Microbial adhesion behavior and participation of adhered and planktonic microorganisms in anaerobic digestion of leaf, epidermis, pith from corn stalk

This study presents deep insights into the microbial adhesion and community dynamics of adhered and planktonic microorganisms during the anaerobic digestion (AD) of leaf, epidermis, and pith of corn stalk (CS). Microbial adhesion regularity varied with the part of CS. Overall, hydrolytic bacteria (Ruminofilibacter xylanolyticum, uncultured Bacteroidetes bacteria RII-AN097, uncultured Prolixibacteriaceae bacteria, Proteiniphilum sp. S20) and fermentative bacteria (Enterobacter hormaechei, Mobilitalia sibirica, Sphaerochaeta associate, Marinatabiaceae bacteria Ai-910, uncultured Planctomycetes bacteria, Kosakonia cowanii) would adhere to the surface of feedstock to synergistically degrade CS according to the full-length 16S rDNA gene sequencing. Acidification (uncultured Sedimentibacteriaceae sp.) and methanogenesis microorganisms (Methanosarcina barkeri str. Fusaro, Methanosateta spp.) mainly played a role in the planktonic phase for acetic acid and methane production. This study enriches the understanding of the adhered and planktonic microbial community involved in the AD, and provides a novel perspective to scientifically regulate microorganisms improving methanogenesis efficiency.

Targeted pretreatment and inoculation strategies for horse manure fermentation: Impact on metabolites and microbial community composition

Horse manure is a lignocellulosic biomass found in significant quantities with a vast indigenous flora, not yet fully valorized apart from anaerobic digestion. Its use in the fermentation process can lead to the production of higher-value metabolites. This study investigates three inoculation strategies coupled with five pretreatment conditions for horse manure fermentation. Two microwave pretreatments (200W and 1000W) were compared with a conventional thermal pretreatment, a thermo-acid pretreatment, and an unpretreated condition. The sole horse manure indigenous microorganisms were used in fermentation and compared with two inoculation strategies using external inoculum, which was i) thermally treated or ii) pretreated simultaneously with manure. A statistically similar total metabolite production (0.088 ± 0.010 gCOD/gVS) was observed, with more than 50 % of acetate produced for all the pretreated conditions. When no pretreatment was performed (Ctrl), methane was produced as a major metabolite. The metabolic profile of the thermo-acid pretreatment condition using solely indigenous microorganisms was different from the other conditions, with ethanol (0.015 ± 0.004 gCOD/gVS) and hydrogen (0.009 ± 0.002 gCOD/gVS) production. This was related to the Klebsiella genus abundance increase recorded for this condition. Both microwave pretreatments shared similar metabolite results and microbial composition with the conventional thermal pretreatment. However, a heat shock is needed to inhibit methane production from archaea and can be performed by microwave or conventional thermal pretreatment. To conclude, indigenous horse manure microorganisms are suitable for fermentation with equivalent yields compared to an external inoculum from a wastewater treatment plant whatever the pretreatment applied. However, a heat shock is needed to inhibit methane production from archaea and can be performed via microwave or conventional thermal pretreatment.

The interplay of hematite and photic biofilm triggers the acceleration of biotic nitrate removal

The soil-water interface is replete with photic biofilm and iron minerals; however, the potential of how iron minerals promote biotic nitrate removal is still unknown. This study investigates the physiological and ecological responses of photic biofilm to hematite (Fe2O3), in order to explore a practically feasible approach for in-situ nitrate removal. The nitrate removal by photic biofilm was significantly higher in the presence of Fe2O3 (92.5%) compared to the control (82.8%). Results show that the presence of Fe2O3 changed the microbial community composition of the photic biofilm, facilitates the thriving of Magnetospirillum and Pseudomonas, and promotes the growth of photic biofilm represented by the extracellular polymeric substance (EPS) and the content of chlorophyll. The presence of Fe2O3 also induces oxidative stress (•O2-) in the photic biofilm, which was demonstrated by electron spin resonance spectrometry. However, the photic biofilm could improve the EPS productivity to prevent the entrance of Fe2O3 to cells in the biofilm matrix and mitigate oxidative stress. The Fe2O3 then promoted the relative abundance of Magnetospirillum and Pseudomonas and the activity of nitrate reductase, which accelerates nitrate reduction by the photic biofilm. This study provides an insight into the interaction between iron minerals and photic biofilm and demonstrates the possibility of combining biotic and abiotic methods to improve the in-situ nitrate removal rate.

