

METHODS

Faecal samples were collected from three populations of Exmoor ponies kept under contrasting management conditions: 29 adult female ponies in groups with low management (LM) (n = 10), medium management (MM) (n = 10) and high management (HM) (n = 9) levels, based on diet, drug use, handling and exercise. Faecal microbial composition was profiled via high-throughput sequencing of the bacterial 16S rRNA gene, and functional metagenome predictions.

RESULTS

We observed profound step-wise changes in microbiome structure in the transition from LM to MM to HM. A relatively high abundance of Proteobacteria and Tenericutes was associated with the HM group; higher abundance of Methanobacteria was observed in the LM group. The MM group had intermediate levels of these taxa and exhibited high 'within group' variation in alpha diversity. Functional predictions revealed increased amino acid and lipid metabolism in HM; energy metabolism in LM and carbohydrate metabolism and immune/metabolic disease pathways in MM.

MAIN LIMITATIONS

Low group sizes, incomplete knowledge of bacterial genomes in equine gut microbiota and it was not possible to assess the relative impact of diet, drug use, handling and exercise on the microbiome as variables were confounded.

CONCLUSIONS

Human-led management factors had profound step-wise effects on faecal microbial composition. Based on functional metagenome predictions, we hypothesise that dietary differences between groups were the major driver of observed differences.

A comprehensive overview of the Chloroflexota community in wastewater treatment plants worldwide

IMPORTANCE

Chloroflexota are often abundant members of the biomass in wastewater treatment plants (WWTPs) worldwide, typically with a filamentous morphology, forming the backbones of the activated sludge floc. However, their overgrowth can often cause operational issues connected to poor settling or foaming, impairing effluent quality and increasing operational costs. Despite their importance, few Chloroflexota genera have been characterized so far. Here, we present a comprehensive overview of Chloroflexota abundant in WWTPs worldwide and an in-depth characterization of their morphology, phylogeny, and ecophysiology, obtaining a broad understanding of their ecological role in activated sludge.

Effect of free nitrous acid on extracellular polymeric substances production and membrane fouling in a nitritation membrane bioreactor

The membrane bioreactor (MBR) with nitritation based nitrogen removal processes has attracted growing interest in recent years, although membrane fouling in the nitritation MBR is a challenging issue. In this study, the inhibitory effect of free nitrous acid (FNA) on microbial extracellular polymeric substances (EPS) production and membrane fouling in a nitritation MBR was investigated. Results showed that EPS played a critical role in the biofouling process, and EPS production was affected by FNA concentration. As FNA concentration increased from 5.10 × 10-3 mg N/L to 1.34 × 10-2 mg N/L, protein (PN) and polysaccharide (PS) contents increased from 8.20 to 60.28 mg/g VSS and 4.74-30.46 mg/g VSS, respectively. However, when FNA concentration was 1.48 × 10-2 mg N/L, PN and PS reduced by 20.0% and 10.9%, respectively, indicating that the higher FNA concentration could reduce EPS production. The EPS reduction could be attributed to reduction in the loosely bound (LB) and tightly bound (TB) EPS but not the soluble microbial products (SMP). It was further revealed that higher FNA concentrations up to 1.48 × 10-2 mg N/L consequently mitigate trans-membrane pressure (TMP) rate in terms of dTMP/dt by 25.5% in the nitritation MBR. High throughput sequencing analysis revealed that the increase in FNA led to enrichment of Nitrosomonas but reduction in heterotrophic bacteria. This study showed that the appropriate FNA concentration affected EPS production and hence membrane fouling, leading to the possibility of membrane fouling mitigation by in-situ generated FNA in the nitritation MBR.

Novel Insights on the Bacterial and Archaeal Diversity of the Panarea Shallow-Water Hydrothermal Vent Field

Current knowledge of the microbial diversity of shallow-water hydrothermal vents is still limited. Recent evidence suggests that these peculiar and heterogeneous systems might host highly diversified microbial assemblages with novel or poorly characterized lineages. In the present work, we used 16S rRNA gene metabarcoding to provide novel insights into the diversity of the bacterial and archaeal assemblages in seawater and sediments of three shallow-water hydrothermal systems of Panarea Island (Tyrrhenian Sea). The three areas were characterized by hot, cold, or intermediate temperatures and related venting activities. Microbial biodiversity in seawater largely differed from the benthic one, both in α-diversity (i.e., richness of amplicon sequence variants-ASVs) and in prokaryotic assemblage composition. Furthermore, at the class level, the pelagic prokaryotic assemblages were very similar among sites, whereas the benthic microbial assemblages differed markedly, reflecting the distinct features of the hydrothermal activities at the three sites we investigated. Our results show that ongoing high-temperature emissions can influence prokaryotic α-diversity at the seafloor, increasing turnover (β-)diversity, and that the intermediate-temperature-venting spot that experienced a violent gas explosion 20 years ago now displays the highest benthic prokaryotic diversity. Overall, our results suggest that hydrothermal vent dynamics around Panarea Island can contribute to an increase in the local heterogeneity of physical-chemical conditions, especially at the seafloor, in turn boosting the overall microbial (γ-)diversity of this peculiar hydrothermal system.

