Changes in Soil Microbial Communities Induced by Biodegradable and Polyethylene Mulch Residues Under Three Different Temperatures

Mulching is a common method increasing crop yield and achieving out-of-season production; nevertheless, their removal poses a significant environmental danger. In this scenario, the use of biodegradable plastic mulches comes up as a solution to increase the sustainability of this practice, as they can be tilled in soil without risk for the environment. In this context, it is important to study the microbial response to this practice, considering their direct involvement in plastic biodegradation. This study evaluated the biodegradation of three commercial mulch residues: one conventional non-biodegradable mulch versus two biodegradable ones (white and black compostable Mater-Bi mulches). The experiment was conducted under three incubation temperatures (room temperature 20-25 °C, 30 °C, and 45 °C) for a 6-month trial using fallow agricultural soil. Soil without plastic mulch residues was used as a control. White mater-bi biodegradable mulch residues showed higher degradation rates up to 88.90% at 30 °C, and up to 69.15% at room temperature. Furthermore, incubation at 45 °C determines the absence of degradation for all types of mulch considered. Moreover, bacterial alpha diversity was primarily influenced by plastic type and temperature, while fungal populations were mainly affected by temperature. Beta diversity was impacted by all experimental variables. Predicted functional genes crucial for degrading complex substrates, including those encoding hydrolases, cutinases, cellobiosidases, and lipases, were derived from 16S rRNA gene sequencing data. Cluster analysis based on predicted enzyme-encoding gene abundance revealed two clusters, mainly linked to sampling time. Finally, core microbiome analysis identified dominant bacterial and fungal taxa in various soil-plastic ecosystems during degradation, pinpointing species potentially involved in plastic breakdown. The present study allows an assessment of how different temperatures affect the degradation of mulch residues in soil, providing important insights for different climatic growing zones. It also fills a gap in the literature by directly comparing the effects of biodegradable and polyethylene mulches on soil microbial communities.

Multi-factor analysis of the quality of cellar mud of Luzhou-flavor liquor in Yibin production area

The aim of this study was to conduct a thorough scientific investigation into the similarities and differences in the quality of the cellars of different Luzhou-flavor liquor wineries in Yibin production area and the reasons for them. This study analyzed cellar mud samples from five wineries in Yibin production area. The analysis of volatile flavor compounds was carried out using headspace solid-phase microextraction and gas chromatography-mass spectrometry. The bacterial and archaeal community structures and their correlations were analyzed by high-throughput sequencing. The study indicates that the Distillery A had the highest levels of ammonium nitrogen and effective phosphorus, Distillery F had the highest humus levels, and Distillery I had the highest pH levels. The community structure of the principal bacterial and archaeal communities in the five subterranean clays exhibited similarity, and all samples were dominated by Firmicutes as the primary bacterial group. However, there was variation in bacterial abundance. The cellar mud also has obvious regional differences, and there are three genera of differentially dominant archaea in the archaea. In summary, significant differences were observed in the physicochemical indexes of bacterial and archaeal abundance across all five samples. These differences led to variations in both the content and composition of volatile constituents.

Soil amendments alter cadmium distribution and bacterial community structure in paddy soils

Soil amendments play a pivotal role in ensuring the safety of food production by inhibiting the transfer of heavy metal ions from soils to crops. Nevertheless, their impact on soil characteristics and the microbial community and their role in reducing cadmium (Cd) accumulation in rice remain unclear. In this study, pot experiments were conducted to investigate the effects of three soil amendments (mineral, organic, and microbial) on the distribution of Cd speciation, organic components, iron oxides, and microbial community structure. The application of soil amendments resulted in significant reductions in the soil available Cd content (16 %-51 %) and brown rice Cd content (16 %-78 %), facilitating the transformation of Cd from unstable forms (decreasing 10 %-20 %) to stable forms (increasing 77 %-150 %) in the soil. The mineral and organic amendments increased the soil cation exchange capacity (CEC) and plant-derived organic carbon (OC), respectively, leading to reduced Cd accumulation in brown rice, while the microbial amendment enhanced OC complexity and the abundances of Firmicutes and Bacteroidota, contributing to the decreased rice Cd uptake. The synchrotron radiation-based Fourier transform infrared (SR-FTIR) spectroscopy indicated that soil amendments regulated soil Cd species by promoting iron oxides and OC coupling. Moreover, both organic and microbial amendments significantly reduced the diversity and richness of the bacterial communities and altered their compositions and structures, by increasing the relative abundances of Bacteroidota and Firmicutes and decreasing those of Acidobacteria, Actinobacteria, and Myxococcota. Soil microbiome analysis revealed that the increase of Firmicutes and Bacteroidota associated with Cd adsorption and sequestration contributed to the suppression of soil Cd reactivity. These findings offer valuable insights into the potential mechanisms by which soil amendments regulate the speciation and bioavailability of Cd, and improve the bacterial communities, thereby providing guidance for agricultural management practices.

Pig manure-derived fulvic acid more strongly drives the fate of arsenic and antibiotic resistance genes in paddy soil

Antibiotic resistance genes (ARGs) can threaten the clean production of rice owing to continuous selective pressure in heavy metal-antibiotic co-contaminated paddy soils. As an important soil carbon reservoir, the role of humic substances from different types of manure in the regulation of soil ARGs remains unclear. In this study, fulvic acid (FA) and humic acid (HA) were extracted from pig manure (PM), cow dung (CD), and chicken manure (CM). The influence of their characteristics and doses on the fate of ARGs was investigated in arsenic (As)-antibiotic co-contaminated paddy soils. The release of As and degradation of antibiotics were promoted in 1% PM-FA treatment, with increases of 4.8%-5.6% and 8.3%-8.8% compared with CM-FA and CD-FA treatments, respectively. The coexistence of FA/HA, Fe, As, and antibiotics in soil pore water affected the environmental behavior of ARGs, with FA showing a more positive effect. Species including Bacillus, Geobacter, Desulfitobacterium, and Christensenellaceae_R-7_group were considered potential hosts of ARGs, and their resistance to co-contamination increased after the addition of FA. Membrane transport is a potential strategy for host bacteria of ARGs to cope with As-antibiotic complex pressure. These results demonstrate the coupling mechanisms of As, antibiotics, and ARGs regulated by different humic substances in co-contaminated paddy soils, which could support the clean production of rice in agricultural practice.

Mechanistic insights into Fe3O4-modified biochar relieving inhibition from erythromycin on anaerobic digestion

Anaerobic digestion (AD) of antibiotic manufacturing wastewater to degrade residual antibiotics and produce mixture of combustible gases has been investigated actively in the past decades. However, detrimental effect of residual antibiotic to microbial activities is commonly faced in AD process, leading to the reduction of treatment efficiency and energy recovery. Herein, the present study systematically evaluated the detoxification effect and mechanism of Fe3O4-modified biochar in AD of erythromycin manufacturing wastewater. Results showed that Fe3O4-modified biochar had stimulatory effect on AD at 0.5 g/L erythromycin existence. A maximum methane yield of 327.7 ± 8.0 mL/g COD was achieved at 3.0 g/L Fe3O4-modified biochar, leading to the increase of 55.7% compared to control group. Mechanistic investigation demonstrated that different levels of Fe3O4-modified biochar could improve methane yield via different metabolic pathways involved in specific bacteria and archaea. Low levels of Fe3O4-modified biochar (i.e., 0.5-1.0 g/L) led to the enrichment of Methanothermobacter sp., strengthening the hydrogenotrophic pathway. On the contrary, high levels of Fe3O4-modified biochar (2.0-3.0 g/L) favored the proliferation of acetogens (e.g., Lentimicrobium sp.) and methanogen (Methanosarcina sp.) and their syntrophic relations played vital role on the simulated AD performance at erythromycin stress. Additionally, the addition of Fe3O4-modified biochar significantly decreased the abundance of representative antibiotic resistant genes (ARGs), benefiting the reduction of environmental risk. The results of this study verified that the application of Fe3O4-modified biochar could be an efficient approach to detoxify erythromycin on AD system, which brings high impacts and positive implications for biological antibiotic wastewater treatment.

