Genome recovery and metatranscriptomic confirmation of functional acetate-oxidizing bacteria from enriched anaerobic biogas digesters

Ammonia-stressed anaerobic digestion: Sensitivity dynamics of key syntrophic interactions and methanogenic pathways-A review

The problematic anaerobic digestion (AD) of protein-rich substrates owing to their high ammonia content continues to hinder optimum methanation despite their high potential for offsetting greenhouse gas (GHG) emissions. This review focuses on the analyses of the sensitivity dynamics of key AD processes as well as the microbial interactions and exchanges that occur with them. Aside from the apparent increased risk associated with thermophilic ammonia-rich substrate AD, the marginally higher energy generation compared to mesophilic systems is not commensurate to the energy requirement. Moreover, while comparable FAN thresholds have been confirmed, TAN thresholds are susceptible to physical chemistry and so vary greatly. Profiling of the metabolic capability of front-end AD microbiome revealed Bacteroidetes, Firmicutes, and Synergistetes as some of the ammonia-resilient bacteria groups while Proteobacteria and Actinobacteria were the most fragile taxa. Besides the predominance of incomplete propionate oxidizing bacteria under ammonia stress conditions, syntrophic propionate oxidation (SPO) is usually shifted from the methylmalonyl CoA to the dismutation pathway. Furthermore, besides their different recoverability potentials, distinct methanogenic groups are differentially impacted by different ammonia species. Prevailing literature evidence suggests that conductive material assisted bioaugmentation with SAO-HM consortia, and in-situ H2 supplementation are the most effective for expediting electron transfer and relieving ammonia stress. These valuable insights should inform the design of targeted ammonia inhibition mitigation strategies.

Temperature-dependent transformation of microbial community: A systematic approach to analyzing functional microbes and biogas production

The stability and effectiveness of the anaerobic digestion (AD) system are significantly influenced by temperature. While majority research has focused on the composition of the microbial community in the AD process, the relationships between functional gene profile deduced from gene expression at different temperatures have received less attention. The current study investigates the AD process of potato peel waste and explores the association between biogas production and microbial gene expression at 15, 25, and 35 °C through metatranscriptomic analysis. The production of total biogas decreased with temperature at 15 °C (19.94 mL/g VS), however, it increased at 35 °C (269.50 mL/g VS). The relative abundance of Petrimonas, Clostridium, Aminobacterium, Methanobacterium, Methanothrix, and Methanosarcina were most dominant in the AD system at different temperatures. At the functional pathways level 3, α-diversity indices, including Evenness (Y = 5.85x + 8.85; R2 = 0.56), Simpson (Y = 2.20x + 2.09; R2 = 0.33), and Shannon index (Y = 1.11x + 4.64; R2 = 0.59), revealed a linear and negative correlation with biogas production. Based on KEGG level 3, several dominant functional pathways associated with Oxidative phosphorylation (ko00190) (25.09, 24.25, 24.04%), methane metabolism (ko00680) (30.58, 32.13, and 32.89%), and Carbon fixation pathways in prokaryotes (ko00720) (27.07, 26.47, and 26.29%), were identified at 15 °C, 25 °C and 35 °C. The regulation of biogas production by temperature possibly occurs through enhancement of central function pathways while decreasing the diversity of functional pathways. Therefore, the methanogenesis and associated processes received the majority of cellular resources and activities, thereby improving the effectiveness of substrate conversion to biogas. The findings of this study illustrated the crucial role of central function pathways in the effective functioning of these systems.