Mapping the microbial diversity associated with different geochemical regimes in the shallow-water hydrothermal vents of the Aeolian archipelago, Italy

Shallow-water hydrothermal vents are unique marine environments ubiquitous along the coast of volcanically active regions of the planet. In contrast to their deep-sea counterparts, primary production at shallow-water vents relies on both photoautotrophy and chemoautotrophy. Such processes are supported by a range of geochemical regimes driven by different geological settings. The Aeolian archipelago, located in the southern Tyrrhenian sea, is characterized by intense hydrothermal activity and harbors some of the best sampled shallow-water vents of the Mediterranean Sea. Despite this, the correlation between microbial diversity, geochemical regimes and geological settings of the different volcanic islands of the archipelago is largely unknown. Here, we report the microbial diversity associated with six distinct shallow-water hydrothermal vents of the Aeolian Islands using a combination of 16S rRNA amplicon sequencing along with physicochemical and geochemical measurements. Samples were collected from biofilms, fluids and sediments from shallow vents on the islands of Lipari, Panarea, Salina, and Vulcano. Two new shallow vent locations are described here for the first time. Our results show the presence of diverse microbial communities consistent in their composition with the local geochemical regimes. The shallow water vents of the Aeolian Islands harbor highly diverse microbial community and should be included in future conservation efforts.

Granular activated carbon remediates antibiotic resistance propagation and methanogenic inhibition induced by polystyrene nanoplastics in sludge anaerobic digestion

Nano/microplastics (NPs/MPs) in sewage sludge can induce oxidative stress to the anaerobic digestion (AD) and also proliferate antibiotic resistance genes (ARGs). Recently, granular activated carbon (GAC) has been used as an additive to enhance methane production in AD via direct interspecies electron transfer (DIET); however, its impact on AD exposed to NPs/MPs is yet to be studied. This study examined the effect of GAC (5 and 15 g/L) on sludge AD exposed to 150 µg/L of polystyrene nanoplastics (PsNPs). PsNPs decreased methane yield by 32.3% due to elevated levels of reactive oxygen species. However, GAC addition counteracted this adverse effect and improved methane production, attributed to the potential enrichment of DIET-active microbes and the adsorption of PsNPs by GAC. Moreover, GAC reduced the total abundance of ARGs, which was increased by PsNPs exposure. Thus, GAC can provide dual benefits in mitigating methanogenic inhibition caused by PsNPs and ARG spread.

Sludge source-redox mediators obtainment and availability for enhancing bioelectrogenesis and acidogenesis: Deciphering characteristics and mechanisms

Anaerobic biological treatment was regarded as one of promising options for realizing concurrent WAS reduction, stabilization and bioenergy/bioresource recycle. But the relatively low treatment efficiency limited its spreading application toward larger scale considerably in China. Aimed at such barrier, this study offered a novel enhancing strategy for achieving high-efficiency of bioenergy/bioresource recycle from WAS anaerobic treatment via improving bioelectrogenesis/acidogenesis using sludge source-redox mediators (SSRMs). SSRMs not only facilitated bioeletrogenesis with an increasing efficiency of 36% for voltage output and 39% for bioelectricity bioconversion, but also enhanced acidogenesis of WAS with a mean elevating efficiency of 37.5% of volatile fatty acids (VFAs) production within 5 d Mechanistic investigations indicated that SSRMs had a potential influence on improving the protein and carbohydrate metabolisms-related genes' expression for enhancing bioelectrogenesis and acidogenesis. Moreover, SSRMs exerted roles of electrochemical "catalysts" or as terminal electron acceptors with affecting functional proteins of complexes of Ⅰ and Ⅳ in electron transfer chains for improving electron transfer efficiency. Meanwhile, the core members' abundance, microbial diversity and community distributive evenness were prompted concurrently for carrying out superior bioelectrogenesis and acidogenesis. A schematic illustration was established for demonstrating the mechanism of SSRMs for enhancing bioelectrogenesis and acidogenesis via changing microbial metabolism functions, enhancing electron transfer efficiency, and regulating functional genes' expression of functional proteins (up-regulating cytochrome c oxidase and down-regulating-NADH dehydrogenase). This study provided an effective enhancing strategy for facilitating WAS bioconversion to bioenergy/bioresource with well-process sustainability.

Genome-centric metagenomic insights into the role of Chloroflexi in anammox, activated sludge and methanogenic reactors

BACKGROUND

The phylum Chloroflexi is highly abundant in a wide variety of wastewater treatment bioreactors. It has been suggested that they play relevant roles in these ecosystems, particularly in degrading carbon compounds and on structuring flocs or granules. Nevertheless, their function is not yet well understood as most species have not been isolated in axenic cultures. Here we used a metagenomic approach to investigate Chloroflexi diversity and their metabolic potential in three environmentally different bioreactors: a methanogenic full-scale reactor, a full-scale activated sludge reactor and a lab scale anammox reactor.

RESULTS

Differential coverage binning approach was used to assemble the genomes of 17 new Chloroflexi species, two of which are proposed as new Candidatus genus. In addition, we recovered the first representative genome belonging to the genus 'Ca. Villigracilis'. Even though samples analyzed were collected from bioreactors operating under different environmental conditions, the assembled genomes share several metabolic features: anaerobic metabolism, fermentative pathways and several genes coding for hydrolytic enzymes. Interestingly, genome analysis from the anammox reactor indicated a putative role of Chloroflexi in nitrogen conversion. Genes related to adhesiveness and exopolysaccharides production were also detected. Complementing sequencing analysis, filamentous morphology was detected by Fluorescent in situ hybridization.

CONCLUSION

Our results suggest that Chloroflexi participate in organic matter degradation, nitrogen removal and biofilm aggregation, playing different roles according to the environmental conditions.

Steering the product spectrum in high-pressure anaerobic processes: CO2 partial pressure as a novel tool in biorefinery concepts

BACKGROUND

Elevated CO₂ partial pressure (pCO₂) has been proposed as a potential steering parameter for selective carboxylate production in mixed culture fermentation. It is anticipated that intermediate product spectrum and production rates, as well as changes in the microbial community, are (in)directly influenced by elevated pCO₂. However, it remains unclear how pCO₂ interacts with other operational conditions, namely substrate specificity, substrate-to-biomass (S/X) ratio and the presence of an additional electron donor, and what effect pCO₂ has on the exact composition of fermentation products. Here, we investigated possible steering effects of elevated pCO₂ combined with (1) mixed substrate (glycerol/glucose) provision; (2) subsequent increments in substrate concentration to increase the S/X ratio; and (3) formate as an additional electron donor.