Investigation on the microbial community of an accelerating stabilization landfill by aeration engineering

The microbial community of the landfill undergoing aerobic stabilization process by aeration engineering was investigated. The municipal solid wastes (MSWs) were sampled from two aeration well sites with different landfill temperatures (65.5°C and 41.7°C) under higher and lower stabilization level. The physical component, chemical property, and microbial population of MSWs were analyzed and compared. The result showed that the phylum Firmicutes was dominant in the aerobic landfill; and the genus Weissella and Syntrophaceticus were more abundant in high, and low temperature site, respectively. The bacterial distribution showed difference on two temperature sites and four landfill depths, mainly affected by the ammonia-nitrogen and moisture content of MSWs. The ecological profiles of the microorganisms responded the aeration engineering were predicted. The anaerobic hydrolytic and acetogenic microorganisms were decreased in abundance, while the facultative Lactobacillus increased when the landfill under a higher stabilization level. The function abundances of methane oxidation, sulfide oxidation, and aerobic chemoheterotrophy were enriched by aeration engineering, which was the microbial mechanism for accelerating the stabilization process of landfill.

Magnetic biochar promotes the risk of mobile genetic elements propagation in sludge anaerobic digestion

Mobile genetic elements (MGEs) mediated horizontal gene transfer is the primary reason for the propagation of antibiotic resistance genes in environment. The behavior of MGEs under magnetic biochar pressure in sludge anaerobic digestion (AD) is still unknown. This study evaluated the effects of different dosage magnetic biochar on the MGEs in AD reactors. The results showed that the biogas yield was highest (106.68 ± 1.16 mL g^-1 VS_added) with adding optimal dosage of magnetic biochar (25 mg g^-1 TS_added), due to it increased the microorganism's abundance involved in hydrolysis and methanogenesis. While, the total absolute abundance of MGEs in the reactors with magnetic biochar addition increased by 11.58%-77.37% compared with the blank reactor. When the dosage of magnetic biochar was 12.5 mg g^-1 TS_added, the relative abundance of most MGEs was the highest. The enrichment effect on ISCR1 was the most significant, and the enrichment rate reached 158.90-214.16%. Only the intI1 abundance was reduced and the removal rates yield 14.38-40.00%, which was inversely proportional to the dosage of magnetic biochar. Co-occurrence network explored that Proteobacteria (35.64%), Firmicutes (19.80%) and Actinobacteriota (15.84%) were the main potential host of MGEs. Magnetic biochar changed MGEs abundance by affecting the potential MGEs-host community structure and abundance. Redundancy analysis and variation partitioning analysis showed that the combined effect of polysaccharides, protein and sCOD exhibited the greatest contribution (accounted for 34.08%) on MGEs variation. These findings demonstrated that magnetic biochar increases the risk of MGEs proliferation in AD system.

Synergetic effects of anaerobic co-digestion of food waste and algae on biogas production

Anaerobic co-digestion of food waste and algae was assessed to offset the drawbacks of anaerobic mono-digestion of each substrate. Batch test results indicated that a food waste and algae mixture ratio of 8:2 facilitated the highest CH₄ yield (334 mL CH₄/g COD_Input). This ratio was applied to the anaerobic co-digestion reactor, resulting in a CH₄ yield that was twice that of the anaerobic mono-digestion reactors, thereby facilitating high operational stability. In contrast to the anaerobic mono-digestion, anaerobic co-digestion resulted in stable CH₄ production by overcoming volatile fatty acid accumulation and a decreased pH, even under a high organic loading rate (3 kg COD/m³∙d). Furthermore, a comparative metagenomic analysis revealed that the abundance of volatile fatty acid-oxidizing bacteria and hydrogenotrophic and methylotrophic methanogens was significantly increased in the anaerobic co-digestion reactor. These findings indicate that the anaerobic co-digestion of food waste and algae significantly improves CH₄ production and process stability.

Understanding the mechanism of enhanced anaerobic biodegradation of biodegradable plastics after alkaline pretreatment

Biodegradable plastics (BPs) tend to replace conventional plastics, which increases the amount of BP waste entering the environment. The anaerobic environment exists extensively in nature, and anaerobic digestion has become a widely used technique for organic waste treatment. Many kinds of BPs have low biodegradability (B_D) and biodegradation rates under anaerobic condition due to the limitation of hydrolysis, so they still have harmful environmental consequences in anaerobic environment. There is an urgent need to find an intervention method to improve the biodegradation of BPs. Therefore, this study aimed to investigate the effectiveness of alkaline pretreatment in accelerating the thermophilic anaerobic degradation of ten widely used BPs, such as poly (lactic acid) (PLA), poly (butylene adipate-co-terephthalate) (PBAT), thermoplastic starch (TPS), poly (butylene succinate-co-butylene adipate) (PBSA), cellulose diacetate (CDA), etc. The results showed that NaOH pretreatment significantly improved the solubility of PBSA, PLA, poly (propylene carbonate) (PPC), and TPS. Except for PBAT, pretreatment with an appropriate NaOH concentration could improve the B_D and degradation rate. The pretreatment also reduced the lag phase in the anaerobic degradation of BPs such as PLA, PPC, and TPS. Specifically, for CDA and PBSA, the B_D increased from 4.6 % and 30.5 % to 85.2 % and 88.7 %, with increments of 1752.2 % and 190.8 %, respectively. Microbial analysis indicated that NaOH pretreatment promoted the dissolution and hydrolysis of PBSA and PLA and the deacetylation of CDA, which contributed to rapid and complete degradation. This work not only provides a promising method for improving the degradation of BP waste but also lays the foundation for its large-scale application and safe disposal.

Absence of oxygen effect on microbial structure and methane production during drying and rewetting events

Natural environments with frequent drainage experience drying and rewetting events that impose fluctuations in water availability and oxygen exposure. These relatively dramatic cycles profoundly impact microbial activity in the environment and subsequent emissions of methane and carbon dioxide. In this study, we mimicked drying and rewetting events by submitting methanogenic communities from strictly anaerobic environments (anaerobic digestors) with different phylogenetic structures to consecutive desiccation events under aerobic (air) and anaerobic (nitrogen) conditions followed by rewetting. We showed that methane production quickly recovered after each rewetting, and surprisingly, no significant difference was observed between the effects of the aerobic or anaerobic desiccation events. There was a slight change in the microbial community structure and a decrease in methane production rates after consecutive drying and rewetting, which can be attributed to a depletion of the pool of available organic matter or the inhibition of the methanogenic communities. These observations indicate that in comparison to the drying and rewetting events or oxygen exposure, the initial phylogenetic structure and the organic matter quantity and quality exhibited a stronger influence on the methanogenic communities and overall microbial community responses. These results change the current paradigm of the sensitivity of strict anaerobic microorganisms to oxygen exposure.

Multivariate insights into enhanced biogas production in thermophilic dry anaerobic co-digestion of food waste with kitchen waste or garden waste: Process properties, microbial communities and metagenomic analyses

Multisubstrate synergetic anaerobic co-digestion can effectively overcome low efficiency of food waste (FW) mono-digestion. This study investigated the effect of supplementing FW with kitchen waste (KW) or garden waste (GW) on thermophilic dry anaerobic co-digestion. FW-KW and FW-GW co-digestion enhanced biogas production by 24.69 % and 44.96 % at organic loading rate (OLR) of 3 g VS L^-1 d^-1, and increased OLR tolerance from 3 to 4 g VS L^-1 d^-1 through mitigating ammonia nitrogen inhibition and volatile fatty acids accumulation. Co-digestion enriched the dominant hydrolytic bacteria Defluviitoga, resulting in an acceleration of substrate hydrolysis. FW-KW co-digestion improved biogas production by increasing gene abundance related to key enzymes in methanogenesis pathways and promoting the conversion of intermediate products into methane. FW-GW co-digestion enhanced biogas production by enriching ABC transporters-associated genes, leading to efficient substrate utilization. This study provides a promising approach for FW treatment with multivariate insights into thermophilic dry anaerobic co-digestion.