Description of Sporanaerobium hydrogeniformans gen. nov., sp. nov., an obligately anaerobic, hydrogen-producing bacterium isolated from Aravali hot spring in India

An obligately anaerobic bacterium XHS1971T, capable of degrading cellulose and xylan, was isolated from a sediment sample of Aravali hot spring, Ratnagiri, India. Cells of strain XHS1971T were Gram-stain-negative, spore-forming, motile, long-rods. Growth was observed at temperatures 30-50 °C (optimum 40-45 °C), pH 5.0-10.0 (optimum pH 8.0) and NaCl concentrations 0-0.5% (optimum 0%). Generation time of strain XHS1971T was 5 h under optimised growth conditions. Strain XHS1971T showed the ability to metabolise different complex and simple sugars constituting lignocellulosic biomass. Glucose was fermented majorly into hydrogen, formic acid, acetic acid, and ethanol, whereas carbon dioxide, butyric acid, lactic acid and succinic acid were produced in traces. 16S rRNA gene analysis of strain XHS1971T revealed < 94.5% homology with Cellulosilyticum lentocellum DSM5427T followed by Cellulosilyticum ruminicola JCM14822T, identifying strain as a distinct member of family Lachnospiraceae. The major cellular fatty acids (> 5%) were C14:0, C16:0, C18:0, and C16:1 ω7c. The genome size of the strain was 3.74 Mb with 35.3 mol% G + C content, and genes were annotated to carbohydrate metabolism, including genes involved in the degradation of cellulose and xylan and the production of hydrogen, ethanol and acetate. The uniqueness of strain was further validated by digital DNA-DNA hybridisation (dDDH), Average Nucleotide Identity (ANI), and Average Amino Acid Identity (AAI) values of 22%, 80%, and 63%, respectively, with nearest phylogenetic affiliates. Based on the detailed analyses, we propose a new genus and species, Sporanaerobium hydrogeniformans gen. nov., sp. nov., for strain XHS1971T (= MCC3498T = KCTC15729T = JCM32657T) within family Lachnospiraceae.

Microbes drive changes in arsenic species distribution during the landfill process

Landfills are considered an anthropogenic source of arsenic (As). The As species mediated by microbes in landfills vary significantly in toxicity. Based on random matrix theory, 16S rRNA genes were used to construct four microbial networks associated with different stages over 12 years of landfill ages. The results indicated that network size and microbial structure varied with landfill age. According to the network scores, about 208 taxa were identified as putative keystones for the whole landfill; the majority of them were Firmicutes, which accounted for 66.8% of all specialists. Random Forest analysis was performed to predict the keystone taxa most responsible for As species distribution under different landfill conditions; 17, 10 and 14 keystone taxa were identified as drivers affecting As species distribution at early, middle, and later landfill stages, respectively.

Variimorphobacter saccharofermentans gen. nov., sp. nov., a new member of the family Lachnospiraceae, isolated from a maize-fed biogas fermenter

Strain MD1^T is an anaerobic, Gram-stain-negative bacterium isolated from a lab-scale biogas fermenter fed with maize silage. It has a rod-shaped morphology with peritrichously arranged appendages and forms long chains of cells and coccoid structures. The colonies of MD1^T were white, circular, slightly convex and had a smooth rim. The isolate is mesophilic, displaying growth between 25 and 45 °C with an optimum at 40 °C. It grew at pH values of pH 6.7-8.2 (optimum, pH 7.1) and tolerated the addition of up to 1.5% (w/v) NaCl to the medium. The main cellular fatty acids of MD1^T are C_14:0 DMA and C_16:0. Strain MD1^T fermented xylose, arabinose, glucose, galactose, cellobiose, maltose, maltodextrin10, lactose starch, and xylan, producing mainly 2-propanol and acetic acid. The genome of the organism has a total length of 4163427 bp with a G+C content of 38.5 mol%. The two closest relatives to MD1^T are Mobilitalea sibirica P3M-3^T and Anaerotaenia torta FH052^T with 96.44 or 95.8 % 16S rRNA gene sequence similarity and POCP values of 46.58 and 50.58%, respectively. As MD1^T showed saccharolytic and xylanolytic properties, it may play an important role in the biogas fermentation process. Closely related variants of MD1^T were also abundant in microbial communities involved in methanogenic fermentation. Based on morphological, phylogenetic and genomic data, the isolated strain can be considered as representing a novel genus in the family Lachnospiraceae, for which the name Variimorphobacter saccharofermentans gen. nov., sp. nov. (type strain MD1^T=DSM 110715^T=JCM 39125^T) is proposed.

Structure-function elucidation of a microbial consortium in degrading rice straw and producing acetic and butyric acids via metagenome combining 16S rDNA sequencing

The characterized microbial consortium can efficiently degrade rice straw to produce acetic and butyric acids in high yields. The rice straw lost 86.9% in weight and degradation rates of hemicellulose, cellulose, and lignin attained were 97.1%, 86.4% and 70.3% within 12 days, respectively. During biodegradation via fermentation of rice straw, average concentrations of acetic and butyric acids reached 1570 mg/L and 1270 mg/L, accounting for 47.2% and 35.4% of the total volatile fatty acids, respectively. The consortium mainly composed of Prevotella, Cellulosilyticum, Pseudomonas, Clostridium and Ruminococcaceae, etc. Metagenomic analyses indicated that glycoside hydrolases (GHs) were the largest enzyme group with a relative abundance of 54.5%. Various lignocellulose degrading enzymes were identified in the top 30 abundant GHs, and were primarily distributed in the dominant genera (Prevotella, Cellulosilyticum and Clostridium). These results provide a new route for the commercial recycling of rice straw to produce organic acids.