Phosphorus cycling in a subterranean estuary seepage face: A seasonal view on inventory composition and linkage with nitrate transformations

Seasonal field surveys (April 2018 to February 2019) were conducted in a subterranean estuary (STE) seepage face in Sanggou Bay (China) aiming to explore the transport and reactivity of phosphorus (P) and biogeochemical linkages with the cycling of nitrogen (N) prior to discharge. Porewater dissolved inorganic phosphorus (DIP) and dissolved organic phosphorus (DOP) together with different fractions of sedimentary P were analyzed in the upper, middle and lower intertidal covering the top 20 cm of sediment (1-4 cm, 5-8 cm, 9-12 cm, 13-16 cm and 17-20 cm depth). The accumulation of sedimentary organic P stimulated the growth of phosphate-solubilizing microorganisms and led to porewater DOP enrichment during spring. During summer, total P (TP), porewater DIP and DOP concentrations decreased, potentially due to enhanced mineralization driven by high ambient temperature. From autumn to winter, pelagic organic matter into the STE lowered, triggering a drop of TP standing stocks. Compared with the significant seasonality, sedimentary P storage was statistically identical along the intertidal. Such spatial homogeneity likely results from the rebalance driven by P adsorption dynamics and pelagic organic matter delivered by tide and wave setup. The vertical distribution of DIP, DOP, and sedimentary TP were linked to nitrate transformations. In the sediment layer with active mineralization and nitrification, concentrations of DOP, sedimentary redox and clay P increased. In the layer with active nitrate removal (2-5 cm depth), both DIP and DOP concentrations decreased. The sedimentary loosely-bound and organic P were also lower there. Notably, a substantial quantity of soluble P seeped out, acting as an important contributor to the dissolved P pool of the receiving waters. The spatial and temporal overlap of high concentrations of N and P in STEs adds variabilities and uncertainties in P out-drainage fluxes and nutrient stoichiometry balances, which should draw attention from coastal researchers and stakeholders.

Diverse electron carriers drive syntrophic interactions in an enriched anaerobic acetate-oxidizing consortium

In many anoxic environments, syntrophic acetate oxidation (SAO) is a key pathway mediating the conversion of acetate into methane through obligate cross-feeding interactions between SAO bacteria (SAOB) and methanogenic archaea. The SAO pathway is particularly important in engineered environments such as anaerobic digestion (AD) systems operating at thermophilic temperatures and/or with high ammonia. Despite the widespread importance of SAOB to the stability of the AD process, little is known about their in situ physiologies due to typically low biomass yields and resistance to isolation. Here, we performed a long-term (300-day) continuous enrichment of a thermophilic (55 °C) SAO community from a municipal AD system using acetate as the sole carbon source. Over 80% of the enriched bioreactor metagenome belonged to a three-member consortium, including an acetate-oxidizing bacterium affiliated with DTU068 encoding for carbon dioxide, hydrogen, and formate production, along with two methanogenic archaea affiliated with Methanothermobacter_A. Stable isotope probing was coupled with metaproteogenomics to quantify carbon flux into each community member during acetate conversion and inform metabolic reconstruction and genome-scale modeling. This effort revealed that the two Methanothermobacter_A species differed in their preferred electron donors, with one possessing the ability to grow on formate and the other only consuming hydrogen. A thermodynamic analysis suggested that the presence of the formate-consuming methanogen broadened the environmental conditions where ATP production from SAO was favorable. Collectively, these results highlight how flexibility in electron partitioning during SAO likely governs community structure and fitness through thermodynamic-driven mutualism, shedding valuable insights into the metabolic underpinnings of this key functional group within methanogenic ecosystems.

Syntrophic entanglements for propionate and acetate oxidation under thermophilic and high-ammonia conditions

Propionate is a key intermediate in anaerobic digestion processes and often accumulates in association with perturbations, such as elevated levels of ammonia. Under such conditions, syntrophic ammonia-tolerant microorganisms play a key role in propionate degradation. Despite their importance, little is known about these syntrophic microorganisms and their cross-species interactions. Here, we present metagenomes and metatranscriptomic data for novel thermophilic and ammonia-tolerant syntrophic bacteria and the partner methanogens enriched in propionate-fed reactors. A metagenome for a novel bacterium for which we propose the provisional name 'Candidatus Thermosyntrophopropionicum ammoniitolerans' was recovered, together with mapping of its highly expressed methylmalonyl-CoA pathway for syntrophic propionate degradation. Acetate was degraded by a novel thermophilic syntrophic acetate-oxidising candidate bacterium. Electron removal associated with syntrophic propionate and acetate oxidation was mediated by the hydrogen/formate-utilising methanogens Methanoculleus sp. and Methanothermobacter sp., with the latter observed to be critical for efficient propionate degradation. Similar dependence on Methanothermobacter was not seen for acetate degradation. Expression-based analyses indicated use of both H2 and formate for electron transfer, including cross-species reciprocation with sulphuric compounds and microbial nanotube-mediated interspecies interactions. Batch cultivation demonstrated degradation rates of up to 0.16 g propionate L-1 day-1 at hydrogen partial pressure 4-30 Pa and available energy was around -20 mol-1 propionate. These observations outline the multiple syntrophic interactions required for propionate oxidation and represent a first step in increasing knowledge of acid accumulation in high-ammonia biogas production systems.

