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Senchenkov VY, Lyakhovchenko NS, Nikishin IA, Myagkov DA, Chepurina AA, Polivtseva VN, Abashina TN, Delegan YA, Nikulicheva TB, Nikulin IS, Bogun AG, Solomentsev VI, Solyanikova IP. Whole-Genome Sequencing and Biotechnological Potential Assessment of Two Bacterial Strains Isolated from Poultry Farms in Belgorod, Russia. Microorganisms 2023; 11:2235. [PMID: 37764079 PMCID: PMC10537646 DOI: 10.3390/microorganisms11092235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/25/2023] [Accepted: 08/28/2023] [Indexed: 09/29/2023] Open
Abstract
Bacteria, designated as A1.1 and A1.2, were isolated from poultry waste based on the ability to form ammonia on LB nutrient medium. Whole genome sequencing identified the studied strains as Peribacillus frigoritolerans VKM B-3700D (A1.1) and Bacillus subtilis VKM B-3701D (A1.2) with genome sizes of 5462638 and 4158287 bp, respectively. In the genome of B. subtilis VKM B-3701D, gene clusters of secondary metabolites of bacillin, subtilisin, bacilisin, surfactin, bacilliacin, fengycin, sactipeptide, and ratipeptide (spore killing factor) with potential antimicrobial activity were identified. Clusters of coronimine and peninodin production genes were found in P. frigoritolerans VKM B-3700D. Information on coronimine in bacteria is extremely limited. The study of the individual properties of the strains showed that the cultures are capable of biosynthesis of a number of enzymes, including amylases. The B. subtilis VKM V-3701D inhibited the growth of bacterial test cultures and reduced the growth rate of the mold fungus Aspergillus unguis VKM F-1754 by 70% relative to the control. The antimicrobial activity of P. frigoritolerans VKM V-3700D was insignificant. At the same time, a mixture of cultures P. frigoritolerans VKM B-3700D/B. subtilis VKM B-3701D reduced the growth rate of A. unguis VKM F-1754 by 24.5%. It has been shown that strain A1.1 is able to use nitrogen compounds for assimilation processes. It can be assumed that P. frigoritolerans VKM V-3700D belongs to the group of nitrifying or denitrifying microorganisms, which may be important in developing methods for reducing nitrogen load and eutrophication.
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Affiliation(s)
- Vladislav Yu. Senchenkov
- Department of Biochemistry, Medical Institute, Belgorod State National Research University, 308015 Belgorod, Russia; (V.Y.S.); (N.S.L.)
| | - Nikita S. Lyakhovchenko
- Department of Biochemistry, Medical Institute, Belgorod State National Research University, 308015 Belgorod, Russia; (V.Y.S.); (N.S.L.)
| | - Ilya A. Nikishin
- Department of Biotechnology and Microbiology, Institute of Pharmacy, Chemistry and Biology, Belgorod State National Research University, 308015 Belgorod, Russia
| | - Dmitry A. Myagkov
- Department of Biology, Institute of Pharmacy, Chemistry and Biology, Belgorod State National Research University, 308015 Belgorod, Russia
| | - Anna A. Chepurina
- Department of Biotechnology and Microbiology, Institute of Pharmacy, Chemistry and Biology, Belgorod State National Research University, 308015 Belgorod, Russia
| | - Valentina N. Polivtseva
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center «Pushchino Scientific Center for Biological Research of Russian Academy of Sciences» (FRC PSCBR RAS), 142290 Pushchino, Russia (T.N.A.); (Y.A.D.)
| | - Tatiana N. Abashina
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center «Pushchino Scientific Center for Biological Research of Russian Academy of Sciences» (FRC PSCBR RAS), 142290 Pushchino, Russia (T.N.A.); (Y.A.D.)
| | - Yanina A. Delegan
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center «Pushchino Scientific Center for Biological Research of Russian Academy of Sciences» (FRC PSCBR RAS), 142290 Pushchino, Russia (T.N.A.); (Y.A.D.)