Time-course analysis of metabolomic and microbial responses in anaerobic digesters exposed to ammonia

Omics longitudinal studies are effective experimental designs to inform on the stability and dynamics of microbial communities in response to perturbations, but time-course analytical frameworks are required to fully exploit the temporal information acquired in this context. In this study we investigate the influence of ammonia on the stability of anaerobic digestion (AD) microbiome with a new statistical framework. Ammonia can severely reduce AD performance. Understanding how it affects microbial communities development and the degradation progress is a key operational issue to propose more stable processes. Thirty batch digesters were set-up with different levels of ammonia. Microbial community structure and metabolomic profiles were monitored with 16 S-metabarcoding and GCMS (gas-chromatography-mass-spectrometry). Digesters were first grouped according to similar degradation performances. Within each group, time profiles of OTUs and metabolites were modelled, then clustered into similar time trajectories, evidencing for example a syntrophic interaction between Syntrophomonas and Methanoculleus that was maintained up to 387 mg FAN/L. Metabolites resulting from organic matter fermentation, such as dehydroabietic or phytanic acid, decreased with increasing ammonia levels. Our analytical framework enabled to fully account for time variability and integrate this parameter in data analysis.

Drivers and ecological consequences of arsenite detoxification in aged semi-aerobic landfill

Microbial populations responsible for arsenite [As(III)] detoxification were examined in aged refuse treated with 75 μM As(III) under semi-aerobic conditions. As(III) was rapidly oxidized to As(V) via microbial activity, and substantial As was fixed in the solid phase. The abundance of arsenite oxidase genes (aioA) was about four times higher in the moderate As(III) stressed treatment than in the untreated control. Network analysis of microbial community 16S rRNA genes based on MRT (random matrix theory) further illuminated details about microbe-microbe interactions, and showed six ecological clusters. A total of 166 "core" taxa were identified by within-module connectivity and among-module connectivity values. When compared with the control treatment without As(III), 12 putative keystone operational taxonomic units were positively correlated with As(III) oxidation, of which 10 of these were annotated to genera level. Eight genera were associated with As(III) detoxification: Pseudomonas, Paenalcaligenes, Proteiniphilum, Moheibacter, Mobilitalea, Anaerosporobacter, Syntrophomonas and Pusillimonas. Most of those putative keystone taxa were rare species in landfill, which suggests that low-abundance taxa might significantly contribute to As(III) oxidation.

Anaerocolumna chitinilytica sp. nov., a chitin-decomposing anaerobic bacterium isolated from anoxic soil subjected to biological soil disinfestation

An obligately anaerobic bacterial strain (CTTW^T) belonging to the family Lachnospiraceae within the class Clostridia was isolated from an anoxic soil sample subjected to biological or reductive soil disinfestation. Cells of the strain were Gram-stain-positive, short rods with peritrichous flagella. The strain was saccharolytic and decomposed polysaccharides, chitin, xylan and β-1,3-glucan. Strain CTTW^T decomposed cell biomass and cell-wall preparations of an ascomycete plant pathogen, Fusarium oxysporum f. sp. spinaciae. The strain produced acetate, ethanol, H₂ and CO₂ as fermentation products from the utilized substrates. The major cellular fatty acids of the strain were C_16 : 1 ω7c dimethylacetal (DMA), C_16 : 0 DMA and C_18 : 1 ω7c DMA. The closely related species of strain CTTW^T based on the 16S rRNA gene sequences were species in the genus Anaerocolumna with sequence similarities of 95.2-97.6 %. Results of genome analyses of strain CTTW^T indicated that the genome size of the strain was 5.62 Mb and the genomic DNA G+C content was 38.3 mol%. Six 16S rRNA genes with five different sequences from each other were found in the genome. Strain CTTW^T had genes encoding chitinase, xylanase, cellulase, β-glucosidase and nitrogenase as characteristic genes in the genome. Homologous genes encoding these proteins were found in the genomes of the related Anaerocolumna species, but the genomic and phenotypic properties of strain CTTW^T were distinct from them. Based on the phylogenetic, genomic and phenotypic analyses, the name Anaerocolumna chitinilytica sp. nov., in the family Lachnospiraceae is proposed for strain CTTW^T (=NBRC 112102^T=DSM 110036^T).

Draft Genome Sequence of Mobilitalea sibirica Strain P3M-3T, the Sole Representative of the Genus Mobilitalea

Mobilitalea sibirica strain P3M-3^T is a strictly anaerobic, halotolerant, organotrophic bacterium of the family Lachnospiraceae that can utilize various plant-derived polysaccharides as its carbon source. The strain was originally isolated by from a microbial mat in western Siberia (Russia). In this study, we present the draft genome sequence of M. sibirica P3M-3^T based on Illumina paired-end sequencing.

