Diversity, localization, and physiological properties of filamentous microbes belonging to Chloroflexi subphylum I in mesophilic and thermophilic methanogenic sludge granules

Performance and mechanism of antibiotic resistance removal by biochar-enhanced sediment microbial fuel cell

This study is the first to explore the performance and mechanism of biochar-impacted sediment microbial fuel cell for removing antibiotic resistance genes (ARGs), and examines the effects of different biochar contents. The addition of 5% biochar produced the highest output voltage and power density, which increased by 100% and 219%, respectively, while simultaneously reducing the abundance and risk of ARGs. Comparatively, the addition of moderate amount of biochar (1-5%) promoted the removal of ARGs, while the opposite was true for excessive (10%) biochar. Biochar affected ARGs through prophages, insertion sequence, and transposons. Biological factors and voltage jointly influenced ARGs variation, with the former accounting for 56%. Further analysis of functional genes indicated that biochar controlled ARGs by regulating the synthesis of genetic material and amino acids to influence metabolism. Overall, findings of this study shed light on the potential removal of ARGs in microbial electrochemical systems.

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.

The resistance of hydrogenotrophic methanogenic microorganisms to ofloxacin in sludge anaerobic digestion process

Ofloxacin (OFL) is a commonly used antibiotic that can enter wastewater treatment plants and be adsorbed by the sludge, resulting in a high OFL concentration in sludge and affecting the subsequent sludge anaerobic digestion process. However, the micro mechanisms involved in this process have not been thoroughly studied. Therefore, this study focuses on the effect of OFL on the sludge anaerobic digestion of sludge to provide such support. The experimental results showed that the maximal methane yield decreased from 277.7 to 164.7 mL/g VSS with the OFL concentration increased from 0 to 300 mg/L. Additionally, OFL hindered the intermediate biochemical processes of hydrolysis, acidogenesis, acetogenesis, and acetoclastic methanogenesis. However, it promoted hydrogenotrophic methanogenesis process, using H2 as substrate, with the concentration of 300 mg/L OFL was 5.54 fold methane production of that in the control. Further investigation revealed that the negative effect of OFL was likely due to the induction of reactive oxygen species, which led to a decrease in cell activity and interference with the activity of key enzymes. Microbiological analysis revealed that OFL reduced the relative abundance of hydrolysis and acidogenesis bacteria, and Methanosaeta archaea, while increasing the relative abundance of hydrogenotrophic methanogenesis microorganism from 36.54% to 51.48% as the OFL concentration increase from 0 to 300 mg/L.

Full-scale study on high-rate low-temperature anaerobic digestion of agro-food wastewater: process performances and microbial community

The fast-growing global population has led to a substantial increase in food production, which generates large volumes of wastewater during the process. Despite most industrial wastewater being discharged at lower ambient temperatures (<20 °C), majority of the high-rate anaerobic reactors are operated at mesophilic temperatures (>30 °C). High-rate low-temperature anaerobic digestion (LtAD) has proven successful in treating industrial wastewater both at laboratory and pilot scales, boasting efficient organic removal and biogas production. In this study, we demonstrated the feasibility of two full-scale high-rate LtAD bioreactors treating meat processing and dairy wastewater, and the microbial communities in both reactors were examined. Both reactors exhibited rapid start-up, achieving considerable chemical oxygen demand (COD) removal efficiencies (total COD removal >80%) and generating high-quality biogas (CH4% in biogas >75%). Long-term operations (6-12 months) underscored the robustness of LtAD bioreactors even during winter periods (average temperature <12 °C), as evidenced by sustained high COD removal rates (total COD removal >80%). The stable performance was underpinned by a resilient microbial community comprising active acetoclastic methanogens, hydrolytic, and fermentative bacteria. These findings underscore the feasibility of high-rate low-temperature anaerobic wastewater treatment, offering promising solutions to the zero-emission wastewater treatment challenge.

Mechanistic understanding of acclimation and energy metabolism of acetoclastic methanogens under different substrate to microorganism ratios

Mechanistic understanding of acetoclastic methanogenesis is pivotal for optimizing anaerobic digestion for efficient methane production. In this study, two different operational modes, continuous flow reactor (CFR) and sequencing batch reactor (SBR), accompanied with solids retention times (SRT) of 10 days (SBR10d and CFR10d) and 25 days (SBR25d and CFR25d) were implemented to elucidate their impacts on microbial communities and energy metabolism of methanogens in acetate-fed systems. Microbial community analysis revealed that the relative abundance of Methanosarcina (16.0%-46.0%) surpassed Methanothrix (3.7%-22.9%) in each reactor. SBRs had the potential to enrich both Methanothrix and Methanosarcina. Compared to SBRs, CFRs had lower total relative abundance of methanogens. Methanosarcina exhibited a superior enrichment in reactors with 10-day SRT, while Methanothrix preferred to be acclimated in reactors with 25-day SRT. The operational mode and SRT were also observed to affect the distribution of acetate-utilizing bacteria, including Pseudomonas, Desulfocurvus, Mesotoga, and Thauera. Regarding enzymes involved in energy metabolism, Ech and Vho/Vht demonstrated higher relative abundances at 10-day SRT compared to 25-day SRT, whereas Fpo and MtrA-H showed higher relative abundances in SBRs than those in CFRs. The relative abundance of genes encoding ATPase harbored by Methanothrix was higher than Methanosarcina at 25-day SRT. Additionally, the relative abundance of V/A-type ATPase (typically for methanogens) was observed higher in SBRs compared to CFRs, while the F-type ATPase (typically for bacteria) exhibited higher relative abundance in CFRs than that in SBRs.

The biotechnological potential of the Chloroflexota phylum

In the next decades, the increasing material and energetic demand to support population growth and higher standards of living will amplify the current pressures on ecosystems and will call for greater investments in infrastructures and modern technologies. A valid approach to overcome such future challenges is the employment of sustainable bio-based technologies that explore the metabolic richness of microorganisms. Collectively, the metabolic capabilities of Chloroflexota, spanning aerobic and anaerobic conditions, thermophilic adaptability, anoxygenic photosynthesis, and utilization of toxic compounds as electron acceptors, underscore the phylum's resilience and ecological significance. These diverse metabolic strategies, driven by the interplay between temperature, oxygen availability, and energy metabolism, exemplify the complex adaptations that enabled Chloroflexota to colonize a wide range of ecological niches. In demonstrating the metabolic richness of the Chloroflexota phylum, specific members exemplify the diverse capabilities of these microorganisms: Chloroflexus aurantiacus showcases adaptability through its thermophilic and phototrophic growth, whereas members of the Anaerolineae class are known for their role in the degradation of complex organic compounds, contributing significantly to the carbon cycle in anaerobic environments, highlighting the phylum's potential for biotechnological exploitation in varying environmental conditions. In this context, the metabolic diversity of Chloroflexota must be considered a promising asset for a large range of applications. Currently, this bacterial phylum is organized into eight classes possessing different metabolic strategies to survive and thrive in a wide variety of extreme environments. This review correlates the ecological role of Chloroflexota in such environments with the potential application of their metabolisms in biotechnological approaches.

CH4 control and nitrogen removal from constructed wetlands by plant combination

Global warming trend is accelerating. This study proposes a green and economical methane (CH4) control strategy by plant combination in constructed wetlands (CWs). In this study, a single planting of Acorus calamus L. hybrid constructed wetland (HCW-A) and a mixed planting of Acorus calamus L. and Eichhornia crassipes (Mart.) Solms hybrid constructed wetland (HCW-EA) were constructed. The differences in nitrogen removal performance and CH4 emissions between HCW-A and HCW-EA were compared and analyzed. The findings indicated that HCW-EA demonstrated significant improvements over HCW-A, with NH4+-N and TN removal rates increasing by 21.61% and 16.38% respectively, and CH4 emissions decreased by 43.36%. The microbiological analysis results showed that plant combination promoted the enrichment of Proteobacteria, Alphaproteobacteria and Bacillus. More nitrifying bacteria carrying nxrA genes and denitrifying bacteria carrying nirK genes accelerated the nitrogen transformation process. In addition, the absolute abundance ratio of pmoA/mcrA increased, reducing the release of CH4.