Effects of various materials used to promote the direct interspecies electron transfer on anaerobic digestion of low-concentration swine manure

The activation of direct interspecies electron transfer (DIET) by the supplementation of conductive materials is one of the effective and available methods to enhance anaerobic digestion (AD). Microorganisms that colonize the surface of these materials form biofilms, the study of which could provide new insights into the character of the DIET process and its effect on AD. The present study focused on AD performance, microbial community, as well as morphological and topological features of biofilms on various materials used to promote DIET during AD of low-concentration swine manure. The best AD characteristics were observed in stainless steel mesh (SM)/digested cow manure (CM) and polyester felt (PF)/digested sewage sludge (SS) combinations used as material/inoculum, respectively. Thus, potential methane yields in CM-SM and SS-PF were up to 26.4% and 26.2% higher compared to the corresponding controls. Microbial analysis of biofilms revealed the dominance of putatively syntrophic bacteria of the MBA03 group of the Limnochordia class in CM inoculated reactors, and syntrophic proteolytic bacteria of the genus Coprothermobacter and acetogenic Clostridium sensu stricto 1, known for their ability to carry out DIET, in SS inoculated reactors. Biofilms on non-conductive materials contained pili-like structures, which were observed only in SS inoculated reactors. Polyester felt tended to biofoul better than carbon felt, resulting in up to 2.8, 3.2 and 1.8 higher nucleic acid, extracellular polymeric substances, and total biomass content, respectively, depending on the inoculum. These results provide new insights into the different types of DIET that can occur in low-loaded AD systems with attached growth.

Insights into Pyrroloquinoline Quinone (PQQ) Effects on Soil Nutrients and Pathogens from Pepper Monocropping Soil under Anaerobic and Aerobic Conditions

Imbalances of soil available nutrients and soilborne diseases have seriously restricted the productivity of crops and jeopardized food security worldwide. Pyrroloquinoline quinone (PQQ), a redox cofactor in some bacteria involved in glucose metabolism and phosphorus mineralization, could be anticipated to alter soil ecosystems to a certain extent. However, there is limited information on PQQ defending soilborne pathogens and regulating soil main nutrients. Here, a pot experiment based on mono-cropping soils of pepper was conducted to examine the effects of PQQ amendment on reconstructing soil microbial communities and soil nutrients under aerobic/anaerobic conditions comprising three treatments, namely, control, PQQ (aerobic), and FL-PQQ (anaerobic). The results revealed that soil microbial community composition and soil nutrients were distinctly altered by PQQ regimes. Compared to control, PQQ treatment significantly increased the content of soil available phosphorus (AP), while FL_PQQ treatment strongly improved the content of soil available nitrogen (AN). In terms of pathogens, relative to control, both PQQ treatments suppressed the abundances of pathogens, of which FL_PQQ treatment significantly decreased the abundance of the pathotrophic fungal by 64% and the abundance of Fusarium oxysporum by 57%, largely attributed to the increase of organic acid generators (Oxobacter, Hydrogenispora) and potential antagonists (Bacillus, Talaromyces). Structural equation modeling (SEM) showed that PQQ regimes suppressed pathogens by indirectly regulating soil physicochemical properties and microbial communities. Overall, we proposed that PQQ application both in aerobic/anaerobic conditions could improve soil available nutrients and suppress soil pathogens in pepper monocropping soils.

IMPORTANCE The attention to PQQ (pyrroloquinoline quinone) effect on soil nutrients and pathogens was less paid in monocropping soils. However, the underlying microbial interacting mechanism remains unclear. Adopting a novel external bio-additive, the effects of PQQ on soil main nutrients and the pathotrophic fungal under aerobic and anaerobic regimes will be investigated, which would help to improve soil quality health. Our main conclusion was that PQQ would help to remediate monocropping obstacle soils in terms of soil nutrients and soil pathogens by associating with the microbial community, and anaerobic PQQ application more favored amelioration of continuous obstacle soils. These results will benefit the health and sustainable development of pepper production as well as other greenhouse vegetable production.

Light alters microbiota and electron transport: Evidence for enhanced mesophilic digestion of municipal sludge

Light as an environmental factor can affect the process of anaerobic digestion, but there is no systematic study in municipal wastewater sludge mesophilic digestion. In this study, the effects of light on the performance of the anaerobic digestion system and photo-anaerobic microbiota (PAM) were evaluated in lighted anaerobic batch digesters (LABRs). The methane yield from the reactor under the dark condition (LABR0) was 179.2 mL CH₄/g COD, which was lower than 305.4 mL CH₄/g COD and 223.0 mL CH₄/g COD (n = 3, p < 0.05) from reactors under the light intensity of 3600 lm (LABR1) and 7200 lm (LABR2), respectively. The dominant genera in the bacterial and archaeal communities were Bacillus and Methanosarcina under light conditions, Enterococcus and Methanobacterium under dark conditions. And these two bacteria acted as electroactive bacterial genera, indicating that light changes the combination of direct interspecies electron transfer (DIET) microbial partners and activates the DIET pathway for methane production. The electron conduction pathways analysis further suggests that biological DIET (bDIET) between microbial biomass, rather than DIET via conductive material (cDIET) between microbes and conductive materials, is promoted and behaves as the dominant factor enhancing methane production under light conditions. The morphology of microorganisms and the amount and properties of EPS corroborate these views. Our findings are guided to anaerobic digester constructions under the outdoor environment with light exposure.

Exploring the microbial mechanism of reducing methanogenesis during dairy manure membrane-covered aerobic composting at industrial scale

In this study, the microbial mechanism of reducing methanogenesis during membrane-covered aerobic composting from solid dairy manure was investigated. An industrial-scale experiment was carried out to compare a static composting group (SC) and a forced aeration composting group (AC) with a semipermeable membrane-covered composting group (MC + AC). The results showed that the semipermeable membrane-covered could improve the oxygen utilization rate and inhibit the anaerobic bacterial genus Hydrogenispora and archaea order Methanobacteriales. During the membrane-covered period, the acetoclastic methanogenesis module in MC + AC, AC and SC decreased by 0.58%, 0.05% and 0.04%, respectively, and the cdhC gene in the acetoclastic pathway was found to be decreased by 65.51% only in MC + AC. Changes in methane metabolism pathways resulted in a 27.48% lower average methane concentration in MC + AC than in SC. Therefore, the semipermeable membrane-covered strategy can effectively reduce methane production during dairy manure aerobic composting by restricting the methanogenesis of the acetoclastic pathway.

Reductive Soil Disinfestation Enhances Microbial Network Complexity and Function in Intensively Cropped Greenhouse Soil

Reductive soil disinfestation (RSD) is an effective practice to eliminate plant pathogens and improve the soil microbial community. However, little is known about how RSD treatment affects microbial interactions and functions. Previous study has shown that RSD-regulated microbiomes may degenerate after re-planting with former crops, while the effect of planting with different crops is still unclear. Here, the effects of both RSD treatment and succession planting with different crops on microbial community composition, interactions, and functions were investigated. Results showed that RSD treatment improves the soil microbial community, decreases the relative abundance of plant pathogens, and effectively enhances microbial interactions and functions. The microbial network associated with RSD treatment was more complex and connected. The functions of hydrocarbon (C, H), nitrogen (N), and sulfur (S) cycling were significantly increased in RSD-treated soil, while the functions of bacterial and fungal plant pathogens were decreased. Furthermore, the bacterial and fungal communities present in the RSD-treated soil, and soil succession planted with different crops, were found to be significantly different compared to untreated soil. In summary, we report that RSD treatment can improve soil quality by regulating the interactions of microbial communities and multifunctionality.

Microbial succession analysis reveals the significance of restoring functional microorganisms during rescue of failed anaerobic digesters by bioaugmentation of nano-biochar-amended digestate

Nano-biochar application was investigated for anaerobic digestion of orange peel waste. The application for methane production focused on the optimization of biochar feedstock, rescue of failed digesters, and microbial succession analysis. It showed that sewage sludge (SS) derived biochar had the highest performance enhancement among the different feedstocks, which could be ascribed to the improvement of electron transfer, interspecies hydrogen transfer, and supply of trace elements. Subsequently, nano SS biochar-amended digestate was evaluated for rescuing failed digesters, and the experimental results indicated its positive roles through gradual bioaugmentation operation. The dynamic analysis of microbial succession indicated the successful application was through the mechanism of restoring partially the functional microbial communities. The major reconstruction of functional microorganisms included bacteria phyla Hydrogenispora (24.5%) and Defluviitoga (18.8%) as well as methanogenic genera of Methanosarcina (41.5%) and Methanobacterium (27.3%). These findings would contribute to rescuing failed anaerobic digesters by bioaugmentation with biochar-amended digestate.