Mobilitalea sibirica strain P3M-3^T is a strictly anaerobic, halotolerant, organotrophic bacterium of the family Lachnospiraceae that can utilize various plant-derived polysaccharides as its carbon source. The strain was originally isolated from a microbial mat in western Siberia (Russia). In this study, we present the draft genome sequence of M. sibirica P3M-3^T based on Illumina paired-end sequencing.

Temporal Responses of Microbial Communities to Anaerobic Soil Disinfestation

Anaerobic soil disinfestation (ASD) is an organic amendment-based management tool for controlling soil-borne plant diseases and is increasingly used in a variety of crops. ASD results in a marked decrease in soil redox potential and other physicochemical changes, and a turnover in the composition of the soil microbiome. Mechanisms of ASD-mediated pathogen control are not fully understood, but appear to depend on the carbon source used to initiate the process and involve a combination of biological (i.e., release of volatile organic compounds) and abiotic (i.e., lowered pH, release of metal ions) factors. In this study, we examined how the soil microbiome changes over time in response to ASD initiated with rice bran, tomato pomace, or red grape pomace as amendments using growth chamber mesocosms that replicate ASD-induced field soil redox conditions. Within 2 days, the soil microbiome rapidly shifted from a diverse assemblage of taxa to being dominated by members of the Firmicutes for all ASD treatments, whereas control mesocosms maintained diverse and more evenly distributed communities. Rice bran and tomato pomace amendments resulted in microbial communities with similar compositions and trajectories that were different from red grape pomace communities. Quantitative PCR showed nitrogenase gene abundances were higher in ASD communities and tended to increase over time, suggesting the potential for altering soil nitrogen availability. These results highlight the need for temporal and functional studies to understand how pathogen suppressive microbial communities assemble and function in ASD-treated soils.

Impact of Fe and Ni Addition on the VFAs' Generation and Process Stability of Anaerobic Fermentation Containing Cd

The effects of Cd, Cd + Fe, and Cd + Ni on the thermophilic anaerobic fermentation of corn stover and cow manure were studied in pilot experiments by investigating the biogas properties, process stability, substrate biodegradation, and microbial properties. The results showed that the addition of Fe and Ni into the Cd-containing fermentation system induced higher cumulative biogas yields and NH₄⁺–N concentrations compared with the only Cd-added group. Ni together with Cd improved and brought forward the peak daily biogas yields, and increased the CH₄ contents to 80.76%. Taking the whole fermentation process into consideration, the promoting impact of the Cd + Ni group was mainly attributed to better process stability, a higher average NH₄⁺–N concentration, and increased utilization of acetate. Adding Fe into the Cd-containing fermentation system increased the absolute abundance of Methanobrevibacter on the 13th day, and Methanobrevibacter and Methanobacterium were found to be positively correlated with the daily biogas yield. This research was expected to provide a basis for the reuse of biological wastes contaminated by heavy metals and a reference for further studies on the influence of compound heavy metals on anaerobic fermentation.

Anaerosacchariphilus polymeriproducens gen. nov., sp. nov., an anaerobic bacterium isolated from a salt field

A Gram-stain-negative oval-rod-shaped, spore-forming anaerobic bacterium, designated as strain MCWD5^T, was isolated from sediment of a salt pond in the Republic of Korea (35° 7' 18″ N 126° 19' 4″ E). The 16S rRNA gene sequence analysis revealed that strain MCWD5^T had low similarity values to members in the family Lachnospiraceae, such as Robinsoniella peoriensis PPC31^T (94.8 %), Ruminococcusgauvreauii CCRI-16110^T (94.2 %) and Lachnotalea glycerini DLD10^T (94.0 %), and its phylogenetic position is unstable. The strain could grow at 20-42 °C (optimum, 38-42 °C), pH 5.5-10.0 (pH 7.0) and with 0-6 % (2.0 %) NaCl. Strain MCWD5^T could not use nitrate, nitrite, sulfate or sulfite as electron acceptors. The strain could utilize various carbohydrates, such as arabinose, cellobiose, glucose, etc., and polymers such as pectin and starch. The major fatty acids of strain MCWD5^T were C14 : 0, C16 : 0, C16 : 1ω7c, C18 : 1ω7c DMA and summed feature 8 (C17 : 1ω8c and/or C17 : 2), which was clearly different from those of related genera. The major polar lipids were diphosphatidyglycerol, phosphatidyglycerol and an unknown phospholipid. Based on the results of phylogenetic, physiologic and chemotaxonomic studies, Anaerosacchariphilus polymeriproducens gen. nov., sp. nov. with the type strain MCWD5^T (=KCTC 15595^T=DSM 105757^T) is proposed in the family Lachnospiraceae.