Biotic and abiotic factors acting on community assembly in parallel anaerobic digestion systems from a brewery wastewater treatment plant

Anaerobic digestion is a complex microbial process that mediates the transformation of organic waste into biogas. The performance and stability of anaerobic digesters relies on the structure and function of the microbial community. In this study, we asked whether the deterministic effect of wastewater composition outweighs the effect of reactor configuration on the structure and dynamics of anaerobic digester archaeal and bacterial communities. Biotic and abiotic factors acting on microbial community assembly in two parallel anaerobic digestion systems, an upflow anaerobic sludge blanket digestor (UASB) and a closed digester tank with a solid recycling system (CDSR), from a brewery WWTP were analysed utilizing 16S rDNA and mcrA amplicon sequencing and genome-centric metagenomics. This study confirmed the deterministic effect of the wastewater composition on bacterial community structure, while the archaeal community composition resulted better explained by organic loading rate (ORL) and volatile free acids (VFA). According to the functions assigned to the differentially abundant metagenome-assembled genomes (MAGs) between reactors, CDSR was enriched in genes related to methanol and methylamines methanogenesis, protein degradation, and sulphate and alcohol utilization. Conversely, the UASB reactor was enriched in genes associated with carbohydrate and lipid degradation, as well as amino acid, fatty acid, and propionate fermentation. By comparing interactions derived from the co-occurrence network with predicted metabolic interactions of the prokaryotic communities in both anaerobic digesters, we conclude that the overall community structure is mainly determined by habitat filtering.

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

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

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.

Viral potential to modulate microbial methane metabolism varies by habitat

Methane is a potent greenhouse gas contributing to global warming. Microorganisms largely drive the biogeochemical cycling of methane, yet little is known about viral contributions to methane metabolism (MM). We analyzed 982 publicly available metagenomes from host-associated and environmental habitats containing microbial MM genes, expanding the known MM auxiliary metabolic genes (AMGs) from three to 24, including seven genes exclusive to MM pathways. These AMGs are recovered on 911 viral contigs predicted to infect 14 prokaryotic phyla including Halobacteriota, Methanobacteriota, and Thermoproteota. Of those 24, most were encoded by viruses from rumen (16/24), with substantially fewer by viruses from environmental habitats (0-7/24). To search for additional MM AMGs from an environmental habitat, we generate metagenomes from methane-rich sediments in Vrana Lake, Croatia. Therein, we find diverse viral communities, with most viruses predicted to infect methanogens and methanotrophs and some encoding 13 AMGs that can modulate host metabolisms. However, none of these AMGs directly participate in MM pathways. Together these findings suggest that the extent to which viruses use AMGs to modulate host metabolic processes (e.g., MM) varies depending on the ecological properties of the habitat in which they dwell and is not always predictable by habitat biogeochemical properties.

Impact of Ecological Restoration on the Physicochemical Properties and Bacterial Communities in Alpine Mining Area Soils

Ecological restoration has notably impacted microbe and soil characteristics in abandoned open pit mines, especially in alpine regions. Yet, the adaptive responses of microbial communities in the initial years of mine site restoration remain largely unexplored. This study endeavors to offer a thorough comprehension of soil properties and microbial dynamics during the initial phases of alpine mining land reclamation. It places emphasis on physicochemical properties and microbial community composition and evaluates the feasibility of phytoremediation, along with proposing subsequent measures. Our study employs spatial sequence instead of time-sequenceal sequence to investigate early-stage changes in soil microbes and physicochemical properties in alpine mining land reclamation. We used high-throughput sequencing for the 16S rRNA amplicon study. Over time, soil physicochemical properties improved noticeably. Soil pH shifted from neutral to alkaline (7.04-8.0), while soil electrical conductivity (EC) decreased to 77 μS·cm-1 in R_6a. Cation exchange capacity (CEC) initially decreased from R_2a (12.30-27.98 cmol·kg-1) and then increased. Soil organic matter increased from 17.7 to 43.2 g·kg-1 over time during mine reclamation and restoration. The dominant bacterial community consisted of Proteobacteria (33.94% to 52.09%), Acidobacteriota (4.94% to 15.88%), Bacteroidota (6.52% to 11.15%), Actinobacteriota (7.18% to 9.61%), and Firmicutes (4.52% to 16.80%) with varying relative abundances. Gene annotation of sequences from various reclamation years revealed general function prediction, translation, ribosome structure, cell wall/membrane/envelope biogenesis, nucleotide translocation, and metabolism, along with other related functions. Mine reclamation improved soil fertility and properties, with the R_6a treatment being the most effective. Starting in the 2nd year of reclamation, the effective phosphorus content and the dominance of microbial bacteria, notably the Bacillus content, decreased. Firmicute fertilization promoted phosphorus and bacterial growth. In conclusion, employing a blend of sequencing and experimental approaches, our study unveils early-stage enhancements in soil microbial and physicochemical properties during the reclamation of alpine mining areas. The results underscore the beneficial impacts of vegetation restoration on key properties, including soil fertility, pore structure, and bacterial community composition. Special attention is given to assessing the effectiveness of the R_6a treatment and identifying deficiencies in the R_2a treatment. It serves as a reference for addressing the challenges associated with soil fertility and microbial community structure restoration in high-altitude mining areas in Qinghai-Tibet. This holds great significance for soil and water conservation as well as vegetation restoration in alpine mining regions. Furthermore, it supports the sustainable restoration of local ecosystems.

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.

Simultaneous partial nitrification, denitrification, and phosphorus removal in sequencing batch reactors via controlled reduced aeration and short-term sludge retention time decrease

Simultaneous bio-treatment processes of organic carbon (C)-, nitrogen (N)-, and phosphorus (P)-containing wastewater are challenged by insufficient carbon sources in the effluent. In the present study, two parallel anaerobic/aerobic sequencing batch reactors (R-1 and R-2) treating low C/N (≤4) wastewater were employed using different partial nitrification start-up strategies, controlled reduced aeration, and decreased sludge retention time. Advanced removal efficiencies for NH4+-N (≥96%), total nitrogen (TN, ≥86%), PO43--P (≥95%), and CODintra (≥91%) were realized, with TN and PO43--P effluent concentrations of 10.0 ± 3.5 and 0.11 ± 0.3 mg/L in R-1 and 9.28 ± 4.0 and 0.11 ± 0.1 mg/L in R-2, respectively. Higher nitrite accumulation rate (nearly 100%) and TN (121.1 ± 0.7 mg TN/g VSS·d) and P (12.5 ± 0.6 mg PO43--P/g VSS·d) removal loadings were obtained in R-2 by a thorough elimination of nitrite-oxidizing bacteria. Moreover, different microbial structures and nutrient removal pathways were identified. Denitrifying glycogen-accumulating organisms (Candidatus Competibacter) and phosphorus-accumulating organisms (PAOs) (Tetrasphaera) removed N and P with partial nitrification-endogenous denitrification pathways and aerobic P removal in R-1. In R-2, aerobic denitrifying bacteria (Psychrobacter) and PAOs ensured N and P removal through the partial nitrification-aerobic denitrification and aerobic P removal pathways. Compared to R-1, R-2 offers greater efficiency, convenience, and scope to further reduce carbon-source demand.

Enhanced degradation of ibuprofen in an integrated constructed wetland-microbial fuel cell: treatment efficiency, electrochemical characterization, and microbial community dynamics

Over the past few decades, there has been a growing concern regarding the fate and transport of pharmaceuticals, particularly antibiotics, as emerging contaminants in the environment. It has been proposed that the presence of antibiotics at concentrations typically found in wastewater can impact the dynamics of bacterial populations and facilitate the spread of antibiotic resistance. The efficiency of currently-used wastewater treatment technologies in eliminating pharmaceuticals is often insufficient, resulting in the release of low concentrations of these compounds into the environment. In this study, we addressed these challenges by evaluating how different influent ibuprofen (IBU) concentrations influenced the efficiency of a laboratory-scale, integrated constructed wetland-microbial fuel cell (CW-MFC) system seeded with Eichhornia crassipes, in terms of organic matter removal, electricity generation, and change of bacterial community structure compared to unplanted, sediment MFC (S-MFC) and abiotic S-MFC (AS-MFC). We observed that the addition of IBU (5 mg L-1) resulted in a notable decrease in chemical oxygen demand (COD) and electricity generation, suggesting that high influent IBU concentrations caused partial inhibition for the electroactive microbial community due to its complexity and aromaticity. However, CW-MFC could recover from IBU inhibition after an acclimation period compared to unplanted S-MFC, even though the influent IBU level was increased up to 20 mg L-1, suggesting that plants in CW-MFCs have a beneficial role in relieving the inhibition of anode respiration due to the presence of high levels of IBU; thus, promoting the metabolic activity of the electroactive microbial community. Similarly, IBU removal efficiency for CW-MFC (i.e., 49-62%) was much higher compared to SMFC (i.e., 29-42%), and AS-MFC (i.e., 20-22%) during all experimental phases. In addition, our high throughput sequencing revealed that the high performance of CW-MFCs compared to S-MFC was associated with increasing the relative abundances of several microbial groups that are closely affiliated with anode respiration and organic matter fermentation. In summary, our results show that the CW-MFC system demonstrates suitability for high removal efficiency of IBU and effective electricity generation.

