201
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Moll J, Kellner H, Leonhardt S, Stengel E, Dahl A, Bässler C, Buscot F, Hofrichter M, Hoppe B. Bacteria inhabiting deadwood of 13 tree species are heterogeneously distributed between sapwood and heartwood. Environ Microbiol 2018; 20:3744-3756. [PMID: 30109768 DOI: 10.1111/1462-2920.14376] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 07/12/2018] [Accepted: 08/07/2018] [Indexed: 01/02/2023]
Abstract
Deadwood represents an important structural component of forest ecosystems, where it provides diverse niches for saproxylic biota. Although wood-inhabiting prokaryotes are involved in its degradation, knowledge about their diversity and the drivers of community structure is scarce. To explore the effect of deadwood substrate on microbial distribution, the present study focuses on the microbial communities of deadwood logs from 13 different tree species investigated using an amplicon based deep-sequencing analysis. Sapwood and heartwood communities were analysed separately and linked to various relevant wood physico-chemical parameters. Overall, Proteobacteria, Acidobacteria and Actinobacteria represented the most dominant phyla. Microbial OTU richness and community structure differed significantly between tree species and between sapwood and heartwood. These differences were more pronounced for heartwood than for sapwood. The pH value and water content were the most important drivers in both wood compartments. Overall, investigating numerous tree species and two compartments provided a remarkably comprehensive view of microbial diversity in deadwood.
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Affiliation(s)
- Julia Moll
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Halle (Saale), Germany
| | - Harald Kellner
- Department of Bio- and Environmental Sciences, Technical University Dresden - International Institute (IHI) Zittau, Zittau, Germany
| | - Sabrina Leonhardt
- Department of Bio- and Environmental Sciences, Technical University Dresden - International Institute (IHI) Zittau, Zittau, Germany
| | - Elisa Stengel
- Department of Bio- and Environmental Sciences, Technical University Dresden - International Institute (IHI) Zittau, Zittau, Germany.,Department of Animal Ecology and Tropical Biology (Zoology III), University of Würzburg, Field Station Fabrikschleichach, Würzburg, Germany
| | - Andreas Dahl
- Biotechnology Center - Deep Sequencing Group - SFB655, Technical University Dresden, Dresden, Germany
| | - Claus Bässler
- Department of Conservation and Research, Bavarian Forest National Park, Grafenau, Germany.,Department of Ecology and Ecosystem management, Technical University of Munich, Chair for Terrestrial Ecology, Freising, Germany
| | - François Buscot
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Halle (Saale), Germany.,German Centre for Integrative Biodiversity Research (iDiv), Leipzig, Germany
| | - Martin Hofrichter
- Department of Bio- and Environmental Sciences, Technical University Dresden - International Institute (IHI) Zittau, Zittau, Germany
| | - Björn Hoppe
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Halle (Saale), Germany.,Julius Kühn-Institute, Institute for National and International Plant Health, Braunschweig, Germany
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202
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Wei H, Peng C, Yang B, Song H, Li Q, Jiang L, Wei G, Wang K, Wang H, Liu S, Liu X, Chen D, Li Y, Wang M. Contrasting Soil Bacterial Community, Diversity, and Function in Two Forests in China. Front Microbiol 2018; 9:1693. [PMID: 30108560 PMCID: PMC6080587 DOI: 10.3389/fmicb.2018.01693] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 07/06/2018] [Indexed: 12/03/2022] Open
Abstract
Bacteria are the highest abundant microorganisms in the soil. To investigate bacteria community structures, diversity, and functions, contrasting them in four different seasons all the year round with/within two different forest type soils of China. We analyzed soil bacterial community based on 16S rRNA gene sequencing via Illumina HiSeq platform at a temperate deciduous broad-leaved forest (Baotianman, BTM) and a tropical rainforest (Jianfengling, JFL). We obtained 51,137 operational taxonomic units (OTUs) and classified them into 44 phyla and 556 known genera, 18.2% of which had a relative abundance >1%. The composition in each phylum was similar between the two forest sites. Proteobacteria and Acidobacteria were the most abundant phyla in the soil samples between the two forest sites. The Shannon index did not significantly differ among the four seasons at BTM or JFL and was higher at BTM than JFL in each season. The bacteria community at both BTM and JFL showed two significant (P < 0.05) predicted functions related to carbon cycle (anoxygenic photoautotrophy sulfur oxidizing and anoxygenic photoautotrophy) and three significant (P < 0.05) predicted functions related to nitrogen cycle (nitrous denitrificaton, nitrite denitrification, and nitrous oxide denitrification). We provide the basis on how changes in bacterial community composition and diversity leading to differences in carbon and nitrogen cycles at the two forests.
