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Rat A, Naranjo HD, Krigas N, Grigoriadou K, Maloupa E, Alonso AV, Schneider C, Papageorgiou VP, Assimopoulou AN, Tsafantakis N, Fokialakis N, Willems A. Endophytic Bacteria From the Roots of the Medicinal Plant Alkanna tinctoria Tausch ( Boraginaceae): Exploration of Plant Growth Promoting Properties and Potential Role in the Production of Plant Secondary Metabolites. Front Microbiol 2021; 12:633488. [PMID: 33633713 PMCID: PMC7901983 DOI: 10.3389/fmicb.2021.633488] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 01/13/2021] [Indexed: 11/13/2022] Open
Abstract
Alkannin and shikonin (A/S) are enantiomeric naphthoquinones produced in the roots of certain plants from the Boraginaceae family such as Lithospermum spp. and Alkanna spp. They possess antimicrobial, anti-tumoral and wound healing properties. The production of secondary metabolites by Alkanna tinctoria might be influenced by its endomicrobiome. To study the interaction between this medicinal plant and its bacterial endophytes, we isolated bacteria from the roots of wild growing Alkanna tinctoria collected near to Athens and Thessaloniki in Greece. Representative strains selected by MALDI-TOF mass spectrometry were identified by partial 16S rRNA gene sequence analysis. In total, 197 distinct phylotypes of endophytic bacteria were detected. The most abundant genera recovered were Pseudomonas, Xanthomonas, Variovorax, Bacillus, Inquilinus, Pantoea, and Stenotrophomonas. Several bacteria were then tested in vitro for their plant growth promoting activity and the production of cell-wall degrading enzymes. Strains of Pseudomonas, Pantoea, Bacillus and Inquilinus showed positive plant growth properties whereas those of Bacteroidetes and Rhizobiaceae showed pectinase and cellulase activity in vitro. In addition, bacterial responses to alkannin and shikonin were investigated through resistance assays. Gram negative bacteria were found to be resistant to the antimicrobial properties of A/S, whereas the Gram positives were sensitive. A selection of bacteria was then tested for the ability to induce A/S production in hairy roots culture of A. tinctoria. Four strains belonging to Chitinophaga sp., Allorhizobium sp., Duganella sp., and Micromonospora sp., resulted in significantly more A/S in the hairy roots than the uninoculated control. As these bacteria can produce cell-wall degrading enzymes, we hypothesize that the A/S induction may be related with the plant-bacteria interaction during colonization.
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Affiliation(s)
- Angélique Rat
- Laboratory of Microbiology, Department Biochemistry and Microbiology, Faculty Sciences, Ghent University, Ghent, Belgium
| | - Henry D Naranjo
- Laboratory of Microbiology, Department Biochemistry and Microbiology, Faculty Sciences, Ghent University, Ghent, Belgium
| | - Nikos Krigas
- Laboratory of Conservation and Evaluation of Native and Floricultural Species, Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization Demeter, Thessaloniki, Greece
| | - Katerina Grigoriadou
- Laboratory of Conservation and Evaluation of Native and Floricultural Species, Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization Demeter, Thessaloniki, Greece
| | - Eleni Maloupa
- Laboratory of Conservation and Evaluation of Native and Floricultural Species, Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization Demeter, Thessaloniki, Greece
| | | | | | - Vassilios P Papageorgiou
- Organic Chemistry Laboratory, School of Chemical Engineering, Aristotle University of Thessaloniki and Center of Interdisciplinary Research and Innovation of AUTh (CIRI-AUTh), Natural Products Research Centre of Excellence (NatPro-AUTH), Thessaloniki, Greece
| | - Andreana N Assimopoulou
- Organic Chemistry Laboratory, School of Chemical Engineering, Aristotle University of Thessaloniki and Center of Interdisciplinary Research and Innovation of AUTh (CIRI-AUTh), Natural Products Research Centre of Excellence (NatPro-AUTH), Thessaloniki, Greece
| | - Nikolaos Tsafantakis
- Division of Pharmacognosy and Natural Products Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Athens, Greece
| | - Nikolas Fokialakis
- Division of Pharmacognosy and Natural Products Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Athens, Greece
| | - Anne Willems
- Laboratory of Microbiology, Department Biochemistry and Microbiology, Faculty Sciences, Ghent University, Ghent, Belgium
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102
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Supanakorn G, Varatkowpairote N, Taokaew S, Phisalaphong M. Alginate as Dispersing Agent for Compounding Natural Rubber with High Loading Microfibrillated Cellulose. Polymers (Basel) 2021; 13:polym13030468. [PMID: 33535720 PMCID: PMC7867155 DOI: 10.3390/polym13030468] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 01/27/2021] [Accepted: 01/28/2021] [Indexed: 11/16/2022] Open
Abstract
Natural rubber (NR) reinforced with high loading of microfibrillated cellulose (MFC) was fabricated in the presence of sodium alginate as a thickening and dispersing agent in NR latex. The tensile strength and Young’s moduli of the 50% wt. MFC loading-NR composites were 13.6 and 1085.7 MPa, which were about 11.3- and 329-times enhanced compared with those of the neat NR film. The maximum elongation at 313.3% was obtained from 30% MFC loading, which was a 3.3-fold increase of that of the NR film. The thermal stability of MFC–NR films was slightly reduced, while the glass transition temperature remained unchanged at −64 °C. The MFC–NR films exhibited high water adsorption ability, toluene resistance, and biodegradability.
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Affiliation(s)
- Goragot Supanakorn
- Department of Chemical Engineering, Faculty of Engineering, Chulalongkorn University, Bangkok 10330, Thailand; (G.S.); (N.V.)
| | - Nanthaphak Varatkowpairote
- Department of Chemical Engineering, Faculty of Engineering, Chulalongkorn University, Bangkok 10330, Thailand; (G.S.); (N.V.)
| | - Siriporn Taokaew
- Department of Materials Science and Technology, School of Engineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan;
| | - Muenduen Phisalaphong
- Department of Chemical Engineering, Faculty of Engineering, Chulalongkorn University, Bangkok 10330, Thailand; (G.S.); (N.V.)
- Correspondence: ; Tel.: +66-2218-6875
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103
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Lee SA, Le VV, Ko SR, Lee N, Oh HM, Ahn CY. Mucilaginibacter inviolabilis sp. nov., isolated from the phycosphere of Haematococcus lacustris NIES 144 culture. Int J Syst Evol Microbiol 2021; 71. [PMID: 33502297 DOI: 10.1099/ijsem.0.004668] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, non-motile, rod-shaped, aerobic bacterial strain, designated HC2T, was isolated from the phycosphere of Haematococcus lacustris NIES 144 culture. Strain HC2T was able to grow at pH 4.5-8.0, at 4-32 °C and in the presence of 0-2 % (w/v) NaCl. Phylogenetic analysis of the 16S rRNA gene sequence revealed that strain HC2T was affiliated to the genus Mucilaginibacter and shared the highest sequence similarity with Mucilaginibacter lappiensis ANJKI2T (98.20 %) and Mucilaginibacter sabulilitoris SMS-12T (98.06 %). Strain HC2T contained summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) and iso-C15 : 0 as the major fatty acids (>10.0 %). The major polar lipids were phosphatidylethanolamine, one unidentified aminophospholipid, one unidentified phospholipid, two unidentified aminolipids and four unidentified lipids. The respiratory quinone was menaquinone 7 (MK-7). The genomic DNA G+C content was 42.0 %. On the basis of the phenotypic, chemotaxonomic and phylogenetic characteristics, strain HC2T represents a novel species of the genus Mucilaginibacter, for which the name Mucilaginibacter inviolabilis sp. nov. is proposed. The type strain is HC2T (=KCTC 82084T=JCM 34116T).
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Affiliation(s)
- Sang-Ah Lee
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea.,Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon 34113, Republic of Korea
| | - Ve Van Le
- Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon 34113, Republic of Korea.,Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - So-Ra Ko
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Nakyeong Lee
- School of Chemical & Biomolecular Engineering, Pusan National University, 2 Busandaehak-ro, Geumjeong-gu, Busan 46241, Republic of Korea
| | - Hee-Mock Oh
- Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon 34113, Republic of Korea.,Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Chi-Yong Ahn
- Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon 34113, Republic of Korea.,Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
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104
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Adamczyk M, Rüthi J, Frey B. Root exudates increase soil respiration and alter microbial community structure in alpine permafrost and active layer soils. Environ Microbiol 2021; 23:2152-2168. [PMID: 33393203 DOI: 10.1111/1462-2920.15383] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 12/22/2020] [Accepted: 12/29/2020] [Indexed: 12/15/2022]
Abstract
Due to climate warming, alpine ecosystems are changing rapidly. Ongoing upward migrations of plants and thus an increase of easily decomposable substrates will strongly affect the soil microbiome. To understand how belowground communities will respond to such changes, we set up an incubation experiment with permafrost and active soil layers from northern (NW) and southern (SE) slopes of a mountain ridge on Muot da Barba Peider in the Swiss Alps and incubated them with or without artificial root exudates (AREs) at two temperatures, 4°C or 15°C. The addition of AREs resulted in elevated respiration across all soil types. Bacterial and fungal alpha diversity decreased significantly, coinciding with strong shifts in microbial community structure in ARE-treated soils. These shifts in bacterial community structure were driven by an increased abundance of fast-growing copiotrophic taxa. Fungal communities were predominantly affected by AREs in SE active layer soils and shifted towards fast-growing opportunistic yeast. In contrast, in the colder NW facing active layer and permafrost soils fungal communities were more influenced by temperature changes. These findings demonstrate the sensitivity of soil microbial communities in high alpine ecosystems to climate change and how shifts in these communities may lead to functional changes impacting biogeochemical processes.
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Affiliation(s)
- Magdalene Adamczyk
- Rhizosphere Processes Group, Swiss Federal Research Institute WSL, Birmensdorf, 8903, Switzerland
| | - Joel Rüthi
- Rhizosphere Processes Group, Swiss Federal Research Institute WSL, Birmensdorf, 8903, Switzerland
| | - Beat Frey
- Rhizosphere Processes Group, Swiss Federal Research Institute WSL, Birmensdorf, 8903, Switzerland
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105
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Napieralski SA, Roden EE. The Weathering Microbiome of an Outcropping Granodiorite. Front Microbiol 2021; 11:601907. [PMID: 33381096 PMCID: PMC7767972 DOI: 10.3389/fmicb.2020.601907] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 11/26/2020] [Indexed: 11/13/2022] Open
Abstract
Microorganisms have long been recognized for their capacity to catalyze the weathering of silicate minerals. While the vast majority of studies on microbially mediated silicate weathering focus on organotrophic metabolism linked to nutrient acquisition, it has been recently demonstrated that chemolithotrophic ferrous iron [Fe(II)] oxidizing bacteria (FeOB) are capable of coupling the oxidation of silicate mineral Fe(II) to metabolic energy generation and cellular growth. In natural systems, complex microbial consortia with diverse metabolic capabilities can exist and interact to influence the biogeochemical cycling of essential elements, including iron. Here we combine microbiological and metagenomic analyses to investigate the potential interactions among metabolically diverse microorganisms in the near surface weathering of an outcrop of the Rio Blanco Quartz Diorite (DIO) in the Luquillo Mountains of Puerto Rico. Laboratory based incubations utilizing ground DIO as metabolic energy source for chemolithotrophic FeOB confirmed the ability of FeOB to grow via the oxidation of silicate-bound Fe(II). Dramatically accelerated rates of Fe(II)-oxidation were associated with an enrichment in microorganisms with the genetic capacity for iron oxidizing extracellular electron transfer (EET) pathways. Microbially oxidized DIO displayed an enhanced susceptibility to the weathering activity of organotrophic microorganisms compared to unoxidized mineral suspensions. Our results suggest that chemolithotrophic and organotrophic microorganisms are likely to coexist and contribute synergistically to the overall weathering of the in situ bedrock outcrop.