- State Research Center for Applied Microbiology and Biotechnology, 142279 Obolensk, Russia; (A.G.B.); (V.I.S.)
| | | | - Ivan S. Nikulin
- Fund of Innovative Scientific Technologies, 308518 Belgorod, Russia; (T.B.N.); (I.S.N.)
| | - Alexander G. Bogun
- State Research Center for Applied Microbiology and Biotechnology, 142279 Obolensk, Russia; (A.G.B.); (V.I.S.)
| | - Viktor I. Solomentsev
- State Research Center for Applied Microbiology and Biotechnology, 142279 Obolensk, Russia; (A.G.B.); (V.I.S.)
| | - Inna P. Solyanikova
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center «Pushchino Scientific Center for Biological Research of Russian Academy of Sciences» (FRC PSCBR RAS), 142290 Pushchino, Russia (T.N.A.); (Y.A.D.)
- Regional Microbiological Center, Belgorod State National Research University, 308015 Belgorod, Russia
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Mohtadi M, James BR, Krasnoff GR, Davis AP. Removal of stormwater dissolved organic nitrogen through biotransformation using activated carbon. Water Environ Res 2022; 94:e10703. [PMID: 35315959 DOI: 10.1002/wer.10703] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 02/28/2022] [Accepted: 03/03/2022] [Indexed: 06/14/2023]
Abstract
Conventional bioretention systems are not effectively designed to remove stormwater dissolved organic nitrogen (DON). Biotransformation study on five organic nitrogenous compounds with different values for adsorption on coal activated carbon (AC) and bioavailability revealed that adsorption is a greater controlling factor for ammonification than bioavailability. This study also showed three apparent benefits: enhancement of the ammonification rate, ammonification of the bio-recalcitrant organic nitrogenous compounds, for example, pyrrole, and bio-regeneration of the adsorbent (coal AC). Low temperature (4°C) did not impact ammonification of leucine at a velocity of 34 cm/h, but negatively affected it at 61 cm/h. It was also observed that bed media height > 30 cm would not appreciably increase ammonification. Under intermittent wetting/draining conditions, the DON removal efficiency was more than 90%, indicating that DON was successfully removed through concurrent adsorption/ammonification, although generated ammonium in the effluent must be properly addressed. PRACTITIONER POINTS: Coal activated carbon appears a better material for DON ammonification compared with charcoal and quartz sand. A temperature as low as 4°C may not adversely impact DON ammonification at a velocity of 34 cm/h or less. A bed media depth of 30 cm is considered as adequate to promote DON ammonification. A larger depth may not be expected to improve ammonification. Ammonification of the bio-recalcitrant organic nitrogenous compounds, for example, pyrrole, and bio-regeneration of the adsorbent, for example, coal activated carbon, may be achieved.
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Affiliation(s)
- Mehrdad Mohtadi
- Department of Civil and Environmental Engineering, University of Maryland, College Park, Maryland, USA
| | - Bruce R James
- Department of Environmental Science and Technology, University of Maryland, College Park, Maryland, USA
| | - Gregory R Krasnoff
- Department of Civil and Environmental Engineering, University of Maryland, College Park, Maryland, USA
| | - Allen P Davis
- Department of Civil and Environmental Engineering, University of Maryland, College Park, Maryland, USA
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Watanabe K, Kitamura T, Ogata Y, Shindo C, Suda W. Flavobacterium ammonificans sp. nov. and Flavobacterium ammoniigenes sp. nov., ammonifying bacteria isolated from surface river water. Int J Syst Evol Microbiol 2022; 72. [PMID: 35344478 DOI: 10.1099/ijsem.0.005307] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Three aerobic, Gram-stain-negative, non-motile, rod-shaped bacteria, designated as strains SHINM13T, GENT5T and GENT11 were isolated from surface river water (Saitama Prefecture, Japan). SHINM13T and GENT11 were positive for catalase, whereas GENT5T was negative. Phylogenetic analyses based on the 16S rRNA gene (1341 bp) or 40 marker gene (34,513 bp) sequences revealed that the strains formed distinct phylogenetic lineages within the genus Flavobacterium. The three strains shared 99.3-99.6 % 16S rRNA gene sequence similarity among each other. The average nucleotide identity by orthology (OrthoANI) and digital DNA-DNA hybridization (dDDH) values between strains SHINM13T and GENT11 were 96.56 and 82.1 %, respectively, and those between SHINM13T and GENT5T were 83.46 % and 52.9 %, respectively. The major cellular fatty acids were C15 : 1ω6c, iso-C15 : 0, iso-C15 : 1G, anteiso-C15 : 0 and iso-C15 : 0 3-OH. The major polar lipid was phosphatidylethanolamine. SHINM13T and GENT5T contained menaquinone-6 (MK-6) as the predominant respiratory quinone, and their DNA G+C contents were 34.4 and 35.1 mol%, respectively. Genome sequencing of the three isolates revealed a genome size of 2.26-2.40 Mbp. Furthermore, all three isolates converted dissolved organic nitrogen to ammonium during cell growth. On the basis of the results of phenotypic and phylogenetic analyses, strains SHINM13T and GENT11 and GENT5T represent two distinct novel species in the genus Flavobacterium, for which the names Flavobacterium ammonificans sp. nov. (type strain SHINM13T =JCM 34684T =NCIMB 15379T) and Flavobacterium ammoniigenes sp. nov. (type strain GENT5T =JCM 32249T=NCIMB 15380T) are proposed.