RESULTS

Metabolite predominance, e.g., propionate vs. butyrate/acetate, and cell density, depended on interaction effects between pCO₂-S/X ratio and pCO₂-formate. Individual substrate consumption rates were negatively impacted by the interaction effect between pCO₂-S/X ratio and were not re-established after lowering the S/X ratio and adding formate. The product spectrum was influenced by the microbial community composition, which in turn, was modified by substrate type and the interaction effect between pCO₂-formate. High propionate and butyrate levels strongly correlated with Negativicutes and Clostridia predominance, respectively. After subsequent pressurized fermentation phases, the interaction effect between pCO₂-formate enabled a shift from propionate towards succinate production when mixed substrate was provided.

CONCLUSIONS

Overall, interaction effects between elevated pCO₂, substrate specificity, high S/X ratio and availability of reducing equivalents from formate, rather than an isolated pCO₂ effect, modified the proportionality of propionate, butyrate and acetate in pressurized mixed substrate fermentations at the expense of reduced consumption rates and increased lag-phases. The interaction effect between elevated pCO₂ and formate was beneficial for succinate production and biomass growth with a glycerol/glucose mixture as the substrate. The positive effect may be attributed to the availability of extra reducing equivalents, likely enhanced carbon fixating activity and hindered propionate conversion due to increased concentration of undissociated carboxylic acids.

Effects of different microbial agents on bedding treatment of ectopic fermentation of buffalo manure

Introduction

The rapid development of the farming industry has increased the amount of manure produced by livestock and poultry, causing increasingly prominent environmental pollution problems. In recent years, due to the increase in conventional bedding material costs, an increasing number of farmers choose to use harmless recycled manure as bedding. Manure bedding treatment of farms can not only solve the problem of manure pollution, but also resource utilization of manure and cost savings.

Methods

This study compared the effects of five microbial agents (Microbial agents A, B, C, E, F) on buffalo manure bedding treatment by testing the temperature, moisture content, pH, microbial bacteria distribution of buffalo manure ectopic fermentation, and screened the lowest cost and most effective agent. The changes of microbial bacteria distribution in different periods of bedding treatment were also detected.

Results

Agent A was eliminated because of poor fermentation effect and low fermentation temperature, which could not achieve the effect of harmless treatment. The other four agents of bacteria achieved a harmless effect, but the bedding treatment effect of agent F was significantly better than agent E, B, and C. In terms of the cost of agents: the cost of agent F required for fermenting 100m^³ buffalo manure was the lowest, 1000yuan, followed by E (1200yuan), C (1750yuan), and B (1980yuan). In the process of ectopic fermentation bedding treatment of buffalo manure, Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, and Chloroflexi were the major bacteria used. The process was divided into three periods; the heating period - high temperature period - cooling period, the high temperature period could reach more than 75°C, and a large number of pathogenic bacteria and harmful bacteria, and other miscellaneous bacteria in the pile were degraded, their species diversity was reduced, and the structure of bacterial flora had significant differences in different treatment periods. In conclusion, this study has provided a guide for the resource utilization of manure in cattle farms and the reduction of manure pollution to the environment.

Evidence of competition between electrogens shaping electroactive microbial communities in microbial electrolysis cells

In single-chamber microbial electrolysis cells (MECs), organic compounds are oxidized at the anode, liberating electrons that are used for hydrogen evolution at the cathode. Microbial communities on the anode and cathode surfaces and in the bulk liquid determine the function of the MEC. The communities are complex, and their assembly processes are poorly understood. We investigated MEC performance and community composition in nine MECs with a carbon cloth anode and a cathode of carbon nanoparticles, titanium, or stainless steel. Differences in lag time during the startup of replicate MECs suggested that the initial colonization by electrogenic bacteria was stochastic. A network analysis revealed negative correlations between different putatively electrogenic Deltaproteobacteria on the anode. Proximity to the conductive anode surface is important for electrogens, so the competition for space could explain the observed negative correlations. The cathode communities were dominated by hydrogen-utilizing taxa such as Methanobacterium and had a much lower proportion of negative correlations than the anodes. This could be explained by the diffusion of hydrogen throughout the cathode biofilms, reducing the need to compete for space.

Synergic role of ferrate and nitrite for triggering waste activated sludge solubilisation and acidogenic fermentation: Effectiveness evaluation and mechanism elucidation

Enhancing anaerobic treatment efficiency of waste activated sludge (WAS) toward preferable resource recovery would be an important requirement for achieving carbon-emission reduction, biosolids minimization, stabilization and security concurrently. This study demonstrated the synergic effect of potassium ferrate (PF) and nitrite on prompting WAS solubilisation and acidogenic fermentation toward harvesting volatile fatty acids (VFAs). The results indicated the PF+NaNO₂ co-pretreatment boosted 7.44 times and 1.32 times higher WAS solubilisation [peak soluble chemical oxygen demand (SCOD) of 2680 ± 52 mg/L] than that by the single nitrite- and PF-pretreatment, respectively, while about 2.77 times and 2.11 times higher VFAs production were achieved (maximum VFAs accumulation of 3536.25 ± 115.24 mg COD/L) as compared with the single pretreatment (nitrite and PF)-fermentations. Afterwards the WAS dewaterability was improved simultaneously after acidogenic fermentation. Moreover, a schematic diagram was established for illustrating mechanisms of the co-pretreatment of PF and nitrite for enhancing the VFAs generation via increasing key hydrolytic enzymes, metabolic functional genes expression, shifting microbial biotransformation pathways and elevating abundances of key microbes in acidogenic fermentation. Furthermore, the mechanistic investigations suggested that the PF addition was conducive to form a relatively conductive fermentation environment for enhancing electron transfer (ET) efficiency, which contributed to the VFAs biotransformation positively. This study provided an effective strategy for enhancing the biodegradation/bioconversion efficiency of WAS organic matters with potential profitable economic returns.