Advancing Insights into Probiotics during Vegetable Fermentation

Fermented vegetables have a long history and are enjoyed worldwide for their unique flavors and health benefits. The process of fermentation improves the nutritional value, taste, and shelf life of foods. Microorganisms play a crucial role in this process through the production of metabolites. The flavors of fermented vegetables are closely related to the evaluation and succession of microbiota. Lactic acid bacteria (LABs) are typically the dominant bacteria in fermented vegetables, and they help inhibit the growth of spoilage bacteria and maintain a healthy gut microbiota in humans. However, homemade and small-scale artisanal products rely on spontaneous fermentation using bacteria naturally present on fresh vegetables or from aged brine, which may introduce external microorganisms and lead to spoilage and substandard products. Hence, understanding the role of LABs and other probiotics in maintaining the quality and safety of fermented vegetables is essential. Additionally, selecting probiotic fermentation microbiota and isolating beneficial probiotics from fermented vegetables can facilitate the use of safe and healthy starter cultures for large-scale industrial production. This review provides insights into the traditional fermentation process of making fermented vegetables, explains the mechanisms involved, and discusses the use of modern microbiome technologies to regulate fermentation microorganisms and create probiotic fermentation microbiota for the production of highly effective, wholesome, safe, and healthy fermented vegetable foods.

Insights into methanogenesis of mesophilic-psychrophilic varied anaerobic digestion of municipal sludge with antibiotic stress

Methane production through anaerobic digestion (AD) of municipal sludge is economic and eco-friendly, which is commonly affected by temperature and pollutants residues. However, little is known about methanogenesis in psychrophilic AD (PAD) with temperature variations that simulating seasonal variations and with antibiotic stress. Here, two groups of AD systems with oxytetracycline (OTC) were operated with temperature maintained at 35 °C and 15 °C or variation to explore the influence to methanogenesis. The acetic acid was noticeably accumulated in OTC groups initially (P < 0.001). Methane production was noticeably inhibited initially in PAD with OTC, but had been stimulated later at 35 °C. The dominant acetoclastic methanogens Methanosaeta gradually decreased to 15.48% and was replaced by methylotrophic Methanomethylovorans (73.43%) in PAD with OTC. Correspondingly, the abundances of functional genes related to methylotrophic methanogenesis were also higher in these groups. Besides, genes involving in methane oxidation had over 50 times higher abundances in PAD with OTC groups in the second phase. Further investigation is essential to understand the main dynamics of methanogenesis in PAD and to clear the related molecular mechanism for future methane production regulation in sludge systems.

An enriched ammonia-oxidizing microbiota enables high removal efficiency of ammonia in antibiotic production wastewater