Metabolic implications for predatory and parasitic bacterial lineages in activated sludge wastewater treatment systems

Deciphering unclear microbial interactions is key to improving biological wastewater treatment processes. Microbial predation and parasitism in wastewater treatment ecosystems are unexplored survival strategies that have long been known and have recently attracted attention because these interspecies interactions may contribute to the reduction of excess sludge. Here, microbial community profiling of 600 activated sludge samples taken from six industrial and one municipal wastewater treatment processes (WWTPs) was conducted. To identify the shared lineages in the WWTPs, the shared microbial constituents were defined as the family level taxa that had ≥ 0.1% average relative abundance and detected in all processes. The microbial community analysis assigned 106 families as the shared microbial constituents in the WWTPs. Correlation analysis showed that 98 of the 106 shared families were significantly correlated with total carbon (TC) and/or total nitrogen (TN) concentrations, suggesting that they may contribute to wastewater remediation. Most possible predatory or parasitic bacteria belonging to the phyla Bdellovibrionota, Myxococcota, and Candidatus Patescibacteria were found to be the shared families and negatively correlated with TC/TN; thus, they were frequently present in the WWTPs and could be involved in the removal of carbon/nitrogen derived from cell components. Shotgun metagenome-resolved metabolic reconstructions indicated that gene homologs associated with predation or parasitism are conserved in the Bdellovibrionota, Myxococcota, and Ca. Patescibacteria genomes (e.g., host interaction (hit) locus, Tad-like secretion complexes, and type IV pilus assembly proteins). This study provides insights into the complex microbial interactions potentially linked to the reduction of excess sludge biomass in these processes.

Validation of 16S rRNA gene sequencing and metagenomics for evaluating microbial immigration in a methanogenic bioreactor

To quantitatively evaluate the impact of microbial immigration from an upstream community on the microbial assembly of a downstream community, an ecological genomics (ecogenomics)-based mass balance (EGMB) model coupled with 16S rRNA gene sequencing was previously developed. In this study, a mock community was used to further validate the EGMB models and demonstrate the feasibility of using metagenome-based EGMB model to reveal both microbial activity and function. The mock community consisting of Aeromonas, Escherichia, and Pseudomonas was fed into a lab-scale methanogenic bioreactor together with dissolved organic substrate. Using qPCR, 16S rRNA gene, 16S rRNA gene copy number normalization (GCN), and metagenome, results showed highly comparable community profiles in the feed. In the bioreactor, Aeromonas and Pseudomonas exhibited negative growth rates throughout the experiment by all approaches. Escherichia's growth rate was negative by most biomarkers but was slightly positive by 16S rRNA gene. Still, all approaches showed a decreasing trend toward negative in the growth rate of Escherichia as reactor operation time increased. Uncultivated populations of phyla Desulfobacterota, Chloroflexi, Actinobacteriota, and Spirochaetota were observed to increase in abundance, suggesting their contribution in degrading the feed biomass. Based on metabolic reconstruction of metagenomes, these populations possessed functions of hydrolysis, fermentation, fatty acid degradation, or acetate oxidation. Overall results supported the application of both 16S rRNA gene- and metagenome-based EGMB models to measure the growth rate of microbes in the bioreactor, and the latter had advantage in providing insights into the microbial functions of uncultivated populations.

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.

Effect of Post-Ruminal Urea Supply on Growth Performance of Grazing Nellore Young Bulls at Dry Season

The objective of this study was to evaluate the effect of the use of post-ruminal urea on performance, nitrogen metabolism and the ruminal environment of Nellore cattle reared on pasture during the dry season. In experiment 1 (Exp. 1), nine ruminal-cannulated Nellore steers, 30 ± 2 months old (651 ± 45 kg body weight (BW)), were allotted to a 3 × 3 Latin triple square. In experiment 2 (Exp. 2), 84 Nellore bulls, 18 ± 3 months old (315 ± 84 kg BW), were distributed in complete randomized blocks, by initial BW. Protein supplements were supplied daily, in the amount of 2 g/kg BW, and consisted of either CONT: protein + conventional urea (50% CP), PRU: protein + post ruminal urea (50% CP) and U + PRU: protein + urea conventional + post-ruminal urea (70% CP). The paddocks were composed of Urochloa brizantha cv. Marandu grass. In Exp. 1, there was no treatment effect for DM, OM, NDF, forage intake, and CP, but there was a higher intake for PRU (p < 0.005) and a higher digestibility for U+ PRU (p = 0.001). There was no effect on ruminal pH or NH3-N concentration (p ≥ 0.232), but there was an interaction between treatment and time for them (p < 0.039). Furthermore, there was a treatment effect on the total SCFA concentration, with CONT being higher than the others. A difference in the acetate:propionate ratio was found (p < 0.027), with a greater relationship for PRU and U + PRU. A treatment effect (p = 0.049) was found for the propionate proportion, with a higher proportion in the CONT. Nitrogen intake was consequently lower for the CONT and higher urinary excretion for the U + PRU (p = 0.002). Animals supplemented with CONT showed a tendency to have more Bacteria and fewer Archaea (p = 0.086). In Exp. 2, there was a treatment effect for the disappearance rate of the supplement (p < 0.001). Intake was faster for PRU and CONT, but performance was not affected by PRU (p = 0.311). The use of post-ruminal urea alters the microbial population, but does not affect performance. Therefore, supplementation with post-ruminal urea presented similar results compared to conventional urea. Ruminal and blood parameters and animal performance were not influenced by treatments.

Enhanced nitrogen removal from municipal wastewater via a novel combined process driven by partial nitrification/anammox (PN/A) and partial denitrification/anammox (PD/A) with an ultra-low hydraulic retention time (HRT)

Anaerobic ammonia oxidation (Anammox) is a highly productive research area in municipal wastewater treatment. A novel combined process driven by partial nitrification/anammox (PN/A) and partial denitrification/anammox (PD/A) was established in this paper using a sequencing batch reactor (SBR) and two up-flow sludge beds (USBs). Municipal wastewater after carbon removal pretreatment in SBR entered PN/A-USB. PN/A process was initiated and enhanced by optimizing the intermittent aeration mode under low dissolved oxygen (DO). After enhancing and stabilizing the PD/A process, PN/A effluent entered the PD/A-USB along with raw municipal wastewater at a ratio of 4:1 and the combined system was established. Through this, this study achieved a nitrogen removal efficiency (NRE) of 84.9 % from municipal wastewater at an ultra-low total hydraulic residence time (HRT) of 3.9 h. Candidatus Brocadia (1.8 % in PN/A, 1.0 % in PD/A) was the only functional anammox bacterium in the combined process.

Process characteristics and energy self-sufficient operation of a low-fouling anaerobic dynamic membrane bioreactor for up-concentrated municipal wastewater treatment

Up-concentration of municipal wastewater using physico-chemical methods can effectively enrich organic matter, facilitating subsequent anaerobic digestion of up-concentrated wastewater for enhanced methanogenesis at reduced energy consumption. An anaerobic dynamic membrane bioreactor (AnDMBR) assisted with biogas-sparging was developed to treat up-concentrated municipal wastewater, focusing on the effects of operating temperature and hydraulic retention time (HRT) as well as COD mass balance and energy balance. The COD removal stabilized at about 98 % over the experimental period, while gaseous and dissolved methane contributed 43-49 % and 2-3 % to the influent COD reducing greenhouse gas emissions. The formed dynamic membrane exists mainly as a heterogeneous cake layer with a uneven distribution feature, ensuring the stable effluent quality. Without adopting any physico-chemical cleaning, the transmembrane pressure (TMP) maintained at a low range (2.7 to 14.67 kPa) with the average TMP increasing rate of 0.089 kPa/d showing a long-term low-fouling operation. Increasing the concentration ratio, the methane production rate decreased from 0.18 to 0.15 L CH₄/gCOD likely due to the accumulation of particulate organics. Microbial community analysis indicated the predominant methanogenic pathway shifted from hydrogenotrophic to acetoclastic methanogenesis in response to the temperature change. Net energy balance (0.003-0.600 kWh/m³) can be achieved only under room temperature (25 °C) rather than mesophilic conditions (36 °C).