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Affiliation(s)
| | - Eric E Roden
- Department of Geoscience, University of Wisconsin-Madison, Madison, WI, United States
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106
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Jia T, Wang Y, Chai B. Bacterial Community Characteristics and Enzyme Activities in Bothriochloa ischaemum Litter Over Progressive Phytoremediation Years in a Copper Tailings Dam. Front Microbiol 2020; 11:565806. [PMID: 33408700 PMCID: PMC7779404 DOI: 10.3389/fmicb.2020.565806] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 12/03/2020] [Indexed: 11/13/2022] Open
Abstract
Litter decomposition is the key link between material circulation and energy flow in ecosystems, resulting from the activity of resident microbes and various enzymes. This study investigated enzyme activity in litter and associated microbial community characteristics to help clarify the internal mechanisms associated with litter decomposition, while also providing researchers a scientific basis for soil remediation in mining areas. Results confirmed that the nutrient content of Bothriochloa ischaemum litter significantly increased as phytoremediation years progressed, while enzyme activities in litter varied over different phytoremediation years. During the litter decomposition process, cellulase predominated in the early phytoremediation stage and catalase predominated in the intermediate phytoremediation stage. Obvious differences were found in bacterial community structure and diversity over progressive phytoremediation years. Predominant bacterial genera mainly included Massilia, Sphingomonas, Curtobacterium, Amnibacterium, and Methylobacterium. Moreover, Methylorosula and Jatrophihabitans had relatively higher betweenness centrality, and played important roles in bacterial community positive interactions. Additionally, total nitrogen (TN) and total zinc in soil, sucrase and catalase activity in litter were the main environmental factors that affected the structural framework of bacteria in B. ischaemum litter. However, TN had the greatest overall effect on the structural framework of bacteria in litter. Results from this study can help our understanding of the role that litter plays in degraded ecosystems. Our results also provide a scientific basis for improving poor quality soil in areas affected by copper tailings while also amending ecological restoration efficiency.
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Affiliation(s)
- Tong Jia
- Shanxi Key Laboratory of Ecological Restoration on Loess Plateau, Institute of Loess Plateau, Shanxi University, Taiyuan, China
| | - Yuwen Wang
- Shanxi Key Laboratory of Ecological Restoration on Loess Plateau, Institute of Loess Plateau, Shanxi University, Taiyuan, China
| | - Baofeng Chai
- Shanxi Key Laboratory of Ecological Restoration on Loess Plateau, Institute of Loess Plateau, Shanxi University, Taiyuan, China
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107
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Yadav S, Pandey AK, Dubey SK. Molecular modeling, docking and simulation dynamics of β-glucosidase reveals high-efficiency, thermo-stable, glucose tolerant enzyme in Paenibacillus lautus BHU3 strain. Int J Biol Macromol 2020; 168:371-382. [PMID: 33310096 DOI: 10.1016/j.ijbiomac.2020.12.059] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 11/26/2020] [Accepted: 12/07/2020] [Indexed: 01/10/2023]
Abstract
The enzyme β-glucosidase mediates the rate limiting step of conversion of cellobiose to glucose and thus plays a vital role in the process of cellulose degradation. The present study deals with analysis of the effective novel strain of Paenibacillus lautus BHU3 for identifying high-efficiency thermostable, glucose tolerant β-glucosidases. Seven counterparts with elevated Tm values ranging from 64.6 to 75.8 °C with high thermo-stability, were revealed through this analysis. The blind molecular docking of the model enzymes structures with cellobiose and pNPG gave high negative interaction energies ranging from -11.33 to -13.29 and -6.43 to -9.054 (kcal mol-1), respectively. The enzyme WP_096774744.1 effectively formed 5 hydrogen bonds with the highest interaction energy (-13.29 kcal mol-1) with cellobiose at its catalytic site. Molecular dynamics simulation analysis performed for the WP_096774744.1-pNPG complex predicted Glu5, Arg7, Lue68, Gly69 and Phe325 as the major contributing residues for accomplishing hydrolysis of β-1-4-linkage. Further, the molecular docking of WP_096774744.1 enzyme with glucose revealed a distinct glucose-binding site distant from the substrate-binding site, thus confirming the deficient competitive inhibition by glucose. Hence, WP_096774744.1 β-glucosidase appears to be an efficient enzyme with enhanced activity to biodegrade the cellulosic materials and highly relevant for waste management and various industrial applications.
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Affiliation(s)
- Suman Yadav
- Molecular Ecology Laboratory, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Anand Kumar Pandey
- Department of Biotechnology Engineering, Institute of Engineering and Technology, Bundelkhand University, Jhansi, 284128, India
| | - Suresh Kumar Dubey
- Molecular Ecology Laboratory, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India.
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108
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Chettri D, Verma AK, Verma AK. Innovations in CAZyme gene diversity and its modification for biorefinery applications. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2020; 28:e00525. [PMID: 32963975 PMCID: PMC7490808 DOI: 10.1016/j.btre.2020.e00525] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 08/04/2020] [Accepted: 08/30/2020] [Indexed: 02/07/2023]
Abstract
For sustainable growth, concept of biorefineries as recourse to the "fossil derived" energy source is important. Here, the Carbohydrate Active enZymes (CAZymes) play decisive role in generation of biofuels and related sugar-based products utilizing lignocellulose as a carbon source. Given their industrial significance, extensive studies on the evolution of CAZymes have been carried out. Various bacterial and fungal organisms have been scrutinized for the development of CAZymes, where advance techniques for strain enhancement such as CRISPR and analysis of specific expression systems have been deployed. Specific Omic-based techniques along with protein engineering have been adopted to unearth novel CAZymes and improve applicability of existing enzymes. In-Silico computational research and functional annotation of new CAZymes to synergy experiments are being carried out to devise cocktails of enzymes for use in biorefineries. Thus, with the establishment of these technologies, increased diversity of CAZymes with broad span of functions and applications is seen.
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109
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Tripathy S, Jali P, Parida C, Pradhan C. Study on biodegradability and thermal behaviour of composites using poly lactic acid and gamma-irradiated fibres of Luffa cylindrica. CHEMOSPHERE 2020; 261:127684. [PMID: 32721687 DOI: 10.1016/j.chemosphere.2020.127684] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 07/08/2020] [Accepted: 07/10/2020] [Indexed: 06/11/2023]
Abstract
Surface modification of natural fibres by gamma irradiation is an economical and potent technique. The biodegradability of gamma irradiated Luffa cylindrica (LC) fibres having response of doses (0.5Gy, 1Gy and 2Gy) is studied. The degradation process is carried out in various environments like compost, sand, soil, salt water, brackish water and sweet water for a period of 90 days and microbial degradation using bacteria and fungi for a period of 90 days. The rate of biodegradation was calculated by measuring the loss of weight of composites at an interval of 30 days in each environmental condition. Preliminary results reported that the bacterial environment was the most prominent medium for degradation than fungi. B8 composites showed degradation of 27.5% and 3.59 in bacterial and fungal medium respectively. A minimum degradation was observed in compost medium (0.29%, 2.52%, 0.21%, 0.08%, 0.11%, 0.13%, 0.17%, 1.25% and 1.51% for B1-B9 respectively). For exploring the use of the composites in the field of biomedical sciences, the LC fibres are modified using calcium salts before reinforcement. The thermal properties like crystallization temperature (Tcc), glass transition temperature (Tg), melting peak temperature (Tm) and thermal stability of the bio-composites were analyzed using Differential scanning calorimetry (DSC) in temperature range from 30 °C to 250 °C and the thermogravimetric analysis (TGA) was done in the temperature range of 20 °C to 700 °C. With increase in irradiation dose, crystallization temperature and glass transition temperature increased. Increasing in the irradiation dose, thermal stability of the composites decreased.
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Affiliation(s)
| | - Pallavi Jali
- Department of Botany, Utkal University, Bhubaneswar, Odisha, India
| | - Chhatrapati Parida
- Department of Physics, College of Basic Sciences and Humanities, OUAT, Bhubaneswar, Odisha, India
| | - Chinmay Pradhan
- Department of Botany, Utkal University, Bhubaneswar, Odisha, India.
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110
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Wu X, Shang Y, Wei Q, Chen J, Zhang H, Chen Y, Gao X, Wang Z, Zhang H. Gut Microbiota in Dholes During Estrus. Front Microbiol 2020; 11:575731. [PMID: 33329438 PMCID: PMC7734286 DOI: 10.3389/fmicb.2020.575731] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 11/09/2020] [Indexed: 12/11/2022] Open
Abstract
The co-evolution of gut microbes and the host plays a vital role in the survival and reproduction of the host. The dhole (Cuon alpinus) has been listed as endangered species by the International Union for Conservation of Nature; therefore, conservation and effective breeding of dholes are essential. Effective estrus can promote reproduction. However, little is known about the relative contribution of estrus in shaping the structure and the functions of fecal microbiota. Here, we investigated the potential association between estrus and the fecal microbiota in dholes using shotgun metagenomic sequencing. We found that the estrus stages in dholes vary significantly in terms of gut bacterial composition and microbiome metabolism and function. Compared with that of non-estrus, adult dholes, the microbiome of estrus adult dholes had a significantly higher abundance of Bacillus faecalis and Veillonella, which play a key role in the synthesis of sex hormones and nucleic acids, energy production, and reproductive cell division. The insulin and energy metabolism-related pathways are significantly enhanced in the gut microbes and the related gluconeogenic enzymes are significantly enriched during estrus. These findings suggest that the structure and metagenome of the fecal microbiome during estrus have a significant effect in promoting estrus in dholes, thus providing a new perspective for dhole conservation.
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Affiliation(s)
- Xiaoyang Wu
- College of Life Sciences, Qufu Normal University, Qufu, China
| | - Yongquan Shang
- College of Life Sciences, Qufu Normal University, Qufu, China
| | - Qinguo Wei
- College of Life Sciences, Qufu Normal University, Qufu, China
| | - Jun Chen
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Huanxin Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yao Chen
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xiaodong Gao
- College of Life Sciences, Qufu Normal University, Qufu, China
| | - Zhiyong Wang
- Shijiazhuang Wildlife Conservation Center, Shijiazhuang, China
| | - Honghai Zhang
- College of Life Sciences, Qufu Normal University, Qufu, China
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111
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Fast Spectrophotometric Method as Alternative for CuO Oxidation to Assess Lignin in Soils with Different Tree Cover. FORESTS 2020. [DOI: 10.3390/f11121262] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Given the ongoing climate change, estimating the amount of less degradable plant compounds that can be stored in the soil, such as lignin, is a topic of primary importance. There are few methods applicable to soils for the determination of lignin, such as the copper oxide (CuO) oxidation method (CuOL). Acetyl bromide spectrophotometric lignin (ABSL) could be a valid alternative providing information that is less detailed compared to CuOL, but it offers data on the bulk amount of lignin and may offer a valid, fast, and cheap alternative to the CuO method. The aim of this work was to compare ABSL with the CuO method on several soils receiving plant residues from different trees. Mineral soil samples from 0 to 10 cm depth were obtained from a former agricultural site in northern Italy (Brusciana, Tuscany), where different tree plantations were established 22 years ago. The plantations were white poplar and common walnut, which were also intercropped with other species such as hazelnut, Italian alder, and autumn olive. Soil samples under these plantations were also compared to soil under an adjacent agricultural field. In general, the amount of lignin in the afforested stands was approximately double than in the agricultural field as determined by either method. The two methods returned a largely different scale of values due to their different mechanisms of action. The acid-to-aldehyde ratio of syringyl structural units highlights that forest plantation provides a plant input material that is more slowly oxidatively degraded compared to arable soil. A linear mixed model proved that ABSL performed well in relation to CuOL, especially when considering the random variation in the model given by the plantation field design. In conclusion, ABSL can be considered a valid proxy of soil C pool derived from structural plant component, although further analyses are needed.