High ammonia concentration hinders the efficient treatment of antibiotic production wastewater (APW). Developing effective ammonia oxidation wastewater treatment strategies is an ideal approach for facilitating APW treatment. Compared with traditional nitrification strategies, the partial nitrification process is more eco-friendly, less energy-intensive, and less excess sludge. The primary limiting factor of the partial nitrification process is increasing ammonia-oxidizing bacteria (AOB) while decreasing nitrite-oxidizing bacteria (NOB). In this study, an efficient AOB microbiota (named AF2) was obtained via enrichment of an aerobic activated sludge (AS0) collected from a pharmaceutical wastewater treatment plant. After a 52-day enrichment of AS0 in 250 mL flasks, the microbiota AE1 with 69.18% Nitrosomonas microorganisms was obtained. Subsequent scaled-up cultivation in a 10 L fermenter led to the AF2 microbiota with 59.22% Nitrosomonas. Low concentration of free ammonia (FA, < 42.01 mg L^-1) had a negligible effect on the activity of AF2, and the nitrite-nitrogen accumulation rate (NAR) of AF2 was 98% when FA concentration was 42.01 mg L^-1. The specific ammonia oxidation rates (SAORs) at 30 °C and 15 °C were 3.64 kg NH₄⁺-N·kg MLVSS^-1·d^-1 and 1.43 kg NH₄⁺-N·kg MLVSS^-1·d^-1 (MLVSS: mixed liquor volatile suspended solids). The SAOR was 0.52 kg NH₄⁺-N·kg MLVSS^-1·d^-1 when the NaCl concentration was increased from 0 to 20 g L^-1, showing that AF2 functioning was stable in a high-level salt environment. The ammonia oxidation performance of AF2 was verified by treating abamectin and lincomycin production wastewater. The NARs of AF2 used for abamectin and lincomycin production wastewater treatment were >90% and the SAORs were 2.39 kg NH₄⁺-N·kg MLVSS^-1·d^-1 and 0.54 kg NH₄⁺-N·kg MLVSS^-1·d^-1, respectively, which was higher than the traditional biological denitrification process. In summary, AF2 was effective for APW treatment via enhanced ammonia removal efficiency, demonstrating great potential for future industrial wastewater treatment.

Effect of the degradation performance on carbon tetrachloride by anaerobic co-metabolism under different external energy sources

In this research, a comprehensive study was carried out on the removal of carbon tetrachloride (CT) in the anaerobic co-metabolism (ACM) reactor. The experiments showed that when the hydraulic retention time (HRT) was 36 h, pH was 7, and influent CT was 2.5mg/L, the average removal efficiency reached 82.45 ± 2.56% in the glucose co-metabolism substrate reactor, exhibiting a dramatic excellent difference in reaction performance from the other two reactors (p < 0.05) and a favorable tolerance on the CT shock loading. The content of extracellular polymeric substances (EPS) and volatile fatty acids (VFA) demonstrated that glucose could supply more energy to protect the microorganisms, which was the appropriate external energy source. Moreover, microbial community structure and biostatistics analysis demonstrated that Pseudomonas was the most important dechlorination bacteria in ACM reactors, which might via dehalogenation process mediate the transformation of CT. The succession of methanogenic bacteria further demonstrated that CT degradation using co-digestion require to destroy hydrogenotrophic methane generation pathway and the external energy substances could make up the lack of hydrogen in the treatment of CT. The change of intermediate products hinted that anaerobic dechlorination process of CT in an ACM reactor was a sequential dechlorination process, and major transformation products measured were CF. Overall, this study has improved our understanding of the roles of CT degradation process in ACM reactors.

Advances in Studies on Microbiota Involved in Nitrogen Removal Processes and Their Applications in Wastewater Treatment

The discharge of excess nitrogenous pollutants in rivers or other water bodies often leads to serious ecological problems and results in the collapse of aquatic ecosystems. Nitrogenous pollutants are often derived from the inefficient treatment of industrial wastewater. The biological treatment of industrial wastewater for the removal of nitrogen pollution is a green and efficient strategy. In the initial stage of the nitrogen removal process, the nitrogenous pollutants are converted to ammonia. Traditionally, nitrification and denitrification processes have been used for nitrogen removal in industrial wastewater; while currently, more efficient processes, such as simultaneous nitrification-denitrification, partial nitrification-anammox, and partial denitrification-anammox processes, are used. The microorganisms participating in nitrogen pollutant removal processes are diverse, but information about them is limited. In this review, we summarize the microbiota participating in nitrogen removal processes, their pathways, and associated functional genes. We have also discussed the design of efficient industrial wastewater treatment processes for the removal of nitrogenous pollutants and the application of microbiome engineering technology and synthetic biology strategies in the modulation of the nitrogen removal process. This review thus provides insights that would help in improving the efficiency of nitrogen pollutant removal from industrial wastewater.