Effects of sulfate concentration on anaerobic treatment of wastewater containing monoethanolamine using an up-flow anaerobic sludge blanket reactor

Monoethanolamine (MEA), a toxic organic chemical, is widely used in industries and is found in their wastewater. Anaerobic MEA degradation is an appropriate strategy to reduce energy and cost for treatment. Industry wastewaters also contain sulfate, but information on the effects of sulfate on MEA degradation is limited. Here, an up-flow anaerobic sludge blanket (UASB) for MEA-containing wastewater treatment was operated under psychrophilic conditions (18-20 ºC) to investigate the effects of sulfate on the microbial characteristics of the retained sludge. To acclimatize the sludge, the proportion of MEA in the influent (containing sucrose, acetate, and propionate) was increased from 15% to 100% of total COD (1500 mg L^-1); sulfate was then added to the influent. The COD removal efficiency remained above 95% despite the increase in MEA and sulfate. However, granular sludge disintegration was observed when sulfate was increased from 20 to 330 mg L^-1. Batch tests revealed that propionate and acetate were produced as the metabolites of MEA degradation. In response to sulfate acclimation, methane-producing activities for propionate and hydrogen declined, while sulfate-reducing activities for MEA, propionate, and hydrogen increased. Accordingly, acclimation and changes in dominant microbial groups promoted the acetogenic reaction of propionate by sulfate reduction.

Pyrite-Based Autotrophic Denitrifying Microorganisms Derived from Paddy Soils: Effects of Organic Co-Substrate Addition

The presence of organic co-substrate in groundwater and soils is inevitable, and much remains to be learned about the roles of organic co-substrates during pyrite-based denitrification. Herein, an organic co-substrate (acetate) was added to a pyrite-based denitrification system, and the impact of the organic co-substrate on the performance and bacterial community of pyrite-based denitrification processes was evaluated. The addition of organic co-substrate at concentrations higher than 48 mg L^-1 inhibited pyrite-based autotrophic denitrification, as no sulfate was produced in treatments with high organic co-substrate addition. In contrast, both competition and promotion effects on pyrite-based autotrophic denitrification occurred with organic co-substrate addition at concentrations of 24 and 48 mg L^-1. The subsequent validation experiments suggested that competition had a greater influence than promotion when organic co-substrate was added, even at a low concentration. Thiobacillus, a common chemolithoautotrophic sulfur-oxidizing denitrifier, dominated the system with a relative abundance of 13.04% when pyrite served as the sole electron donor. With the addition of organic co-substrate, Pseudomonas became the dominant genus, with 60.82%, 61.34%, 70.37%, 73.44%, and 35.46% abundance at organic matter concentrations of 24, 48, 120, 240, and 480 mg L^-1, respectively. These findings provide an important theoretical basis for the cultivation of pyrite-based autotrophic denitrifying microorganisms for nitrate removal in soils and groundwater.

Potential metabolic and genetic interaction among viruses, methanogen and methanotrophic archaea, and their syntrophic partners

The metabolism of methane in anoxic ecosystems is mainly mediated by methanogens and methane-oxidizing archaea (MMA), key players in global carbon cycling. Viruses are vital in regulating their host fate and ecological function. However, our knowledge about the distribution and diversity of MMA viruses and their interactions with hosts is rather limited. Here, by searching metagenomes containing mcrA (the gene coding for the α-subunit of methyl-coenzyme M reductase) from a wide variety of environments, 140 viral operational taxonomic units (vOTUs) that potentially infect methanogens or methane-oxidizing archaea were retrieved. Four MMA vOTUs (three infecting the order Methanobacteriales and one infecting the order Methanococcales) were predicted to cross-domain infect sulfate-reducing bacteria. By facilitating assimilatory sulfur reduction, MMA viruses may increase the fitness of their hosts in sulfate-depleted anoxic ecosystems and benefit from synthesis of the sulfur-containing amino acid cysteine. Moreover, cell-cell aggregation promoted by MMA viruses may be beneficial for both the viruses and their hosts by improving infectivity and environmental stress resistance, respectively. Our results suggest a potential role of viruses in the ecological and environmental adaptation of methanogens and methane-oxidizing archaea.

Characterization of the Bacterial Community in the Ecosystem of Sea Cucumber (Apostichopus japonicus) Culture Ponds: Correlation and Specificity in Multiple Media

The bacterial community is an essential component of the aquaculture pond ecosystem, which not only improves and restores the aquaculture environment but also maintains a stable ecological equilibrium with the external environment. Here, Illumina 16S rRNA sequencing was conducted to characterize the bacterial community in the ecosystem of sea cucumber Apostichopus japonicus culture ponds, as well as their correlation with overall community structures. The alpha-diversities of bacterial community among water, sediment, and the gut of A. japonicus were consistent across culture ponds from different areas. Specifically, the richness and diversity of bacterial communities were the highest in sediment, followed by the gut, and the lowest in water. The dominant bacterial community among multiple media was Proteobacteria, which occupies a large proportion of the bacterial community structure, followed by Bacteroidetes and Verrucomicrobia. Highly similar bacterial community structures were present in multiple media among different areas, which provides evidence for deterministic natural evolution. Meanwhile, there was a significant difference (p < 0.05) in the specific bacterial communities across the multiple media. The specific functions of the multiple media in the ecosystem are the main reason for the formation of different bacterial communities. This work demonstrates that bacterial communities are the result of natural evolution within the ecosystem during adaptation to the required environment.

The rhizosphere effect of native legume Albizzia julibrissin on coastal saline soil nutrient availability, microbial modulation, and aggregate formation

In the coastal zones, numerous ecological shelterbelt projects were conducted to protect against natural hazards. However, it is still not fully understood whether phytoremediation with native legume Albizzia julibrissin plantation can improve saline soil structural development or microbial community structure. In this study, a field experiment was conducted to investigate the responses of rhizosphere soil salinity, nutrients, bacterial community, and aggregate structure to A. julibrissin plantation in a recently reclaimed area along Zhejiang coast, China. After ~3-year plantation, rhizosphere soil pH and EC reduced to 8.25 and 0.14 dS·m^-1, respectively, belonging to non-saline soil. Meanwhile, total organic carbon (TOC), permanganate-oxidizable carbon (POXC), total nitrogen (TN), alkali-hydrolyzable nitrogen (AN), and ammonium nitrogen (NH₄⁺-N) were significantly increased in rhizosphere soil compared with bare land (P < 0.05). Consequently, rhizosphere soil had favorable habitat condition for copiotrophic bacterial taxa (e.g., Chloroflexi, Acidobacteria, and Bacteroidates), as well as high diversity, complex co-occurrence network, and catabolism related with nutrient cycling. The soil particle size of bare land was < 0.053 mm, while microaggregate (0.053-0.25 mm) and macroaggregate (0.25-2 mm) were formed in the rhizosphere and coupled with C accumulation and Fe removal. Soil aggregates were of great importance to soil fertility with more efficient bacterial network and biogeochemical cycles of nutrients. N-fixing Rhizobiales preferred to inhabit large soil particle and might primarily contribute to N accumulation. Generally, A. julibrissin was a suitable pioneer tree for mudflat reclamation projects, which effectively improved saline soil rhizosphere environment by reducing salinity, accumulating C and N, and promoting microbial community succession, as well as aggregate structure formation.