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112
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Steiner E, Margesin R. Production and partial characterization of a crude cold-active cellulase (CMCase) from Bacillus mycoides AR20-61 isolated from an Alpine forest site. ANN MICROBIOL 2020. [DOI: 10.1186/s13213-020-01607-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Purpose
To evaluate the production of a cold-active CMCase (endoglucanase) by Bacillus mycoides AR20-61 isolated from Alpine forest soil and to characterize the crude enzyme.
Methods
After studying the effect of cultivation parameters (medium composition, temperature, NaCl concentration, pH) on bacterial growth and enzyme production, the crude enzyme was characterized with regard to the effect of pH, temperature, and inhibitors on enzyme activity and stability.
Result
Optimum growth and enzyme production occurred at 20–25 °C, pH 7, and 1–1.5% (w/v) CMC. Despite high biomass production over the whole growth temperature range (10–35 °C), enzyme production was low at 10 and 35 °C. CMC concentration had a minor effect on growth, independent of the growth temperature, but a significant effect on CMCase production at temperatures ≥ 20 °C. The crude enzyme was active over a broad temperature range (0–60 °C); the apparent optimum temperature for activity was at 40–50 °C. The cultivation temperature influenced the effect of temperature on enzyme activity and stability. A significantly higher thermosensitivity of the enzyme produced at a cultivation temperature of 10 °C compared to that produced at 25 °C was noted at 50 and 65 °C. The enzyme was highly active over a pH range of 4–6 and showed optimum activity at pH 5. No activity was lost after 60 min of incubation at 30 °C and pH 4–9. The CMCase was resistant against a number of monovalent and divalent metal ions, metal-chelating agents, and phenol.
Conclusion
The CMCase produced by the studied strain is characterized by high activities in the low temperature range (down to 0 °C) and acidic pH range, high stability over a broad pH range, and high resistance against a number of effectors. Our results also demonstrate the different, independent roles of temperature in bacterial growth, enzyme production, nutrient requirements during enzyme production, and enzyme characteristics regarding thermosensitivity, which has not yet been described for cellulases.
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Evdokimova EV, Gladkov GV, Kuzina NI, Ivanova EA, Kimeklis AK, Zverev AO, Kichko AA, Aksenova TS, Pinaev AG, Andronov EE. The difference between cellulolytic 'culturomes' and microbiomes inhabiting two contrasting soil types. PLoS One 2020; 15:e0242060. [PMID: 33216789 PMCID: PMC7678988 DOI: 10.1371/journal.pone.0242060] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 10/27/2020] [Indexed: 11/18/2022] Open
Abstract
High-throughput 16S rRNA sequencing was performed to compare the microbiomes inhabiting two contrasting soil types-sod-podzolic soil and chernozem-and the corresponding culturome communities of potentially cellulolytic bacteria cultured on standard Hutchinson media. For each soil type, soil-specific microorganisms have been identified: for sod-podzolic soil-Acidothermus, Devosia, Phenylobacterium and Tumebacillus, and for chernozem soil-Sphingomonas, Bacillus and Blastococcus. The dynamics of differences between soil types for bulk soil samples and culturomes varied depending on the taxonomic level of the corresponding phylotypes. At high taxonomic levels, the number of common taxa between soil types increased more slowly for bulk soil than for culturome. Differences between soil-specific phylotypes were detected in bulk soil at a low taxonomic level (genus, species). A total of 13 phylotypes were represented both in soil and in culturome. No relationship was shown between the abundance of these phylotypes in soil and culturome.
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Affiliation(s)
- Elizaveta V. Evdokimova
- Saint-Petersburg State University, Saint-Petersburg, Russia
- All-Russia research institute for agricultural microbiology, Saint-Petersburg, Russia
| | - Grigory V. Gladkov
- Saint-Petersburg State University, Saint-Petersburg, Russia
- All-Russia research institute for agricultural microbiology, Saint-Petersburg, Russia
| | - Natalya I. Kuzina
- All-Russia research institute for agricultural microbiology, Saint-Petersburg, Russia
| | | | - Anastasiia K. Kimeklis
- Saint-Petersburg State University, Saint-Petersburg, Russia
- All-Russia research institute for agricultural microbiology, Saint-Petersburg, Russia
| | - Aleksei O. Zverev
- Saint-Petersburg State University, Saint-Petersburg, Russia
- All-Russia research institute for agricultural microbiology, Saint-Petersburg, Russia
| | - Arina A. Kichko
- Saint-Petersburg State University, Saint-Petersburg, Russia
- All-Russia research institute for agricultural microbiology, Saint-Petersburg, Russia
| | - Tatyana S. Aksenova
- All-Russia research institute for agricultural microbiology, Saint-Petersburg, Russia
| | - Alexander G. Pinaev
- All-Russia research institute for agricultural microbiology, Saint-Petersburg, Russia
| | - Evgeny E. Andronov
- Saint-Petersburg State University, Saint-Petersburg, Russia
- All-Russia research institute for agricultural microbiology, Saint-Petersburg, Russia
- Dokuchaev Soil Institute, Moscow, Russia
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Díaz-García L, Bugg TDH, Jiménez DJ. Exploring the Lignin Catabolism Potential of Soil-Derived Lignocellulolytic Microbial Consortia by a Gene-Centric Metagenomic Approach. MICROBIAL ECOLOGY 2020; 80:885-896. [PMID: 32572536 DOI: 10.1007/s00248-020-01546-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 06/15/2020] [Indexed: 05/25/2023]
Abstract
An exploration of the ligninolytic potential of lignocellulolytic microbial consortia can improve our understanding of the eco-enzymology of lignin conversion in nature. In this study, we aimed to detect enriched lignin-transforming enzymes on metagenomes from three soil-derived microbial consortia that were cultivated on "pre-digested" plant biomass (wheat straw, WS1-M; switchgrass, SG-M; and corn stover, CS-M). Of 60 selected enzyme-encoding genes putatively involved in lignin catabolism, 20 genes were significantly abundant in WS1-M, CS-M, and/or SG-M consortia compared with the initial forest soil inoculum metagenome (FS1). These genes could be involved in lignin oxidation (e.g., superoxide dismutases), oxidative stress responses (e.g., catalase/peroxidases), generation of protocatechuate (e.g., vanAB genes), catabolism of gentisate, catechol and 3-phenylpropionic acid (e.g., gentisate 1,2-dioxygenases, muconate cycloisomerases, and hcaAB genes), the beta-ketoadipate pathway (e.g., pcaIJ genes), and tolerance to lignocellulose-derived inhibitors (e.g., thymidylate synthases). The taxonomic affiliation of 22 selected lignin-transforming enzymes from WS1-M and CS-M consortia metagenomes revealed that Pseudomonadaceae, Alcaligenaceae, Sphingomonadaceae, Caulobacteraceae, Comamonadaceae, and Xanthomonadaceae are the key bacterial families in the catabolism of lignin. A predictive "model" was sketched out, where each microbial population has the potential to metabolize an array of aromatic compounds through different pathways, suggesting that lignin catabolism can follow a "task division" strategy. Here, we have established an association between functions and taxonomy, allowing a better understanding of lignin transformations in soil-derived lignocellulolytic microbial consortia, and pinpointing some bacterial taxa and catabolic genes as ligninolytic trait-markers.
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Affiliation(s)
- Laura Díaz-García
- Microbiomes and Bioenergy Research Group, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | | | - Diego Javier Jiménez
- Microbiomes and Bioenergy Research Group, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia.
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Santos-Júnior CD, Sarmento H, de Miranda FP, Henrique-Silva F, Logares R. Uncovering the genomic potential of the Amazon River microbiome to degrade rainforest organic matter. MICROBIOME 2020; 8:151. [PMID: 33126925 PMCID: PMC7597016 DOI: 10.1186/s40168-020-00930-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 10/06/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND The Amazon River is one of the largest in the world and receives huge amounts of terrestrial organic matter (TeOM) from the surrounding rainforest. Despite this TeOM is typically recalcitrant (i.e. resistant to degradation), only a small fraction of it reaches the ocean, pointing to a substantial TeOM degradation by the river microbiome. Yet, microbial genes involved in TeOM degradation in the Amazon River were barely known. Here, we examined the Amazon River microbiome by analysing 106 metagenomes from 30 sampling points distributed along the river. RESULTS We constructed the Amazon River basin Microbial non-redundant Gene Catalogue (AMnrGC) that includes ~ 3.7 million non-redundant genes, affiliating mostly to bacteria. We found that the Amazon River microbiome contains a substantial gene-novelty compared to other relevant known environments (rivers and rainforest soil). Genes encoding for proteins potentially involved in lignin degradation pathways were correlated to tripartite tricarboxylates transporters and hemicellulose degradation machinery, pointing to a possible priming effect. Based on this, we propose a model on how the degradation of recalcitrant TeOM could be modulated by labile compounds in the Amazon River waters. Our results also suggest changes of the microbial community and its genomic potential along the river course. CONCLUSIONS Our work contributes to expand significantly our comprehension of the world's largest river microbiome and its potential metabolism related to TeOM degradation. Furthermore, the produced gene catalogue (AMnrGC) represents an important resource for future research in tropical rivers. Video abstract.