Insight into the Interaction Between Microplastics and Microorganisms Based on a Bibliometric and Visualized Analysis

Microplastics are abundant in the environment and have been proven to affect ecosystems and human health. Microorganisms play essential roles in the ecological fate of microplastics pollution, potentially yielding positive and negative effects. This study reviews the research progress of interaction between microplastics and microorganisms based on a bibliometric and visualized analysis. Publication numbers, subjects, countries, institutions, highly cited papers, and keywords were investigated by statistical analysis. VOSviewer software was applied to visualize the co-occurrence and aggregation of national collaboration, subjects, and keywords. Results revealed trends of rapidly increasing publication output that involved multiple disciplines. Contributing countries and their institutions were also identified in this study. Keywords, co-occurrence network visualization, highly cited papers analysis, and knowledge-based mining were all used to give insight into microorganisms or microbiota related to microplastics pollution, and the potential impacts that microplastics biodegradation may cause. In the future, research efforts need to focus on the following areas: microbial degradation processes and mechanisms, assessment of ecological microplastics risks, and potential effects of microplastics bioaccumulation and human exposure. This study provides a holistic view of ongoing microplastics and related microbial research, which may be useful for future microplastics biodegradation studies.

Syntrophic metabolism facilitates Methanosarcina-led methanation in the anaerobic digestion of lipidic slaughterhouse waste

Different inoculum to slaughterhouse waste (SHW) ratios (Ino/SHW) influences the digester performance, substrate utilization, and methane yield through microbial shift and their metabolic syntrophy. Acetoclastic Methanosarcina (68-87%) was dominant in the exponential phase, overpowering the initial abundance of Methanosaeta (86% of methanogens) in the SHW digesters. Positive interactions among acetogenic and acetate-oxidizing species of Clostridium (11%) with Methanosarcina (84% of methanogens) improved the methanogenic activity (292 mL g^-1 VS_initial d^-1) and final VS utilization (90%) at the highest Ino/SHW loading. In contrast, significant improvement of methane yield (152% higher than the control) at the lowest Ino/SHW loading was attributed to strong syntrophy among Methanosaeta (24% of methanogens) and its exoelectrogenic partners, Bythopirellula (0.52%) and Mariniphaga (0.08%) and the acetogenic Cloacimonas (0.16%) and Longilinea (0.32%). These syntrophic interactions among the core microbiota induced major metabolic activities, including butanoate, glycine, serine and threonine, methane, propanoate, and pyruvate metabolism, and quorum sensing.

Draft Genome Sequence of an Epiphytic Strain, Bacillus sp. Strain WL1, Isolated from the Surface of Nostoc flagelliforme Colonies in Yinchuan, Ningxia, China

Bacillus species are Gram-positive, aerobic, spore-forming bacteria that are widely spread in soil, dust, and water. One strain, Bacillus sp. strain WL1, was isolated from the surface of the cyanobacterium Nostoc flagelliforme in Yinchuan, Ningxia, China. The draft genome sequence of this strain was 5.62 Mbp.

Exploring Gut Microbiota in Patients with Colorectal Disease Based on 16S rRNA Gene Amplicon and Shallow Metagenomic Sequencing