Biogas Production and Microbial Communities of Mesophilic and Thermophilic Anaerobic Co-Digestion of Animal Manures and Food Wastes in Costa Rica

Biomass generated from agricultural operations in Costa Rica represents an untapped renewable resource for bioenergy generation. This study investigated the effects of two temperatures and three mixture ratios of manures and food wastes on biogas production and microbial community structure. Increasing the amount of fruit and restaurant wastes in the feed mixture significantly enhanced the productivity of the systems (16% increase in the mesophilic systems and 41% in the thermophilic). The methane content of biogas was also favored at higher temperatures. Beta diversity analysis, based on high-throughput sequencing of 16S rRNA gene, showed that microbial communities of the thermophilic digestions were more similar to each other than the mesophilic digestions. Species richness of the thermophilic digestions was significantly greater than the corresponding mesophilic digestions (F = 40.08, p = 0.003). The mesophilic digesters were dominated by Firmicutes and Bacteroidetes while in thermophilic digesters, the phyla Firmicutes and Chloroflexi accounted for up to 90% of all sequences. Methanosarcina represented the key methanogen and was more abundant in thermophilic digestions. These results demonstrate that increasing digestion temperature and adding food wastes can alleviate the negative impact of low C:N ratios on anaerobic digestion.

In-situ biogas upgrading assisted by bioaugmentation with hydrogenotrophic methanogens during mesophilic and thermophilic co-digestion

In this study, the effects of bioaugmentation of typically dominant hydrogenotrophic methanogens to CSTR co-digesting cheese whey and manure, under in-situ biomethanation operations were investigated. Reactors working at mesophilic (37 °C) and thermophilic (55 °C) conditions were independently treated and examined in terms of microbial composition and process dynamics. Addition of Methanoculleus bourgensis in the mesophilic reactor led to a stable biomethanation, and an improved microbial metabolism, resulting in 11% increase in CH₄ production rate. 16S rRNA and biochemical analyses revealed an enrichment in syntrophic and acidogenic species abundance. Moreover, nearly total volatile fatty acids conversion was observed. Differently, Methanothermobacter thermautotrophicus addition in the thermophilic reactor did not promote biogas upgrading performance due to incomplete H₂ conversion and inefficient community adaptation to H₂ excess, ultimately favoring acetoclastic methanogenesis. Bioaugmentation constitutes a viable tool to strengthen in-situ upgrading processes and paves the way to the development of more sophisticated and robust microbial inoculants.

Analysis of Major Bacteria and Diversity of Surface Soil to Discover Biomarkers Related to Soil Health

The discovery of biomarkers for assessing soil health requires the exploration of organisms that can explain the core functions of soil and identification of species with major roles in these functions. However, identifying specific keystone markers within the soil microbiota is challenging. Next-generation sequencing (NGS)-based molecular-biological methods have revealed information on soil biodiversity; however, whether this biodiversity is related to soil health remains unclear. In this study, we performed NGS on grassland surface soil to compare the prokaryotic and eukaryotic genetic diversity to determine the chemical soil quality and examined markers associated with soil health. Microorganisms associated with the nitrogen cycle, bioremediation, plant pathogenicity, antibiotic production, and material degradation showed potential for use as markers. To propose a framework for soil health assessment, we not only used traditional indicators, such as chemical and physical measures, but also assessed metagenomics data of soil by land use to identify the major factors influencing the microbial structure in soil. Moreover, major keystone species were identified. Furthermore, the microbial genetic diversity of generally healthy surface soil, such as forests, farmland, and parks, was determined. These findings provide basic data for exploring soil health-related biomarkers.

Quantitative assessment of exposure to fecal contamination in urban environment across nine cities in low-income and lower-middle-income countries and a city in the United States

BACKGROUND

During 2014 to 2019, the SaniPath Exposure Assessment Tool, a standardized set of methods to evaluate risk of exposure to fecal contamination in the urban environment through multiple exposure pathways, was deployed in 45 neighborhoods in ten cities, including Accra and Kumasi, Ghana; Vellore, India; Maputo, Mozambique; Siem Reap, Cambodia; Atlanta, United States; Dhaka, Bangladesh; Lusaka, Zambia; Kampala, Uganda; Dakar, Senegal.

OBJECTIVE

Assess and compare risk of exposure to fecal contamination via multiple pathways in ten cities.

METHODS

In total, 4053 environmental samples, 4586 household surveys, 128 community surveys, and 124 school surveys were collected. E. coli concentrations were measured in environmental samples as an indicator of fecal contamination magnitude. Bayesian methods were used to estimate the distributions of fecal contamination concentration and contact frequency. Exposure to fecal contamination was estimated by the Monte Carlo method. The contamination levels of ten environmental compartments, frequency of contact with those compartments for adults and children, and estimated exposure to fecal contamination through any of the surveyed environmental pathways were compared across cities and neighborhoods.

RESULTS

Distribution of fecal contamination in the environment and human contact behavior varied by city. Universally, food pathways were the most common dominant route of exposure to fecal contamination across cities in low-income and lower-middle-income countries. Risks of fecal exposure via water pathways, such as open drains, flood water, and municipal drinking water, were site-specific and often limited to smaller geographic areas (i.e., neighborhoods) instead of larger areas (i.e., cities).

CONCLUSIONS

Knowledge of the relative contribution to fecal exposure from multiple pathways, and the environmental contamination level and frequency of contact for those "dominant pathways" could provide guidance for Water, Sanitation, and Hygiene (WASH) programming and investments and enable local governments and municipalities to improve intervention strategies to reduce the risk of exposure to fecal contamination.

The chemical-microbial release and transformation of arsenic induced by citric acid in paddy soil

Citric acid (CA) is the major exudate of rice roots, yet the effects of CA on arsenic (As) transformation and microbial community in flooded paddy soil have not been clearly elucidated. In this study, microcosms were established by amending CA to As contaminated paddy soils, mimicking the rhizosphere environment. Results showed that 0.5% CA addition significantly enhanced As mobilization after one-hour incubation, increased total As in porewater by about 20-fold. CA addition induced arsenate release into porewater, and subsequently formed ternary complex of As, iron and organic matters, inhibiting further As transformation (including arsenate reduction and arsenite methylation). Furthermore, the results of linear discriminant analysis (LDA) effect size (LEfSe) and network analysis revealed that CA addition significantly enriched bacteria associated with arsenic and iron reductions, such as Clostridium (up to 35-fold) and Desulfitobacterium (up to 4-fold). Our results suggest that CA exhibits robust ability to mobilize As through both chemical and microbial processes, increasing the risk of As accumulation by rice. This study sheds light on our understanding of As mobilization and transformation in rhizosphere soil, potentially providing effective strategies to restrict As accumulation in food crops by screening or cultivating varieties with low CA exuding.

Effect of biochar combined with a biotrickling filter on deodorization, nitrogen retention, and microbial community succession during chicken manure composting

The high-nitrogen content and dense structure of poultry manure compost cause volatilization of N to ammonia (NH₃). This study evaluated the combined application of biochar and biotrickling filtration (BTF) to remove of odor in chicken manure mixed straw compost (w/w, 2.5:1). Adding of 10% biochar reduced NH₃, hydrogen sulfide (H₂S), and total volatile organic compounds (TVOCs) contents by 20.04%, 16.18%, and 17.55% respectively, and decreased the N loss rate by 8.27%, compared with those observed in control. The organic matter content decreased by 28.11% and germination index reached 97.36% in the experimental group. Meanwhile, the N-cycling microorganisms such as Pusillimonas and Pseudomonas became more active, and the relative abundance of sulfur-cycling microorganisms Hydrogenispora decreased in the experimental group. Following BTF application, the NH₃, H₂S, and TVOCs removal rates reached 95%, 97%, and 53%, respectively.

The synergistic effect of rumen cellulolytic bacteria and activated carbon on thermophilic digestion of cornstalk

To explore the bioaugmentation of rumen cellulolytic bacteria (RCB) and activated carbon (AC) on thermophilic digestion of cornstalk, biochemical methane potential tests were carried out. Adding RCB or AC can improve methane production, while simultaneous existence of AC (10 g/L) and RCB (5%) obtained the best performance. The maximum cellulose degradation rate, methane production rate and methane yield were 66.92%, 32.2 L/(kgVS·d), and 144.9 L/kgVS, which increased by 30.23%, 51.17%, and 20.35% compared with control group. The cellulolytic and fermentative bacteria (Hydrogenispora), syntrophic acetate-oxidizing bacteria (norank_o_MBA03), and hydrogenotrophic Methanothermobacter were crucial for thermophilic digestion of cornstalk. The enhancement of AC was due to the enrichment of Hydrogenispora and Methanothermobacter, while RCB can increase the abundance of cellulolytic bacteria (Halocella and norank_o_M55-D21) and mixotrophic Methanosarcina. The synergetic effect of AC and RCB owing to the enriched cellulolytic bacteria, the enhanced syntrophic acetate oxidation and the concentrated carbon metabolic flow to methane.

