keyword
https://read.qxmd.com/read/38517167/tartrate-fermentation-with-h-2-production-by-a-new-member-of-sporomusaceae-enriched-from-rice-paddy-soil
#1
JOURNAL ARTICLE
Luciana Pereira-Mora, Leandro D Guerrero, Leonardo Erijman, Ana Fernández-Scavino
In rice paddies, soil and plant-derived organic matter are degraded anaerobically to methane (CH4 ), a powerful greenhouse gas. The highest rate of methane emission occurs during the reproductive stage of the plant when mostly dicarboxylic acids are exudated by the roots. The emission of methane at this stage depends largely on the cooperative interaction between dicarboxylic acid-fermenting bacteria and methanogenic archaea in the rhizosphere. The fermentation of tartrate, one of the major acids exudated, has been scarcely explored in rice paddy soils...
March 22, 2024: Applied and Environmental Microbiology
https://read.qxmd.com/read/38499204/formation-characterization-of-humin-mediated-anaerobic-granular-sludge-and-enhanced-methanogenic-performance
#2
JOURNAL ARTICLE
Ningli Zhou, Zhixing Xiao, Dan Chen
This study presents a novel method for accelerating the granulation of methanogenic anaerobic granular sludge (AnGS) in an upflow anaerobic sludge blanket (UASB) reactor using solid-phase humin (HM). The results demonstrated that HM-mediated AnGS (HM-AnGS) formed rapidly within 50 days. The increase in particle size, settling velocity and mechanical strength was attributed to the rapid granulation of the HM-AnGS. The maximum methane yield of the HM-AnGS was 5-fold higher than that of the control group...
March 16, 2024: Bioresource Technology
https://read.qxmd.com/read/38486809/functional-prediction-of-proteins-from-the-human-gut-archaeome
#3
JOURNAL ARTICLE
Polina V Novikova, Susheel Bhanu Busi, Alexander J Probst, Patrick May, Paul Wilmes
The human gastrointestinal tract contains diverse microbial communities, including archaea. Among them, Methanobrevibacter smithii represents a highly active and clinically relevant methanogenic archaeon, being involved in gastrointestinal disorders, such as inflammatory bowel disease and obesity. Herein, we present an integrated approach using sequence and structure information to improve the annotation of M. smithii proteins using advanced protein structure prediction and annotation tools, such as AlphaFold2, trRosetta, ProFunc, and DeepFri...
January 2024: ISME Commun
https://read.qxmd.com/read/38468562/isolation-of-an-h-2-dependent-electron-bifurcating-co-2-reducing-megacomplex-with-mvhb-polyferredoxin-from-methanothermobacter-marburgensis
#4
JOURNAL ARTICLE
Shunsuke Nomura, Nicole Paczia, Jörg Kahnt, Seigo Shima
In the hydrogenotrophic methanogenic pathway, formylmethanofuran dehydrogenase (Fmd) catalyzes the formation of formylmethanofuran through reducing CO2 . Heterodisulfide reductase (Hdr) provides two low potential electrons for the Fmd reaction using a flavin-based electron-bifurcating mechanism. [NiFe]-hydrogenase (Mvh) or formate dehydrogenase (Fdh) complexes with Hdr and provides electrons to Hdr from H2 and formate, or the reduced form of F420 , respectively. Recently, an Fdh-Hdr complex was purified as a 3-MDa megacomplex that contained Fmd, and its three-dimensional structure was elucidated by cryo-electron microscopy...
March 12, 2024: FEBS Journal
https://read.qxmd.com/read/38443373/effect-of-model-methanogens-on-the-electrochemical-activity-stability-and-microbial-community-structure-of-geobacter-spp-dominated-biofilm-anodes
#5
JOURNAL ARTICLE
Daniel Dzofou Ngoumelah, Tonje Marita Bjerkan Heggeset, Tone Haugen, Snorre Sulheim, Alexander Wentzel, Falk Harnisch, Jörg Kretzschmar
Combining anaerobic digestion (AD) and microbial electrochemical technologies (MET) in AD-MET holds great potential. Methanogens have been identified as one cause of decreased electrochemical activity and deterioration of Geobacter spp. biofilm anodes. A better understanding of the different interactions between methanogenic genera/species and Geobacter spp. biofilms is needed to shed light on the observed reduction in electrochemical activity and stability of Geobacter spp. dominated biofilms as well as observed changes in microbial communities of AD-MET...