The dosage-effect of biochar on anaerobic digestion under the suppression of oily sludge: Performance variation, microbial community succession and potential detoxification mechanisms

This study investigated the dosage-effect of biochar on the suppressed mesophilic digestion of oily sludge (OS) containing naphthalene (recalcitrant compound) and starch (easily bioavailable substrate). Methanogenesis was inhibited in control with OS, where biomethane yield (63.33 mL/gVS) was obviously lower than theoretical yield (260.55 mL/gVS). With adding optimal dose of biochar (0.60 g/gVS OS), the highest CH₄ yield (138.41 mL/gVS) was 2.19 times of control. Meanwhile, the efficiencies of hydrolysis, acidogenesis and acetogenesis were significantly enhanced. However, excessive biochar (4.80 g/gVS OS) caused negative effects with methanogenic efficiency diminished by 32.5% and lag phase prolonged by 5.72 h. Dissolved organic matter (DOM) analysis showed that humic acid-like and fulvic acid-like components percentages of fluorescence regional integration were decreased because of the adsorption of biochar. In addition, biochar mediating interspecies electron transfer selectively enriched electroactive fermentation bacteria (Clostridium and Bacteroides) and acetoclastic Methanosaeta, which was responsible for promoting mesophilic digestion performance. The functional genes related to metabolism and environmental information processing were potentially activated by biochar. Above results indicate that moderate biochar application may mitigate the bio-toxicity suppression of OS, which help to provide a promising pathway for reinforcing oily wastes bio-treatment.

Microbial characteristics in anaerobic membrane bioreactor treating domestic sewage: Effects of HRT and process performance

Two anaerobic membrane bioreactors (AnMBRs) equipped with different membrane pore size (0.4 or 0.05 µm) were operated at 25˚C and fed with domestic wastewater. The hydraulic retention time (HRT) of the reactors was shortened. The microbial communities of the two AnMBRs were investigated by 16S rRNA gene amplicon sequencing to see the effects of HRT. The predominant Archaea was an aceticlastic methanogen Methanosaeta. The composition of hydrogenotrophic methanogens changed with the HRTs: the population of Methanobacterium was higher for longer HRTs, whereas the population of unclassified Methanoregulaceae was higher for shorter HRTs. The Anaerolineae, Bacteroidia and Clostridia bacteria were dominant in both of the reactors, with a combined relative abundance of over 55%. The relative abundance of Anaerolineae was proportional to the biogas production performance. The change in the population of hydrogenotrophic methanogens or Anaerolineae can be used as an indicator for process monitoring. The sum of the relative abundance of Anaerolineae and Clostridia fluctuated slightly with changes in the HRT in both AnMBRs when the reactor was stably operated. The co-occurrence analysis revealed the relative abundance of the operational taxonomic units belonging to Anaerolineae and Clostridia was functionally equivalent during the treatment of real domestic sewage. A principal coordination analysis revealed that the changes in the microbial community in each reactor were consistent with the change of HRT. In addition, both the HRT and the stability of the process are important factors for maintaining microbial community structures.

Different soil salinity imparts clear alteration in rhizospheric bacterial community dynamics in rice and peanut

The rhizospheric microbiome is capable of changing the physio-chemical properties of its own micro-environment and found to be indispensable in the overall health of the hostplant. The interplay between the rhizospheric environment and the microbiota residing therein tune the physiology of the associated plant. In this study, we have determined how the soil properties and the host-plant remains as an important parameter for microbial community dynamics in the rhizosphere of rice and peanut. In addition to check the physio-chemical parameters of the rhizospheric soil, we have also prepared the metagenomic DNA from each rhizospheric soil followed by high-throughput sequencing and sequence analysis to predict the OTUs that represents the community structure. The alpha-diversity of the bacterial community in the RRN sample was highest, while the lowest was in PRS sample. Actinobacteria is the most predominant phylum in PRN, PRS and RRN, whereas Acidobacteria in RRS. We found a clear shift in bacterial community over the rice and peanut rhizosphere and also over these host-rhizospheres from normal and high saline region. The rhizospheric bacterial community composition found to be affected by the close-by environmental factors. Thus, the rhizospheric bacterial community structure is related to both the adjoining soil characters and the type of the hosts.

Sulfidogenic fluidized-bed bioreactor kinetics for co-treatment of hospital wastewater and acid mine drainage

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Bioremediation process for acidic mine water co-treatment with hospital wastewater.

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Metal precipitation reached 98% and soluble concentrations of Fe and Zn were less than 0.1 mg/l.

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SO₄²⁻ removal was above 90% in the sulfidogenic bioreactor.

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Naproxen, ibuprofen, ketoprofen, and diclofenac partially removed during the co-treatment process.

A passive co-treatment of acid mine drainage and hospital wastewater previously demonstrated a promising bioremediation viable approach for both toxic streams. The study of inhibition kinetics and microbial communities is essential to understand better the diverse species and the reaction mechanisms within the system. The kinetics and microbiology diversity in the sulfidogenic fluidized-bed reactor (at 30 °C) for co-treatment of hospital wastewater and metal-containing acidic water were examined. The alkalinity from organic oxidation raised the pH of the effluent from 2.3 to 6.1–8.2. Michaelis-Menten modeling yielded (K_m =7.3 mg/l, V_max = 0.12 mg/l min⁻¹) in the batch bioreactor treatment using sulfate-reducing bacteria. For COD oxidation, the dissolved sulfide inhibition constant (K_i) was 3.6 mg/l, and the K_i value for H₂S was 9 mg/l. The dominant species in the treatment process belong to the Proteobacteria group (especially Deltaproteobacteria). The ibuprofen and diclofenac compounds achieved the highest removal rates in the bioreactor of 58.6% and 52.3%, respectively; while, ketoprofen and naproxen of 41.9% and 46.6%, respectively. The findings in COD kinetics, sulfate-reducing bacteria abundance, and selected pharmaceutical concentration reduction provide insight into this co-treatment process's capability.

Evaluation of biochar addition and circulation control strengthening measures on efficiency and microecology of food waste treatment in anaerobic reactor

The process of strengthening an expanded granular sludge blanket (EGSB) reactor under ammonia nitrogen stress conditions and by adopting three strengthening measures, namely, opening the circulation (OC), adding modified biochar (MB), adding modified biochar along with opening the circulation (MBOC), to treat food waste was studied. When the ammonia nitrogen concentration of influent increased to 1200 mg/L, the removal rate of COD reduced to about 75%, while the removal rate of ammonia nitrogen was about 6%. The average COD removal rate of the anaerobic reactor in the last 5 days of each operating cycle i.e. OC, MB and MBOC, was 85.51%, 84.11% and 90.03%, respectively. At the 30th day of each treatment-OC, MB and MBOC, the protease content in the sludge was 44.61, 42.47, 46.24 NH₂-N (mg)/mg, respectively. and the content of coenzyme F₄₂₀ was 0.244, 0.217 and 0.267 mmol/g, respectively. Proteobacteria was the most abundant phylum in the stage I (OC), reaching 34.36%. It was accounted for 16.68% and 21.38%, respectively, in the stage II (MB) and stage III (MBOC). The dominant archaea in the three stages were Methanosaeta, whose abundance was 38.98% in stage I, which increased to 64.94% and 64.01% in stage II and III, respectively. Among the active carbohydrate enzymes, the gene abundance of Glycoside transferases in the MBOC stage was the largest among the three stages.

Effect of pH on volatile fatty acid production and the microbial community during anaerobic digestion of Chinese cabbage waste

The effects of pH on the production of volatile fatty acids (VFAs) and the evolution of microbial community structure were studied via anaerobic fermentation of Chinese cabbage waste. The results showed that the concentration of total VFAs was highest at 20,241.4 mg COD/L at pH 6.0, followed by pH 7.0. Ethanol, acetate and butyrate were dominant under the acidic condition. The main products at pH 7.0 were acetate, propionate, and butyrate. Ethanol, acetate and butyrate were rapidly produced during the initial stage. The hexanoate concentration increased quickly from day 6 due to the chain extension between ethanol and butyrate, and was 4,885.1 mg COD/L on day 8, accounting for 30.4% of the total VFAs. As fermentation was extended, Bacteroidia and Clostridia were dominant at pH 6.0 and the uncontrolled pH, respectively. Clostridium IV, Ruminococcus, and Candida, were suspected to be related to hexanoate production.