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Affiliation(s)
- Célio Dias Santos-Júnior
- Molecular Biology Laboratory, Department of Genetics and Evolution – DGE, Universidade Federal de São Carlos – UFSCar, Rod. Washington Luis KM 235 - Monjolinho, São Carlos, SP 13565-905 Brazil
- Institute of Science and Technology for Brain-Inspired Intelligence – ISTBI, Fudan University, Handan Rd 220, Wu Jiao Chang, Yangpu, Shanghai, 200433 China
| | - Hugo Sarmento
- Laboratory of Microbial Processes & Biodiversity, Department of Hydrobiology – DHB, Universidade Federal de São Carlos – UFSCar, Via Washington Luis KM 235 - Monjolinho, São Carlos, SP 13565-905 Brazil
| | - Fernando Pellon de Miranda
- Centro de Pesquisas e Desenvolvimento Leopoldo Américo Miguez de Mello, Petróleo Brasileiro S.A. (Petrobras), Av. Horácio Macedo 950, Rio de Janeiro, RJ 21941-915 Brazil
| | - Flávio Henrique-Silva
- Molecular Biology Laboratory, Department of Genetics and Evolution – DGE, Universidade Federal de São Carlos – UFSCar, Rod. Washington Luis KM 235 - Monjolinho, São Carlos, SP 13565-905 Brazil
| | - Ramiro Logares
- Institute of Marine Sciences (ICM), CSIC, Passeig Marítim de la Barceloneta 37-49, ES08003, Barcelona, Catalonia Spain
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116
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Metabarcoding Analysis of Bacterial Communities Associated with Media Grow Bed Zones in an Aquaponic System. Int J Microbiol 2020; 2020:8884070. [PMID: 33061984 PMCID: PMC7547338 DOI: 10.1155/2020/8884070] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 09/21/2020] [Indexed: 12/14/2022] Open
Abstract
The development of environmentally sustainable plant and fish production in aquaponic systems requires a complete understanding of the systems' biological components. In order to better understand the role of microorganisms in this association, we studied the bacterial communities in the dry, root, and mineralized zones of a flood-and-drain media bed aquaponic system. Bacterial communities were characterized using metabarcoding of the V3-V4 16S rRNA regions obtained from paired-end Illumina MiSeq reads. Proteobacteria, Actinobacteria, and Bacteroidetes accounted for more than 90% of the total community in the dry zone and the effluent water. These phyla also accounted for more than 68% of the total community in the root and mineralized zones. The genera Massilia, Mucilaginibacter, Mizugakiibacter, and Rhodoluna were most dominant in the dry, root, and mineralized zones and in the effluent water, respectively. The number of shared operational taxonomic units (OTUs) for the three zones was 241, representing 7.15% of the total observed OTUs. The number of unique OTUs in samples from dry zone, root zone, mineralized zone, and effluent water was 485, 638, 445, and 383, respectively. The samples from the root zone harbored more diverse communities than either the dry or mineralized zones. This study is the first to report on the bacterial community within the zones of a flood-and-drain media bed. Thus, this information will potentially accelerate studies on other microbial communities involved in the bioconversion of nitrogen compounds and mineralization within these types of aquaponic systems.
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Prada-Salcedo LD, Wambsganss J, Bauhus J, Buscot F, Goldmann K. Low root functional dispersion enhances functionality of plant growth by influencing bacterial activities in European forest soils. Environ Microbiol 2020; 23:1889-1906. [PMID: 32959469 DOI: 10.1111/1462-2920.15244] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 09/16/2020] [Accepted: 09/18/2020] [Indexed: 11/29/2022]
Abstract
Current studies show that multispecies forests are beneficial regarding biodiversity and ecosystem functionality. However, there are only little efforts to understand the ecological mechanisms behind these advantages of multispecies forests. Bacteria are among the key plant growth-promoting microorganisms that support tree growth and fitness. Thus, we investigated links between bacterial communities, their functionality and root trait dispersion within four major European forest types comprising multispecies and monospecific plots. Bacterial diversity revealed no major changes across the root functional dispersion gradient. In contrast, predicted gene profiles linked to plant growth activities suggest an increasing bacterial functionality from monospecific to multispecies forest. In multispecies forest plots, the bacterial functionality linked to plant growth activities declined with the increasing functional dispersion of the roots. Our findings indicate that enriched abundant bacterial operational taxonomic units are decoupled from bacterial functionality. We also found direct effects of tree species identity on bacterial community composition but no significant relations with root functional dispersion. Additionally, bacterial network analyses indicated that multispecies forests have a higher complexity in their bacterial communities, which points towards more stable forest systems with greater functionality. We identified a potential of root dispersion to facilitate bacterial interactions and consequently, plant growth activities.
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Affiliation(s)
- Luis Daniel Prada-Salcedo
- Department of Soil Ecology, Helmholtz-Centre for Environmental Research - UFZ, Halle (Saale), Theodor-Lieser-Straße 4, 06120, Germany.,Department of Biology, University of Leipzig, Leipzig, Johannisallee 21, 04103, Germany
| | - Janna Wambsganss
- Chair of Silviculture, Faculty of Environment and Natural Resources, University of Freiburg, Freiburg, Tennenbacherstr. 4, 79085, Germany.,Chair of Geobotany, Faculty of Biology, University of Freiburg, Freiburg, Schänzlestraße 1, 79104, Germany
| | - Jürgen Bauhus
- Chair of Silviculture, Faculty of Environment and Natural Resources, University of Freiburg, Freiburg, Tennenbacherstr. 4, 79085, Germany
| | - François Buscot
- Department of Soil Ecology, Helmholtz-Centre for Environmental Research - UFZ, Halle (Saale), Theodor-Lieser-Straße 4, 06120, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Deutscher Platz 5e, 04103, Germany
| | - Kezia Goldmann
- Department of Soil Ecology, Helmholtz-Centre for Environmental Research - UFZ, Halle (Saale), Theodor-Lieser-Straße 4, 06120, Germany
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118
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Malik A, Kim YR, Kim SB. Genome Mining of the Genus Streptacidiphilus for Biosynthetic and Biodegradation Potential. Genes (Basel) 2020; 11:genes11101166. [PMID: 33022985 PMCID: PMC7601586 DOI: 10.3390/genes11101166] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 09/26/2020] [Accepted: 09/29/2020] [Indexed: 12/23/2022] Open
Abstract
The genus Streptacidiphilus represents a group of acidophilic actinobacteria within the family Streptomycetaceae, and currently encompasses 15 validly named species, which include five recent additions within the last two years. Considering the potential of the related genera within the family, namely Streptomyces and Kitasatospora, these relatively new members of the family can also be a promising source for novel secondary metabolites. At present, 15 genome data for 11 species from this genus are available, which can provide valuable information on their biology including the potential for metabolite production as well as enzymatic activities in comparison to the neighboring taxa. In this study, the genome sequences of 11 Streptacidiphilus species were subjected to the comparative analysis together with selected Streptomyces and Kitasatospora genomes. This study represents the first comprehensive comparative genomic analysis of the genus Streptacidiphilus. The results indicate that the genomes of Streptacidiphilus contained various secondary metabolite (SM) producing biosynthetic gene clusters (BGCs), some of them exclusively identified in Streptacidiphilus only. Several of these clusters may potentially code for SMs that may have a broad range of bioactivities, such as antibacterial, antifungal, antimalarial and antitumor activities. The biodegradation capabilities of Streptacidiphilus were also explored by investigating the hydrolytic enzymes for complex carbohydrates. Although all genomes were enriched with carbohydrate-active enzymes (CAZymes), their numbers in the genomes of some strains such as Streptacidiphilus carbonis NBRC 100919T were higher as compared to well-known carbohydrate degrading organisms. These distinctive features of each Streptacidiphilus species make them interesting candidates for future studies with respect to their potential for SM production and enzymatic activities.
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Affiliation(s)
- Adeel Malik
- Department of Microbiology and Molecular Biology, Chungnam National University, Daejeon 34134, Korea; (A.M.); (Y.R.K.)
- Institute of Intelligence Informatics Technology, Sangmyung University, Seoul 03016, Korea
| | - Yu Ri Kim
- Department of Microbiology and Molecular Biology, Chungnam National University, Daejeon 34134, Korea; (A.M.); (Y.R.K.)
| | - Seung Bum Kim
- Department of Microbiology and Molecular Biology, Chungnam National University, Daejeon 34134, Korea; (A.M.); (Y.R.K.)
- Correspondence:
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Genomic and Transcriptome Analyses of a Thermophilic Bacterium Geobacillus stearothermophilus B5 Isolated from Compost Reveal Its Enzymatic Basis for Lignocellulose Degradation. Microorganisms 2020; 8:microorganisms8091357. [PMID: 32899798 PMCID: PMC7564440 DOI: 10.3390/microorganisms8091357] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 09/01/2020] [Accepted: 09/03/2020] [Indexed: 02/02/2023] Open
Abstract
A lignocellulose-degrading strain isolated from thermophilic compost was identified as Geobacillus stearothermophilus B5, and found able to secrete considerable amounts of enzymes at optimal temperature (60 °C) and pH (7.5). One circular contig of 3.37 Mbp was assembled from raw data, and 3371 protein-coding genes were predicted. Clusters of orthologous groups (COG) analysis revealed various genes with functions in polymeric substrate degradation, especially for Carbohydrate Active enZymes (CAZymes), such as glycoside hydrolases (GHs) and glycosyl transferases (GTs). Furthermore, the transcriptional responses of B5 at different temperatures—with rice straw provided as the sole carbon source—were analyzed. The results revealed that B5 could resist high temperature by upregulating heat shock proteins (HSPs), enhancing protein synthesis, and decreasing carbon catabolism. Briefly, B5 possesses the ability of lignocellulose degradation, and might be considered a potential inoculant for improving composting efficiency.
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120
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Starke R, Morais D, Větrovský T, López Mondéjar R, Baldrian P, Brabcová V. Feeding on fungi: genomic and proteomic analysis of the enzymatic machinery of bacteria decomposing fungal biomass. Environ Microbiol 2020; 22:4604-4619. [PMID: 32743948 DOI: 10.1111/1462-2920.15183] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 07/21/2020] [Accepted: 07/31/2020] [Indexed: 11/29/2022]
Abstract
Dead fungal biomass is an abundant source of nutrition in both litter and soil of temperate forests largely decomposed by bacteria. Here, we have examined the utilization of dead fungal biomass by the five dominant bacteria isolated from the in situ decomposition of fungal mycelia using a multiOMIC approach. The genomes of the isolates encoded a broad suite of carbohydrate-active enzymes, peptidases and transporters. In the extracellular proteome, only Ewingella americana expressed chitinases while the two Pseudomonas isolates attacked chitin by lytic chitin monooxygenase, deacetylation and deamination. Variovorax sp. expressed enzymes acting on the side-chains of various glucans and the chitin backbone. Surprisingly, despite its genomic potential, Pedobacter sp. did not produce extracellular proteins to decompose fungal mycelia but presumably feeds on simple substrates. The ecological roles of the five individual strains exhibited complementary features for a fast and efficient decomposition of dead fungal biomass by the entire bacterial community.
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Affiliation(s)
- Robert Starke
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Daniel Morais
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Tomáš Větrovský
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Ruben López Mondéjar
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Vendula Brabcová
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
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Reynaud C, Thoury M, Dazzi A, Latour G, Scheel M, Li J, Thomas A, Moulhérat C, Didier A, Bertrand L. In-place molecular preservation of cellulose in 5,000-year-old archaeological textiles. Proc Natl Acad Sci U S A 2020; 117:19670-19676. [PMID: 32747556 PMCID: PMC7443972 DOI: 10.1073/pnas.2004139117] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The understanding of fossilization mechanisms at the nanoscale remains extremely challenging despite its fundamental interest and its implications for paleontology, archaeology, geoscience, and environmental and material sciences. The mineralization mechanism by which cellulosic, keratinous, and silk tissues fossilize in the vicinity of archaeological metal artifacts offers the most exquisite preservation through a mechanism unexplored on the nanoscale. It is at the center of the vast majority of ancient textiles preserved under nonextreme conditions, known through extremely valuable fragments. Here we show the reconstruction of the nanoscale mechanism leading to the preservation of an exceptional collection of ancient cellulosic textiles recovered in the ancient Near East (4,000 to 5,000 years ago). We demonstrate that even the most mineralized fibers, which contain inorganic compounds throughout their histology, enclose preserved cellulosic remains in place. We evidence a process that combines the three steps of water transport of biocidal metal cations and soil solutes, degradation and loss of crystallinity of cellulosic polysaccharides, and silicification.