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Affiliation(s)
- Hua Wei
- Center for Ecological Forecasting and Global Change, College of Forestry, Northwest A&F University, Yangling, China.,Medical College, Baoji Vocational Technology College, Baoji, China
| | - Changhui Peng
- Center for Ecological Forecasting and Global Change, College of Forestry, Northwest A&F University, Yangling, China.,Départment des Sciences Biologiques, Institut des Sciences de l'Environnement, Université du Québec à Montréal, Montreal, QC, Canada
| | - Bin Yang
- Center for Ecological Forecasting and Global Change, College of Forestry, Northwest A&F University, Yangling, China
| | - Hanxiong Song
- Center for Ecological Forecasting and Global Change, College of Forestry, Northwest A&F University, Yangling, China
| | - Quan Li
- Center for Ecological Forecasting and Global Change, College of Forestry, Northwest A&F University, Yangling, China
| | - Lin Jiang
- Center for Ecological Forecasting and Global Change, College of Forestry, Northwest A&F University, Yangling, China
| | - Gang Wei
- Center for Ecological Forecasting and Global Change, College of Forestry, Northwest A&F University, Yangling, China
| | - Kefeng Wang
- Center for Ecological Forecasting and Global Change, College of Forestry, Northwest A&F University, Yangling, China
| | - Hui Wang
- Center for Ecological Forecasting and Global Change, College of Forestry, Northwest A&F University, Yangling, China
| | - Shirong Liu
- Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
| | - Xiaojing Liu
- Baotianman Natural Reserve Administration, Neixiang, China
| | - Dexiang Chen
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
| | - Yide Li
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
| | - Meng Wang
- Center for Ecological Forecasting and Global Change, College of Forestry, Northwest A&F University, Yangling, China.,State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, Institute for Peat and Mire Research, Northeast Normal University, Changchun, China
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203
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Lladó Fernández S, Větrovský T, Baldrian P. The concept of operational taxonomic units revisited: genomes of bacteria that are regarded as closely related are often highly dissimilar. Folia Microbiol (Praha) 2018; 64:19-23. [DOI: 10.1007/s12223-018-0627-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 06/12/2018] [Indexed: 02/07/2023]
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204
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Nie Y, Wang M, Zhang W, Ni Z, Hashidoko Y, Shen W. Ammonium nitrogen content is a dominant predictor of bacterial community composition in an acidic forest soil with exogenous nitrogen enrichment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 624:407-415. [PMID: 29262382 DOI: 10.1016/j.scitotenv.2017.12.142] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 12/11/2017] [Accepted: 12/12/2017] [Indexed: 06/07/2023]
Abstract
Soil pH is a dominant factor affecting bacterial community composition in acidic, neutral, and alkaline soils but not in severely acidic soils (pH<4.5). We conducted a nitrogen (N) addition experiment in the field in severely acidic forest soil to determine the response of the soil bacterial community and identified the dominant factor in determining community composition. Using a high-throughput Illumina HiSeq sequencing platform, we found that high levels of N addition significantly decreased soil bacterial diversity and altered the composition of the soil bacterial community. The addition of nitrogen increased the relative abundance of copiotrophic taxa (Proteobacteria and Actinobacteria phyla) but decreased the relative abundance of oligotrophic taxa (Acidobacteria, Verrucomicrobia, Planctomycetes, and WD272). In particular, the relative abundance of N-cycling-related microbes (e.g., Burkholderia and Rhizomicrobium genera) also increased upon addition of N. Our correlation analysis showed that soil ammonium nitrogen concentration, rather than pH or nitrate nitrogen concentration, was a key environmental parameter determining the composition of the soil bacterial community. However, these bacterial response behaviors were observed only in the dry season and not in the wet season, indicating that high temperature and precipitation in the wet season may alleviate the impact of the addition of N on soil bacterial diversity and community composition. These results suggest that the soil bacterial community shifted to copiotrophic taxa with higher N demands under increased N addition in severely acidic forest soil.