Variation in the Distribution of Hydrogen Producers from the Clostridiales Order in Biogas Reactors Depending on Different Input Substrates

With growing demand for clean and cheap energy resources, biogas production is emerging as an ideal solution, as it provides relatively cheap and clean energy, while also tackling the problematic production of excessive organic waste from crops and animal agriculture. Behind this process stands a variety of anaerobic microorganisms, which turn organic substrates into valuable biogas. The biogas itself is a mixture of gases, produced mostly as metabolic byproducts of the microorganisms, such as methane, hydrogen, or carbon dioxide. Hydrogen itself figures as a potent bio-fuel, however in many bioreactors it serves as the main substrate of methanogenesis, thus potentially limiting biogas yield. With help of modern sequencing techniques, we tried to evaluate the composition in eight bioreactors using different input materials, showing shifts in the microbial consortia depending on the substrate itself. In this paper, we provide insight on the occurrence of potentially harmful microorganisms such as Clostridium novyi and Clostridium septicum, as well as key genera in hydrogen production, such as Clostridium stercorarium, Mobilitalea sp., Herbinix sp., Herbivorax sp., and Acetivibrio sp.

Influence of CO2 Degassing on the Microbial Community in a Dry Mofette Field in Hartoušov, Czech Republic (Western Eger Rift)

The Cheb Basin (CZ) is a shallow Neogene intracontinental basin filled with fluvial and lacustrine sediments that is located in the western part of the Eger Rift. The basin is situated in a seismically active area and is characterized by diffuse degassing of mantle-derived CO₂ in mofette fields. The Hartoušov mofette field shows a daily CO₂ flux of 23-97 tons of CO₂ released over an area of 0.35 km² and a soil gas concentration of up to 100% CO₂. The present study aims to explore the geo-bio interactions provoked by the influence of elevated CO₂ concentrations on the geochemistry and microbial community of soils and sediments. To sample the strata, two 3-m cores were recovered. One core stems from the center of the degassing structure, whereas the other core was taken 8 m from the ENE and served as an undisturbed reference site. The sites were compared regarding their geochemical features, microbial abundances, and microbial community structures. The mofette site is characterized by a low pH and high TOC/sulfate contents. Striking differences in the microbial community highlight the substantial impact of elevated CO₂ concentrations and their associated side effects on microbial processes. The abundance of microbes did not show a typical decrease with depth, indicating that the uprising CO₂-rich fluid provides sufficient substrate for chemolithoautotrophic anaerobic microorganisms. Illumina MiSeq sequencing of the 16S rRNA genes and multivariate statistics reveals that the pH strongly influences microbial composition and explains around 38.7% of the variance at the mofette site and 22.4% of the variance between the mofette site and the undisturbed reference site. Accordingly, acidophilic microorganisms (e.g., OTUs assigned to Acidobacteriaceae and Acidithiobacillus) displayed a much higher relative abundance at the mofette site than at the reference site. The microbial community at the mofette site is characterized by a high relative abundance of methanogens and taxa involved in sulfur cycling. The present study provides intriguing insights into microbial life and geo-bio interactions in an active seismic region dominated by emanating mantle-derived CO₂-rich fluids, and thereby builds the basis for further studies, e.g., focusing on the functional repertoire of the communities. However, it remains open if the observed patterns can be generalized for different time-points or sites.

Whole-genome sequence data and analysis of type strains 'Pusillimonas nitritireducens' and 'Pusillimonas subterraneus' isolated from nitrate- and radionuclide-contaminated groundwater in Russia

Two strains, 'Pusillimonas nitritireducens' JR1/69-2-13^T and 'Pusillimonas subterraneus' JR1/69-3-13^T, of aerobic, motile, Gram-negative, non-spore-forming, organotrophic, psychrotolerant bacteria were isolated from a sample of nitrate- and radionuclide-contaminated groundwater in Russia. Here we describe the draft genomes of these strains. The sequenced and annotated genome of the strain JR1/69-2-13^T contained 4.3 Mbp with 4108 protein-coding genes. The genome of the strain JR1/69-3-13^T contained 4.5 Mbp with 4260 protein-coding genes. Genome analysis of both strains provides an insight into the genomic basis of their resistance to nitrate, heavy metals and metalloids. The draft genome sequences of strains 'Pusillimonas nitritireducens' JR1/69-2-13^T and 'Pusillimonas subterraneus' JR1/69-3-13^T are available at DDBJ/EMBL/GenBank under the accession nos. https://www.ncbi.nlm.nih.gov/nuccore/PDNV00000000 and https://www.ncbi.nlm.nih.gov/nuccore/PDNW00000000, respectively.