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Affiliation(s)
- Keiji Watanabe
- Center for Environmental Science in Saitama, 914 Kamitanadare, Kazo, Saitama 347-0115, Japan
| | - Tatsumi Kitamura
- Ibaraki Kasumigaura Environmental Science Center, 1853 Okijyuku-machi, Tsuchiura, Ibaraki 300-0023, Japan
| | - Yusuke Ogata
- RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Chie Shindo
- RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Wataru Suda
- RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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Liu M, Ma ZL. [Effects of experimental warming on soil nitrogen transformation in alpine scrubland of eastern Qinghai-Tibet Plateau, China]. Ying Yong Sheng Tai Xue Bao 2021; 32:2045-2052. [PMID: 34212610 DOI: 10.13287/j.1001-9332.202106.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
We investigated the effects of warming on soil nitrogen cycling process in alpine scrub ecosystem, with an in-situ simulated warming experiment at Sibiraea angustata alpine scrubland on the eastern Qinghai-Tibet Plateau, China. We examined the responses of soil nitrogen transformation rate to warming in three critical periods (the early, late, and non-growing seasons). The results showed that warming increased soil temperature by 1.2 ℃, but decreased soil moisture by 2.5%. The soil net nitrogen mineralization rates (i.e., ammonification and nitrification) in the growing season were significantly higher than those in the non-growing season. The rates of soil net nitrogen fixation in the non-growing season were significantly higher than that in the growing season. Soil nitrification was the major process of soil nitrogen transformation in the early growing season, while soil ammonification was the major one in the late growing season and non-growing season. The effects of experimental warming on soil nitrogen transformation differed among those three periods. Experimental warming significantly increased soil net ammonification, nitrification, nitrogen mine-ralization and fixation in the early growing season, and enhanced soil net nitrification and nitrogen mineralization in the non-growing season. However, warming significantly decreased soil net nitrification, nitrogen mineralization and fixation in the late growing season and soil net ammonification in the non-growing season. Moreover, warming did not affect soil net nitrogen fixation rates in the non-growing season and soil net nitrification rates in the late growing season. Future climate warming would significantly change soil nitrogen transformation by accelerating soil nitrogen cycling in the alpine scrub ecosystem on the eastern Qinghai-Tibet Plateau.