The gastrointestinal tract, the largest human microbial reservoir, is highly dynamic. The gut microbes play essential roles in causing colorectal diseases. In the present study, we explored potential keystone taxa during the development of colorectal diseases in central China. Fecal samples of some patients were collected and were allocated to the adenoma (Group A), colorectal cancer (Group C), and hemorrhoid (Group H) groups. The 16S rRNA amplicon and shallow metagenomic sequencing (SMS) strategies were used to recover the gut microbiota. Microbial diversities obtained from 16S rRNA amplicon and SMS data were similar. Group C had the highest diversity, although no significant difference in diversity was observed among the groups. The most dominant phyla in the gut microbiota of patients with colorectal diseases were Bacteroidetes, Firmicutes, and Proteobacteria, accounting for >95% of microbes in the samples. The most abundant genera in the samples were Bacteroides, Prevotella, and Escherichia/Shigella, and further species-level and network analyses identified certain potential keystone taxa in each group. Some of the dominant species, such as Prevotella copri, Bacteroides dorei, and Bacteroides vulgatus, could be responsible for causing colorectal diseases. The SMS data recovered diverse antibiotic resistance genes of tetracycline, macrolide, and beta-lactam, which could be a result of antibiotic overuse. This study explored the gut microbiota of patients with three different types of colorectal diseases, and the microbial diversity results obtained from 16S rRNA amplicon sequencing and SMS data were found to be similar. However, the findings of this study are based on a limited sample size, which warrants further large-scale studies. The recovery of gut microbiota profiles in patients with colorectal diseases could be beneficial for future diagnosis and treatment with modulation of the gut microbiota. Moreover, SMS data can provide accurate species- and gene-level information, and it is economical. It can therefore be widely applied in future clinical metagenomic studies.

Novel strains with superior degrading efficiency for lincomycin manufacturing biowaste

As the antibiotic pollution source in the environment, a large amount of biowastes generated from antibiotic fermentation manufacture needs proper disposal. Recycling the biowaste as resources and nutrients is of great interest. Besides, degradation or removal of antibiotics is indispensable for the reclamation of antibiotic manufacturing biowaste. To establish environmentally friendly disposal strategies for lincomycin manufacturing biowaste (LMB), we screened the microbial strains that could efficiently degrade lincomycin from the antibiotic wastewater treatment plant. Among them, three novel strains were identified as Bacillus subtilis (strain LMB-A), Rhodotorula mucilaginosa (strain LMB-D) and Penicillium oxalicum (strain LMB-E), respectively. LMB-A and LMB-D could degrade 92.69% and 74.05% of lincomycin with an initial concentration of 1117.55 mg/L in 144 h, respectively. The lincomycin degradation products were formed by the breakage of amide bond or losing N-demethyl/thiomethyl group from the pyrrolidine/pyranose ringcata cata catalyzed by the strains. Moreover, LMB-A could decontaminate LMB, and the decontaminated LMB could be used as a nitrogen source to culture salt-resistant bacteria and other useful microorganisms. LMB-A and LMB-D have the potential to be used for the bioremediation of water and soil polluted by lincomycin and its analogs. LMB-E could degrade 88.20% LMB after 144-h cultivation. In summary, this study gives an insight into the green disposal of LMB, and the established strategy has potential application for biotreatment of other antibiotic fermentation manufacturing biowastes.

Discriminating Microbial Community Structure Between Peri-Implantitis and Periodontitis With Integrated Metagenomic, Metatranscriptomic, and Network Analysis

Peri-implantitis and periodontitis are both polymicrobial diseases induced by subgingival plaque accumulation, with some differing clinical features. Studies on the microbial and gene transcription activity of peri-implantitis microbiota are limited. This study aimed to verify the hypothesis that disease-specific microbial and gene transcription activity lead to disease-specific clinical features, using an integrated metagenomic, metatranscriptomic, and network analysis. Metagenomic data in peri-implantitis and periodontitis were obtained from the same 21 subjects and metatranscriptomic data from 12 subjects were obtained from a database. The microbial co-occurrence network based on metagenomic analysis had more diverse species taxa and correlations than the network based on the metatranscriptomic analysis. Solobacterium moorei and Prevotella denticola had high activity and were core species taxa specific to peri-implantitis in the co-occurrence network. Moreover, the activity of plasmin receptor/glyceraldehyde-3-phosphate dehydrogenase genes was higher in peri-implantitis. These activity differences may increase complexity in the peri-implantitis microbiome and distinguish clinical symptoms of the two diseases. These findings should help in exploring a novel biomarker that assist in the diagnosis and preventive treatment design of peri-implantitis.