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Affiliation(s)
- Yanxia Nie
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China
| | - Mengcen Wang
- Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou 310058, PR China
| | - Wei Zhang
- College of Urban and Environmental Sciences, Peking University, Beijing 100871, PR China
| | - Zhuang Ni
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China; University of Chinese Academy of Sciences, Beijing 10049, PR China
| | - Yasuyuki Hashidoko
- Graduate School of Agriculture, Hokkaido University, Sapporo 060 8589, Japan
| | - Weijun Shen
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China.
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205
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Drivers of microbial community structure in forest soils. Appl Microbiol Biotechnol 2018; 102:4331-4338. [DOI: 10.1007/s00253-018-8950-4] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 03/13/2018] [Accepted: 03/14/2018] [Indexed: 10/17/2022]
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206
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Pent M, Hiltunen M, Põldmaa K, Furneaux B, Hildebrand F, Johannesson H, Ryberg M, Bahram M. Host genetic variation strongly influences the microbiome structure and function in fungal fruiting-bodies. Environ Microbiol 2018; 20:1641-1650. [DOI: 10.1111/1462-2920.14069] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 02/06/2018] [Accepted: 02/07/2018] [Indexed: 02/01/2023]
Affiliation(s)
- Mari Pent
- Institute of Ecology and Earth Sciences; University of Tartu; Tartu Estonia
| | - Markus Hiltunen
- Department of Organismal Biology; Uppsala University; Uppsala Sweden
| | - Kadri Põldmaa
- Institute of Ecology and Earth Sciences; University of Tartu; Tartu Estonia
| | - Brendan Furneaux
- Department of Organismal Biology; Uppsala University; Uppsala Sweden
| | - Falk Hildebrand
- Structural and Computational Biology, European Molecular Biology Laboratory; Heidelberg Germany
| | - Hanna Johannesson
- Department of Organismal Biology; Uppsala University; Uppsala Sweden
| | - Martin Ryberg
- Department of Organismal Biology; Uppsala University; Uppsala Sweden
| | - Mohammad Bahram
- Institute of Ecology and Earth Sciences; University of Tartu; Tartu Estonia
- Department of Organismal Biology; Uppsala University; Uppsala Sweden
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207
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López-Mondéjar R, Brabcová V, Štursová M, Davidová A, Jansa J, Cajthaml T, Baldrian P. Decomposer food web in a deciduous forest shows high share of generalist microorganisms and importance of microbial biomass recycling. ISME JOURNAL 2018; 12:1768-1778. [PMID: 29491492 DOI: 10.1038/s41396-018-0084-2] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Revised: 01/21/2018] [Accepted: 01/27/2018] [Indexed: 01/08/2023]
Abstract
Forest soils represent important terrestrial carbon (C) pools where C is primarily fixed in the plant-derived biomass but it flows further through the biomass of fungi and bacteria before it is lost from the ecosystem as CO2 or immobilized in recalcitrant organic matter. Microorganisms are the main drivers of C flow in forests and play critical roles in the C balance through the decomposition of dead biomass of different origins. Here, we track the path of C that enters forest soil by following respiration, microbial biomass production, and C accumulation by individual microbial taxa in soil microcosms upon the addition of 13C-labeled biomass of plant, fungal, and bacterial origin. We demonstrate that both fungi and bacteria are involved in the assimilation and mineralization of C from the major complex sources existing in soil. Decomposer fungi are, however, better suited to utilize plant biomass compounds, whereas the ability to utilize fungal and bacterial biomass is more frequent among bacteria. Due to the ability of microorganisms to recycle microbial biomass, we suggest that the decomposer food web in forest soil displays a network structure with loops between and within individual pools. These results question the present paradigms describing food webs as hierarchical structures with unidirectional flow of C and assumptions about the dominance of fungi in the decomposition of complex organic matter.