Identification of key steps and associated microbial populations for efficient anaerobic digestion under high ammonium or salinity conditions

Ammonium (NH₄⁺) and salinity are major inhibitors of CH₄ production in anaerobic digestion. This study evaluated their inhibitory effects on CH₄ production and explored the key populations for efficient CH₄ production under high NH₄⁺ and NaCl concentrations to understand their inhibition mechanisms. Comparative batch experiments for mesophilic anaerobic digestion were conducted using three seeding sludges under different concentrations of NH₄⁺ (1-5 gNH₄-N/L) and NaCl (10-30 g/L). Although all sludges tolerated 3 gNH₄-N/L and 10 g/L NaCl, NH₄⁺ or NaCl concentrations higher than these substantially reduced CH₄ production, depending on the seeding sludge, primarily by impairing the initial hydrolysis and methanogenesis steps. In addition, propionate was found to be a deterministic factor affecting CH₄ production. Based on microbial community analysis, Candidatus Brevefilum was identified as a potential syntrophic propionate-oxidizing bacterium that facilitates the mitigation of propionate accumulation, allowing the maintenance of unaffected CH₄ production under high inhibitory conditions.

Deposit-feeding worms control subsurface ecosystem functioning in intertidal sediment with strong physical forcing

Intertidal sands are global hotspots of terrestrial and marine carbon cycling with strong hydrodynamic forcing by waves and tides and high macrofaunal activity. Yet, the relative importance of hydrodynamics and macrofauna in controlling these ecosystems remains unclear. Here, we compare geochemical gradients and bacterial, archaeal, and eukaryotic gene sequences in intertidal sands dominated by subsurface deposit-feeding worms (Abarenicola pacifica) to adjacent worm-free areas. We show that hydrodynamic forcing controls organismal assemblages in surface sediments, while in deeper layers selective feeding by worms on fine, algae-rich particles strongly decreases the abundance and richness of all three domains. In these deeper layers, bacterial and eukaryotic network connectivity decreases, while percentages of clades involved in degradation of refractory organic matter, oxidative nitrogen, and sulfur cycling increase. Our findings reveal macrofaunal activity as the key driver of biological community structure and functioning, that in turn influence carbon cycling in intertidal sands below the mainly physically controlled surface layer.

Polystyrene nanoplastics shape microbiome and functional metabolism in anaerobic digestion

Nanoplastics (NPs) and microplastics (MPs) are ubiquitous in the natural environment, social production, and life. However, our understanding of the effects of NPs and MPs on shaping the microbiome and functional metabolism of anaerobic microorganisms is limited. We investigated the response of core microbiomes and functional genes to polystyrene (PS) NPs and MPs exposure in a representative anaerobic micro-ecosystem of waste activated sludge. Independent anaerobic digestion (AD) experiment indicated that PS nanobeads suppressed acidogenesis by inhibiting the activity of acetate kinase, and subsequently reduced methane production. Our findings confirmed that MPs (1 and 10 μm) had no perceptible effect on methane production, yet 50 nm NPs resulted in a 15.5% decrease in methane yield, perhaps driven by the behavior of dominant genera Sulfurovum, Candidatus Methanofastidiosum, and Methanobacterium. Assays revealed that NPs contributed to the simplest network assemblies in bacterial communities, contrary to empirical networks in archaeal communities. NPs significantly reduced the abundance of genes involved in carbon degradation: lig, naglu and xylA, as well as gcd and phnK related to phosphorus cycling. The absolute abundance of mcrA encoding methyl-coenzyme M reductase was 54.4% of the control assay. PS NPs might adversely affect the biodiversity and biogeochemical cycles in natural and artificial ecosystems through their negative impact on biomass energy conversion by anaerobic microorganisms.

Characterization of the bacterial microbiota in different gut and oral compartments of splendid japalure (Japalura sensu lato)

Background

Gut and oral microbes form complex communities and play key roles in co-evolution with their hosts. However, little is understood about the bacterial community in lizards.

Results

In this study, we investigated the gut and oral bacterial communities in Japalura sensu lato from Sichuan Province, China, using 16S rRNA gene sequencing. Results showed that Bacteroidota (36.5%) and Firmicutes (32.8%) were the main phyla in the gut, while Proteobacteria, Bacteroidota, Firmicutes, and Actinobacteriota were the dominant phyla in the oral cavity. 16 S rRNA sequencing analysis of fecal samples showed that: (1) Bacteroidota was the most abundant in Japalura sensu lato, which was different from the bacterial community of insectivorous animals; (2) Bacteroidota, Firmicutes, Actinobacteriota, Fusobacteriota, and Cyanobacteria were the most abundant phylum in Japalura sensu lato. (3) Proteobacteria was the dominant phylum in Japalura sensu lato and other domestic insectivorous lizards (Shinisaurus crocodilurus, Phrynocephalus vlangalii, and Takydromus septentrionalis); (4) Comparing with the bacterial community of Shinisaurus crocodilurus, Phrynocephalus vlangalii, Takydromus septentrionalis, Liolaemus parvus, L. ruibali, and Phymaturus williamsi, Desulfobacterota was uniquely present in the gut of Japalura sensu lato. 16 S rRNA sequencing of oral samples showed that Chloroflexi and Deinococcota phyla were enriched in the oral cavity, which may have a significant influence on living in extreme environments.