Investigation on hydrogen production from paper sludge without inoculation and its enhancement by Clostridium thermocellum

The feasibility and performance of hydrogen production from paper sludge without inoculation was investigated under thermophilic conditions. The maximum hydrogen production reached 64.32 mM with 7.4% PS. The dynamic changes in bacterial community structures during hydrogen production were investigated by analyzing 16S rDNA gene sequences using high throughput sequencing technology. The results showed that microbial community was dominated by order Clostridiales and Thermoanaerobacterales. Genus Thermoanaerobacterium and Ruminiclostridium played a leading role in the fermentation process, which was responsible for the hydrolysis of PS and hydrogen production. Effect of inoculation with Clostridium thermocellum on hydrogen production from PS was also studied. The results showed that C. thermocellum supplement significantly increased hydrogen yield and holocellulose degradation rate by 96.80% and 32.95%, respectively. In addition, inoculation of C. thermocellum enhanced VFA generation and shortened the lag phase of hydrogen production. The present study lays the foundation on the valorization of waste lignocellulose.

Biodegradation of nonylphenol during aerobic composting of sewage sludge under two intermittent aeration treatments in a full-scale plant

The urbanization and industrialization of cities around the coastal region of the Bohai Sea have produced large amounts of sewage sludge from sewage treatment plants. Research on the biodegradation of nonylphenol (NP) and the influencing factors of such biodegradation during sewage sludge composting is important to control pollution caused by land application of sewage sludge. The present study investigated the effect of aeration on NP biodegradation and the microbe community during aerobic composting under two intermittent aeration treatments in a full-scale plant of sewage sludge, sawdust, and returned compost at a ratio of 6:3:1. The results showed that 65% of NP was biodegraded and that Bacillus was the dominant bacterial species in the mesophilic phase. The amount of NP biodegraded in the mesophilic phase was 68.3%, which accounted for 64.6% of the total amount of biodegraded NP. The amount of NP biodegraded under high-volume aeration was 19.6% higher than that under low-volume aeration. Bacillus was dominant for 60.9% of the composting period under high-volume aeration, compared to 22.7% dominance under low-volume aeration. In the thermophilic phase, high-volume aeration promoted the biodegradation of NP and Bacillus remained the dominant bacterial species. In the cooling and stable phases, the contents of NP underwent insignificant change while different dominant bacteria were observed in the two treatments. NP was mostly biodegraded by Bacillus, and the rate of biodegradation was significantly correlated with the abundance of Bacillus (r = 0.63, p < 0.05). Under aeration, Bacillus remained the dominant bacteria, especially in the thermal phase; this phenomenon possibly increased the biodegradation efficiency of NP. High-volume aeration accelerated the activity and prolonged the survival of Bacillus. The risk of organic pollution could be decreased prior to sewage sludge reuse in soil by adjusting the ventilation strategies of aerobic compost measurements.

Draft Genome Sequence of Roseomonas aestuarii Strain JR1/69-1-13 Isolated from Nitrate- and Radionuclide-Contaminated Groundwater in Russia

The draft genome sequence of Roseomonas aestuarii strain JR1/69-1-13, an aerobic chemoorganotrophic bacterium isolated from nitrate- and radionuclide-contaminated groundwater in Russia, is presented here. The genome was annotated to elucidate the genomic basis for the strain’s adaptation to the environment and its resistance to nitrate, heavy metals, and metalloids.

Draft Genome Sequence of a Dissimilatory U(VI)-Reducing Bacterium, Shewanella xiamenensis Strain DCB2-1, Isolated from Nitrate- and Radionuclide-Contaminated Groundwater in Russia

Here, we describe the draft genome sequence of Shewanella xiamenensis strain DCB2-1, isolated from nitrate- and radionuclide-contaminated groundwater. This strain is able to reduce nitrate, Tc(VII), Cr(VI), Fe(III), and U(VI), and its genome sequence contains several gene sets encoding denitrification, resistance to heavy metals, and reduction of metals and metalloids.

Extremophiles for microbial-electrochemistry applications: A critical review

Extremophiles, notably archaea and bacteria, offer a good platform for treating industrial waste streams that were previously perceived as hostile to the model organisms in microbial electrochemical systems (MESs). Here we present a critical overview of the fundamental and applied biology aspects of halophiles and thermophiles in MESs. The current study suggests that extremophiles enable the MES operations under a seemingly harsh conditions imposed by the physical (pressure, radiation, and temperature) and geochemical extremes (oxygen levels, pH, and salinity). We highlight a need to identify the underpinning mechanisms that define the exceptional electrocatalytic performance of extremophiles in MESs.