Enhanced anaerobic digestion of waste-activated sludge via bioaugmentation strategy-Phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt2) analysis through hydrolytic enzymes and possible linkage to system performance

In this study, anaerobic digestion of waste-activated sludge was bioaugmented with hydrolytic bacteria, Bacteroidetes uniformis (Bacteroidetes, B) and Clostridium sp. (Firmicutes, F) at various dosages. Bioaugmentation resulted in enhanced methane conversion of waste-activated sludge. The highest methane yield of 298.1 mL CH₄/g-COD, 85.2% COD conversion efficiency was obtained when Bacteroidetes uniformis and Clostridium sp. were augmented at 100 and 900 CFU/mL, respectively. The microbial community analysis demonstrated that bioaugmentation increased the proportion of Bacteroidetes, Firmicutes, and Proteobacteria. Furthermore, at the highest methane yield, the principal methanogenic pathway was altered from acetoclastic to a mixture of hydrogenotrophic and acetoclastic; the major species shifted from Methanosaeta concilii to Methanobacterium subterraneum. Predicted gene analysis revealed that increased expression of hydrolases resulted in enhanced methane conversion through bioaugmentation.

Statistical optimization of methane production from brewery spent grain: Interaction effects of temperature and substrate concentration

This study evaluated the effects of thermal pretreatment of brewery spent grain (BSG) (by autoclave 121 °C, 1.45 atm for 30 min) on methane production (CH₄). Operation temperature (31-59 °C) and substrate concentration (8.3-19.7 g BSG.L^-1) factors were investigated by Response Surface Methodology (RSM) and Central Composite Design (CCD). Values ranging from 81.1 ± 2.0 to 290.1 ± 3.5 mL CH₄.g^-1 TVS were obtained according to operation temperature and substrate concentration variation. The most adverse condition for methanogenesis (81.1 ± 2.0 mL CH₄.g^-1 TVS) was at 59 °C and 14 g BSG.L^-1, in which there was increase in the organic matter concentration from 173.6 ± 4.94 to 3036 ± 7.78 mg.L^-1) result of a higher final concentration of volatile fatty acids (VFA, 2662.7 mg.L^-1). On the other hand, the optimum condition predicted by the statistical model was at 35 °C and 18 g BSG.L^-1 (289.1 mL CH₄.g^-1 TVS), which showed decrease in the organic matter concentration of 78.6% and a lower final concentration of VFA (533.2 mg.L^-1). Hydrogenospora and Methanosaeta were identified in this optimum CH₄ production condition, where acetoclastic methanogenic pathway prevailed. The CH₄ production enhancement was concomitant to acetic acid concentration decrease (from 578.9 to 135.7 mg.L^-1).

Molecular characterization of microbial communities in a peat-rich aquifer system contaminated with chlorinated aliphatic compounds

In an aquifer-aquitard system in the subsoil of the city of Ferrara (Emilia-Romagna region, northern Italy) highly contaminated with chlorinated aliphatic toxic organics such as trichloroethylene (TCE) and tetrachloroethylene (PCE), a strong microbial-dependent dechlorination activity takes place during migration of contaminants through shallow organic-rich layers with peat intercalations. The in situ microbial degradation of chlorinated ethenes, formerly inferred by the utilization of contaminant concentration profiles and Compound-Specific Isotope Analysis (CSIA), was here assessed using Illumina sequencing of V4 hypervariable region of 16S rRNA gene and by clone library analysis of dehalogenase metabolic genes. Taxon-specific investigation of the microbial communities catalyzing the chlorination process revealed the presence of not only dehalogenating genera such as Dehalococcoides and Dehalobacter but also of numerous other groups of non-dehalogenating bacteria and archaea thriving on diverse metabolisms such as hydrolysis and fermentation of complex organic matter, acidogenesis, acetogenesis, and methanogenesis, which can indirectly support the reductive dechlorination process. Besides, the diversity of genes encoding some reductive dehalogenases was also analyzed. Geochemical and 16S rRNA and RDH gene analyses, as a whole, provided insights into the microbial community complexity and the distribution of potential dechlorinators. Based on the data obtained, a possible network of metabolic interactions has been hypothesized to obtain an effective reductive dechlorination process.

Evidence of thermophilic waste decomposition at a landfill exhibiting elevated temperature regions

There have been several reports of landfills exhibiting temperatures as high as 80 to 100 °C. This observation has motivated researchers to understand the causes of the elevated temperatures and to develop predictive models of landfill temperature. The objective of this research was to characterize the methanogenic activity of microbial communities that were derived from landfill samples excavated from a section of a landfill exhibiting gas well temperatures above 55 °C. Specific objectives were to: (1) determine the upper temperature limit for methane production; (2) evaluate the kinetics of methane generation when landfill-derived microcosms are incubated above and below their excavation temperature and derive a temperature inhibition function; and (3) evaluate microbial community shifts in response to temperature perturbations. Landfill microcosms were derived from 57 excavated landfill samples and incubated within ±2.5 °C of their excavation temperature between 42.5 °C and 87.5 °C. Results showed an optimum temperature for methane generation of ~57 °C and a 95% reduction in methane yield at ~72 °C. When select cultures were perturbed between 5 °C below and 15 °C above their in-situ temperature, both the rate and maximum methane production decreased as incubation temperature increased. Microbial community characterization using 16S rRNA amplicon sequencing suggests that thermophilic methanogenic activity can be attributed to methanogens of the genus Methanothermobacter. This study demonstrated that from a microbiological standpoint, landfills may maintain active methanogenic processes while experiencing temperatures in the thermophilic regime (<72 °C).

Comparison of microbial community structures between mesophilic and thermophilic anaerobic digestion of vegetable waste

The anaerobic digestion performance correlates with the functional microbial community. Mesophilic and thermophilic digestions of vegetable waste were conducted, and dynamics of the microbial community were investigated. The mesophilic and thermophilic collapsed stages occurred at organic loading rates of 1.5 and 2.0 g VS/(L d) due to the accumulation of volatile fatty acids with final concentrations of 2276 and 6476 mg/L, respectively. A high concentration of volatile fatty acids caused the severe inhibition of methanogens, which finally led to the imbalance between acetogenesis and methanogenesis. The mesophilic digestion exhibited a higher microbial diversity and richness than the thermophilic digestion. Syntrophic acetate-oxidizing coupled with hydrogenotrophic methanogenesis was the dominant pathway in the thermophilic stable system, and acetoclastic methanogenesis in the mesophilic stable system. The dominant acidogens, syntrophus, and methanogens were unclassified_f__Anaerolineaceae (8.68%), Candidatus_Cloacamonas (19.70%), Methanosaeta (6.10%), and Methanosarcina (4.08%) in the mesophilic stable stage, and Anaerobaculum (12.59%), Syntrophaceticus (4.84%), Methanosarcina (30.58%), and Methanothermobacter (3.17%) in thermophilic stable stage. Spirochaetae and Thermotogae phyla were the characteristic microorganisms in the mesophilic and thermophilic collapsed stages, respectively. These findings provided valuable information for the deep understanding of the difference of the microbial community and methane-producing mechanism between mesophilic and thermophilic digestion of vegetable waste.

