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Degrune F, Theodorakopoulos N, Colinet G, Hiel MP, Bodson B, Taminiau B, Daube G, Vandenbol M, Hartmann M. Temporal Dynamics of Soil Microbial Communities below the Seedbed under Two Contrasting Tillage Regimes. Front Microbiol 2017; 8:1127. [PMID: 28674527 PMCID: PMC5474472 DOI: 10.3389/fmicb.2017.01127] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 06/01/2017] [Indexed: 12/01/2022] Open
Abstract
Agricultural productivity relies on a wide range of ecosystem services provided by the soil biota. Plowing is a fundamental component of conventional farming, but long-term detrimental effects such as soil erosion and loss of soil organic matter have been recognized. Moving towards more sustainable management practices such as reduced tillage or crop residue retention can reduce these detrimental effects, but will also influence structure and function of the soil microbiota with direct consequences for the associated ecosystem services. Although there is increasing evidence that different tillage regimes alter the soil microbiome, we have a limited understanding of the temporal dynamics of these effects. Here, we used high-throughput sequencing of bacterial and fungal ribosomal markers to explore changes in soil microbial community structure under two contrasting tillage regimes (conventional and reduced tillage) either with or without crop residue retention. Soil samples were collected over the growing season of two crops (Vicia faba and Triticum aestivum) below the seedbed (15-20 cm). Tillage, crop and growing stage were significant determinants of microbial community structure, but the impact of tillage showed only moderate temporal dependency. Whereas the tillage effect on soil bacteria showed some temporal dependency and became less strong at later growing stages, the tillage effect on soil fungi was more consistent over time. Crop residue retention had only a minor influence on the community. Six years after the conversion from conventional to reduced tillage, soil moisture contents and nutrient levels were significantly lower under reduced than under conventional tillage. These changes in edaphic properties were related to specific shifts in microbial community structure. Notably, bacterial groups featuring copiotrophic lifestyles or potentially carrying the ability to degrade more recalcitrant compounds were favored under conventional tillage, whereas taxa featuring more oligotrophic lifestyles were more abundant under reduced tillage. Our study found that, under the specific edaphic and climatic context of central Belgium, different tillage regimes created different ecological niches that select for different microbial lifestyles with potential consequences for the ecosystem services provided to the plants and their environment.
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Affiliation(s)
- Florine Degrune
- Microbiology and Genomics, Department of AGROBIOCHEM, Gembloux Agro-Bio Tech, University of LiègeGembloux, Belgium
- TERRA-AgricultureIsLife, Gembloux Agro-Bio Tech, University of LiègeGembloux, Belgium
| | - Nicolas Theodorakopoulos
- Microbiology and Genomics, Department of AGROBIOCHEM, Gembloux Agro-Bio Tech, University of LiègeGembloux, Belgium
| | - Gilles Colinet
- Exchanges Ecosystems – Atmosphere, Department of BIOSE, Gembloux Agro-Bio Tech, University of LiègeGembloux, Belgium
| | - Marie-Pierre Hiel
- Microbiology and Genomics, Department of AGROBIOCHEM, Gembloux Agro-Bio Tech, University of LiègeGembloux, Belgium
- Crop Sciences, Department of AGROBIOCHEM, Gembloux Agro-Bio Tech, University of LiègeGembloux, Belgium
| | - Bernard Bodson
- Crop Sciences, Department of AGROBIOCHEM, Gembloux Agro-Bio Tech, University of LiègeGembloux, Belgium
| | | | - Georges Daube
- Food Microbiology, University of LiègeLiège, Belgium
| | - Micheline Vandenbol
- Microbiology and Genomics, Department of AGROBIOCHEM, Gembloux Agro-Bio Tech, University of LiègeGembloux, Belgium
| | - Martin Hartmann
- Forest Soils and Biogeochemistry, Research Institute for Forest, Snow and Landscape Research WSLBirmensdorf, Switzerland
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Jiménez DJ, Dini-Andreote F, van Elsas JD. Metataxonomic profiling and prediction of functional behaviour of wheat straw degrading microbial consortia. BIOTECHNOLOGY FOR BIOFUELS 2014; 7:92. [PMID: 24955113 PMCID: PMC4064818 DOI: 10.1186/1754-6834-7-92] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Accepted: 05/23/2014] [Indexed: 05/09/2023]
Abstract