March 5, 2024: NPJ Biofilms and Microbiomes
https://read.qxmd.com/read/38426740/radical-sam-enzyme-pylb-generates-a-lysyl-radical-intermediate-in-the-biosynthesis-of-pyrrolysine-by-using-sam-as-a-cofactor
#6
JOURNAL ARTICLE
Baixu Ma, R David Britt, Lizhi Tao
Pyrrolysine, the 22nd amino acid encoded by the natural genetic code, is essential for methanogenic archaea to catabolize methylamines into methane. The structure of pyrrolysine consists of a methylated pyrroline carboxylate that is linked to the ε-amino group of the l-lysine via an amide bond. The biosynthesis of pyrrolysine requires three enzymes: PylB, PylC, and PylD. PylB is a radical S -adenosyl-l-methionine (SAM) enzyme and catalyzes the first biosynthetic step, the isomerization of l-lysine into methylornithine...
March 1, 2024: Journal of the American Chemical Society
https://read.qxmd.com/read/38387351/landfill-bacteriology-role-in-waste-bioprocessing-elevated-landfill-gaseselimination-and-heat-management
#7
REVIEW
Shalini Dhiman, Kanika Khanna, Jaspreet Kour, Arun Dev Singh, Tamanna Bhardwaj, Kamini Devi, Neerja Sharma, Vinod Kumar, Renu Bhardwaj
This study delves into the critical role of microbial ecosystems in landfills, which are pivotal for handling municipal solid waste (MSW). Within these landfills, a complex interplay of several microorganisms (aerobic/anaerobic bacteria, archaea or methanotrophs), drives the conversion of complex substrates into simplified compounds and complete mineralization into the water, inorganic salts, and gases, including biofuel methane gas. These landfills have dominant biotic and abiotic environments where various bacterial, archaeal, and fungal groups evolve and interact to decompose substrate by enabling hydrolytic, fermentative, and methanogenic processes...
February 21, 2024: Journal of Environmental Management
https://read.qxmd.com/read/38373456/a-low-methane-rice-with-high-yield-potential-realized-via-optimized-carbon-partitioning
#8
JOURNAL ARTICLE
Jia Hu, Mathilde Bettembourg, Lihong Xue, Ronggui Hu, Anna Schnürer, Chuanxin Sun, Yunkai Jin, Jens F Sundström
Global rice cultivation significantly contributes to anthropogenic methane emissions. The methane emissions are caused by methane-producing microorganisms (methanogenic archaea) that are favoured by the anoxic conditions of paddy soils and small carbon molecules released from rice roots. However, different rice cultivars are associated with differences in methane emission rates suggesting that there is a considerable natural variation in this trait. Starting from the hypothesis that sugar allocation within a plant is an important factor influencing both yields and methane emissions, the aim of this study was to produce high-yielding rice lines associated with low methane emissions...
February 17, 2024: Science of the Total Environment
https://read.qxmd.com/read/38365034/magnetite-alleviating-calcification-of-anaerobic-granular-sludge-angs-electron-transfer-enhancement-and-ion-competition
#9
JOURNAL ARTICLE
Linlin Chen, Ruoxuan Yuan, Xiangyang Xu, Liang Zhu
Calcification accompanied by deactivation of anaerobic granular sludge (AnGS) is a continuing challenge for high calcium wastewater treatment. The interaction between Ca2+ and extracellular polymeric substances (EPS) is a precondition for this problem. In this study, magnetite for activity recovery and calcification alleviation simultaneously of AnGS under high calcium stress was investigated. The results showed that, in the presence of magnetite, the relative biogas production increased by 13.2 % with the higher activities of key enzymes involved in methanogenesis...
April 10, 2024: Science of the Total Environment
https://read.qxmd.com/read/38309618/polyphasic-molecular-approach-to-the-characterization-of-methanogens-in-the-saliva-of-tunisian-adults
#10
JOURNAL ARTICLE
Fériel Bouzid, Imen Gtif, Salma Charfeddine, Leila Abid, Najla Kharrat
BACKGROUND: Methanogenic archaea are a minor component of human oral microbiota. Due to their relatively low abundance, the detection of these neglected microorganisms is challenging. OBJECTIVE: This study concerns the presence of methanogens in salivary samples collected from Tunisian adults to evaluate their prevalence and burden using a polyphasic molecular approach. METHODS: A total of 43 saliva samples were included. Metagenomic and standard 16S rRNA sequencing were performed as an initial screening to detect the presence of methanogens in the oral microbiota of Tunisian adults...