Fusimonas intestini gen. nov., sp. nov., a novel intestinal bacterium of the family Lachnospiraceae associated with diabetes in mice

Our previous study shows that an anaerobic intestinal bacterium strain AJ110941^P contributes to type 2 diabetes development in mice. Here we phylogenetically and physiologically characterized this unique mouse gut bacterium. The 16S rRNA gene analysis revealed that the strain belongs to the family Lachnospiraceae but shows low sequence similarities ( < 92.5%) to valid species, and rather formed a distinct cluster with uncultured mouse gut bacteria clones. In metagenomic database survey, the 16S sequence of AJ110941^P also matched with mouse gut-derived datasets (56% of total datasets) with > 99% similarity, suggesting that AJ110941^P-related bacteria mainly reside in mouse digestive tracts. Strain AJ110941^P shared common physiological traits (e.g., Gram-positive, anaerobic, mesophilic, and fermentative growth with carbohydrates) with relative species of the Lachnospiraceae. Notably, the biofilm-forming capacity was found in both AJ110941^P and relative species. However, AJ110941^P possessed far more strong ability to produce biofilm than relative species and formed unique structure of extracellular polymeric substances. Furthermore, AJ110941^P cells are markedly long fusiform-shaped rods (9.0–62.5 µm) with multiple flagella that have never been observed in any other Lachnospiraceae members. Based on the phenotypic and phylogenetic features, we propose a new genus and species, Fusimonas intestini gen. nov., sp. nov. for strain AJ110941^P (FERM BP-11443).

Investigation of foaming causes in three mesophilic food waste digesters: reactor performance and microbial analysis

Foaming negatively affects anaerobic digestion of food waste (FW). To identify the causes of foaming, reactor performance and microbial community dynamics were investigated in three mesophilic digesters treating FW. The digesters were operated under different modes, and foaming was induced with several methods. Proliferation of specific bacteria and accumulation of surface active materials may be the main causes of foaming. Volatile fatty acids (VFAs) and total ammonia nitrogen (TAN) accumulated in these reactors before foaming, which may have contributed to foam formation by decreasing the surface tension of sludge and increasing foam stability. The relative abundance of acid-producing bacteria (Petrimonas, Fastidiosipila, etc.) and ammonia producers (Proteiniphilum, Gelria, Aminobacterium, etc.) significantly increased after foaming, which explained the rapid accumulation of VFAs and NH4+ after foaming. In addition, the proportions of microbial genera known to contribute to foam formation and stabilization significantly increased in foaming samples, including bacteria containing mycolic acid in cell walls (Actinomyces, Corynebacterium, etc.) and those capable of producing biosurfactants (Corynebacterium, Lactobacillus, 060F05-B-SD-P93, etc.). These findings improve the understanding of foaming mechanisms in FW digesters and provide a theoretical basis for further research on effective suppression and early warning of foaming.

Genomics and prevalence of bacterial and archaeal isolates from biogas-producing microbiomes

BACKGROUND

To elucidate biogas microbial communities and processes, the application of high-throughput DNA analysis approaches is becoming increasingly important. Unfortunately, generated data can only partialy be interpreted rudimentary since databases lack reference sequences.

RESULTS

Novel cellulolytic, hydrolytic, and acidogenic/acetogenic Bacteria as well as methanogenic Archaea originating from different anaerobic digestion communities were analyzed on the genomic level to assess their role in biomass decomposition and biogas production. Some of the analyzed bacterial strains were recently described as new species and even genera, namely Herbinix hemicellulosilytica T3/55^T, Herbinix luporum SD1D^T, Clostridium bornimense M2/40^T, Proteiniphilum saccharofermentans M3/6^T, Fermentimonas caenicola ING2-E5B^T, and Petrimonas mucosa ING2-E5A^T. High-throughput genome sequencing of 22 anaerobic digestion isolates enabled functional genome interpretation, metabolic reconstruction, and prediction of microbial traits regarding their abilities to utilize complex bio-polymers and to perform specific fermentation pathways. To determine the prevalence of the isolates included in this study in different biogas systems, corresponding metagenome fragment mappings were done. Methanoculleus bourgensis was found to be abundant in three mesophilic biogas plants studied and slightly less abundant in a thermophilic biogas plant, whereas Defluviitoga tunisiensis was only prominent in the thermophilic system. Moreover, several of the analyzed species were clearly detectable in the mesophilic biogas plants, but appeared to be only moderately abundant. Among the species for which genome sequence information was publicly available prior to this study, only the species Amphibacillus xylanus, Clostridium clariflavum, and Lactobacillus acidophilus are of importance for the biogas microbiomes analyzed, but did not reach the level of abundance as determined for M. bourgensis and D. tunisiensis.

CONCLUSIONS

Isolation of key anaerobic digestion microorganisms and their functional interpretation was achieved by application of elaborated cultivation techniques and subsequent genome analyses. New isolates and their genome information extend the repository covering anaerobic digestion community members.