Evaluation of Three Prokaryote Primers for Identification of Prokaryote Community Structure and Their Abode Preference in Three Distinct Wetland Ecosystems

The ultimate role of prokaryote (bacteria and archaea), the decomposer of the wetland ecosystem, depends on its community structure and its interaction with the environment. The present study has used three universal prokaryote primers to compare prokaryote community structure and diversity of three distinctly different wetlands. The study results revealed that α-diversity indices and phylogenetic differential abundance patterns did not differ significantly among primers, but they did differ significantly across wetlands. Microbial community composition revealed a distinct pattern for each primer in each wetland. Overall comparison of prokaryote communities in sediments of three wetlands revealed the highest prokaryote richness and diversity in Bhomra (freshwater wetland) followed by Malencho (brackish-water wetland) and East Kolkata wetland (EKW) (sewage-fed wetland). Indicator genus analysis identified 21, 4, and 29 unique indicator genera, having preferential abode for Bhomra, EKW, and Malencho, respectively. Prediction of potential roles of these microbes revealed a preference for sulfate-reducing microbes in Malencho and methanogens in Bhomra. The distinct phylogenetic differential abundance pattern, microbial abode preference, and their potential functional role predict ecosystem variables shaping microbial diversity. The variation in community composition of prokaryotes in response to ecosystem variables can serve as the most sensitive bioindicator of wetland ecosystem assessment and management.

Combined Stochastic and Deterministic Processes Drive Community Assembly of Anaerobic Microbiomes During Granule Flotation

Advances in null-model approaches have resulted in a deeper understanding of community assembly mechanisms for a variety of complex microbiomes. One under-explored application is assembly of communities from the built-environment, especially during process disturbances. Anaerobic digestion for biological wastewater treatment is often underpinned by retaining millions of active granular biofilm aggregates. Flotation of granules is a major problem, resulting in process failure. Anaerobic aggregates were sampled from three identical bioreactors treating dairy wastewater. Microbiome structure was analysed using qPCR and 16S rRNA gene amplicon sequencing from DNA and cDNA. A comprehensive null-model approach quantified assembly mechanisms of floating and settled communities. Significant differences in diversity were observed between floating and settled granules, in particular, we highlight the changing abundances of Methanosaeta and Lactococcus. Both stochastic and deterministic processes were important for community assembly. Homogeneous selection was the primary mechanism for all categories, but dispersal processes also contributed. The lottery model was used to identify clade-level competition driving community assembly. Lottery “winners” were identified with different winners between floating and settled groups. Some groups changed their winner status when flotation occurred. Spirochaetaceae, for example, was only a winner in settled biomass (cDNA-level) and lost its winner status during flotation. Alternatively, Arcobacter butzerli gained winner status during flotation. This analysis provides a deeper understanding of changes that occur during process instabilities and identified groups which may be washed out—an important consideration for process control.

Land-Use System and Forest Floor Explain Prokaryotic Metacommunity Structuring and Spatial Turnover in Amazonian Forest-to-Pasture Conversion Areas

Advancing extensive cattle production is a major threat to biodiversity conservation in Amazonia. The dominant vegetation cover has a drastic impact on soil microbial communities, affecting their composition, structure, and ecological services. Herein, we explored relationships between land-use, soil types, and forest floor compartments on the prokaryotic metacommunity structuring in Western Amazonia. Soil samples were taken in sites under high anthropogenic pressure and distributed along a ±800 km gradient. Additionally, the litter and a root layer, characteristic of the forest environment, were sampled. DNA was extracted, and metacommunity composition and structure were assessed through 16S rRNA gene sequencing. Prokaryotic metacommunities in the bulk soil were strongly affected by pH, base and aluminum saturation, Ca + Mg concentration, the sum of bases, and silt percentage, due to land-use management and natural differences among the soil types. Higher alpha, beta, and gamma diversities were observed in sites with higher soil pH and fertility, such as pasture soils or fertile soils of the state of Acre. When taking litter and root layer communities into account, the beta diversity was significantly higher in the forest floor than in pasture bulk soil for all study regions. Our results show that the forest floor's prokaryotic metacommunity performs a spatial turnover hitherto underestimated to the regional scale of diversity.

16S rRNA gene amplicon-based metagenomic analysis of bacterial communities in the rhizospheres of selected mangrove species from Mida Creek and Gazi Bay, Kenya

Prokaryotic communities play key roles in biogeochemical transformation and cycling of nutrients in the productive mangrove ecosystem. In this study, the vertical distribution of rhizosphere bacteria was evaluated by profiling the bacterial diversity and community structure in the rhizospheres of four mangrove species (Sonneratia alba, Rhizophora mucronata, Ceriops tagal and Avicennia marina) from Mida Creek and Gazi Bay, Kenya, using DNA-metabarcoding. Alpha diversity was not significantly different between sites, but, significantly higher in the rhizospheres of S. alba and R. mucronata in Gazi Bay than in Mida Creek. Chemical parameters of the mangrove sediments significantly correlated inversely with alpha diversity metrics. The bacterial community structure was significantly differentiated by geographical location, mangrove species and sampling depth, however, differences in mangrove species and sediment chemical parameters explained more the variation in bacterial community structure. Proteobacteria (mainly Deltaproteobacteria and Gammaproteobacteria) was the dominant phylum while the families Desulfobacteraceae, Pirellulaceae and Syntrophobacteraceae were dominant in both study sites and across all mangrove species. Constrained redundancy analysis indicated that calcium, potassium, magnesium, electrical conductivity, pH, nitrogen, sodium, carbon and salinity contributed significantly to the species–environment relationship. Predicted functional profiling using PICRUSt2 revealed that pathways for sulfur and carbon metabolism were significantly enriched in Gazi Bay than Mida Creek. Overall, the results indicate that bacterial community composition and their potential function are influenced by mangrove species and a fluctuating influx of nutrients in the mangrove ecosystems of Gazi Bay and Mida Creek.

Database Mining to Unravel the Ecology of the Phylum Chloroflexi in Methanogenic Full Scale Bioreactors

Although microbial communities of anaerobic bioreactors have been extensively studied using DNA-based tools, there are still several knowledge gaps regarding the microbiology of the process, in particular integration of all generated data is still limited. One understudied core phylum within anaerobic bioreactors is the phylum Chloroflexi, despite being one of the most abundant groups in anaerobic reactors. In order to address the abundance, diversity and phylogeny of this group in full-scale methanogenic reactors globally distributed, a compilation of 16S ribosomal RNA gene sequence data from 62 full-scale methanogenic reactors studied worldwide, fed either with wastewater treatment anaerobic reactors (WTARs) or solid-waste treatment anaerobic reactors (STARs), was performed. One of the barriers to overcome was comparing data generated using different primer sets and different sequencing platforms. The sequence analysis revealed that the average abundance of Chloroflexi in WTARs was higher than in STARs. Four genera belonging to the Anaerolineae class dominated both WTARs and STARs but the core populations were different. According to the phylogenetic analysis, most of the sequences formed clusters with no cultured representatives. The Anaerolineae class was more abundant in reactors with granular biomass than in reactors with disperse biomass supporting the hypothesis that Anaerolineae play an important role in granule formation and structure due to their filamentous morphology. Cross-study comparisons can be fruitfully used to understand the complexity of the anaerobic digestion process. However, more efforts are needed to standardize protocols and report metadata information.

Chemotaxis-selective colonization of mangrove rhizosphere microbes on nine different microplastics

Microplastics pollution poses a new threat to the environment of intertidal zone. The sea forest, mangrove, has been polluted by a large number of plastic debris worldwide. To fill the gaps in knowledge of mangrove rhizosphere microbes connected with the 'plasticsphere', a semi-controlled in situ exposure experiment for nine different types of microplastics were conducted in mangrove ecosystem. A sign of biodegrading was observed on polyethylene, polyamide 6 and polyvinyl chloride microplastics surface after 3 months exposure. We discovered that the metabolic activities of the dominant bacteria on certain microplastics were related to the specific groups on polymers molecule. The selective colonization may be driven by the chemotaxis of bacteria. Specially, microplastics biofilms of polyethylene, polyamide 6, polyvinyl chloride and expanded polystyrene possess distinctive dominant bacteria assemblages which have great significance in ecosystem processes involving carbon cycle or sulfur cycle. Community of mangrove soil microorganism and microplastic biofilm varies as the seasons changes. As a new niche, microplastics has higher inclusivity to bacteria than surrounding soil. Additionally, pathogens for human beings (Vibrio parahaemolyticus and Escherichia-Shigella) were detected both in microplastics and soil. We stress that the interaction between microplastics and rhizosphere microorganisms may affect the growth and health of mangrove plants. Besides, we point out that mangrove rhizosphere microorganism can be an ideal candidate for plastics-degradation.