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Affiliation(s)
- Ruben López-Mondéjar
- Institute of Microbiology of the CAS, Průmyslová 595, 252 50, Vestec, Czech Republic
| | - Vendula Brabcová
- Institute of Microbiology of the CAS, Průmyslová 595, 252 50, Vestec, Czech Republic
| | - Martina Štursová
- Institute of Microbiology of the CAS, Průmyslová 595, 252 50, Vestec, Czech Republic
| | - Anna Davidová
- Institute of Microbiology of the CAS, Průmyslová 595, 252 50, Vestec, Czech Republic
| | - Jan Jansa
- Institute of Microbiology of the CAS, Průmyslová 595, 252 50, Vestec, Czech Republic
| | - Tomaš Cajthaml
- Institute of Microbiology of the CAS, Průmyslová 595, 252 50, Vestec, Czech Republic
| | - Petr Baldrian
- Institute of Microbiology of the CAS, Průmyslová 595, 252 50, Vestec, Czech Republic.
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208
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Nguyen STC, Freund HL, Kasanjian J, Berlemont R. Function, distribution, and annotation of characterized cellulases, xylanases, and chitinases from CAZy. Appl Microbiol Biotechnol 2018; 102:1629-1637. [PMID: 29359269 DOI: 10.1007/s00253-018-8778-y] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 01/06/2018] [Accepted: 01/09/2018] [Indexed: 11/30/2022]
Abstract
The enzymatic deconstruction of structural polysaccharides, which relies on the production of specific glycoside hydrolases (GHs), is an essential process across environments. Over the past few decades, researchers studying the diversity and evolution of these enzymes have isolated and biochemically characterized thousands of these proteins. The carbohydrate-active enzymes database (CAZy) lists these proteins and provides some metadata. Here, the sequences and metadata of characterized sequences derived from GH families associated with the deconstruction of cellulose, xylan, and chitin were collected and discussed. First, although few polyspecific enzymes are identified, characterized GH families are mostly monospecific. Next, the taxonomic distribution of characterized GH mirrors the distribution of identified sequences in sequenced genomes. This provides a rationale for connecting the identification of GH sequences to specific reactions or lineages. Finally, we tested the annotation of the characterized GHs using HMM scan and the protein families database (Pfam). The vast majority of GHs targeting cellulose, xylan, and chitin can be identified using this publicly accessible approach.
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Affiliation(s)
- Stanley T C Nguyen
- Department of Biological Sciences, California State University-Long Beach, 1250 Bellflower Blvd., Long Beach, CA, 90840-9502, USA
| | - Hannah L Freund
- Department of Biological Sciences, California State University-Long Beach, 1250 Bellflower Blvd., Long Beach, CA, 90840-9502, USA
| | - Joshua Kasanjian
- Department of Biological Sciences, California State University-Long Beach, 1250 Bellflower Blvd., Long Beach, CA, 90840-9502, USA
| | - Renaud Berlemont
- Department of Biological Sciences, California State University-Long Beach, 1250 Bellflower Blvd., Long Beach, CA, 90840-9502, USA.