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Affiliation(s)
- Mei Liu
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang 621000, Sichuan, China
| | - Zhi-Liang Ma
- College of Life Science, China West Normal University, Nanchong 637009, Sichuan, China
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Liu Q, Tang S, Meng X, Zhu H, Zhu Y, Liu D, Shen Q. Proteomic Analysis Demonstrates a Molecular Dialog Between Trichoderma guizhouense NJAU 4742 and Cucumber ( Cucumis sativus L.) Roots: Role in Promoting Plant Growth. Mol Plant Microbe Interact 2021; 34:631-644. [PMID: 33496609 DOI: 10.1094/mpmi-08-20-0240-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Trichoderma is a genus of filamentous fungi that play notable roles in stimulating plant growth after colonizing the root surface. However, the key proteins and molecular mechanisms governing this stimulation have not been completely elucidated. In this study, Trichoderma guizhouense NJAU 4742 was investigated in a hydroponic culture system after interacting with cucumber roots. The total proteins of the fungus were characterized, and the key metabolic pathways along with related genes were analyzed through proteomic and transcriptomic analyses. The roles played by the regulated proteins during the interaction between plants and NJAU 4742 were further examined. The intracellular or extracellular proteins from NJAU 4742 and extracellular proteins from cucumber were quantified, and the high-abundance proteins were determined which were primarily involved in the shikimate pathway (tryptophan, tyrosine, and phenylalanine metabolism, auxin biosynthesis, and secondary metabolite synthesis). Moreover, 15N-KNO3 labeling analysis indicated that NJAU 4742 had a strong ability to convert nitrogenous amino acids, nitrate, nitrile, and amines into ammonia. The auxin synthesis and ammonification metabolism pathways of NJAU 4742 significantly contributed to plant growth. The results of this study demonstrated the crucial metabolic pathways involved in the interactions between Trichoderma spp. and plants.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Qiumei Liu
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, Peoples Republic of China
| | - Siyu Tang
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, Peoples Republic of China
| | - Xiaohui Meng
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, Peoples Republic of China
| | - Han Zhu
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, Peoples Republic of China
| | - Yiyong Zhu
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, Peoples Republic of China
| | - Dongyang Liu
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, Peoples Republic of China
| | - Qirong Shen
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, Peoples Republic of China
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Sato Y, Tanaka E, Hori T, Futamata H, Murofushi K, Takagi H, Akachi T, Miwa T, Inaba T, Aoyagi T, Habe H. Efficient conversion of organic nitrogenous wastewater to nitrate solution driven by comammox Nitrospira. Water Res 2021; 197:117088. [PMID: 33813172 DOI: 10.1016/j.watres.2021.117088] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 03/17/2021] [Accepted: 03/23/2021] [Indexed: 06/12/2023]
Abstract
A bacterium capable of complete ammonia oxidation (comammox) has been widely found in various environments, whereas its industrial application is limited due to the difficulty of cultivation and/or enrichment. We developed a biological system to produce a high-quality nitrate solution for use in hydroponic fertilizer. The system was composed of two separate reactors for ammonification and nitrification and was found to have a stable and efficient performance in the conversion of organic nitrogen to nitrate. To determine the key microbes involved and better understand the system, the microbial communities in the reactors were analyzed by 16S rRNA gene sequencing in combination with a shotgun metagenomic analysis. Canonical ammonia-oxidizing bacteria, which can only catalyze the oxidation of ammonia to nitrite, were detected with negligible relative abundances, while a comammox Nitrospira-related operational taxonomic unit (OTU) dominated the nitrification reactor. Furthermore, the comammox-type ammonia monooxygenase was found to be 500 times more highly expressed than the canonical one by quantitative PCR, indicating that comammox was the main driver of the stable and efficient ammonia oxidation in the system. A microbial co-occurrence analysis revealed a strong positive correlation between Nitrospira and several OTUs, some of which, such as Anaerolinea OTU, have been found to co-exist with comammox Nitrospira in the biofilms of water treatment systems. Given that these OTUs were abundant only on microbe-attached carriers in the system, their co-existence within the biofilm could be beneficial to stabilize the Nitrospira abundance, possibly by physically preventing oxygen exposure as well as cell spillage.
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Affiliation(s)
- Yuya Sato
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki 305-8569, Japan.