Conclusions

Thus, based on 16 S rRNA sequencing analysis of the community composition of the gut and oral microbiomes, this study firstly represents a foundation for understanding the gut and oral microbial ecology of Japalura sensu lato, and constitutes a detail account of the diversity of the microbiota inhabiting the gut and oral cavity of Japalura sensu lato. Further researches will continue to reveal how gut and oral microbial communities may be impacting the ecology and evolution of lizards.

Supplementary information

The online version contains supplementary material available at 10.1186/s12917-022-03300-w.

Community Structure and Microbial Associations in Sediment-Free Methanotrophic Enrichment Cultures from a Marine Methane Seep

Syntrophic consortia of anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB) consume large amounts of methane and serve as the foundational microorganisms in marine methane seeps. Despite their importance in the carbon cycle, research on the physiology of ANME-SRB consortia has been hampered by the slow growth and complex physicochemical environment the consortia inhabit. Here, we report successful sediment-free enrichment of ANME-SRB consortia from deep-sea methane seep sediments in the Santa Monica Basin, California. Anoxic Percoll density gradients and size-selective filtration were used to separate ANME-SRB consortia from sediment particles and single cells to accelerate the cultivation process. Over a 3-year period, a subset of the sediment-associated ANME and SRB lineages, predominantly comprised of ANME-2a/2b ("Candidatus Methanocomedenaceae") and their syntrophic bacterial partners, SEEP-SRB1/2, adapted and grew under defined laboratory conditions. Metagenome-assembled genomes from several enrichments revealed that ANME-2a, SEEP-SRB1, and Methanococcoides in different enrichments from the same inoculum represented distinct species, whereas other coenriched microorganisms were closely related at the species level. This suggests that ANME, SRB, and Methanococcoides are more genetically diverse than other members in methane seeps. Flow cytometry sorting and sequencing of cell aggregates revealed that Methanococcoides, Anaerolineales, and SEEP-SRB1 were overrepresented in multiple ANME-2a cell aggregates relative to the bulk metagenomes, suggesting they were physically associated and possibly interacting. Overall, this study represents a successful case of selective cultivation of anaerobic slow-growing microorganisms from sediments based on their physical characteristics, introducing new opportunities for detailed genomic, physiological, biochemical, and ecological analyses. IMPORTANCE Biological anaerobic oxidation of methane (AOM) coupled with sulfate reduction represents a large methane sink in global ocean sediments. Methane consumption is carried out by syntrophic archaeal-bacterial consortia and fuels a unique ecosystem, yet the interactions in these slow-growing syntrophic consortia and with other associated community members remain poorly understood. The significance of this study is the establishment of sediment-free enrichment cultures of anaerobic methanotrophic archaea and sulfate-reducing bacteria performing AOM with sulfate using selective cultivation approaches based on size, density, and metabolism. By reconstructing microbial genomes and analyzing community composition of the enrichment cultures and cell aggregates, we shed light on the diversity of microorganisms physically associated with AOM consortia beyond the core syntrophic partners. These enrichment cultures offer simplified model systems to extend our understanding of the diversity of microbial interactions within marine methane seeps.

Sodium hypochlorite induced inhibition in anaerobic digestion and possible approach to maintain methane fermentation performance

Since sodium hypochlorite (NaClO), a commonly used chemical to deal with membrane fouling, is toxic to microorganisms, it is a major concern in the membrane cleaning process. In this study, the concentration-dependent effects of NaClO (0-9 g/L) on the biodegradation performance and microbial activity were investigated via batch experiments. The methane production (obtained approximately 140 mL) and microbial community revealed by principal coordinates analysis were almost unaffected when the NaClO concentration ranged between 0 and 3 g/L. A follow-up batch experiment was conducted and revealed that the microbial products could help protect or recover the activity of anaerobic microorganisms at a high NaClO concentration of 10 g/L. Additionally, correlation analysis was used to investigate the associations between the 15 major bacterial genera. Moreover, the microbial analysis results indicated that the top 10 operational taxonomic units most affected by NaClO were primarily coryneform and filamentous bacteria.

Microbial communities reveal impacts of unconventional oil and gas development on headwater streams

The demand for natural gas has led to the development of techniques used to access unconventional oil and natural gas (UOG) resources, due to the novelty of UOG, the potential impacts to freshwater ecosystems are not fully understood. We used a dual pronged approach to study the effects of UOG development on microbial biodiversity and function via a laboratory microcosm experiment and a survey study of streams with and without UOG development within their watersheds. The microcosm experiment simulated stream contamination with produced water, a byproduct of UOG operations, using sediment collected from one high water-quality stream and two low water-quality streams. For the survey study, biofilm and sediment samples were collected from streams experiencing varying levels of UOG development. In the microcosm experiment, produced water decreased microbial aerobic and anaerobic CO₂ production in the high water-quality stream sediment but had a positive effect on this microbial activity in the lower water-quality stream sediments, suggesting habitat degradation alters the response of microbes to contaminants. Results from the stream survey indicate UOG development alters stream water temperature, chemistry, sediment aerobic and anaerobic CO₂ production, and microbial community biodiversity in both sediments and biofilms. Correlations among UOG associated land use, environmental, and microbial variables suggest increases in light availability and sediment delivery to streams, due to deforestation and land disturbance, impact stream microbial communities and their function. Consistent changes in the relative abundance of bacterial taxa suggest microorganisms may be good indicators of the environmental changes associated with UOG development. The observed impacts of UOG development on microbial community composition and carbon cycling could have cascading effects on stream health and broader ecosystem function.