February 1, 2024: Anaerobe
https://read.qxmd.com/read/38259075/metabolism-of-novel-potential-syntrophic-acetate-oxidizing-bacteria-in-thermophilic-methanogenic-chemostats
#11
JOURNAL ARTICLE
Yan Zeng, Dan Zheng, Lan-Peng Li, Miaoxiao Wang, Min Gou, Yoichi Kamagata, Ya-Ting Chen, Masaru Konishi Nobu, Yue-Qin Tang
Acetate is a major intermediate in the anaerobic digestion of organic waste to produce CH4 . In methanogenic systems, acetate degradation is carried out by either acetoclastic methanogenesis or syntrophic degradation by acetate oxidizers and hydrogenotrophic methanogens. Due to challenges in the isolation of syntrophic acetate-oxidizing bacteria (SAOB), the diversity and metabolism of SAOB and the mechanisms of their interactions with methanogenic partners are not fully characterized. In this study, the in situ activity and metabolic characteristics of potential SAOB and their interactions with methanogens were elucidated through metagenomics and metatranscriptomics...
January 23, 2024: Applied and Environmental Microbiology
https://read.qxmd.com/read/38253195/the-function-and-keystone-microbiota-in-typical-habitats-under-the-influence-of-anthropogenic-activities-in-baiyangdian-lake
#12
JOURNAL ARTICLE
Hongjie Wang, Zhixin Wang, Jie Yu, Congli Ma, Ling Liu, Dong Xu, Jing Zhang
Microbe is an essential driver in regulating the biochemical cycles of carbon, nitrogen, and sulfur. In freshwater lake, microbial communities and functions are influenced by multiple factors, especially anthropogenic activities. Baiyangdian Lake consisted of various habitats, and was frequently interfered with human activities. In this study, 16 S rRNA sequencing and metagenomic sequencing were performed to characterize the microbial communities, determine keystone taxa and reveal dominated metabolic functions in typical habitats in Baiyangdian Lake...
January 20, 2024: Environmental Research
https://read.qxmd.com/read/38243071/differences-in-regulation-mechanisms-of-glutamine-synthetases-from-methanogenic-archaea-unveiled-by-structural-investigations
#13
JOURNAL ARTICLE
Marie-Caroline Müller, Olivier N Lemaire, Julia M Kurth, Cornelia U Welte, Tristan Wagner
Glutamine synthetases (GS) catalyze the ATP-dependent ammonium assimilation, the initial step of nitrogen acquisition that must be under tight control to fit cellular needs. While their catalytic mechanisms and regulations are well-characterized in bacteria and eukaryotes, only limited knowledge exists in archaea. Here, we solved two archaeal GS structures and unveiled unexpected differences in their regulatory mechanisms. GS from Methanothermococcus thermolithotrophicus is inactive in its resting state and switched on by 2-oxoglutarate, a sensor of cellular nitrogen deficiency...
January 19, 2024: Communications Biology
https://read.qxmd.com/read/38194798/comparison-of-anaerobic-digestion-of-starch-and-petro-based-bioplastic-under-hydrogen-rich-conditions
#14
JOURNAL ARTICLE
Eun Seo Lee, Seon Yeong Park, Chang Gyun Kim
To identify an economically viable waste management system for bioplastics, thermoplastic starch (TPS) and poly(butylene adipate-co-terephthalate) (PBAT) were anaerobically digested under hydrogen (H2 )/carbon dioxide (CO2 ) and nitrogen (N2 ) gas-purged conditions to compare methane (CH4 ) production and biodegradation. Regardless of the type of bioplastics, CH4 production was consistently higher with H2 /CO2 than with N2 . The highest amount of CH4 was produced at 307.74 mL CH4 /g volatile solids when TPS digested with H2 /CO2 ...
January 8, 2024: Waste Management
https://read.qxmd.com/read/38179920/a-shift-between-mineral-and-nonmineral-sources-of-iron-and-sulfur-causes-proteome-wide-changes-in-methanosarcina-barkeri
#15
JOURNAL ARTICLE
Hunter Fausset, Rachel L Spietz, Savannah Cox, Gwendolyn Cooper, Scott Spurzem, Monika Tokmina-Lukaszewska, Jennifer DuBois, Joan B Broderick, Eric M Shepard, Eric S Boyd, Brian Bothner
The methanogenic archaeon Methanosarcina barkeri holds great potential for industrial bio-mining and energy generation technologies. Much of the biochemistry of this microbe is poorly understood, and its characterization will provide a glimpse into biological processes that evolved close to life's origin. The discovery of its ability to extract iron and sulfur from bulk, solid-phase minerals shifted a longstanding paradigm that these elements were inaccessible to biological systems. The full elucidation of this process has the potential to help scientists and engineers extract valuable metals from low-grade ore and mine waste generating energy in the form of methane while doing so...