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Affiliation(s)
- Corentin Reynaud
- Université Paris-Saclay, CNRS, Ministère de la Culture, UVSQ, Institut photonique d'analyse non-destructive européen des matériaux anciens, 91192, Saint-Aubin, France
| | - Mathieu Thoury
- Université Paris-Saclay, CNRS, Ministère de la Culture, UVSQ, Institut photonique d'analyse non-destructive européen des matériaux anciens, 91192, Saint-Aubin, France
| | - Alexandre Dazzi
- Université Paris-Saclay, CNRS, Institut de Chimie Physique, 91405, Orsay, France
| | - Gaël Latour
- Laboratoire d'Optique et Biosciences, École Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128 Palaiseau, France
- Université Paris-Saclay, 91190, Saint-Aubin, France
| | - Mario Scheel
- Synchrotron SOLEIL, 91192 Gif-sur-Yvette, France
| | - Jiayi Li
- Université Paris-Saclay, CNRS, Ministère de la Culture, UVSQ, Institut photonique d'analyse non-destructive européen des matériaux anciens, 91192, Saint-Aubin, France
| | | | | | - Aurore Didier
- Archéologies et Sciences de l'Antiquité, CNRS, UMR 7041, Univ Paris-Nanterre, Univ. Paris I Panthéon-Sorbonne, Ministère de la Culture, 92000 Nanterre, France
| | - Loïc Bertrand
- Université Paris-Saclay, CNRS, Ministère de la Culture, UVSQ, Institut photonique d'analyse non-destructive européen des matériaux anciens, 91192, Saint-Aubin, France;
- Synchrotron SOLEIL, 91192 Gif-sur-Yvette, France
- Université Paris-Saclay, ENS Paris-Saclay, CNRS, Photophysique et Photochimie Supramoléculaires et Macromoléculaires, 91190 Gif-sur-Yvette, France
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122
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Long-term decomposition of litter in the montane forest and the definition of fungal traits in the successional space. FUNGAL ECOL 2020. [DOI: 10.1016/j.funeco.2020.100913] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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123
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Jia T, Guo T, Chai B. Bacterial community characteristics and enzyme activities in Imperata cylindrica litter as phytoremediation progresses in a copper tailings dam. PeerJ 2020; 8:e9612. [PMID: 33194335 PMCID: PMC7391973 DOI: 10.7717/peerj.9612] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 07/06/2020] [Indexed: 12/04/2022] Open
Abstract
This study analyzed Imperata cylindrica litter to determine variation in bacterial community composition and function along with enzyme activity as phytoremediation progresses. We found significant differences in physical and chemical properties of soil and litter in the different sub-dams investigated. The Actinobacteria, Gammaproteobacteria and Alphaproteobacteria were the dominant bacteria found in the litter of the different sub-dams. The alpha diversity (α-diversity) of litter bacterial community increased over as phytoremediation progressed, while total soil carbon and total litter carbon content were positively correlated to bacterial α-diversity. Total litter carbon and total nitrogen were the key factors that influenced bacterial community structure. Heavy metal can influence the degradation of litters by altering the composition of the microbial community. Furthermore, bacterial communities encoded with alpha-amylase (α-amylase) dominated during the initial phytoremediation stage; however, bacterial communities encoded with hemicellulase and peroxidase gradually dominated as phytoremediation progressed. Findings from this study provide a basis for exploring litter decomposition mechanisms in degraded ecosystems, which is critically important to understand the circulation of substances in copper tailings dams.
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Affiliation(s)
- Tong Jia
- Shanxi Key Laboratory of Ecological Restoration on Loess Plateau, Institute of Loess Plateau, Shanxi University, Taiyuan, China
| | - Tingyan Guo
- Shanxi Key Laboratory of Ecological Restoration on Loess Plateau, Institute of Loess Plateau, Shanxi University, Taiyuan, China
| | - Baofeng Chai
- Shanxi Key Laboratory of Ecological Restoration on Loess Plateau, Institute of Loess Plateau, Shanxi University, Taiyuan, China
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Comparative Genomic Study of Polar Lichen-Associated Hymenobacter sp. PAMC 26554 and Hymenobacter sp. PAMC 26628 Reveals the Presence of Polysaccharide-Degrading Ability Based on Habitat. Curr Microbiol 2020; 77:2940-2952. [PMID: 32681312 DOI: 10.1007/s00284-020-02120-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 07/07/2020] [Indexed: 12/20/2022]
Abstract
The genus Hymenobacter is classified in the family Hymenobacteraceae under the phylum Bacteroidetes. They have been isolated from diverse environments, such as air, soil, and lichen, along with extreme polar environments, including the Arctic and Antarctic regions. The polar regions have attracted intense research interest for the discovery of novel microorganisms and their functions. Analysis of the polysaccharide utilization-related carbohydrate-active enzyme among the two lichen-associated polar organisms Hymenobacter sp. PAMC 26554 and Hymenobacter sp. PAMC 26628 was performed, along with its comparison with the complete genome of the same genus available in the NCBI database. The study was conducted relying on the AZCL screening data for the two polar lichen-associated species. While comparing with eight other complete genomes, differences in polysaccharide preferences based on the isolation environment and biosample source were discovered. All the species showed almost similar percentage of cellulose synthesis and degradation genes. However, the polar lichen-associated microorganism was found to have a high percentage of hemicellulose degradation genes, and less starch and laminarin degradation. The Hymenobacter species with higher number of hemicellulose degradation genes was found to have a lower number of starch and laminarin degradation genes and vice versa, highlighting the differences in polysaccharide utilization among the species.
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Yamada T, Teranishi W, Park K, Jiang J, Tachikawa T, Furusato S, Sajiki H. Development of Carbon‐Neutral Cellulose‐Supported Heterogeneous Palladium Catalysts for Chemoselective Hydrogenation. ChemCatChem 2020. [DOI: 10.1002/cctc.202000805] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Tsuyoshi Yamada
- Laboratory of Organic Chemistry Gifu Pharmaceutical University 1-25-4 Daigaku-nishi Gifu 501-1196 Japan
| | - Wataru Teranishi
- Laboratory of Organic Chemistry Gifu Pharmaceutical University 1-25-4 Daigaku-nishi Gifu 501-1196 Japan
| | - Kwihwan Park
- Laboratory of Organic Chemistry Gifu Pharmaceutical University 1-25-4 Daigaku-nishi Gifu 501-1196 Japan
| | - Jing Jiang
- Laboratory of Organic Chemistry Gifu Pharmaceutical University 1-25-4 Daigaku-nishi Gifu 501-1196 Japan
| | - Takumu Tachikawa
- Laboratory of Organic Chemistry Gifu Pharmaceutical University 1-25-4 Daigaku-nishi Gifu 501-1196 Japan
| | - Shinichi Furusato
- Production engineering department JNC Corporation 1-1 Noguchi, Minamata Kumamoto 867-8501 Japan
| | - Hironao Sajiki
- Laboratory of Organic Chemistry Gifu Pharmaceutical University 1-25-4 Daigaku-nishi Gifu 501-1196 Japan
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Kumla J, Suwannarach N, Sujarit K, Penkhrue W, Kakumyan P, Jatuwong K, Vadthanarat S, Lumyong S. Cultivation of Mushrooms and Their Lignocellulolytic Enzyme Production Through the Utilization of Agro-Industrial Waste. Molecules 2020; 25:molecules25122811. [PMID: 32570772 PMCID: PMC7355594 DOI: 10.3390/molecules25122811] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 06/13/2020] [Accepted: 06/15/2020] [Indexed: 12/18/2022] Open
Abstract
A large amount of agro-industrial waste is produced worldwide in various agricultural sectors and by different food industries. The disposal and burning of this waste have created major global environmental problems. Agro-industrial waste mainly consists of cellulose, hemicellulose and lignin, all of which are collectively defined as lignocellulosic materials. This waste can serve as a suitable substrate in the solid-state fermentation process involving mushrooms. Mushrooms degrade lignocellulosic substrates through lignocellulosic enzyme production and utilize the degraded products to produce their fruiting bodies. Therefore, mushroom cultivation can be considered a prominent biotechnological process for the reduction and valorization of agro-industrial waste. Such waste is generated as a result of the eco-friendly conversion of low-value by-products into new resources that can be used to produce value-added products. Here, we have produced a brief review of the current findings through an overview of recently published literature. This overview has focused on the use of agro-industrial waste as a growth substrate for mushroom cultivation and lignocellulolytic enzyme production.
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Affiliation(s)
- Jaturong Kumla
- Research Center of Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai 50200, Thailand; (J.K.); (N.S.); (K.J.); (S.V.)
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Nakarin Suwannarach
- Research Center of Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai 50200, Thailand; (J.K.); (N.S.); (K.J.); (S.V.)
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Kanaporn Sujarit
- Division of Biology, Faculty of Science and Technology, Rajamangala University of Technology Thanyaburi, Thanyaburi, Pathumthani 12110, Thailand;
| | - Watsana Penkhrue
- School of Preclinic, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand;
- Center of Excellence in Microbial Technology for Agricultural Industry, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Pattana Kakumyan
- School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand;
| | - Kritsana Jatuwong
- Research Center of Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai 50200, Thailand; (J.K.); (N.S.); (K.J.); (S.V.)
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Santhiti Vadthanarat
- Research Center of Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai 50200, Thailand; (J.K.); (N.S.); (K.J.); (S.V.)
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Saisamorn Lumyong
- Research Center of Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai 50200, Thailand; (J.K.); (N.S.); (K.J.); (S.V.)
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
- Academy of Science, The Royal Society of Thailand, Bangkok 10300, Thailand
- Correspondence: ; Tel.: +668-1881-3658
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Successional trajectory of bacterial communities in soil are shaped by plant-driven changes during secondary succession. Sci Rep 2020; 10:9864. [PMID: 32555419 PMCID: PMC7299987 DOI: 10.1038/s41598-020-66638-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 04/27/2020] [Indexed: 11/08/2022] Open
Abstract
This study investigated the potential role of a nitrogen-fixing early-coloniser Alnus Nepalensis D. Don (alder) in driving the changes in soil bacterial communities during secondary succession. We found that bacterial diversity was positively associated with alder growth during course of ecosystem development. Alder development elicited multiple changes in bacterial community composition and ecological networks. For example, the initial dominance of actinobacteria within bacterial community transitioned to the dominance of proteobacteria with stand development. Ecological networks approximating species associations tend to stabilize with alder growth. Janthinobacterium lividum, Candidatus Xiphinematobacter and Rhodoplanes were indicator species of different growth stages of alder. While the growth stages of alder has a major independent contribution to the bacterial diversity, its influence on the community composition was explained conjointly by the changes in soil properties with alder. Alder growth increased trace mineral element concentrations in the soil and explained 63% of variance in the Shannon-diversity. We also found positive association of alder with late-successional Quercus leucotrichophora (Oak). Together, the changes in soil bacterial community shaped by early-coloniser alder and its positive association with late-successional oak suggests a crucial role played by alder in ecosystem recovery of degraded habitats.