Continuous-mode acclimation and operation of lignocellulosic sulfate-reducing bioreactors for enhanced metal immobilization from acidic mining-influenced water

Lignocellulosic sulfate-reducing bioreactors are an inexpensive passive approach for treatment of mining-influenced water (MIW). Typically, microbial community acclimation to MIW involves bioreactor batch-mode operation to initiate lignocellulose hydrolysis and fermentation and provide electron donors for sulfate-reducing bacteria. However, batch-mode operation could significantly prolong bioreactor start-up times (up to several months) and select for slow-growing microorganisms. In this study we assessed the feasibility of bioreactor continuous-mode acclimation to MIW (pH 2.5, 6.5 mM SO₄^2-, 18 metal(loid)s) as an alternate start-up method. Results showed that bioreactors with spent brewing grains and sugarcane bagasse achieved acclimation in continuous mode at hydraulic retention times (HRTs) of 7-12-d within 16-22 days. During continuous-mode acclimation, extensive SO₄^2- reduction (80 ± 20% -91 ± 3%) and > 98% metal(loid) removal was observed. Operation at a 3-d HRT further yielded a metal(loid) removal of 97.5 ± 1.3 -98.8 ± 0.9% until the end of operation. Sulfate-reducing microorganisms were detected closer to the influent in the spent brewing grains bioreactors, and closer to the effluent in the sugarcane bagasse bioreactors, giving insight as to where SO₄^2- reduction was occurring. Results strongly support that a careful selection of lignocellulose and bioreactor operating parameters can bypass typical batch-mode acclimation, shortening bioreactor start-up times and promoting effective MIW metal(loid) immobilization and treatment.

When FLOW-FISH met FACS: Combining multiparametric, dynamic approaches for microbial single-cell research in the total environment

In environmental microbiology, the ability to assess, in a high-throughput way, single-cells within microbial communities is key to understand their heterogeneity. Fluorescence in situ hybridization (FISH) uses fluorescently labeled oligonucleotide probes to detect, identify, and quantify single cells of specific taxonomic groups. The combination of Flow Cytometry (FLOW) with FISH (FLOW-FISH) enables high-throughput quantification of complex whole cell populations, which when associated with fluorescence-activated cell sorting (FACS) enables sorting of target microorganisms. These sorted cells may be investigated in many ways, for instance opening new avenues for cytomics at a single-cell scale. In this review, an overview of FISH and FLOW methodologies is provided, addressing conventional methods, signal amplification approaches, common fluorophores for cell physiology parameters evaluation, and model variation techniques as well. The coupling of FLOW-FISH-FACS is explored in the context of different downstream applications of sorted cells. Current and emerging applications in environmental microbiology to outline the interactions and processes of complex microbial communities within soil, water, animal microbiota, polymicrobial biofilms, and food samples, are described.

Constructed wetlands for polishing oil and gas produced water releases

Produced water (PW) is the largest waste stream associated with oil and gas (O&G) operations and contains petroleum hydrocarbons, heavy metals, salts, naturally occurring radioactive materials and any remaining chemical additives. In some areas in Wyoming, constructed wetlands (CWs) are used to polish PW downstream of National Pollutant Discharge Elimination System (NPDES) PW release points. In recent years, there has been increased interest in finding lower cost options, such as CWs, for PW treatment. The goal of this study was to understand the efficacy of removal and environmental fate of O&G organic chemical additives in CW systems used to treat PW released for agricultural beneficial reuse. To achieve this goal, we analyzed water and sediment samples for organic O&G chemical additives and conducted 16S rRNA gene sequencing for microbial community characterization on three such systems in Wyoming, USA. Three surfactants (polyethylene glycols, polypropylene glycols, and nonylphenol ethoxylates) and one biocide (alkyldimethylammonium chloride) were detected in all three PW discharges and >94% removal of all species from PW was achieved after treatment in two CWs in series. These O&G extraction additives were detected in all sediment samples collected downstream of PW discharges. Chemical and microbial analyses indicated that sorption and biodegradation were the main attenuation mechanisms for these species. Additionally, all three discharges showed a trend of increasingly diverse, but similar, microbial communities with greater distance from NPDES PW discharge points. Results of this study can be used to inform design and management of constructed wetlands for produced water treatment.

Significance of different mixing conditions on performance and microbial communities in anaerobic digester amended with granular and powdered activated carbon

Conductive materials amendment in anaerobic digestion (AD) is a promising strategy for boosting the methanogenesis process. Despite mixing is a critical parameter, the behavior of digesters amended with conductive additives upon different mixing conditions has rarely been investigated. This study investigated continuous mixing, intermittent mixing (10 min in every 12 h), and non-mixing conditions for digesters amended with granular activated carbon (GAC) and powdered activated carbon (PAC). The non-mixed GAC digester provided the highest methane yield (318 ± 28 mL/g COD) from synthetic blackwater, while intermittently mixed GAC and control exhibited similar methane yields (290-294 mL/g COD). For non-mixed systems, microbial richness and diversity increased with GAC and PAC amendment. In contrast, continuous and intermittent mixing increased microbial diversity and richness in control reactors while reduced the same in GAC and PAC amended reactors. Overall, various mixing conditions distinctly changed the degree of enrichment/retention of microbes and consequently influenced methane recovery.