Microbiome analysis of rhizospheres of plant and winter-initiated ratoon crops of sugarcane grown in sub-tropical India: utility to improve ratoon crop productivity

One plant and one to two ratoon crops are the predominant patterns of sugarcane cultivation in sub-tropical part of India. Despite high agricultural inputs, yield of ratoon crop gets dwindled in the subsequent years. The microbial community, particularly bacteria and fungi, in the rhizosphere and their interaction with the root system, in general influences plant productivity. For the present study, an early maturing sugarcane variety (CoLk 94184), was used to establish plant and winter-initiated ratoon crops in 2016-2018. Soils pertaining to both plant and ratoon rhizospheres were subjected to biochemical analysis, microbial DNA isolation and high-throughput sequencing of 16S rRNA genes to assess the microbial diversity and associated characteristics impacting cane yield. Although alpha diversity of bacterial community was observed high in the soils of both plant and ratoon crops, the species richness/diversity was more in plant crop. Bacterial community structure in the rhizosphere of plant crop was predominantly consisted of phyla Actinobacteria (35.68%), Gemmatimonadetes (29.26%), Chloroflexi (26.73%) and Proteobacteria (16.68%), while ratoon rhizosphere revealed dominance of Acidobacteria (20.77%) and Bacteroidetes (10.7%). Though studies revealed the presence of rich bacterial community in the rhizospheres of both plant and ratoon crops of sugarcane, dominance of Acidobacteria and meager proportion of Actinobacteria and Proteobacteria in ratoon crop possibly limited its productivity. Along with high total phenols (7.27 mg/g dry wt), ratoon crop depicted less active root system as revealed by scanning electron microscopy. Dominance of thermophilic bacterial phyla Chloroflexi and Gemmatimonadetes which was observed in sugarcane rhizosphere supports better crop growth in drought. However, management of soil microbial community is required to improve the ratoon crop productivity.

On-Site Blackwater Treatment Fosters Microbial Groups and Functions to Efficiently and Robustly Recover Carbon and Nutrients

Wastewater is considered a renewable resource water and energy. An advantage of decentralized sanitation systems is the separation of the blackwater (BW) stream, contaminated with human pathogens, from the remaining household water. However, the composition and functions of the microbial community in BW are not known. In this study, we used shotgun metagenomics to assess the dynamics of microbial community structure and function throughout a new BW anaerobic digestion system installed at The Netherlands Institute of Ecology. Samples from the influent (BW), primary effluent (anaerobic digested BW), sludge and final effluent of the pilot upflow anaerobic sludge blanket (UASB) reactor and microalgae pilot tubular photobioreactor (PBR) were analyzed. Our results showed a decrease in microbial richness and diversity followed by a decrease in functional complexity and co-occurrence along the different modules of the bioreactor. The microbial diversity and function decrease were reflected both changes in substrate composition and wash conditions. Our wastewater treatment system also decreased microbial functions related to pathogenesis. In summary, the new sanitation system studied here fosters microbial groups and functions that allow the system to efficiently and robustly recover carbon and nutrients while reducing pathogenic groups, ultimately generating a final effluent safe for discharge and reuse.

Diversity, enrichment, and genomic potential of anaerobic methane- and ammonium-oxidizing microorganisms from a brewery wastewater treatment plant

Anaerobic wastewater treatment offers several advantages; however, the effluent of anaerobic digesters still contains high levels of ammonium and dissolved methane that need to be removed before these effluents can be discharged to surface waters. The simultaneous anaerobic removal of methane and ammonium by denitrifying (N-damo) methanotrophs in combination with anaerobic ammonium-oxidizing (anammox) bacteria could be a potential solution to this challenge. After a molecular survey of a wastewater plant treating brewery effluent, indicating the presence of both N-damo and anammox bacteria, we started an anaerobic bioreactor with a continuous supply of methane, ammonium, and nitrite to enrich these anaerobic microorganisms. After 14 months of operation, a stable enrichment culture containing two types of 'Candidatus Methylomirabilis oxyfera' bacteria and two strains of 'Ca. Brocadia'-like anammox bacteria was achieved. In this community, anammox bacteria converted 80% of the nitrite with ammonium, while 'Ca. Methylomirabilis' contributed to 20% of the nitrite consumption. The analysis of metagenomic 16S rRNA reads and fluorescence in situ hybridization (FISH) correlated well and showed that, after 14 months, 'Ca. Methylomirabilis' and anammox bacteria constituted approximately 30 and 20% of the total microbial community. In addition, a substantial part (10%) of the community consisted of Phycisphaera-related planctomycetes. Assembly and binning of the metagenomic sequences resulted in high-quality draft genome of two 'Ca. Methylomirabilis' species containing the marker genes pmoCAB, xoxF, and nirS and putative NO dismutase genes. The anammox draft genomes most closely related to 'Ca. Brocadia fulgida' included the marker genes hzsABC, hao, and hdh. Whole-reactor and batch anaerobic activity measurements with methane, ammonium, nitrite, and nitrate revealed an average anaerobic methane oxidation rate of 0.12 mmol h^-1 L^-1 and ammonium oxidation rate of 0.5 mmol h^-1 L^-1. Together, this study describes the enrichment and draft genomes of anaerobic methanotrophs from a brewery wastewater treatment plant, where these organisms together with anammox bacteria can contribute significantly to the removal of methane and ammonium in a more sustainable way. KEY POINTS: • An enrichment culture containing both N-damo and anammox bacteria was obtained. • Simultaneous consumption of ammonia, nitrite, and methane under anoxic conditions. • In-depth metagenomic biodiversity analysis of inoculum and enrichment culture.

Effects of Drinking Water Temperature and Flow Rate during Cold Season on Growth Performance, Nutrient Digestibility and Cecum Microflora of Weaned Piglets

Simple Summary

Water is an essential nutrient pigs need to sustain life and ensure growth. Determining the appropriate drinking water supply parameters during cold weather are critical for the welfare and growth of pigs, especially vulnerable weaned piglets. This study explored different combinations of drinking water temperature (DWT) and flow rate (DWF) for weaned piglets during winter. It measured their growth performance, nutrient digestibility and cecum microbial diversity, aiming to figure out the optimal water supplying conditions for weaned piglets. The results indicated that a combination of DWT of 30 °C and DWF of 300 mL/min decreased diarrhea occurrence. Furthermore, this increased growth performance and nutrient digestibility, accompanied by improvement of the dominant cecum microflora, mainly manifested in a reduced abundance of Proteobacteria and increased abundance of Bacteroidetes. This study enriches our understanding of the connection between water supply, growth performance and cecum microbiota on weaned piglets during the cold season.

Abstract

Although water is one of the most important nutrients and is essential for various physiological processes within the body, it does not receive adequate consideration when ensuring optimal nutrition and growth performance in piglets. This study was conducted to investigate the effects of drinking water temperature (DWT) and flow rate (DWF) on growth performance, nutrient digestibility and cecum microflora in weaned piglets during cold weather. Sixty-four piglets with an average body weight of 8.60 ± 0.5 kg were allotted into four groups with four replicates in each group and four pigs in each replicate. The DWT and DWF were set for each group as follows: (1) 13 °C + 300 mL/min, (2) 13 °C + 700 mL/min, (3) 30 °C + 300 mL/min and (4) 30 °C + 700 mL/min, respectively. All groups were fed the same diet during the 28 d trial. The body weight at day 0 and day 29, as well as daily feed intake, were recorded. Diarrhea severity was assessed every day. Fresh fecal samples were collected for four consecutive days at the end of the experiment for the digestibility test. Cecum content was collected after sacrifice for microbial composition analysis. The results indicated that: (1) DWT at 30 °C promoted the average daily gain (ADG) of weaned piglets considerably (p = 0.043) and decreased feed to weight ratio when compared with DWT at 13 °C (p = 0.045). DWF had no substantial effect on the growth performance of piglets (p > 0.05). (2) The 30 °C DWT groups had higher apparent digestibility of crude protein, crude fat and energy than the 13 °C DWT groups (p < 0.05), while DWF had no significant effect on the apparent digestibility of nutrients (p > 0.05). (3) DWT at 30 °C increased the Bacteroidetes abundance and decreased the Proteobacteria abundance in cecum digesta. The change in these two factors may be related to a decrease in diarrhea and the improvement of growth performance. Different DWF had no substantial effect on the cecum microbial structure. To sum up, providing a DWT of 30 °C to weaned piglets in cold weather reduced the abundance of harmful bacteria in the cecum and improved the apparent nutrient digestibility, which is beneficial for maintaining a healthy intestinal microenvironment and promoting growth performance. A lower DWF of 300 mL/min had no adverse effect on growth performance. Therefore, a combination of 30 °C + 300 mL/min is recommended for weaned piglets during cold weather for the consideration of animal welfare and production efficiency.