BACKGROUND Mixed microbial cultures, in which bacteria and fungi interact, have been proposed as an efficient way to deconstruct plant waste. The characterization of specific microbial consortia could be the starting point for novel biotechnological applications related to the efficient conversion of lignocellulose to cello-oligosaccharides, plastics and/or biofuels. Here, the diversity, composition and predicted functional profiles of novel bacterial-fungal consortia are reported, on the basis of replicated aerobic wheat straw enrichment cultures. RESULTS In order to set up biodegradative microcosms, microbial communities were retrieved from a forest soil and introduced into a mineral salt medium containing 1% of (un)treated wheat straw. Following each incubation step, sequential transfers were carried out using 1 to 1,000 dilutions. The microbial source next to three sequential batch cultures (transfers 1, 3 and 10) were analyzed by bacterial 16S rRNA gene and fungal ITS1 pyrosequencing. Faith's phylogenetic diversity values became progressively smaller from the inoculum to the sequential batch cultures. Moreover, increases in the relative abundances of Enterobacteriales, Pseudomonadales, Flavobacteriales and Sphingobacteriales were noted along the enrichment process. Operational taxonomic units affiliated with Acinetobacter johnsonii, Pseudomonas putida and Sphingobacterium faecium were abundant and the underlying strains were successfully isolated. Interestingly, Klebsiella variicola (OTU1062) was found to dominate in both consortia, whereas K. variicola-affiliated strains retrieved from untreated wheat straw consortia showed endoglucanase/xylanase activities. Among the fungal players with high biotechnological relevance, we recovered members of the genera Penicillium, Acremonium, Coniochaeta and Trichosporon. Remarkably, the presence of peroxidases, alpha-L-fucosidases, beta-xylosidases, beta-mannases and beta-glucosidases, involved in lignocellulose degradation, was indicated by predictive bacterial metagenome reconstruction. Reassuringly, tests for specific (hemi)cellulolytic enzymatic activities, performed on the consortial secretomes, confirmed the presence of such gene functions. CONCLUSION In an in-depth characterization of two wheat straw degrading microbial consortia, we revealed the enrichment and selection of specific bacterial and fungal taxa that were presumably involved in (hemi) cellulose degradation. Interestingly, the microbial community composition was strongly influenced by the wheat straw pretreatment. Finally, the functional bacterial-metagenome prediction and the evaluation of enzymatic activities (at the consortial secretomes) revealed the presence and enrichment of proteins involved in the deconstruction of plant biomass.
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Affiliation(s)
- Diego Javier Jiménez
- Department of Microbial Ecology, Center for Ecological and Evolutionary Studies (CEES), University of Groningen (RUG), Nijenborgh 7, 9747AG Groningen, The Netherlands
| | - Francisco Dini-Andreote
- Department of Microbial Ecology, Center for Ecological and Evolutionary Studies (CEES), University of Groningen (RUG), Nijenborgh 7, 9747AG Groningen, The Netherlands
| | - Jan Dirk van Elsas
- Department of Microbial Ecology, Center for Ecological and Evolutionary Studies (CEES), University of Groningen (RUG), Nijenborgh 7, 9747AG Groningen, The Netherlands
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Deangelis KM, Sharma D, Varney R, Simmons B, Isern NG, Markilllie LM, Nicora C, Norbeck AD, Taylor RC, Aldrich JT, Robinson EW. Evidence supporting dissimilatory and assimilatory lignin degradation in Enterobacter lignolyticus SCF1. Front Microbiol 2013; 4:280. [PMID: 24065962 PMCID: PMC3777014 DOI: 10.3389/fmicb.2013.00280] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Accepted: 08/29/2013] [Indexed: 01/05/2023] Open
Abstract
Lignocellulosic biofuels are promising as sustainable alternative fuels, but lignin inhibits access of enzymes to cellulose, and by-products of lignin degradation can be toxic to cells. The fast growth, high efficiency and specificity of enzymes employed in the anaerobic litter deconstruction carried out by tropical soil bacteria make these organisms useful templates for improving biofuel production. The facultative anaerobe Enterobacter lignolyticus SCF1 was initially cultivated from Cloud Forest soils in the Luquillo Experimental Forest in Puerto Rico, based on anaerobic growth on lignin as sole carbon source. The source of the isolate was tropical forest soils that decompose litter rapidly with low and fluctuating redox potentials, where bacteria using oxygen-independent enzymes likely play an important role in decomposition. We have used transcriptomics and proteomics to examine the observed increased growth of SCF1 grown on media amended with lignin compared to unamended growth. Proteomics suggested accelerated xylose uptake and metabolism under lignin-amended growth, with up-regulation of proteins involved in lignin degradation via the 4-hydroxyphenylacetate degradation pathway, catalase/peroxidase enzymes, and the glutathione biosynthesis and glutathione S-transferase (GST) proteins. We also observed increased production of NADH-quinone oxidoreductase, other electron transport chain proteins, and ATP synthase and ATP-binding cassette (ABC) transporters. This suggested the use of lignin as terminal electron acceptor. We detected significant lignin degradation over time by absorbance, and also used metabolomics to demonstrate moderately significant decreased xylose concentrations as well as increased metabolic products acetate and formate in stationary phase in lignin-amended compared to unamended growth conditions. Our data show the advantages of a multi-omics approach toward providing insights as to how lignin may be used in nature by microorganisms coping with poor carbon availability.