Stable and Variable Parts of Microbial Community in Siberian Deep Subsurface Thermal Aquifer System Revealed in a Long-Term Monitoring Study

The goal of this work was to study the diversity of microorganisms inhabiting a deep subsurface aquifer system in order to understand their functional roles and interspecies relations formed in the course of buried organic matter degradation. A microbial community of a deep subsurface thermal aquifer in the Tomsk Region, Western Siberia was monitored over the course of 5 years via a 2.7 km deep borehole 3P, drilled down to a Palaeozoic basement. The borehole water discharges with a temperature of ca. 50°C. Its chemical composition varies, but it steadily contains acetate, propionate, and traces of hydrocarbons and gives rise to microbial mats along the surface flow. Community analysis by PCR-DGGE 16S rRNA genes profiling, repeatedly performed within 5 years, revealed several dominating phylotypes consistently found in the borehole water, and highly variable diversity of prokaryotes, brought to the surface with the borehole outflow. The major planktonic components of the microbial community were Desulfovirgula thermocuniculi and Methanothermobacter spp. The composition of the minor part of the community was unstable, and molecular analysis did not reveal any regularity in its variations, except some predominance of uncultured Firmicutes. Batch cultures with complex organic substrates inoculated with water samples were set in order to enrich prokaryotes from the variable part of the community. PCR-DGGE analysis of these enrichments yielded uncultured Firmicutes, Chloroflexi, and Ignavibacteriae. A continuous-flow microaerophilic enrichment culture with a water sample amended with acetate contained Hydrogenophilus thermoluteolus, which was previously detected in the microbial mat developing at the outflow of the borehole. Cultivation results allowed us to assume that variable components of the 3P well community are hydrolytic organotrophs, degrading buried biopolymers, while the constant planktonic components of the community degrade dissolved fermentation products to methane and CO2, possibly via interspecies hydrogen transfer. Occasional washout of minor community components capable of oxygen respiration leads to the development of microbial mats at the outflow of the borehole where residual dissolved fermentation products are aerobically oxidized. Long-term community analysis with the combination of molecular and cultivation techniques allowed us to characterize stable and variable parts of the community and propose their environmental roles.

Mobilisporobacter senegalensis gen. nov., sp. nov., an anaerobic bacterium isolated from tropical shea cake

A Gram-stain positive, endospore-forming, strictly anaerobic bacterium, designated strain Gal1^T, was isolated from shea cake, a waste material from the production of shea butter, originating from Saraya, Senegal. The cells were rod-shaped, slightly curved, and motile with peritrichous flagella. The strain was oxidase-negative and catalase-negative. Growth was observed at temperatures ranging from 15 to 45 °C (optimum 30 °C) and at pH 6.5-9.3 (optimum pH 7.8). The salinity range for growth was 0-3.5 % NaCl (optimum 1 %). Yeast extract was required for growth. Strain Gal1^T fermented various carbohydrates such as mannose, mannitol, arabinose, cellobiose, fructose, glucose, maltose, sucrose, trehalose and lactose and the major end-products were ethanol and acetate. The only major cellular fatty acid was C16 : 0 (19.6 %). The DNA base G+C content of strain Gal1^T was 33.8 mol%. Analysis of the 16S rRNA gene sequence of the isolate indicated that this strain was related to Mobilitalea sibirica DSM 26468^T with 94.27 % similarity, Clostridium populeti ATTC 35295^T with 93.94 % similarity, and Clostridium aminovalericum DSM 1283^T and Anaerosporobacter mobilis DSM 15930^T with 93.63 % similarity. On the basis of phenotypic characteristics, phylogenetic analysis and the results of biochemical and physiological tests, strain Gal1^T was clearly distinguished from closely related genera, and strain Gal1^T can be assigned to a novel species of a new genus for which the name Mobilisporobacter senegalensis gen. nov., sp. nov. is proposed. The type strain is Gal1^T ( = DSM 26537^T = JCM 18753^T).

Herbinix hemicellulosilytica gen. nov., sp. nov., a thermophilic cellulose-degrading bacterium isolated from a thermophilic biogas reactor

Phenotypic and phylogenetic studies were performed on new isolates of a novel Gram-stain-positive, anaerobic, non-sporulating, rod-shaped bacterium isolated from a thermophilic biogas plant. The novel organisms were able to degrade crystalline cellulose. 16S rRNA gene comparative sequence analysis demonstrated that the isolates formed a hitherto unknown subline within the family Lachnospiraceae. As a representative of the whole group of isolates, strain T3/55T was further characterized. The closest relative of T3/55T among the taxa with validly published names is Mobilitalea sibirica, sharing 93.9 % 16S rRNA gene sequence similarity. Strain T3/55T was catalase-negative, indole-negative, and produced acetate, ethanol and propionic acid as major end products from cellulose metabolism. The major cellular fatty acids (>1 %) were 16 : 0 dimethyl acetal, 16 : 0 fatty acid methyl ester and 16 : 0 aldehyde. The DNA G+C content was 36.6 mol%. A novel genus and species, Herbinix hemicellulosilytica gen. nov., sp. nov., is proposed based on phylogenetic analysis and physiological properties of the novel isolate. Strain T3/55T ( = DSM 29228T = CECT 8801T), represents the type strain of Herbinix hemicellulosilytica gen. nov., sp. nov.