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128
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Gill AS, Purnell K, Palmer MI, Stein J, McGuire KL. Microbial Composition and Functional Diversity Differ Across Urban Green Infrastructure Types. Front Microbiol 2020; 11:912. [PMID: 32582043 PMCID: PMC7291602 DOI: 10.3389/fmicb.2020.00912] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 04/17/2020] [Indexed: 01/04/2023] Open
Abstract
Functional and biogeographical properties of soil microbial communities in urban ecosystems are poorly understood despite their role in metabolic processes underlying valuable ecosystem services. The worldwide emergence of engineered habitats in urban landscapes-green roofs, bioswales, and other types of soil-based green infrastructure-highlights the importance of understanding how environmental changes affect the community assembly processes that shape urban microbial diversity and function. In this study we investigated (1) whether engineered green roofs and bioswales in New York City had distinct microbial community composition and trait-associated diversity compared to non-engineered soils in parks and tree pits, and (2) if these patterns were consistent with divergent community assembly processes associated with engineered specifications of green infrastructure habitats not present in conventional, non-engineered green infrastructure; specifically, tree pit and park lawn soils. We found that green roofs and bioswales each had distinct bacterial and fungal communities, but that community composition and diversity were not significantly associated with geographic distance, suggesting that the processes structuring these differences are related to aspects of the habitats themselves. Bioswales, and to a lesser extent green roofs, also contained increased functional potential compared to conventional GI soils, based on the diversity and abundance of taxa associated with nitrogen cycling, biodegradation, decomposition, and traits positively associated with plant growth. We discuss these results in the context of community assembly theory, concluding that urban soil microbial community composition and diversity in engineered habitats are driven largely by environmental filtering, whereas stochastic processes are more important among non-engineered soils.
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Affiliation(s)
- Aman S. Gill
- Department of Environmental Science and Policy Management, University of California, Berkeley, Berkeley, CA, United States
| | - Kai Purnell
- Department of Biology, Barnard College, New York, NY, United States
| | - Matthew I. Palmer
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, United States
| | - Jaime Stein
- Programs for Sustainable Planning and Development, School of Architecture, Pratt Institute, Brooklyn, NY, United States
| | - Krista L. McGuire
- Department of Biology, Institute of Ecology and Evolution, University of Oregon, Eugene, OR, United States
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129
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Quintieri L, Fanelli F, Zühlke D, Caputo L, Logrieco AF, Albrecht D, Riedel K. Biofilm and Pathogenesis-Related Proteins in the Foodborne P. fluorescens ITEM 17298 With Distinctive Phenotypes During Cold Storage. Front Microbiol 2020; 11:991. [PMID: 32670211 PMCID: PMC7326052 DOI: 10.3389/fmicb.2020.00991] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 04/23/2020] [Indexed: 12/22/2022] Open
Abstract
In food chain, Pseudomonas spp. cause spoilage by reducing shelf life of fresh products, especially during cold storage, with a high economic burden for industries. However, recent studies have shed new light on health risks occurring when they colonize immunocompromised patient tissues. Likewise to P. aeruginosa, they exhibit antibiotic resistance and biofilm formation, responsible for their spread and persistence in the environment. Biofilm formation might be induced by environmental stresses, such as temperature fluctuations causing physiological and metabolic changes exacerbating food spoilage (by protease and pigment synthesis), and the production of adhesion molecules, chemotactic or underestimated virulence factors. In order to provide a new insight into phenotypic biodiversity of Pseudomonas spoilers isolated from cold stored cheese, in this work 19 Pseudomonas spp. were investigated for biofilm, pigments, exopolysaccharide production and motility at low temperature. Only nine strains showed these phenotypic traits and the blue pigmenting cheese strain P. fluorescens ITEM 17298 was the most distinctive. In addition, this strain decreased the survival probability of infected Galleria mellonella larvae, showing, for the first time, a pathogenic potential. Genomic and proteomic analyses performed on the ITEM 17298 planktonic cells treated or not with lactoferrin derived antibiofilm peptides allowed to reveal specific biofilm related-pathways as well as proteins involved in pathogenesis. Indeed, several genes were found related to signaling system by cGMP-dependent protein kinases, cellulose, rhamnolipid and alginate synthesis, antibiotic resistance, adhesion and virulence factors. The proteome of the untreated ITEM 17298, growing at low temperature, showed that most of the proteins associated with biofilm regulation, pigmentation motility, antibiotic resistance and pathogenecity were repressed, or decreased their levels in comparison to that of the untreated cultures. Thus, the results of this work shed light on the complex pathways network allowing psychrotrophic pseudomonads to adapt themselves to food-refrigerated conditions and enhance their spoilage. In addition, the discovery of virulence factors and antibiotic resistance determinants raises some questions about the need to deeper investigate these underestimated bacteria in order to increase awareness and provide input to update legislation on their detection limits in foods.
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Affiliation(s)
- Laura Quintieri
- Institute of Sciences of Food Production, Italian National Research Council, Bari, Italy
| | - Francesca Fanelli
- Institute of Sciences of Food Production, Italian National Research Council, Bari, Italy
| | - Daniela Zühlke
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Leonardo Caputo
- Institute of Sciences of Food Production, Italian National Research Council, Bari, Italy
| | | | - Dirk Albrecht
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Katharina Riedel
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
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130
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Wu F, You Y, Werner D, Jiao S, Hu J, Zhang X, Wan Y, Liu J, Wang B, Wang X. Carbon nanomaterials affect carbon cycle-related functions of the soil microbial community and the coupling of nutrient cycles. JOURNAL OF HAZARDOUS MATERIALS 2020; 390:122144. [PMID: 32006845 DOI: 10.1016/j.jhazmat.2020.122144] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 01/13/2020] [Accepted: 01/19/2020] [Indexed: 05/23/2023]
Abstract
Many studies have examined changes in soil microbial community structure and composition by carbon nanomaterials (CNMs). Few, however, have investigated their impact on microbial community functions. This study explored how fullerene (C60) and multi-walled carbon nanotubes (M50) altered functionality of an agricultural soil microbial community (Archaea, Bacteria and Eukarya), using microcosm experiments combined with GeoChip microarray. M50 had a stronger effect than C60 on alpha diversity of microbial functional genes; both CNMs increased beta diversity, resulting in functional profiles distinct from the control. M50 exerted a broader, severer impact on microbially mediated nutrient cycles. Together, these two CNMs affected CO2 fixation pathways, microbial degradation of diverse carbohydrates, secondary plant metabolites, lipids and phospholipids, proteins, as well as methanogenesis and methane oxidation. They also suppressed nitrogen fixation, nitrification, dissimilatory nitrogen reduction, eukaryotic assimilatory nitrogen reduction, and anaerobic ammonium oxidation (anammox). Phosphorus and sulfur cycles were less vulnerable; only phytic acid hydrolysis and sulfite reduction were inhibited by M50 but not C60. Network analysis suggested decoupling of nutrient cycles by CNMs, manifesting closer and more hierarchical gene networks. This work reinforces profound impact of CNMs on soil microbial community functions and ecosystem services, laying a path for future investigation in this direction.
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Affiliation(s)
- Fan Wu
- Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing, 100871, China
| | - Yaqi You
- Department of Civil and Environmental Engineering, University of Nevada, Reno, NV, 89557, USA
| | - David Werner
- School of Engineering, Newcastle University, Newcastle upon Tyne, UK
| | - Shuo Jiao
- Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing, 100871, China
| | - Jing Hu
- Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing, 100871, China
| | - Xinyu Zhang
- Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing, 100871, China
| | - Yi Wan
- Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing, 100871, China
| | - Junfeng Liu
- Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing, 100871, China
| | - Bin Wang
- School of Public Health, Peking University, Beijing, 100191, China
| | - Xilong Wang
- Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing, 100871, China.
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131
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Cortes-Tolalpa L, Wang Y, Salles JF, van Elsas JD. Comparative Genome Analysis of the Lignocellulose Degrading Bacteria Citrobacter freundii so4 and Sphingobacterium multivorum w15. Front Microbiol 2020; 11:248. [PMID: 32194522 PMCID: PMC7065263 DOI: 10.3389/fmicb.2020.00248] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Accepted: 02/03/2020] [Indexed: 01/19/2023] Open
Abstract
Two bacterial strains, denoted so4 and w15, isolated from wheat straw (WS)-degrading microbial consortia, were found to grow synergistically in media containing WS as the single carbon and energy source. They were identified as Citrobacter freundii so4 and Sphingobacterium multivorum w15 based on 16S rRNA gene sequencing and comparison to the respective C. freundii and S. multivorum type strains. In order to identify the mechanisms driving the synergistic interactions, we analyzed the draft genomes of the two strains and further characterized their metabolic potential. The latter analyses revealed that the strains had largely complementary substrate utilization patterns, with only 22 out of 190 compounds shared. The analyses further indicated C. freundii so4 to primarily consume amino acids and simple sugars, with laminarin as a key exception. In contrast, S. multivorum w15 showed ample capacity to transform complex polysaccharides, including intermediates of starch degradation. Sequence analyses revealed C. freundii so4 to have a genome of 4,883,214 bp, with a G + C content of 52.5%, 4,554 protein-encoding genes and 86 RNA genes. S. multivorum w15 has a genome of 6,678,278 bp, with a G + C content of 39.7%, 5,999 protein-encoding genes and 76 RNA genes. Genes for motility apparatuses (flagella, chemotaxis) were present in the genome of C. freundii so4, but absent from that of S. multivorum w15. In the genome of S. multivorum w15, 348 genes had regions matching CAZy family enzymes and/or carbohydrate-binding modules (CBMs), with 193 glycosyl hydrolase (GH) and 50 CBM domains. Remarkably, 22 domains matched enzymes of glycoside hydrolase family GH43, suggesting a strong investment in the degradation of arabinoxylan. In contrast, 130 CAZy family genes were found in C. freundii so4, with 61 GH and 12 CBM domains identified. Collectively, our results, based on both metabolic potential and genome analyses, revealed the two strains to harbor complementary catabolic armories, with S. multivorum w15 primarily attacking the WS hemicellulose and C. freundii so4 the cellobiose derived from cellulose, next to emerging oligo- or monosaccharides. Finally, C. freundii so4 may secrete secondary metabolites that S. multivorum w15 can consume, and detoxify the system by reducing the levels of (toxic) by-products.
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Affiliation(s)
- Larisa Cortes-Tolalpa
- Cluster of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
| | - Yanfang Wang
- Cluster of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
| | - Joana Falcao Salles
- Cluster of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
| | - Jan Dirk van Elsas
- Cluster of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
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132
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Li Y, Lei L, Zheng L, Xiao X, Tang H, Luo C. Genome sequencing of gut symbiotic Bacillus velezensis LC1 for bioethanol production from bamboo shoots. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:34. [PMID: 32140179 PMCID: PMC7048129 DOI: 10.1186/s13068-020-1671-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 01/29/2020] [Indexed: 06/10/2023]
Abstract
BACKGROUND Bamboo, a lignocellulosic feedstock, is considered as a potentially excellent raw material and evaluated for lignocellulose degradation and bioethanol production, with a focus on using physical and chemical pre-treatment. However, studies reporting the biodegradation of bamboo lignocellulose using microbes such as bacteria and fungi are scarce. RESULTS In the present study, Bacillus velezensis LC1 was isolated from Cyrtotrachelus buqueti, in which the symbiotic bacteria exhibited lignocellulose degradation ability and cellulase activities. We performed genome sequencing of B. velezensis LC1, which has a 3929,782-bp ring chromosome and 46.5% GC content. The total gene length was 3,502,596 bp using gene prediction, and the GC contents were 47.29% and 40.04% in the gene and intergene regions, respectively. The genome contains 4018 coding DNA sequences, and all have been assigned predicted functions. Carbohydrate-active enzyme annotation identified 136 genes annotated to CAZy families, including GH, GTs, CEs, PLs, AAs and CBMs. Genes involved in lignocellulose degradation were identified. After a 6-day treatment, the bamboo shoot cellulose degradation efficiency reached 39.32%, and the hydrolysate was subjected to ethanol fermentation with Saccharomyces cerevisiae and Escherichia coli KO11, yielding 7.2 g/L of ethanol at 96 h. CONCLUSIONS These findings provide an insight for B. velezensis strains in converting lignocellulose into ethanol. B. velezensis LC1, a symbiotic bacteria, can potentially degrade bamboo lignocellulose components and further transformation to ethanol, and expand the bamboo lignocellulosic bioethanol production.