| | - Eiji Tanaka
- Department of Eco Farm, IAI Corporation, 577-1 Obane, Shimizu, Shizuoka 424-0103, Japan
| | - Tomoyuki Hori
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki 305-8569, Japan
| | - Hiroyuki Futamata
- Research Institution of Green Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, Shizuoka 422-8529, Japan; Graduate School of Science and Technology, Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu, Shizuoka 432-8011, Japan
| | - Keita Murofushi
- Department of Environment and Energy, Industrial Research Institute of Shizuoka Prefecture, 2078 Makigaya, Aoi-ku, Shizuoka, Shizuoka 421-1298, Japan
| | - Hiroshi Takagi
- Numazu Technical Support Center, Industrial Research Institute of Shizuoka Prefecture, 3981-1 Ohoka, Numazu, Shizuoka 410-0022, Japan
| | - Takuto Akachi
- Department of Eco Farm, IAI Corporation, 577-1 Obane, Shimizu, Shizuoka 424-0103, Japan
| | - Teruhiko Miwa
- Department of Eco Farm, IAI Corporation, 577-1 Obane, Shimizu, Shizuoka 424-0103, Japan
| | - Tomohiro Inaba
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki 305-8569, Japan
| | - Tomo Aoyagi
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki 305-8569, Japan
| | - Hiroshi Habe
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki 305-8569, Japan
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Quistad SD, Doulcier G, Rainey PB. Experimental manipulation of selfish genetic elements links genes to microbial community function. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190681. [PMID: 32200751 PMCID: PMC7133536 DOI: 10.1098/rstb.2019.0681] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Microbial communities underpin the Earth's biological and geochemical processes, but their complexity hampers understanding. Motivated by the challenge of diversity and the need to forge ways of capturing dynamical behaviour connecting genes to function, biologically independent experimental communities comprising hundreds of microbial genera were established from garden compost and propagated on nitrogen-limited minimal medium with cellulose (paper) as sole carbon source. After 1 year of bi-weekly transfer, communities retained hundreds of genera. To connect genes to function, we used a simple experimental manipulation that involved the periodic collection of selfish genetic elements (SGEs) from separate communities, followed by pooling and redistribution across communities. The treatment was predicted to promote amplification and dissemination of SGEs and thus horizontal gene transfer. Confirmation came from comparative metagenomics, which showed the substantive movement of ecologically significant genes whose dynamic across space and time could be followed. Enrichment of genes implicated in nitrogen metabolism, and particularly ammonification, prompted biochemical assays that revealed a measurable impact on community function. Our simple experimental strategy offers a conceptually new approach for unravelling dynamical processes affecting microbial community function. This article is part of the theme issue ‘Conceptual challenges in microbial community ecology’.
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Affiliation(s)
- Steven D Quistad
- Laboratoire de Génétique de l'Evolution, Chemistry, Biology and Innovation (CBI) UMR8231, ESPCI Paris, CNRS, PSL Research University, 10 rue Vauquelin, Paris, France
| | - Guilhem Doulcier
- Laboratoire de Génétique de l'Evolution, Chemistry, Biology and Innovation (CBI) UMR8231, ESPCI Paris, CNRS, PSL Research University, 10 rue Vauquelin, Paris, France
| | - Paul B Rainey
- Laboratoire de Génétique de l'Evolution, Chemistry, Biology and Innovation (CBI) UMR8231, ESPCI Paris, CNRS, PSL Research University, 10 rue Vauquelin, Paris, France.,Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany
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Vuono DC, Read RW, Hemp J, Sullivan BW, Arnone JA, Neveux I, Blank RR, Loney E, Miceli D, Winkler MKH, Chakraborty R, Stahl DA, Grzymski JJ. Resource Concentration Modulates the Fate of Dissimilated Nitrogen in a Dual-Pathway Actinobacterium. Front Microbiol 2019; 10:3. [PMID: 30723459 PMCID: PMC6349771 DOI: 10.3389/fmicb.2019.00003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 01/07/2019] [Indexed: 11/30/2022] Open
Abstract
Respiratory ammonification and denitrification are two evolutionarily unrelated dissimilatory nitrogen (N) processes central to the global N cycle, the activity of which is thought to be controlled by carbon (C) to nitrate (NO3 -) ratio. Here we find that Intrasporangium calvum C5, a novel dual-pathway denitrifier/respiratory ammonifier, disproportionately utilizes ammonification rather than denitrification when grown under low C concentrations, even at low C:NO3 - ratios. This finding is in conflict with the paradigm that high C:NO3 - ratios promote ammonification and low C:NO3 - ratios promote denitrification. We find that the protein atomic composition for denitrification modules (NirK) are significantly cost minimized for C and N compared to ammonification modules (NrfA), indicating that limitation for C and N is a major evolutionary selective pressure imprinted in the architecture of these proteins. The evolutionary precedent for these findings suggests ecological importance for microbial activity as evidenced by higher growth rates when I. calvum grows predominantly using its ammonification pathway and by assimilating its end-product (ammonium) for growth under ammonium-free conditions. Genomic analysis of I. calvum further reveals a versatile ecophysiology to cope with nutrient stress and redox conditions. Metabolite and transcriptional profiles during growth indicate that enzyme modules, NrfAH and NirK, are not constitutively expressed but rather induced by nitrite production via NarG. Mechanistically, our results suggest that pathway selection is driven by intracellular redox potential (redox poise), which may be lowered when resource concentrations are low, thereby decreasing catalytic activity of upstream electron transport steps (i.e., the bc1 complex) needed for denitrification enzymes. Our work advances our understanding of the biogeochemical flexibility of N-cycling organisms, pathway evolution, and ecological food-webs.