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209
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Griffin EA, Carson WP. Tree Endophytes: Cryptic Drivers of Tropical Forest Diversity. ENDOPHYTES OF FOREST TREES 2018. [DOI: 10.1007/978-3-319-89833-9_4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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210
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Sergaki C, Lagunas B, Lidbury I, Gifford ML, Schäfer P. Challenges and Approaches in Microbiome Research: From Fundamental to Applied. FRONTIERS IN PLANT SCIENCE 2018; 9:1205. [PMID: 30174681 PMCID: PMC6107787 DOI: 10.3389/fpls.2018.01205] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 07/26/2018] [Indexed: 05/07/2023]
Abstract
We face major agricultural challenges that remain a threat for global food security. Soil microbes harbor enormous potentials to provide sustainable and economically favorable solutions that could introduce novel approaches to improve agricultural practices and, hence, crop productivity. In this review we give an overview regarding the current state-of-the-art of microbiome research by discussing new technologies and approaches. We also provide insights into fundamental microbiome research that aim to provide a deeper understanding of the dynamics within microbial communities, as well as their interactions with different plant hosts and the environment. We aim to connect all these approaches with potential applications and reflect how we can use microbial communities in modern agricultural systems to realize a more customized and sustainable use of valuable resources (e.g., soil).
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Affiliation(s)
- Chrysi Sergaki
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
- *Correspondence: Chrysi Sergaki,
| | - Beatriz Lagunas
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Ian Lidbury
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Miriam L. Gifford
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
- Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry, United Kingdom
| | - Patrick Schäfer
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
- Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry, United Kingdom
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211
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Kamimura N, Takahashi K, Mori K, Araki T, Fujita M, Higuchi Y, Masai E. Bacterial catabolism of lignin-derived aromatics: New findings in a recent decade: Update on bacterial lignin catabolism. ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:679-705. [PMID: 29052962 DOI: 10.1111/1758-2229.12597] [Citation(s) in RCA: 160] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 09/26/2017] [Accepted: 10/03/2017] [Indexed: 05/21/2023]
Abstract
Lignin is the most abundant phenolic polymer; thus, its decomposition by microorganisms is fundamental to carbon cycling on earth. Lignin breakdown is initiated by depolymerization catalysed by extracellular oxidoreductases secreted by white-rot basidiomycetous fungi. On the other hand, bacteria play a predominant role in the mineralization of lignin-derived heterogeneous low-molecular-weight aromatic compounds. The outline of bacterial catabolic pathways for lignin-derived bi- and monoaryls are typically composed of the following sequential steps: (i) funnelling of a wide variety of lignin-derived aromatics into vanillate and syringate, (ii) O demethylation of vanillate and syringate to form catecholic derivatives and (iii) aromatic ring-cleavage of the catecholic derivatives to produce tricarboxylic acid cycle intermediates. Knowledge regarding bacterial catabolic systems for lignin-derived aromatic compounds is not only important for understanding the terrestrial carbon cycle but also valuable for promoting the shift to a low-carbon economy via biological lignin valorisation. This review summarizes recent progress in bacterial catabolic systems for lignin-derived aromatic compounds, including newly identified catabolic pathways and genes for decomposition of lignin-derived biaryls, transcriptional regulation and substrate uptake systems. Recent omics approaches on catabolism of lignin-derived aromatic compounds are also described.
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Affiliation(s)
- Naofumi Kamimura
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
| | - Kenji Takahashi
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
| | - Kosuke Mori
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
| | - Takuma Araki
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
| | - Masaya Fujita
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
| | - Yudai Higuchi
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
| | - Eiji Masai
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
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212
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Rice SA. Interactions between microbial community members. ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:471-473. [PMID: 28772026 DOI: 10.1111/1758-2229.12571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Affiliation(s)
- Scott A Rice
- The Singapore Centre for Environmental Life Sciences Engineering and the School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- The ithree institute, The University of Technology Sydney, Sydney, NSW, Australia
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