Transformation of redox-sensitive to redox-stable iron-bound phosphorus in anoxic lake sediments under laboratory conditions

Phosphorus (P) can be retained in mineral association with ferrous iron (Fe) as vivianite, Fe(II)₃(PO₄)₂ ∙ 8 H₂O, in lake sediments. The mineral is formed and remains stable under anoxic non-sulphidogenic conditions and, therefore, acts as a long-term P sink. In laboratory experiments under anoxic conditions, we investigated whether P adsorbed to amorphous Fe(III)-hydroxide functioned as a precursor phase of vivianite when added to different sediments as a treatment. The untreated sediments served as controls and were naturally Fe-rich (559 µmol/g DW) and Fe-poor (219 µmol/g DW), respectively. The solid P binding forms analysed by sequential extraction and X-ray diffraction were related to coinciding pore water analyses and the bacterial community compositions of the sediments by bacterial 16S rRNA gene amplicon sequencing. In the treatments, within a period of 40 d, 70 % of the redox-sensitive Fe(III)-P was transformed into redox-stable P, which contained vivianite. The mineral was supersaturated in the pore water, but the presence of Fe(III)-P functioning as a precursor was sufficient for measurable vivianite formation. The composition of the microbial community did not differ significantly (PERMANOVA, p = 0.09) between treatment and control of the naturally Fe-rich sediment. In the naturally Fe-poor sediment, the microbial community changed significantly (PERMANOVA, p = 0.001) in response to the addition of Fe(III)-P to the sediment. The freshly formed redox-stable P was not retransferred to a redox-sensitive compound by aeration for 24 h until 90 % O₂ saturation was reached in the sediment slurry. We conclude that 1) Fe(III)-hydroxide bound P, resulting from oxic conditions at the sediment-water interface, is immobilised during anoxic conditions and stable even after re-oxygenation; 2) the process is feasible within the time scales of anoxic lake stratification periods; and 3) in relatively Fe-poor lakes, Fe dosing can provide excess Fe to form the precursor.

Symbiotic chitin degradation by a novel anaerobic thermophilic bacterium Hydrogenispora sp. UUS1-1 and the bacterium Tepidanaerobacter sp. GT38

Chitin is the second most abundant organic compound in nature. Although mesophilic bacteria degrade insoluble chitin, there is a paucity of data describing degradation of insoluble chitin by anaerobic thermophilic bacteria. In this report, we screened cow manure compost for new chitin degradation systems, and identified a chitinolytic bacterial community (CBC) that showed high chitin degradation activity under thermophilic conditions, i.e., 1% (w/v) chitin powder degraded completely within 7 days at 60 °C. Metagenomic analysis revealed that the CBC was dominated by two bacterial genera from Hydrogenispora, an uncultured taxonomic group, and Tepidanaerobacter. Hydrogenispora were abundant in the early-to-mid stages of culturing with chitin, whereas the population of Tepidanaerobacter increased during the later stages of culturing. Strains UUS1-1 and GT38, which were isolated as pure cultures using the roll-tube method with colloidal chitin, N-acetyl-d-glucosamine, and glucose as carbon sources, were found to be closely related to H. ethanolica and T. acetatoxydans, respectively. Strain UUS1-1 readily degraded chitin and is the first anaerobic thermophilic chitinolytic bacterium reported, whereas strain GT38 showed no chitinolytic activity. Based on phylogenetic analysis, UUS1-1 and GT38 should be classified as novel genera and species. Zymogram analysis revealed that UUS1-1 produces at least two chitinases with molecular weights of 150 and 40 kDa. A coculture of UUS1-1 and GT38 degraded crystalline chitin faster with lower accumulation of lactate compared with UUS1-1 alone, indicating that the strains maintained a symbiotic association through assimilation of organic acids in chitin degradation and that strain GT38 consumed end-products to reduce end-product inhibition and enhance the degradation of crystalline chitin.

Draft genome sequence data of the anaerobic, thermophilic, chitinolytic bacterium strain UUS1-1 belonging to genus Hydrogenispora of the uncultured taxonomic OPB54 cluster

Strain UUS1-1 (=JCM33882 =DSM111537) is a novel chitinolytic, thermophilic, anaerobic bacterium belonging to the genus Hydrogenispora of the uncultured taxonomic OPB54 cluster within the phylum Firmicutes. Strain UUS1-1 has a unique, long, hair-like rod morphology and a strong ability to degrade crystalline chitin. The whole genome of strain UUS1-1 was sequenced on an Ion GeneStudio S5 system, which yielded 86 contigs comprising 2,482,547 bp, 2235 protein-coding sequences, and a G+C content of 52.1 mol%. Strain UUS1-1 is the second cultivable isolate, besides H. ethanolica, within the OPB54 cluster and may be classified as a novel species. The genomic data have been deposited at the National Center for Biotechnology Information (NCBI) under accession number JAAKDE00000000.

Thermophilic Biogas Upgrading via ex Situ Addition of H2 and CO2 Using Codigested Feedstocks of Cow Manure and the Organic Fraction of Solid Municipal Waste

Bioconversion of renewable H₂ and waste CO₂ using methanogenic archaea is a promising technology for obtaining high-purity CH₄, which can serve as an alternative for natural gas. This process is known as ex situ biogas upgrading. This work highlights the pathway toward the bioconversion of renewable H₂ and CO₂ into high-purity biomethane by exploiting highly accessible agro-municipal residues: cow manure (CM) and the organic fraction of solid municipal waste (OFSMW), which used to be called "waste materials". More specifically, an ex situ thermophilic (55 °C) biogas upgrading process was conducted by CM and OFSMW codigestion at different mass proportions: 100:0, 80:20, 70:30, 60:40, and 50:50. Maximum CH₄ concentrations of 92-97 vol % and biogas volumetric production rates of 4954-6605 NmL/L.d were obtained from a batch reactor of 3 L working volume. Feedstock characterization, pH monitoring, and the carbon-to-nitrogen ratio were critical parameters to evaluate during biogas upgrading experiments. In this work, the usefulness of agro-municipal substrates is highlighted by producing high-purity biomethane-an energetic chemical to facilitate renewable energy conversion, which supports various end-use applications. This process therefore provides a solution to renewable energy storage challenges and future sustainable and green energy supply.

Bioconversion of swine manure into high-value products of medium chain fatty acids

This research proposes and demonstrates, for the first time, the utilization of swine manure as a complex feedstock to produce high-value medium chain fatty acids (MCFA). The two-stage anaerobic digestion (AD) carboxylates platform was adopted for the conversion of swine manure to short chain fatty acids (SCFAs) and then SCFAs to MCFA (n-caproate, n-heptanoate, and n-caprylate) with ethanol supplementation. We defined the appropriate initial pH of 10.0 for SCFAs production with a carbon conversion rate of 71.2%, and acetate, propionate were the main products, which accounted for around 72.9% of the total SCFAs in the primary stage (I). Through the addition of ethanol, 61.3% of the converted carbon in the complex SCFAs solution was converted into MCFA (C6-C8) in the chain elongation stage (II), while only 6.7% was attributed to methane formation. The concentrations of n-caproate, n-heptanoate, and n-caprylate reached 8.6 g COD/L (3.9 g/L), 6.4 g COD/L (2.7 g/L), and 2.6 g COD/L (1.07 g/L), respectively. This study achieved a relatively higher concentration of n-heptanoate compared with past studies of MCFA from other feedstock. These findings demonstrated a new route for resource recovery and the operating parameters for producing MCFA from swine manure.

Culturing Bacteria From Fermentation Pit Muds of Baijiu With Culturomics and Amplicon-Based Metagenomic Approaches

The Baijiu-making microbiota has an important role in the alcohol production, flavor, and character of Baijiu. 16S rRNA gene sequencing revolutionized the understanding of Baijiu-making microbiota. In this study, nine phyla, 23 classes, 49 orders, 99 families, and 201 genera were detected in pit muds (PMs) by 16S rRNA gene sequencing. Firmicutes and Bacteroidetes predominated (>99%). At the order level, Clostridiales, Bacteroidales, and Bacillales predominated (>92%). At the genus level, Hydrogenispora, Petrimonas, Proteiniphilum, and Sedimentibacter predominated. The pure culture of Baijiu-making prokaryotes was essential to elucidating the role of these microbes in the fermentation of Baijiu. According to the theory of microbial culturomics, a culturing approach with multiple culture conditions was adopted, combining 16S rRNA gene sequencing. We identified 215 prokaryotic strains, which were assigned to 66 species, 41 genera, four phyla, and 19 potential new species. Gas conditions were key factors in culturomics. In addition, culturomics significantly increased the number of species isolated from the fermentation PM compared with previous reports. With culturomics, the diversity spectrum of culturable bacteria in the PM was increased 273.33% at the genus level. This study confirms the complementary role of culturomics in the exploration of complex microbiota.