Enhanced Volatile Fatty Acid Production from Oil Palm Empty Fruit Bunch through Acidogenic Fermentation—A Novel Resource Recovery Strategy for Oil Palm Empty Fruit Bunch

The glucan-rich fraction, hemicellulosic compounds-rich fraction, and a mixture of both fractions obtained from organosolv pretreatment of oil palm empty fruit bunch (OPEFB) were used as substrates to produce volatile fatty acids (VFAs) in acidogenic fermentation. In this study, the effects of medium adjustment (carbon to nitrogen ratio and trace elements supplementation) and methanogenesis inhibition (through the addition of 2-bromoethanesulfonate or by heat shock) to enhance VFAs yield were investigated. The highest VFA yield was 0.50 ± 0.00 g VFAs/g volatile solid (VS), which was obtained when methanogens were inhibited by heat shock and cultivated in a mixture of glucan-rich and hemicellulosic compounds-rich fractions. Under these conditions, the fermentation produced acetic acid as the only VFA. Based on the results, the mass balance of the whole process (from pretreatment and fermentation) showed the possibility to obtain 30.4 kg acetic acid and 20.3 kg lignin with a 70% purity from 100 kg OPEFB.

Insights into the removal of pharmaceutically active compounds from sewage sludge by two-stage mesophilic anaerobic digestion

The removal efficiencies (REs) of twenty-seven pharmaceutically active compounds (PhACs) (eight analgesic/anti-inflammatories, six antibiotics, four β-blockers, two antihypertensives/diuretics, three lipid regulators and four psychiatric drugs) were evaluated in a pilot-scale two-stage mesophilic anaerobic digestion (MAD) system treating thickened sewage sludge from a pilot-scale A²O™ wastewater treatment plant (WWTP) which was fed with wastewater from the pre-treatment of the full-scale WWTP Murcia Este (Murcia, Spain). The MAD system was long-term operated using two different sets of sludge retention times (SRTs) for the acidogenic (AcD) and methanogenic (MD) digesters (phase I, 2 and 12 days; and phase II, 5 and 24 days, in AcD and MD, respectively). Quantitative PCR (qPCR) and Illumina MiSeq sequencing were used to estimate the absolute abundance of Bacteria, Archaea, and Fungi and investigate the structure, diversity and population dynamics of their communities in the AcD and MD effluents. The extension of the SRT from 12 (phase I) to 24 days (phase II) in the MD was significantly linked with an improved removal of carbamazepine, clarithromycin, codeine, gemfibrozil, ibuprofen, lorazepam, and propranolol. The absolute abundances of total Bacteria and Archaea were higher in the MD regardless of the phase, while the diversity of bacterial and archaeal communities was lower in phase II, in both digesters. Non-metric multidimensional scaling (MDS) plots showed strong negative correlations among phyla Proteobacteria and Firmicutes and between genera Methanosaeta and Methanosarcina throughout the full experimental period. Strong positive correlations were revealed between the relative abundances of Methanospirillum and Methanoculleus and the methanogenesis performance parameters (volatile solids removal, CH₄ recovery rate and %CH₄ in the biogas), which were also related to longer SRT. The REs of several PhACs (naproxen, ketoprofen, ofloxacin, fenofibrate, trimethoprim, and atenolol) correlated positively (r > 0.75) with the relative abundances of specific bacterial and archaeal groups, suggesting their participation in biodegradation/biotransformation pathways.

Deciphering the molecular signal from past and alive bacterial communities in aquatic sedimentary archives

Lake sediments accumulate information on biological communities thus acting as natural archives. Traditionally paleolimnology has focussed on fossilized remains of organisms, however, many organisms do not leave fossil evidence, meaning major ecosystem components are missing from environmental reconstructions. Many paleolimnology studies now incorporate molecular methods, including investigating microbial communities using environmental DNA (eDNA), but there is uncertainty about the contribution of living organisms to molecular inventories. In the present study, we obtained DNA and RNA inventories from sediment spanning 700 years to investigate the contribution of past and active communities to the molecular signal from sedimentary archives. Additionally, a droplet digital PCR (ddPCR) targeting the 16S ribosomal RNA (16S rRNA) gene of the photosynthetic cyanobacterial genera Microcystis was used to explore if RNA signals were from legacy RNA. We posit that the RNA signal is a mixture of legacy RNA, dormant cells, living bacteria and modern-day trace level contaminants that were introduced during sampling and preferentially amplified. The presence of legacy RNA was confirmed by the detection of Microcystis in sediments aged to ~200 years ago. Recent comparisons between 16S rRNA gene metabarcoding and traditional paleo proxies showed that past changes in bacterial communities can be reconstructed from sedimentary archives. The recovery of RNA in the present study has provided new insights into the origin of these signals. However, caution is required during analysis and interpretation of 16S rRNA gene metabarcoding data especially in recent sediments were there are potentially active bacteria.

Tracking the transition to agriculture in Southern Europe through ancient DNA analysis of dental calculus

Archaeological dental calculus, or mineralized plaque, is a key tool to track the evolution of oral microbiota across time in response to processes that impacted our culture and biology, such as the rise of farming during the Neolithic. However, the extent to which the human oral flora changed from prehistory until present has remained elusive due to the scarcity of data on the microbiomes of prehistoric humans. Here, we present our reconstruction of oral microbiomes via shotgun metagenomics of dental calculus in 44 ancient foragers and farmers from two regions playing a pivotal role in the spread of farming across Europe-the Balkans and the Italian Peninsula. We show that the introduction of farming in Southern Europe did not alter significantly the oral microbiomes of local forager groups, and it was in particular associated with a higher abundance of the species Olsenella sp. oral taxon 807. The human oral environment in prehistory was dominated by a microbial species, Anaerolineaceae bacterium oral taxon 439, that diversified geographically. A Near Eastern lineage of this bacterial commensal dispersed with Neolithic farmers and replaced the variant present in the local foragers. Our findings also illustrate that major taxonomic shifts in human oral microbiome composition occurred after the Neolithic and that the functional profile of modern humans evolved in recent times to develop peculiar mechanisms of antibiotic resistance that were previously absent.