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Affiliation(s)
- Kristen M Deangelis
- Department of Microbiology, University of Massachusetts Amherst Amherst, MA, USA
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Hibi M, Hatahira S, Nakatani M, Yokozeki K, Shimizu S, Ogawa J. Extracellular oxidases of Cerrena sp. complementarily functioning in artificial dye decolorization including laccase, manganese peroxidase, and novel versatile peroxidases. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2012. [DOI: 10.1016/j.bcab.2012.03.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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DeAngelis KM, Allgaier M, Chavarria Y, Fortney JL, Hugenholtz P, Simmons B, Sublette K, Silver WL, Hazen TC. Characterization of trapped lignin-degrading microbes in tropical forest soil. PLoS One 2011; 6:e19306. [PMID: 21559391 PMCID: PMC3084812 DOI: 10.1371/journal.pone.0019306] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2011] [Accepted: 04/01/2011] [Indexed: 02/01/2023] Open
Abstract
Lignin is often the most difficult portion of plant biomass to degrade, with fungi generally thought to dominate during late stage decomposition. Lignin in feedstock plant material represents a barrier to more efficient plant biomass conversion and can also hinder enzymatic access to cellulose, which is critical for biofuels production. Tropical rain forest soils in Puerto Rico are characterized by frequent anoxic conditions and fluctuating redox, suggesting the presence of lignin-degrading organisms and mechanisms that are different from known fungal decomposers and oxygen-dependent enzyme activities. We explored microbial lignin-degraders by burying bio-traps containing lignin-amended and unamended biosep beads in the soil for 1, 4, 13 and 30 weeks. At each time point, phenol oxidase and peroxidase enzyme activity was found to be elevated in the lignin-amended versus the unamended beads, while cellulolytic enzyme activities were significantly depressed in lignin-amended beads. Quantitative PCR of bacterial communities showed more bacterial colonization in the lignin-amended compared to the unamended beads after one and four weeks, suggesting that the lignin supported increased bacterial abundance. The microbial community was analyzed by small subunit 16S ribosomal RNA genes using microarray (PhyloChip) and by high-throughput amplicon pyrosequencing based on universal primers targeting bacterial, archaeal, and eukaryotic communities. Community trends were significantly affected by time and the presence of lignin on the beads. Lignin-amended beads have higher relative abundances of representatives from the phyla Actinobacteria, Firmicutes, Acidobacteria and Proteobacteria compared to unamended beads. This study suggests that in low and fluctuating redox soils, bacteria could play a role in anaerobic lignin decomposition.
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Affiliation(s)
- Kristen M DeAngelis
- Earth Sciences Division, Ecology Department, Lawrence Berkeley National Lab, Berkeley, California, United States of America.
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Two laccase isoenzymes and a peroxidase of a commercial laccase-producing basidiomycete, Trametes sp. Ha1. N Biotechnol 2010; 27:317-23. [DOI: 10.1016/j.nbt.2010.02.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2009] [Revised: 02/10/2010] [Accepted: 02/19/2010] [Indexed: 11/19/2022]
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Almeida CC, Romão CV, Lindley PF, Teixeira M, Saraiva LM. The Role of the Hybrid Cluster Protein in Oxidative Stress Defense. J Biol Chem 2006; 281:32445-50. [PMID: 16928682 DOI: 10.1074/jbc.m605888200] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Hybrid cluster proteins (HCP) contain two types of Fe/S clusters, namely a [4Fe-4S](2+/1+) or [2Fe-2S](2+/1+) cluster and a novel type of hybrid cluster, [4Fe-2S-2O], in the as-isolated state. Although first isolated from anaerobic sulfate-reducing bacteria, the analysis of the genomic sequences reveals that genes encoding putative hybrid cluster proteins are present in a wide range of organisms, aerobic, anaerobic, or facultative, from the Bacteria, Archaea, and Eukarya domains. Despite a detailed spectroscopic and structural characterization, the precise physiological function of these proteins remained unknown. The present work shows that the transcription of the Escherichia coli hcp gene is induced by hydrogen peroxide, and this induction is regulated by the redox-sensitive transcriptional activator, OxyR. The E. coli hcp mutant strain exhibits higher sensitivity to hydrogen peroxide, a behavior that reverts to the wild type phenotype once a plasmid carrying the hcp gene is reintroduced. Furthermore, the purified HCPs from E. coli and Desulfovibrio desulfuricans ATCC 27774 show an alternative enzymatic activity, which under physiological conditions exhibited K(m) values for hydrogen peroxide (approximately 0.3 mM) within the range of other peroxidases. Altogether, the results reveal that HCP is involved in oxidative stress protection.