Disentangling Large- and Small-Scale Abiotic and Biotic Factors Shaping Soil Microbial Communities in an Alpine Cushion Plant System

Microorganisms play a crucial role in biogeochemical cycles and ecosystem processes, but the key factors driving microbial community structure are poorly understood, particularly in alpine environments. In this study, we aim to disentangle the relative contribution of abiotic and biotic factors shaping bacterial and fungal community structure at large and small spatial and integration scales in an alpine system dominated by a stress-tolerant cushion species Thylacospermum ceaspitosum. These effects were assessed in two mountain ranges of northwest China and for two contrasting phenotypes of the cushion species inhabiting two different microtopographic positions. The large- and small-scale abiotic effects include the site and microhabitat effects, respectively, while the large- and small-scale biotic effects include the effects of cushion presence and cushion phenotype, respectively. Soil microbial communities were characterized by Illumina Miseq sequencing. Uni- and multivariate statistics were used to test the effects of abiotic and biotic factors at both scales. Results indicated that the site effect representing the soil pH and abiotic hydrothermal conditions mainly affected bacterial community structure, whereas fungal community structure was mainly affected by biotic factors with an equal contribution of cushion presence and cushion phenotype effects. Future studies should analyze the direct factors contributing to shaping microbial community structure in particular of the cushion phenotypes.

Separating and Characterizing Functional Nitrogen Degraders via Magnetic Nanoparticle-Mediated Isolation

Magnetic nanoparticle-mediated isolation (MMI) is a new method for isolating active functional microbes from complex microorganisms without substrate labeling. In this study, the composition and properties of magnetic nanoparticles (MNPs) were characterized by a number of techniques, indicating that MNPs have characteristics such as microinterfaces and can be efficiently fixed on the surface of microbial cells. It also introduced the MMI technology in activated sludge after stable long-term treatment. With further addition of promotor carbon sources, the enrichment of the functional nitrogen degraders in MMI was significantly higher than in samples without MNPs, showing the advantages of MMI in identifying the active degraders. Redundancy analysis (RDA) also showed that the functional nitrogen degraders such as Comamonadaceae_unclassified and Thiobacillus absolutely dominated in situ ammonia degradation, and the change in dominant genera had the same trend as the degradation rate of ammonia nitrogen. In the magnetically functionalized system, the separated functional nitrogen degraders significantly improved ammonia nitrogen degradation efficiency, making it basically stable at more than 80%, up to 91.6%. These results prove that the complex flora created after the addition of MNPs is more adaptable to newly introduced pollutants, and MMI is a powerful tool for studying pollutant-degrading microorganisms under in situ conditions.

Diverse Microbial Community Profiles of Propionate-Degrading Cultures Derived from Different Sludge Sources of Anaerobic Wastewater Treatment Plants

Anaerobic digestion (AD) has been used for wastewater treatment and production of renewable energy or biogas. Propionate accumulation is one of the important problems leading to an unstable system and low methane production. Revealing propionate-degrading microbiome is necessary to gain a better knowledge for alleviation of the problem. Herein, we systematically investigated the propionate-degrading cultures enriched from various anaerobic sludge sources of agro-industrial wastewater treatment plants using 16S rRNA gene sequencing. Different microbial profiles were shown even though the methanogenic activities of all cultures were similar. Interestingly, non-classical propionate-degrading key players Smithella, Syntrophomonas, and Methanosaeta were observed as common prevalent taxa in our enriched cultures. Moreover, different hydrogenotrophic methanogens were found specifically to the different sludge sources. The enriched culture of high salinity sludge showed a distinct microbial profile compared to the others, containing mainly Thermovirga, Anaerolinaceae, Methanosaeta, Syntrophobactor, and Methanospirillum. Our microbiome analysis revealed different propionate-degrading community profiles via mainly the Smithella pathway and offers inside information for microbiome manipulation in AD systems to increase biogas production corresponding to their specific microbial communities.

High Throughput Sediment DNA Sequencing Reveals Azo Dye Degrading Bacteria Inhabit Nearshore Sediments

Estuaries and coastal environments are often regarded as a critical resource for the bioremediation of organic pollutants such as azo dyes due to their high abundance and diversity of extremophiles. Bioremediation through the activities of azoreductase, laccase, and other associated enzymes plays a critical role in the removal of azo dyes in built and natural environments. However, little is known about the biodegradation genes and azo dye degradation genes residing in sediments from coastal and estuarine environments. In this study, high-throughput sequencing (16S rRNA) of sediment DNA was used to explore the distribution of azo-dye degrading bacteria and their functional genes in estuaries and coastal environments. Unlike laccase genes, azoreductase (azoR), and naphthalene degrading genes were ubiquitous in the coastal and estuarine environments. The relative abundances of most functional genes were higher in the summer compared to winter at locations proximal to the mouths of the Hanjiang River and its distributaries. These results suggested inland river discharges influenced the occurrence and abundance of azo dye degrading genes in the nearshore environments. Furthermore, the azoR genes had a significant negative relationship with total organic carbon, Hg, and Cr (p < 0.05). This study provides critical insights into the biodegradation potential of indigenous microbial communities in nearshore environments and the influence of environmental factors on microbial structure, composition, and function which is essential for the development of technologies for bioremediation in azo dye contaminated sites.

Correlations between microbial population dynamics, bamA gene abundance and performance of anaerobic sequencing batch reactor (ASBR) treating increasing concentrations of phenol

The relevant microorganims driving efficiency changes in anaerobic digestion of phenol remains uncertain. In this study correlations were established between microbial population and the process performance in an anaerobic sequencing batch reactor (ASBR) treating increasing concentrations of phenol (from 120 to 1200 mg L^-1). Sludge samples were taken at different operational stages and microbial community dynamics was analyzed by 16S rRNA sequencing. In addition, bamA gene was quantified in order to evaluate the dynamics of anaerobic aromatic degraders. The microbial community was dominated by Anaerolineae, Bacteroidia, Clostridia, and Methanobacteria classes. Correlation analysis between bamA gene copy number and phenol concentration were highly significant, suggesting that the increase of aromatic degraders targeted by bamA assay was due to an increase in the amount of phenol degraded over time. The incremental phenol concentration affected hydrogenotrophic archaea triggering a linear decrease of Methanobacterium and the growth of Methanobrevibacter. The best performance in the reactor was at 800 mg L^-1 of phenol. At this stage, the highest relative abundances of Syntrophorhabdus, Chloroflexus, Smithella, Methanolinea and Methanosaeta were observed and correlated positively with initial degradation rate, suggesting that these microorganisms are relevant players to maintain a good performance in the ASBR.

The microbiome driving anaerobic digestion and microbial analysis

The microbiome residing in anaerobic digesters drives the anaerobic digestion (AD) process to convert various feedstocks to biogas as a renewable source of energy. This microbiome has been investigated in numerous studies in the last century. The early studies used cultivation-based methods and analysis to identify the four guilds (or functional groups) of microorganisms. Molecular biology techniques overcame the limitations of cultivation-based methods and allowed the identification of unculturable microorganisms, revealing the high diversity of microorganisms involved in AD. In the past decade, omics technologies, including metataxonomics, metagenomics, metatranscriptomics, metaproteomics, and metametabolomics, have been or start to be used in comprehensive analysis and studies of biogas-producing microbiomes. In this chapter, we reviewed the utilities and limitations of these analysis methods, techniques, and technologies when they were used in studies of biogas-producing microbiomes, as well as the new information on diversity, composition, metabolism, and syntrophic interactions of biogas-producing microbiomes. We also discussed the current knowledge gaps and the research needed to further improve AD efficiency and stability.