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Affiliation(s)
- David C. Vuono
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Reno, NV, United States
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, United States
| | - Robert W. Read
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Reno, NV, United States
| | - James Hemp
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, United States
| | - Benjamin W. Sullivan
- Department of Natural Resources and Environmental Science, University of Nevada, Reno, Reno, NV, United States
| | - John A. Arnone
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Reno, NV, United States
| | - Iva Neveux
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Reno, NV, United States
| | - Robert R. Blank
- Agricultural Research Service, United States Department of Agriculture, Reno, NV, United States
| | - Evan Loney
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Reno, NV, United States
| | - David Miceli
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Reno, NV, United States
| | - Mari-Karoliina H. Winkler
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, United States
| | - Romy Chakraborty
- Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - David A. Stahl
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, United States
| | - Joseph J. Grzymski
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Reno, NV, United States
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Sun Y, De Vos P, Willems A. Influence of nitrate and nitrite concentration on N 2 O production via dissimilatory nitrate/nitrite reduction to ammonium in Bacillus paralicheniformis LMG 6934. Microbiologyopen 2018; 7:e00592. [PMID: 29504271 PMCID: PMC6079178 DOI: 10.1002/mbo3.592] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 12/17/2017] [Accepted: 12/29/2017] [Indexed: 12/28/2022] Open
Abstract
Until now, the exact mechanisms for N2 O production in dissimilatory nitrate/nitrite reduction to ammonium (DNRA) remain underexplored. Previously, we investigated this mechanism in Bacillus licheniformis and Bacillus paralicheniformis, ubiquitous gram-positive bacteria with many industrial applications, and observed significant strain dependency and media dependency in N2 O production which was thought to correlate with high residual NO2- . Here, we further studied the influence of several physicochemical factors on NO3- (or NO2- ) partitioning and N2 O production in DNRA to shed light on the possible mechanisms of N2 O production. The effects of NO3- concentrations under variable or fixed C/N-NO3- ratios, NO2- concentrations under variable or fixed C/N-NO2- ratios, and NH4+ concentrations under fixed C/N-NO3- ratios were tested during anaerobic incubation of soil bacterium B. paralicheniformis LMG 6934 (previously known as B. licheniformis), a strain with a high nitrite reduction capacity. Monitoring of growth, NO3- , NO2- , NH4+ concentration, and N2 O production in physiological tests revealed that NO3- as well as NO2- concentration showed a linear correlation with N2 O production. Increased NO3- concentration under fixed C/N-NO3- ratios, NO2- concentration, and NH4+ concentration had a significant positive effect on NO3- (or NO2- ) partitioning ([N-NH4+ ]/[N-N2 O]) toward N2 O, which may be a consequence of the (transient) accumulation and subsequent detoxification of NO2- . These findings extend the information on several physiological parameters affecting DNRA and provide a basis for further study on N2 O production during this process.