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Affiliation(s)
- Yuanqiu Li
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, Leshan Normal University, No. 778, Binhe Road, Central District, Leshan, 614000 China
| | - Lu Lei
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, Leshan Normal University, No. 778, Binhe Road, Central District, Leshan, 614000 China
| | - Li Zheng
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, Leshan Normal University, No. 778, Binhe Road, Central District, Leshan, 614000 China
| | - Ximeng Xiao
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, Leshan Normal University, No. 778, Binhe Road, Central District, Leshan, 614000 China
| | - Hao Tang
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, Leshan Normal University, No. 778, Binhe Road, Central District, Leshan, 614000 China
| | - Chaobing Luo
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, Leshan Normal University, No. 778, Binhe Road, Central District, Leshan, 614000 China
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133
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Ma L, Zhao Y, Meng L, Wang X, Yi Y, Shan Y, Liu B, Zhou Y, Lü X. Isolation of Thermostable Lignocellulosic Bacteria From Chicken Manure Compost and a M42 Family Endocellulase Cloning From Geobacillus thermodenitrificans Y7. Front Microbiol 2020; 11:281. [PMID: 32174898 PMCID: PMC7054444 DOI: 10.3389/fmicb.2020.00281] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 02/07/2020] [Indexed: 01/01/2023] Open
Abstract
The composting ecosystem provides a potential resource for finding new microorganisms with the capability for cellulose degradation. In the present study, Congo red method was used for the isolating of thermostable lignocellulose-degrading bacteria from chicken manure compost. A thermophilic strain named as Geobacillus thermodenitrificans Y7 with acid-resident property was successfully isolated and employed to degrade raw switchgrass at 60°C for 5 days, which resulted in the final degradation rates of cellulose, xylan, and acid-insoluble lignin as 18.64, 12.96, and 17.21%, respectively. In addition, GC-MS analysis about aromatic degradation affirm the degradation of lignin by G. thermodenitrificans Y7. Moreover, an endocellulase gene belong to M42 family was successfully cloned from G. thermodenitrificans Y7 and expressed in Escherichia coli BL21. Recombinant enzyme Cel-9 was purified by Ni-NTA column based the His-tag, and the molecular weight determined as 40.4 kDa by SDA-PAGE. The characterization of the enzyme Cel-9 indicated that the maximum enzyme activity was realized at 50°C and pH 8.6 and, Mn2+ could greatly improve the CMCase enzyme activity of Cel-9 at 10 mM, which was followed by Fe2+ and Co2+. Besides, it also found that the β-1,3-1,4, β-1,3, β-1,4, and β-1,6 glucan linkages all could be hydrolyzed by enzyme Cel-9. Finally, during the application of enzyme Cel-9 to switchgrass, the saccharification rates achieved to 1.81 ± 0.04% and 2.65 ± 0.03% for 50 and 100% crude enzyme, respectively. All these results indicated that both the strain G. thermodenitrificans Y7 and the recombinant endocellulase Cel-9 have the potential to be applied to the biomass industry.
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Affiliation(s)
- Lingling Ma
- Laboratory of Bioresources, College of Food Science and Engineering, Northwest A&F University, Yangling, China
| | - Yuchun Zhao
- Laboratory of Bioresources, College of Food Science and Engineering, Northwest A&F University, Yangling, China
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Limin Meng
- Laboratory of Bioresources, College of Food Science and Engineering, Northwest A&F University, Yangling, China
| | - Xin Wang
- Laboratory of Bioresources, College of Food Science and Engineering, Northwest A&F University, Yangling, China
| | - Yanglei Yi
- Laboratory of Bioresources, College of Food Science and Engineering, Northwest A&F University, Yangling, China
| | - Yuanyuan Shan
- Laboratory of Bioresources, College of Food Science and Engineering, Northwest A&F University, Yangling, China
| | - Bianfang Liu
- Laboratory of Bioresources, College of Food Science and Engineering, Northwest A&F University, Yangling, China
| | - Yuan Zhou
- Laboratory of Bioresources, College of Food Science and Engineering, Northwest A&F University, Yangling, China
| | - Xin Lü
- Laboratory of Bioresources, College of Food Science and Engineering, Northwest A&F University, Yangling, China
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134
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Wang ZY, Wang RX, Zhou JS, Cheng JF, Li YH. An assessment of the genomics, comparative genomics and cellulose degradation potential of Mucilaginibacter polytrichastri strain RG4-7. BIORESOURCE TECHNOLOGY 2020; 297:122389. [PMID: 31757614 DOI: 10.1016/j.biortech.2019.122389] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 10/22/2019] [Accepted: 11/06/2019] [Indexed: 06/10/2023]
Abstract
In this study, whole genome sequencing and comparative genomic analyses were performed for Mucilaginibacter polytrichastri RG4-7 and its carboxymethyl cellulose degradation potential was assessed. The results showed that the genome of strain RG4-7 was 5.84 Mb and contained 5019 predicted genes, in which a high proportion of strain-specific genes were related to carbohydrate metabolism. The carboxymethyl cellulose (CMC) degradation and cellulase activity tests revealed the strong cellulose degradation ability, CMCase and β-glucosidase activity in strain RG4-7. Real-time RT-PCR testing of most cellulose degradation related glycoside hydrolase (GH) families showed that GH9 (OKS85969), GH1 (OKS85832), GH3 (OKS89331 and OKS85615) were significantly up-regulated when strain RG4-7 was inoculated with CMC-Na, which suggested that GH9, GH1 and GH3 might determine its cellulose degradation ability. Certainly, further research need to be done to elucidate cellulose degradation mechanisms in strain RG4-7 in order to develop its industrial application value in lignocellulosic biomass degradation and waste management.
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Affiliation(s)
- Zi Yue Wang
- College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Rui Xue Wang
- College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Jun Shi Zhou
- College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Jian Fei Cheng
- College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Yan Hong Li
- College of Life Sciences, Capital Normal University, Beijing 100048, China.
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135
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Campanaro S, Treu L, Rodriguez-R LM, Kovalovszki A, Ziels RM, Maus I, Zhu X, Kougias PG, Basile A, Luo G, Schlüter A, Konstantinidis KT, Angelidaki I. New insights from the biogas microbiome by comprehensive genome-resolved metagenomics of nearly 1600 species originating from multiple anaerobic digesters. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:25. [PMID: 32123542 PMCID: PMC7038595 DOI: 10.1186/s13068-020-01679-y] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 02/08/2020] [Indexed: 05/20/2023]
Abstract
BACKGROUND Microorganisms in biogas reactors are essential for degradation of organic matter and methane production. However, a comprehensive genome-centric comparison, including relevant metadata for each sample, is still needed to identify the globally distributed biogas community members and serve as a reliable repository. RESULTS Here, 134 publicly available metagenomes derived from different biogas reactors were used to recover 1635 metagenome-assembled genomes (MAGs) representing different biogas bacterial and archaeal species. All genomes were estimated to be > 50% complete and nearly half ≥ 90% complete with ≤ 5% contamination. In most samples, specialized microbial communities were established, while only a few taxa were widespread among the different reactor systems. Metabolic reconstruction of the MAGs enabled the prediction of functional traits related to biomass degradation and methane production from waste biomass. An extensive evaluation of the replication index provided an estimation of the growth dynamics for microbes involved in different steps of the food chain. CONCLUSIONS The outcome of this study highlights a high flexibility of the biogas microbiome, allowing it to modify its composition and to adapt to the environmental conditions, including temperatures and a wide range of substrates. Our findings enhance our mechanistic understanding of the AD microbiome and substantially extend the existing repository of genomes. The established database represents a relevant resource for future studies related to this engineered ecosystem.
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Affiliation(s)
- Stefano Campanaro
- Department of Biology, University of Padova, Via U. Bassi 58/b, 35121 Padua, Italy
- CRIBI Biotechnology Center, University of Padova, 35131 Padua, Italy
| | - Laura Treu
- Department of Biology, University of Padova, Via U. Bassi 58/b, 35121 Padua, Italy
- Department of Environmental Engineering, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Luis M. Rodriguez-R
- School of Civil & Environmental Engineering and School of Biological Sciences (Adjunct), Georgia Institute of Technology, 311 Ferst Drive, Atlanta, GA 30332-0512 USA
| | - Adam Kovalovszki
- Department of Environmental Engineering, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Ryan M. Ziels
- Department of Civil Engineering, University of British Columbia, Vancouver, BC Canada
| | - Irena Maus
- Genome Research of Industrial Microorganisms, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstr. 27, 33615 Bielefeld, Germany
| | - Xinyu Zhu
- Department of Environmental Engineering, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Panagiotis G. Kougias
- Hellenic Agricultural Organization DEMETER, Soil and Water Resources Institute, Thermi-Thessaloniki, Greece
| | - Arianna Basile
- Department of Biology, University of Padova, Via U. Bassi 58/b, 35121 Padua, Italy
| | - Gang Luo
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai, 200433 China
| | - Andreas Schlüter
- Hellenic Agricultural Organization DEMETER, Soil and Water Resources Institute, Thermi-Thessaloniki, Greece
| | - Konstantinos T. Konstantinidis
- School of Civil & Environmental Engineering and School of Biological Sciences (Adjunct), Georgia Institute of Technology, 311 Ferst Drive, Atlanta, GA 30332-0512 USA
| | - Irini Angelidaki
- Department of Environmental Engineering, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
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Schiano‐di‐Cola C, Kołaczkowski B, Sørensen TH, Christensen SJ, Cavaleiro AM, Windahl MS, Borch K, Morth JP, Westh P. Structural and biochemical characterization of a family 7 highly thermostable endoglucanase from the fungusRasamsonia emersonii. FEBS J 2019; 287:2577-2596. [DOI: 10.1111/febs.15151] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 11/01/2019] [Accepted: 11/20/2019] [Indexed: 01/21/2023]
Affiliation(s)
| | | | - Trine Holst Sørensen
- Department of Science and Environment Roskilde University Denmark
- Novozymes A/S Lyngby Denmark
| | | | | | - Michael Skovbo Windahl
- Department of Science and Environment Roskilde University Denmark
- Novozymes A/S Lyngby Denmark
| | | | - Jens Preben Morth
- Department of Biotechnology and Biomedicine Technical University of Denmark Lyngby Denmark
| | - Peter Westh
- Department of Science and Environment Roskilde University Denmark
- Department of Biotechnology and Biomedicine Technical University of Denmark Lyngby Denmark
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137
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López-Mondéjar R, Algora C, Baldrian P. Lignocellulolytic systems of soil bacteria: A vast and diverse toolbox for biotechnological conversion processes. Biotechnol Adv 2019; 37:107374. [DOI: 10.1016/j.biotechadv.2019.03.013] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 03/06/2019] [Accepted: 03/21/2019] [Indexed: 12/12/2022]
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138
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Bani A, Borruso L, Matthews Nicholass KJ, Bardelli T, Polo A, Pioli S, Gómez-Brandón M, Insam H, Dumbrell AJ, Brusetti L. Site-Specific Microbial Decomposer Communities Do Not Imply Faster Decomposition: Results from a Litter Transplantation Experiment. Microorganisms 2019; 7:microorganisms7090349. [PMID: 31547404 PMCID: PMC6780308 DOI: 10.3390/microorganisms7090349] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 09/09/2019] [Accepted: 09/09/2019] [Indexed: 12/28/2022] Open
Abstract
Microbes drive leaf litter decomposition, and their communities are adapted to the local vegetation providing that litter. However, whether these local microbial communities confer a significant home-field advantage in litter decomposition remains unclear, with contrasting results being published. Here, we focus on a litter transplantation experiment from oak forests (home site) to two away sites without oak in South Tyrol (Italy). We aimed to produce an in-depth analysis of the fungal and bacterial decomposer communities using Illumina sequencing and qPCR, to understand whether local adaptation occurs and whether this was associated with litter mass loss dynamics. Temporal shifts in the decomposer community occurred, reflecting changes in litter chemistry over time. Fungal community composition was site dependent, while bacterial composition did not differ across sites. Total litter mass loss and rates of litter decomposition did not change across sites. Litter quality influenced the microbial community through the availability of different carbon sources. Additively, our results do not support the hypothesis that locally adapted microbial decomposers lead to a greater or faster mass loss. It is likely that high functional redundancy within decomposer communities regulated the decomposition, and thus greater future research attention should be given to trophic guilds rather than taxonomic composition.