Novel insights of impacts of solid content on high solid anaerobic digestion of cow manure: Kinetics and microbial community dynamics

High solid anaerobic digestion has become the mainstream technology for sustainable on-farm treatment of solid wastes but has not been optimized with respect to increasing solid content in cow manure (CM). In the present study, CM was batch digested at total solid (TS) of 5%, 10%, 15% and 20% and microbial communities were investigated. The process remained stable up to 15% TS. The biomethane production rate at TS of 10% and 15% was reported to be 352.2 mL g^-1 VS and 318.6 mL g^-1 VS, reaching up to 83% and 75% of TS 5% biomethane, respectively. Kinetics results disclosed that the biodegradable organics could be utilized at increasing solid content with decreasing hydrolysis rate. The abundances of hydrogenotrophic and methylotrophic methanogens increased significantly with increasing solid content. This study is of great importance for understanding and application of high solid anaerobic digestion of cow manure.

Ex and In Situ Reactivity and Sorption of Selenium in Opalinus Clay in the Presence of a Selenium Reducing Microbial Community

79Se is a critical radionuclide concerning the safety of deep geological disposal of certain radioactive wastes in clay-rich formations. To study the fate of selenium oxyanions in clayey rocks in the presence of a selenium reducing microbial community, in situ tests were performed in the Opalinus Clay at the Mont Terri Rock Laboratory (Switzerland). Furthermore, biotic and abiotic batch tests were performed to assess Se(VI) and Se(IV) reactivity in the presence of Opalinus Clay and/or stainless steel, in order to support the interpretation of the in situ tests. Geochemical modeling was applied to simulate Se(VI) reduction, Se(IV) sorption and solubility, and diffusion processes. This study shows that microbial activity is required to transform Se(VI) into more reduced and sorbing Se species in the Opalinus Clay, while in abiotic conditions, Se(VI) remains unreactive. On the other hand, Se(IV) can be reduced by microorganisms but can also sorb in the presence of clay without microorganisms. In situ microbial reduction of Se oxyanions can occur with electron donors provided by the clay itself. If microorganisms would be active in the clay surrounding a disposal facility, microbial reduction of leached Se could thus contribute to the overall retention of Se in clayey host rocks.

Bioconversion of food waste to volatile fatty acids: Impact of microbial community, pH and retention time

Bio-based production of materials from waste streams is a pivotal aspect in a circular economy. This study aimed to investigate the influence of inoculum (three different sludge taken from anaerobic digestors), pH (5 & 10) and retention time on production of total volatile fatty acids (VFAs), VFA composition as well as the microbial community during anaerobic digestion of food waste. The highest VFA production was ∼22000 ± 1036 mg COD/L and 12927 ± 1029 mg COD/L on day 15 using the inoculum acclimated to food waste at pH 10 and pH 5, respectively. Acetic acid was the dominant VFA in the batch reactors with initial alkaline conditions, whereas both propionic and acetic acids were the dominant products in the acidic condition. Firmicutes, Chloroflexi and Bacteroidetes had the highest relative abundance in the reactors. VFA generation was positively correlated to the relative abundance of Firmicutes.

Sasso Pisano Geothermal Field Environment Harbours Diverse Ktedonobacteria Representatives and Illustrates Habitat-Specific Adaptations

The hydrothermal steam environment of Sasso Pisano (Italy) was selected to investigate the associated microbial community and its metabolic potential. In this context, 16S and 18S rRNA gene partial sequences of thermophilic prokaryotes and eukaryotes inhabiting hot springs and fumaroles as well as mesophilic microbes colonising soil and water were analysed by high-throughput amplicon sequencing. The eukaryotic and prokaryotic communities from hot environments clearly differ from reference microbial communities of colder soil sites, though Ktedonobacteria showed high abundances in various hot spring samples and a few soil samples. This indicates that the hydrothermal steam environments of Sasso Pisano represent not only a vast reservoir of thermophilic but also mesophilic members of this Chloroflexi class. Metabolic functional profiling revealed that the hot spring microbiome exhibits a higher capability to utilise methane and aromatic compounds and is more diverse in its sulphur and nitrogen metabolism than the mesophilic soil microbial consortium. In addition, heavy metal resistance-conferring genes were significantly more abundant in the hot spring microbiome. The eukaryotic diversity at a fumarole indicated high abundances of primary producers (unicellular red algae: Cyanidiales), consumers (Arthropoda: Collembola sp.), and endoparasite Apicomplexa (Gregarina sp.), which helps to hypothesise a simplified food web at this hot and extremely nutrient-deprived acidic environment.

Machine Learning Approach Reveals the Assembly of Activated Sludge Microbiome with Different Carbon Sources during Microcosm Startup

Activated sludge (AS) microcosm experiments usually begin with inoculating a bioreactor with an AS mixed culture. During the bioreactor startup, AS communities undergo, to some extent, a distortion in their characteristics (e.g., loss of diversity). This work aimed to provide a predictive understanding of the dynamic changes in the community structure and diversity occurring during aerobic AS microcosm startups. AS microcosms were developed using three frequently used carbon sources: acetate (A), glucose (G), and starch (S), respectively. A mathematical modeling approach quantitatively determined that 1.7–2.4 times the solid retention time (SRT) was minimally required for the microcosm startups, during which substantial divergences in the community biomass and diversity (33–45% reduction in species richness and diversity) were observed. A machine learning modeling application using AS microbiome data could successfully (>95% accuracy) predict the assembly pattern of aerobic AS microcosm communities responsive to each carbon source. A feature importance analysis pinpointed specific taxa that were highly indicative of a microcosm feed source (A, G, or S) and significantly contributed for the ML-based predictive classification. The results of this study have important implications on the interpretation and validity of microcosm experiments using AS.