Influence of terminal electron-accepting conditions on the soil microbial community and degradation of organic contaminants of emerging concern

Better understanding of the fate and persistence of trace organic contaminants of emerging concern (CEC) in agricultural soils is critical for assessing the risks associated with using treated wastewater effluent to irrigate crops and land application of wastewater biosolids. This study reports on the influence of prevailing terminal electron-accepting processes (TEAPs, i.e., aerobic, nitrate-reducing, iron(III)-reducing, and sulfate-reducing conditions) and exposure to a mixture of nine trace CEC (90 ng/g each) on both the microbial community structure and CEC degradation in agricultural soil. DNA analysis revealed significant differences in microbial community composition following establishment of different TEAPs, but no significant change upon exposure to the mixture of CEC. The largest community shift was observed after establishing nitrate-reducing conditions and the smallest shift for sulfate-reducing conditions. Two of the CEC (atrazine and sulfamethoxazole) showed significant degradation in both bioactive and abiotic (i.e., sterilized) conditions, with half-lives ranging from 1 to 64 days for different TEAPs, while six of the CEC (amitriptyline, atenolol, trimethoprim, and three organophosphate flame retardants) only degraded in bioactive samples, with half-lives ranging from 27 to 90 days; carbamazepine did not degrade appreciably within 90 days in any of the incubations. Amplicon sequence variants (ASVs) from Firmicutes Hydrogenispora, Gemmatimonadetes Gemmatimonadaceae, and Verrucomicrobia OPB34 soil group were identified as potentially responsible for the biodegradation of organophosphate flame retardants, and ASVs from other taxa groups were suspected to be involved in biodegrading the other target CEC. These results demonstrate that CEC fate and persistence in agricultural soils is influenced by the prevailing TEAPs and their influence on the microbial community, suggesting the need to incorporate these factors into contaminant fate models to improve risk assessment predictions.

pH and Phosphate Induced Shifts in Carbon Flow and Microbial Community during Thermophilic Anaerobic Digestion

pH is a central environmental factor influencing CH4 production from organic substrates, as every member of the complex microbial community has specific pH requirements. Here, we show how varying pH conditions (5.0-8.5, phosphate buffered) and the application of a phosphate buffer per se induce shifts in the microbial community composition and the carbon flow during nine weeks of thermophilic batch digestion. Beside monitoring the methane production as well as volatile fatty acid concentrations, amplicon sequencing of the 16S rRNA gene was conducted. The presence of 100 mM phosphate resulted in reduced CH4 production during the initial phase of the incubation, which was characterized by a shift in the dominant methanogenic genera from a mixed Methanosarcina and Methanoculleus to a pure Methanoculleus system. In buffered samples, acetate strongly accumulated in the beginning of the batch digestion and subsequently served as a substrate for methanogens. Methanogenesis was permanently inhibited at pH values ≤5.5, with the maximum CH4 production occurring at pH 7.5. Adaptations of the microbial community to the pH variations included shifts in the archaeal and bacterial composition, as less competitive organisms with a broad pH range were able to occupy metabolic niches at unfavorable pH conditions.

Salt tolerance of Cressa cretica and its rhizosphere microbiota

The dwarf shrub Cressa cretica is a thermocosmopolitan halophilic species. Different mechanisms confer salt stress tolerance such as tissue and osmotic tolerance and ion exclusion, as well as the associated microbiota. The aims were (i) to investigate the best conditions for C. cretica seed germination and to examine the tolerance of germinated seeds and seedlings to different salt concentrations and (ii) to characterize the rhizosphere and bulk soil microbiota. Germination and growth experiments were conducted to address plant salt tolerance, and with Illumina sequencing the microbiota of rhizosphere and bulk soil was investigated. While high salt concentrations (600, 800, and 1000 mM NaCl) inhibited C.cretica seed germination, recovery of ungerminated seeds under non-saline conditions was high, indicating osmotic rather than toxic effects of high salt concentrations. The microbiota found in rhizosphere and bulk soil showed high similarity with that found in previous studies on halophyte-associated microbiota, among the Planctomyces, Halomonas and Jeotgalibacillus. Concluding, salt stress responses on the plant level were shown, as has the involvement of associated halotolerant bacteria. Still, the potential role for mitigating saline stress by the bacterial associates of C. cretica, most of them microbial dark matter, will have to be investigated, as will the contributions of archaea and fungi.

Prokaryotic communities in multidimensional bottom-pit-mud from old and young pits used for the production of Chinese Strong-Flavor Baijiu

The pit mud (PM) prokaryotic communities with obvious difference between old and young PM is essential for solid-fermentation of Chinese Strong-Flavor Baijiu. The bottom-PM (BPM) is considered more important. In this study, the multidimensional prokaryotic communities of old and young BPMs were investigated. The old BPM presented stratified difference within the depth of 0-7 cm, especially, the surface 0-1 cm was characteristic of dominant Caproiciproducens (34.79%). The young BPM showed significant difference between quarter/center and deep corner (1-7 cm), the former were characteristic of abundant Lactobacillus (12.80%-42.72%), while the deep corner was distinctive of dominant Caproiciproducens (17.85%-64.45%). The lactic acid, pH and soluble Ca²⁺ were considered as the 3 most significant environmental factors through redundancy analysis (RDA). This study may help illuminate the BPM aging process, and allow the future artificial regulation of young BPM.

Microbial and Phenyl Acid Dynamics during the Start-up Phase of Anaerobic Straw Degradation in Meso- and Thermophilic Batch Reactors

Aromatic compounds like phenyl acids derived from lignocellulose degradation have been suspected to negatively influence biogas production processes. However, results on this topic are still inconclusive. To study phenyl acid formation in batch reactors during the start-up phase of anaerobic degradation, different amounts of straw from grain were mixed with mesophilic and thermophilic sludge, respectively. Molecular biological parameters were assessed using next-generation sequencing and qPCR analyses. Metagenomic predictions were done via the program, piphillin. Methane production, concentrations of phenylacetate, phenylpropionate, phenylbutyrate, and volatile fatty acids were monitored chromatographically. Methanosarcina spp. was the dominant methanogen when high straw loads were effectively degraded, and thus confirmed its robustness towards overload conditions. Several microorganisms correlated negatively with phenyl acids; however, a negative effect, specifically on methanogens, could not be proven. A cascade-like increase/decrease from phenylacetate to phenylpropionate, and then to phenylbutyrate could be observed when methanogenesis was highly active. Due to these results, phenylacetate was shown to be an early sign for overload conditions, whereas an increase in phenylbutyrate possibly indicated a switch from degradation of easily available to more complex substrates. These dynamics during the start-up phase might be relevant for biogas plant operators using complex organic wastes for energy exploitation.

Enhanced hydrolysis-acidification of high-solids and low-organic-content sludge by biological thermal-alkaline synergism

In this study, a biological thermal-alkaline synergistic system was successfully established to enhance the hydrolysis-acidification efficiency of high-solids and low-organic-content sludge (HS-LOC-S). The results indicated that the highest hydrolysis rate was obtained at pH of 12 (52.62%) leading to the highest production of soluble chemical oxygen demand (SCOD) and soluble protein (SP). The highest acidification rate was observed at pH of 10 (32.15%), leading to the highest production of volatile fatty acids (VFAs). At pH of 10, average sludge size reduced by 24.60%, and the proportion of biodegradable dissolved organic matter (DOM) produced by synergistic system increased by 15.82%, when compared with those of raw sludge. Moreover, results of 16S rRNA clearly validated that the relative abundance of hydrolytic and acidogenic microbes (e.g. Tepidimicrobium, Coprothermobacter) abundantly enriched at pH of 10 (49.88%) was greatly higher than others, which was the main reason for its maximum VFAs accumulation.

Air-side ammonia stripping coupled to anaerobic digestion indirectly impacts anaerobic microbiome

Air-side stripping without a prior solid-liquid phase separation step is a feasible and promising process to control ammonia concentration in thermophilic digesters. During the process, part of the anaerobic biomass is exposed to high temperature, high pH and aerobic conditions. However, there are no studies assessing the effects of those harsh conditions on the microbial communities of thermophilic digesters. To fill this knowledge gap, the microbiomes of two thermophilic digesters (55°C), fed with a mixture of pig manure and nitrogen-rich co-substrates, were investigated under different organic loading rates (OLR: 1.1-5.2 g COD l-1  day-1 ), ammonia concentrations (0.2-1.5 g free ammonia nitrogen l-1 ) and stripping frequencies (3-5 times per week). The bacterial communities were dominated by Firmicutes and Bacteroidetes phyla, while the predominant methanogens were Methanosarcina sp archaea. Increasing co-substrate fraction, OLR and free ammonia nitrogen (FAN) favoured the presence of genera Ruminiclostridium, Clostridium and Tepidimicrobium and of hydrogenotrophic methanogens, mainly Methanoculleus archaea. The data indicated that the use of air-side stripping did not adversely affect thermophilic microbial communities, but indirectly modulated them by controlling FAN concentrations in the digester. These results demonstrate the viability at microbial community level of air side-stream stripping process as an adequate technology for the ammonia control during anaerobic co-digestion of nitrogen-rich substrates.