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Affiliation(s)
- Yihua Sun
- Laboratory of MicrobiologyDepartment of Biochemistry and MicrobiologyGhent UniversityGentBelgium
| | - Paul De Vos
- Laboratory of MicrobiologyDepartment of Biochemistry and MicrobiologyGhent UniversityGentBelgium
| | - Anne Willems
- Laboratory of MicrobiologyDepartment of Biochemistry and MicrobiologyGhent UniversityGentBelgium
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Sidorova NA, Popov VL, Lavrukova OS, Prikhod'ko AN, Lyabzina SN, Tikhomirova EI. [The specific features of corpse putrification under the influence of necrobiome enzymatic systems]. Sud Med Ekspert 2017; 60:18-22. [PMID: 28980549 DOI: 10.17116/sudmed201760518-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The objective of the present study was to characterize the specific features of corpse putrification under the influence of necrobiome enzymatic systems depending on the duration of the post-mortem period. We present the results of investigations into the enzymatic activity of the dominant species of microorganisms making up the post-mortem microbiome. The domestic pork carcasses weighing 50-70 kg were used as an experimental putrification model. The study revealed the characteristic features of protein decomposition under the influence of proteolytic enzymes of pseudomonads, bacilli, and clostridia, such as alteration in the amount of necrobionts producing proteases in the entire carcass and its fragments during biodegradation in the air over 30 and 136 days of the post-mortem period. A series of experiments designed to evaluate the effectiveness of protein hydrolysis by necrobionts have demonstrated the dependence of the rate of biodegradation on the environmental temperature, duration of the putrification pocess, and the species composition of the necrobiome.
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Affiliation(s)
- N A Sidorova
- Department of Neurology, Psychiatrics and Microbiology, Petrozavodsk State University, Petrozavodsk, Russia, 185910
| | - V L Popov
- Department of Forensic Medicine and Legal Studies, I.P. Pavlov First Saint-Petersburg State Medical University, Saint-Petersburg, Russia, 197022
| | - O S Lavrukova
- Department of Anatomy, Topographic Anatomy and Emergency Surgery, Pathological Anatomy and Forensic Medicine, Petrozavodsk State University, Petrozavodsk, Russia, 185910
| | - A N Prikhod'ko
- Bureau of Forensic Medical Expertise of Republic Karelia, Petrozavodsk, Russia, 185003
| | - S N Lyabzina
- Department of Zoology and Ecology, Petrozavodsk State University, Petrozavodsk, Russia, 185910
| | - E I Tikhomirova
- Medical Institute, Petrozavodsk State University, Petrozavodsk, Russia, 185910
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Saijai S, Ando A, Inukai R, Shinohara M, Ogawa J. Analysis of microbial community and nitrogen transition with enriched nitrifying soil microbes for organic hydroponics. Biosci Biotechnol Biochem 2016; 80:2247-2254. [PMID: 27351990 DOI: 10.1080/09168451.2016.1200459] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Nitrifying microbial consortia were enriched from bark compost in a water system by regulating the amounts of organic nitrogen compounds and by controlling the aeration conditions with addition of CaCO3 for maintaining suitable pH. Repeated enrichment showed reproducible mineralization of organic nitrogen via the conversion of ammonium ions ( ) and nitrite ions ( ) into nitrate ions ( ). The change in microbial composition during the enrichment was investigated by PCR-DGGE analysis with a focus on prokaryote, ammonia-oxidizing bacteria, nitrite-oxidizing bacteria, and eukaryote cell types. The microbial transition had a simple profile and showed clear relation to nitrogen ions transition. Nitrosomonas and Nitrobacter were mainly detected during and oxidation, respectively. These results revealing representative microorganisms acting in each ammonification and nitrification stages will be valuable for the development of artificial simple microbial consortia for organic hydroponics that consisted of identified heterotrophs and autotrophic nitrifying bacteria.