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Affiliation(s)
- Cláudia C Almeida
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
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Amperometric Flow-Injection Determination of Phenolic Compounds Using a Biosensor with Immobilized Laccase, Peroxidase and Tyrosinase. ELECTROANAL 2005. [DOI: 10.1002/elan.200403343] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Ogawa J, Sulistyaningdyah WT, Tanaka H, Kano K, Ikeda T, Shimizu S. Bilirubin dehydrogenase, an enzyme in Aspergillus ochraceus IB-3 useful for diagnostic measurement of bilirubin. Biosci Biotechnol Biochem 2002; 66:2376-81. [PMID: 12506975 DOI: 10.1271/bbb.66.2376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Bilirubin dehydrogenase, a membrane-bound enzyme that catalyzes the one-step oxidation of ditaurobilirubin and bilirubin to ditaurobiliverdin and biliverdin, respectively, in the presence of an electron acceptor, was found in Aspergillus ochraceus IB-3, and purified from the membrane fraction through solubilization by Triton X-100. Phenazine and quinone derivatives acted as electron acceptors. Accumulation of ditaurobiliverdin and biliverdin by enzyme catalysis increased the absorbance at 660 nm, which is far from the range of wavelengths affected by serum ingredients. The enzyme selectively oxidized ditaurobilirubin at low pH, so changes in the reaction pH enable the enzyme to discriminate between the bilirubin fractions ditaurobilirubin (an example of conjugated bilirubin) and bilirubin (an example of unconjugated bilirubin). Using the enzyme, 2 to 80 microM of ditaurobilirubin were measured accurately by monitoring the changes in absorbance at 660 nm.
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Affiliation(s)
- Jun Ogawa
- Division of Applied Life Sciences, Laboratory of Fermentation Physiology and Applied Microbiology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
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Ogawa J, Takeda S, Xie SX, Hatanaka H, Ashikari T, Amachi T, Shimizu S. Purification, characterization, and gene cloning of purine nucleosidase from Ochrobactrum anthropi. Appl Environ Microbiol 2001; 67:1783-7. [PMID: 11282633 PMCID: PMC92797 DOI: 10.1128/aem.67.4.1783-1787.2001] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A bacterium, Ochrobactrum anthropi, produced a large amount of a nucleosidase when cultivated with purine nucleosides. The nucleosidase was purified to homogeneity. The enzyme has a molecular weight of about 170,000 and consists of four identical subunits. It specifically catalyzes the irreversible N-riboside hydrolysis of purine nucleosides, the K(m) values being 11.8 to 56.3 microM. The optimal activity temperature and pH were 50 degrees C and pH 4.5 to 6.5, respectively. Pyrimidine nucleosides, purine and pyrimidine nucleotides, NAD, NADP, and nicotinamide mononucleotide are not hydrolyzed by the enzyme. The purine nucleoside hydrolyzing activity of the enzyme was inhibited (mixed inhibition) by pyrimidine nucleosides, with K(i) and K(i)' values of 0.455 to 11.2 microM. Metal ion chelators inhibited activity, and the addition of Zn(2+) or Co(2+) restored activity. A 1.5-kb DNA fragment, which contains the open reading frame encoding the nucleosidase, was cloned, sequenced, and expressed in Escherichia coli. The deduced 363-amino-acid sequence including a 22-residue leader peptide is in agreement with the enzyme molecular mass and the amino acid sequences of NH(2)-terminal and internal peptides, and the enzyme is homologous to known nucleosidases from protozoan parasites. The amino acid residues forming the catalytic site and involved in binding with metal ions are well conserved in these nucleosidases.
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Affiliation(s)
- J Ogawa
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
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