January 5, 2024: Microbiology Spectrum
https://read.qxmd.com/read/38167520/a-unified-compendium-of-prokaryotic-and-viral-genomes-from-over-300-anaerobic-digestion-microbiomes
#16
JOURNAL ARTICLE
Victor Borin Centurion, Alessandro Rossi, Esteban Orellana, Gabriele Ghiotto, Balázs Kakuk, Maria Silvia Morlino, Arianna Basile, Guido Zampieri, Laura Treu, Stefano Campanaro
BACKGROUND: The anaerobic digestion process degrades organic matter into simpler compounds and occurs in strictly anaerobic and microaerophilic environments. The process is carried out by a diverse community of microorganisms where each species has a unique role and it has relevant biotechnological applications since it is used for biogas production. Some aspects of the microbiome, including its interaction with phages, remains still unclear: a better comprehension of the community composition and role of each species is crucial for a cured understanding of the carbon cycle in anaerobic systems and improving biogas production...
January 2, 2024: Environmental microbiome
https://read.qxmd.com/read/38138100/a-pcr-based-survey-of-methane-cycling-archaea-in-methane-soaked-subsurface-sediments-of-guaymas-basin-gulf-of-california
#17
JOURNAL ARTICLE
John E Hinkle, Paraskevi Mara, David J Beaudoin, Virginia P Edgcomb, Andreas P Teske
The Guaymas Basin in the Gulf of California is characterized by active seafloor spreading, the rapid deposition of organic-rich sediments, steep geothermal gradients, and abundant methane of mixed thermogenic and microbial origin. Subsurface sediment samples from eight drilling sites with distinct geochemical and thermal profiles were selected for DNA extraction and PCR amplification to explore the diversity of methane-cycling archaea in the Guaymas Basin subsurface. We performed PCR amplifications with general (mcrIRD), and ANME-1 specific primers that target the alpha (α) subunit of methyl coenzyme M reductase ( mcrA )...
December 10, 2023: Microorganisms
https://read.qxmd.com/read/38128305/breakdown-of-hardly-degradable-carbohydrates-lignocellulose-in-a-two-stage-anaerobic-digestion-plant-is-favored-in-the-main-fermenter
#18
JOURNAL ARTICLE
Robert Heyer, Patrick Hellwig, Irena Maus, Daniel Walke, Andreas Schlüter, Julia Hassa, Alexander Sczyrba, Tom Tubbesing, Michael Klocke, Torsten Mächtig, Kay Schallert, Ingolf Seick, Udo Reichl, Dirk Benndorf
The yield and productivity of biogas plants depend on the degradation performance of their microbiomes. The spatial separation of the anaerobic digestion (AD) process into a separate hydrolysis and a main fermenter should improve cultivation conditions of the microorganisms involved in the degradation of complex substrates like lignocellulosic biomass (LCB) and, thus, the performance of anaerobic digesters. However, relatively little is known about such two-stage processes. Here, we investigated the process performance of a two-stage agricultural AD over one year, focusing on chemical and technical process parameters and metagenome-centric metaproteomics...
December 17, 2023: Water Research
https://read.qxmd.com/read/38123082/understanding-petroleum-vapor-fate-and-transport-through-high-resolution-analysis-of-two-distinct-vapor-plumes
#19
JOURNAL ARTICLE
Junjie Guan, Jierui Huang, Yue Sun, Chong Li, Yuruo Wan, Guo Wei, Rifeng Kang, Hongwei Pang, Quan Shi, Thomas McHugh, Jie Ma
No field study has provided a detailed characterization of the molecular composition and spatial distribution of a vadose zone plume of petroleum volatile organic compounds (VOCs), which is critical to improve the current understanding of petroleum VOC transport and fate. This is study reports a high-resolution analysis of two distinct vapor plumes emanating from two different light non-aqueous phase liquid (LNAPL) sources (an aliphatic-rich LNAPL for Zone #1vs an aromatic-rich LNAPL for Zone #2) at a large petrochemical site...
December 18, 2023: Science of the Total Environment
https://read.qxmd.com/read/38112444/a-rumen-virosphere-with-implications-of-contribution-to-fermentation-and-methane-production-and-endemism-in-cattle-breeds-and-individuals
#20
JOURNAL ARTICLE
Yoshiaki Sato, Hiroaki Takebe, Kento Tominaga, Jumpei Yasuda, Hajime Kumagai, Hiroyuki Hirooka, Takashi Yoshida
Here, we investigated the individual and breed differences of the rumen viral community in Japanese cattle. In the process, we reconstructed putative novel complete viral genomes related to rumen fiber-degrading bacteria and methanogen. The finding strongly suggests that rumen viruses contribute to cellulose and hemicellulose digestion and methanogenesis. Notably, this study also found that rumen viruses are highly rumen and individual specific, suggesting that rumen viruses may not be transmitted through environmental exposure...
December 19, 2023: Applied and Environmental Microbiology
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