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Affiliation(s)
- Sakuntala Saijai
- a Division of Applied Life Sciences , Graduate School of Agriculture, Kyoto University , Kyoto , Japan
| | - Akinori Ando
- a Division of Applied Life Sciences , Graduate School of Agriculture, Kyoto University , Kyoto , Japan.,b Research Unit for the Physiological Chemistry , Kyoto University , Kyoto , Japan
| | - Ryuya Inukai
- a Division of Applied Life Sciences , Graduate School of Agriculture, Kyoto University , Kyoto , Japan
| | - Makoto Shinohara
- c National Institute of Vegetable and Tea Science, National Agriculture Research Organization , Tsu , Japan
| | - Jun Ogawa
- a Division of Applied Life Sciences , Graduate School of Agriculture, Kyoto University , Kyoto , Japan.,b Research Unit for the Physiological Chemistry , Kyoto University , Kyoto , Japan
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Decleyre H, Heylen K, Van Colen C, Willems A. Dissimilatory nitrogen reduction in intertidal sediments of a temperate estuary: small scale heterogeneity and novel nitrate-to-ammonium reducers. Front Microbiol 2015; 6:1124. [PMID: 26528270 PMCID: PMC4604302 DOI: 10.3389/fmicb.2015.01124] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 09/28/2015] [Indexed: 11/13/2022] Open
Abstract
The estuarine nitrogen cycle can be substantially altered due to anthropogenic activities resulting in increased amounts of inorganic nitrogen (mainly nitrate). In the past, denitrification was considered to be the main ecosystem process removing reactive nitrogen from the estuarine ecosystem. However, recent reports on the contribution of dissimilatory nitrate reduction to ammonium (DNRA) to nitrogen removal in these systems indicated a similar or higher importance, although the ratio between both processes remains ambiguous. Compared to denitrification, DNRA has been underexplored for the last decades and the key organisms carrying out the process in marine environments are largely unknown. Hence, as a first step to better understand the interplay between denitrification, DNRA and reduction of nitrate to nitrite in estuarine sediments, nitrogen reduction potentials were determined in sediments of the Paulina polder mudflat (Westerschelde estuary). We observed high variability in dominant nitrogen removing processes over a short distance (1.6 m), with nitrous oxide, ammonium and nitrite production rates differing significantly between all sampling sites. Denitrification occurred at all sites, DNRA was either the dominant process (two out of five sites) or absent, while nitrate reduction to nitrite was observed in most sites but never dominant. In addition, novel nitrate-to-ammonium reducers assigned to Thalassospira, Celeribacter, and Halomonas, for which DNRA was thus far unreported, were isolated, with DNRA phenotype reconfirmed through nrfA gene amplification. This study demonstrates high small scale heterogeneity among dissimilatory nitrate reduction processes in estuarine sediments and provides novel marine DNRA organisms that represent valuable alternatives to the current model organisms.
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Affiliation(s)
- Helen Decleyre
- Laboratory of Microbiology (LM-UGent), Department of Biochemistry and Microbiology, Ghent University Ghent, Belgium
| | - Kim Heylen
- Laboratory of Microbiology (LM-UGent), Department of Biochemistry and Microbiology, Ghent University Ghent, Belgium
| | - Carl Van Colen
- Marine Biology Research Group, Department of Biology, Ghent University Ghent, Belgium
| | - Anne Willems
- Laboratory of Microbiology (LM-UGent), Department of Biochemistry and Microbiology, Ghent University Ghent, Belgium
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Heylen K, Keltjens J. Redundancy and modularity in membrane-associated dissimilatory nitrate reduction in Bacillus. Front Microbiol 2012; 3:371. [PMID: 23087684 PMCID: PMC3475470 DOI: 10.3389/fmicb.2012.00371] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2012] [Accepted: 09/28/2012] [Indexed: 11/13/2022] Open
Abstract
The genomes of two phenotypically denitrifying type strains of the genus Bacillus were sequenced and the pathways for dissimilatory nitrate reduction were reconstructed. Results suggest that denitrification proceeds in the periplasmic space and in an analogous fashion as in Gram-negative organisms, yet with the participation of proteins that tend to be membrane-bound or membrane-associated. A considerable degree of functional redundancy was observed with marked differences between B. azotoformans LMG 9581(T) and B. bataviensis LMG 21833(T). In addition to the already characterized menaquinol/cyt c-dependent nitric oxide reductase (Suharti et al., 2001, 2004) of which the encoding genes could be identified now, evidence for another novel nitric oxide reductase (NOR) was found. Also, our analyses confirm earlier findings on branched electron transfer with both menaquinol and cytochrome c as reductants. Quite unexpectedly, both bacilli have the disposal of two parallel pathways for nitrite reduction enabling a life style as a denitrifier and as an ammonifying bacterium.
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Affiliation(s)
- Kim Heylen
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, University of Ghent Gent, Belgium
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