Different response of bacteria, archaea and fungi to process parameters in nine full-scale anaerobic digesters

Biogas production is a biotechnological process realized by complex bacterial, archaeal and likely fungal communities. Their composition was assessed in nine full-scale biogas plants with distinctly differing feedstock input and process parameters. This study investigated the actually active microbial community members by using a comprehensive sequencing approach based on ribosomal 16S and 28S rRNA fragments. The prevailing taxonomical units of each respective community were subsequently linked to process parameters. Ribosomal rRNA of bacteria, archaea and fungi, respectively, showed different compositions with respect to process parameters and supplied feedstocks: (i) bacterial communities were affected by the key factors temperature and ammonium concentration; (ii) composition of archaea was mainly related to process temperature; and (iii) relative abundance of fungi was linked to feedstocks supplied to the digesters. Anaerobic digesters with a high methane yield showed remarkably similar bacterial communities regarding identified taxonomic families. Although archaeal communities differed strongly on genus level from each other, the respective digesters still showed high methane yields. Functional redundancy of the archaeal communities may explain this effect. 28S rRNA sequences of fungi in all nine full-scale anaerobic digesters were primarily classified as facultative anaerobic Ascomycota and Basidiomycota. Since the presence of ribosomal 28S rRNA indicates that fungi may be active in the biogas digesters, further research should be carried out to examine to which extent they are important players in anaerobic digestion processes.

Augmentation of Granular Anaerobic Sludge with Algalytic Bacteria Enhances Methane Production from Microalgal Biomass

The efficiency of anaerobic digestion relies upon activity of the inoculum converting organic substrate into biogas. Often, metabolic capacity of the inoculum needs to be augmented with new capabilities to accommodate changes in the substrate feed composition. However, bioaugmentation is not a widely used strategy possibly due to the lack of studies demonstrating successful applications. This study describes the bioaugmentation of granular anaerobic sludge digesting mixed algal biomass in batch-scale reactors. The addition of an algalytic bacterial mixture to the granular consortium increased methane yield by 11%. This study also investigated changes in the microbial 16SrRNA composition of the augmented and non-augmented granular inoculum, which demonstrates a significant change in the hydrolytic microbial community. Overall, the studies’ results aim to provide a feasible checklist to assess the success rates of bioaugmentation of anaerobic digestion applications.

Immediate Effects of Ammonia Shock on Transcription and Composition of a Biogas Reactor Microbiome

The biotechnological process of biogas production from organic material is carried out by a diverse microbial community under anaerobic conditions. However, the complex and sensitive microbial network present in anaerobic degradation of organic material can be disturbed by increased ammonia concentration introduced into the system by protein-rich substrates and imbalanced feeding. Here, we report on a simulated increase of ammonia concentration in a fed batch lab-scale biogas reactor experiment. Two treatment conditions were used simulating total ammonia nitrogen concentrations of 4.9 and 8.0 g/L with four replicate reactors. Each reactor was monitored concerning methane generation and microbial composition using 16S rRNA gene amplicon sequencing, while the transcriptional activity of the overall process was investigated by metatranscriptomic analysis. This allowed investigating the response of the microbial community in terms of species composition and transcriptional activity to a rapid upshift to high ammonia conditions. Clostridia and Methanomicrobiales dominated the microbial community throughout the entire experiment under both experimental conditions, while Methanosarcinales were only present in minor abundance. Transcription analysis demonstrated clostridial dominance with respect to genes encoding for enzymes of the hydrolysis step (cellulase, EC 3.2.1.4) as well as dominance of key genes for enzymes of the methanogenic pathway (methyl-CoM reductase, EC 2.8.4.1; heterodisulfide reductase, EC 1.8.98.1). Upon ammonia shock, the selected marker genes showed significant changes in transcriptional activity. Cellulose hydrolysis as well as methanogenesis were significantly reduced at high ammonia concentrations as indicated by reduced transcription levels of the corresponding genes. Based on these experiments we concluded that, apart from the methanogenic archaea, hydrolytic cellulose-degrading microorganisms are negatively affected by high ammonia concentrations. Further, Acholeplasma and Erysipelotrichia showed lower abundance under increased ammonia concentrations and thus might serve as indicator species for an earlier detection in order to counteract against ammonia crises.

Biogas upgrading and biochemical production from gas fermentation: Impact of microbial community and gas composition

The present study proposes a novel alternative method of the current biogas upgrading techniques by converting CO₂ (in the biogas) into valuable chemicals (e.g., volatile fatty acids) using H₂ as energy source and acetogenic mixed culture as biocatalyst. The influence of thermal treatment (90 °C) on the inhibition of the methanogenic archaea and enriching the acetogenic bacteria in different inocula (mesophilic and thermophilic) was initially tested. The most efficient inoculum that achieved the highest performance through the fermentation process was further used to define the optimum H₂/CO₂ gas ratio that secures maximum production yield of chemicals and maximum biogas upgrading efficiency. In addition, 16S rRNA analysis of the microbial community was conducted at the end of the experimental period to target functional microbes. The maximum biogas content (77% (v/v)) and acetate yield (72%) were achieved for 2H₂:1CO₂ ratio (v/v), with Moorella sp. 4 as the most dominant thermophilic acetogenic bacterium.

Coupling metabolisms of arsenic and iron with humic substances through microorganisms in paddy soil

Humic acid (HA) and fulvic acid (FA) are dominating humic substances (HS) in soil. In this study, the effects of HA and FA addition (0.2%-1.5%) on arsenic (As) mobility and microbial community composition in paddy soil were investigated. FA significantly increased the concentrations of As (12-fold), iron (Fe; 20-fold), manganese (Mn; 3-fold) and acetic acid (3-fold) in soil porewater, and also caused significant enrichment of Desulfitobacterium (41-fold). Furthermore, the FA addition significantly increased the relative abundance of Bathyarchaeota (4-fold), a microorganism that is suggested to be important for FA degradation. In contrast, HA slightly increased As (1.2-fold) in porewater, had little effect on Fe, Mn and acetic acid, and 1.5% HA addition significantly decreased As in porewater at day 14 (45%). Both HA and FA addition promoted As methylation. HA increased dimethylarsenate concentration and FA increased monomethylarsenate concentration in porewater. These results highlight the contrasting effects of different (HA vs. FA) organic substances on As fate in paddy soil and advance our understanding of the associations among As, Fe and organic substances through microorganisms in paddy soil.

Contribution analysis of methane production from food waste in bulk solution and on bio-electrode in a bio-electrochemical anaerobic digestion reactor

Quantitative evaluation of methane production either in bulk sludge or biofilm on electrodes was performed in a bio-electrochemical anaerobic digestion (BEAD) reactor with a lower electrode surface area/reactor working volume (A/V) ratio (7.0 m²/m³). Methane production by electrochemical reaction was also evaluated in the BEAD reactor with a biofilm-free electrode under the same conditions as in other experimental sets. The contributions of bulk sludge, biofilms on the electrodes, and electrochemical reactions in the BEAD reactor, on methane production, were 70.2%, 29.8%, and 0%, respectively. The principal methane-producing reactions occurred in the bulk sludge facilitated by H₂-dependent methylotrophic and hydrogenotrophic methanogens. Hydrogenotrophic methanogenesis was also the main methane-producing reaction in the biofilms attached to the bio-electrodes. Quantitative analysis of methane production (29.8%) in the biofilm revealed that bio-electrochemical processes involving H₂ and direct bio-electrochemical methane production contributed 8.7% and less than 0.1%, respectively. Interestingly, biochemical processes (21.1%) contributed the most to the overall production of methane in the biofilm. Bulk sludge contributed more to methane production than the biofilm, but the methane production per unit mass of volatile solid on the electrodes was about 1.6-times higher than that of bulk sludge. Methane was not produced in the BEAD reactor with biofilm-free electrodes. Therefore, formation and maintenance of biofilms on the electrodes are essential for improved methane production in BEAD reactors.