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Affiliation(s)
- Alessia Bani
- Faculty of Science and Technology, Free University of Bozen/Bolzano, Piazza Università 5, 39100 Bolzano, Italy.
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, UK.
| | - Luigimaria Borruso
- Faculty of Science and Technology, Free University of Bozen/Bolzano, Piazza Università 5, 39100 Bolzano, Italy.
| | | | - Tommaso Bardelli
- Department of Agrifood and Environmental Science, University of Florence, Piazzale delle Cascine 18, 50144 Florence, Italy.
- Institute of Microbiology, University of Innsbruck, Technikerstraβe 25d, 6020 Innsbruck, Austria.
| | - Andrea Polo
- Faculty of Science and Technology, Free University of Bozen/Bolzano, Piazza Università 5, 39100 Bolzano, Italy.
| | - Silvia Pioli
- Faculty of Science and Technology, Free University of Bozen/Bolzano, Piazza Università 5, 39100 Bolzano, Italy.
| | - María Gómez-Brandón
- Institute of Microbiology, University of Innsbruck, Technikerstraβe 25d, 6020 Innsbruck, Austria.
- Departamento de Ecoloxía e Bioloxía Animal, Universidade de Vigo, E-36310 Vigo, Spain.
| | - Heribert Insam
- Institute of Microbiology, University of Innsbruck, Technikerstraβe 25d, 6020 Innsbruck, Austria.
| | - Alex J Dumbrell
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, UK.
| | - Lorenzo Brusetti
- Faculty of Science and Technology, Free University of Bozen/Bolzano, Piazza Università 5, 39100 Bolzano, Italy.
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139
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Quintieri L, Zühlke D, Fanelli F, Caputo L, Liuzzi VC, Logrieco AF, Hirschfeld C, Becher D, Riedel K. Proteomic analysis of the food spoiler Pseudomonas fluorescens ITEM 17298 reveals the antibiofilm activity of the pepsin-digested bovine lactoferrin. Food Microbiol 2019; 82:177-193. [DOI: 10.1016/j.fm.2019.02.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 02/04/2019] [Accepted: 02/06/2019] [Indexed: 11/29/2022]
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140
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Prasad RK, Chatterjee S, Mazumder PB, Gupta SK, Sharma S, Vairale MG, Datta S, Dwivedi SK, Gupta DK. Bioethanol production from waste lignocelluloses: A review on microbial degradation potential. CHEMOSPHERE 2019; 231:588-606. [PMID: 31154237 DOI: 10.1016/j.chemosphere.2019.05.142] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 04/02/2019] [Accepted: 05/17/2019] [Indexed: 05/15/2023]
Abstract
Tremendous explosion of population has led to about 200% increment of total energy consumptions in last twenty-five years. Apart from conventional fossil fuel as limited energy source, alternative non-conventional sources are being explored worldwide to cater the energy requirement. Lignocellulosic biomass conversion for biofuel production is an important alternative energy source due to its abundance in nature and creating less harmful impacts on the environment in comparison to the coal or petroleum-based sources. However, lignocellulose biopolymer, the building block of plants, is a recalcitrant substance and difficult to break into desirable products. Commonly used chemical and physical methods for pretreating the substrate are having several limitations. Whereas, utilizing microbial potential to hydrolyse the biomass is an interesting area of research. Because of the complexity of substrate, several enzymes are required that can act synergistically to hydrolyse the biopolymer producing components like bioethanol or other energy substances. Exploring a range of microorganisms, like bacteria, fungi, yeast etc. that utilizes lignocelluloses for their energy through enzymatic breaking down the biomass, is one of the options. Scientists are working upon designing organisms through genetic engineering tools to integrate desired enzymes into a single organism (like bacterial cell). Studies on designer cellulosomes and bacteria consortia development relating consolidated bioprocessing are exciting to overcome the issue of appropriate lignocellulose digestions. This review encompasses up to date information on recent developments for effective microbial degradation processes of lignocelluloses for improved utilization to produce biofuel (bioethanol in particular) from the most plentiful substances of our planet.
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Affiliation(s)
- Rajesh Kumar Prasad
- Defence Research Laboratory, DRDO, Tezpur, 784001, Assam, India; Assam University, Silchar, 788011, Assam, India
| | | | | | | | - Sonika Sharma
- Defence Research Laboratory, DRDO, Tezpur, 784001, Assam, India
| | | | | | | | - Dharmendra Kumar Gupta
- Gottfried Wilhelm Leibniz Universität Hannover, Institut für Radioökologie und Strahlenschutz (IRS), HerrenhäuserStr. 2, 30419, Hannover, Germany
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141
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Sietiö OM, Santalahti M, Putkinen A, Adamczyk S, Sun H, Heinonsalo J. Restriction of plant roots in boreal forest organic soils affects the microbial community but does not change the dominance from ectomycorrhizal to saprotrophic fungi. FEMS Microbiol Ecol 2019; 95:5554003. [DOI: 10.1093/femsec/fiz133] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 08/22/2019] [Indexed: 12/17/2022] Open
Abstract
ABSTRACT
Boreal forest soils store significant amounts of carbon and are cohabited by saprotrophic and ectomycorrhizal fungi (ECM). The ‘Gadgil effect’ implies antagonistic interactions between saprotrophic fungi and ECM. Plant photosynthates support the competitive fitness of the ECM, and may also shape the soil bacterial communities. Many ‘Gadgil effect’ experiments have focused on litter layer (OL) or have litter and root-fragments present, and thus possibly favor the saprotrophs. We compared how the restriction of plant roots and exudates affect soil microbial community structures in organic soil (mixed OF and OH). For this, we established a 3-yr field experiment with 3 different mesh treatments affecting the penetration of plant roots and external fungal hyphae. Exclusion of plant photosynthates induced modest changes in both fungal and bacterial community structures, but not to potential functionality of the microbial community. The microbial community was resilient towards rather short-term disturbances. Contrary to the ‘Gadgil effect’, mesh treatments restricting the entrance of plant roots and external fungal hyphae did not favor saprotrophs that originally inhabited the soil. Thus, we propose that different substrate preferences (fresh litter vs. fermented or humified soil), rather than antagonism, maintain the spatial separation of saprotrophs and mycorrhizal fungi in boreal forest soils.
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Affiliation(s)
- Outi-Maaria Sietiö
- Department of Microbiology, University of Helsinki, P.O.Box 56, FIN-00014 Helsinki, Finland
- Institute for Atmospheric and Earth System Research/Forest Sciences, Faculty of Agriculture and Forestry, University of Helsinki, P.O.Box 27, FIN-00014 Helsinki, Finland
| | - Minna Santalahti
- Department of Microbiology, University of Helsinki, P.O.Box 56, FIN-00014 Helsinki, Finland
- Institute for Atmospheric and Earth System Research/Forest Sciences, Faculty of Agriculture and Forestry, University of Helsinki, P.O.Box 27, FIN-00014 Helsinki, Finland
- Department of Agricultural Sciences, University of Helsinki, P.O.Box 56, FIN-00014 Helsinki, Finland
| | - Anuliina Putkinen
- Department of Microbiology, University of Helsinki, P.O.Box 56, FIN-00014 Helsinki, Finland
- Institute for Atmospheric and Earth System Research/Forest Sciences, Faculty of Agriculture and Forestry, University of Helsinki, P.O.Box 27, FIN-00014 Helsinki, Finland
- Department of Agricultural Sciences, University of Helsinki, P.O.Box 56, FIN-00014 Helsinki, Finland
| | - Sylwia Adamczyk
- Natural Resources Institute Finland, P.O.Box 2, 00791 Helsinki, Finland
| | - Hui Sun
- Collaborative Innovation Center of Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, NO.159, Longpan Road, Nanjing, 210037, China
| | - Jussi Heinonsalo
- Department of Microbiology, University of Helsinki, P.O.Box 56, FIN-00014 Helsinki, Finland
- Institute for Atmospheric and Earth System Research/Forest Sciences, Faculty of Agriculture and Forestry, University of Helsinki, P.O.Box 27, FIN-00014 Helsinki, Finland
- Finnish Meteorological Institute FMI, Climate System Research, P.O.Box 503, FIN-00101 Helsinki, Finland
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142
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Birolli WG, Lima RN, Porto ALM. Applications of Marine-Derived Microorganisms and Their Enzymes in Biocatalysis and Biotransformation, the Underexplored Potentials. Front Microbiol 2019; 10:1453. [PMID: 31481935 PMCID: PMC6710449 DOI: 10.3389/fmicb.2019.01453] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 06/11/2019] [Indexed: 12/19/2022] Open
Abstract
Biodiversity has been explored in the search for novel enzymes, including forests, savannas, tundras, deserts, and finally the sea. Marine microorganisms and their enzymes are capable of being active in high-salt concentration, large range of temperature, and high incidence of light and pressure, constituting an important source of unique biocatalysts. This review presents studies employing whole-cell processes of marine bacteria and fungi, aiming for new catalysts for different reactions in organic synthesis, such as reduction, oxidation, hydroxylation, hydrolysis, elimination, and conjugation. Genomics and protein engineering studies were also approached, and reactions employing isolated enzymes from different classes (oxidoreductases, hydrolases, lyases, and ligases) were described and summarized. Future biotechnological studies and process development should focus on molecular biology for the obtention of enzymes with interesting, fascinating and enhanced properties, starting from the exploration of microorganisms from the marine environment. This review approaches the literature about the use of marine-derived bacteria, fungi, and their enzymes for biocatalytic reactions of organic compounds, promoting a discussion about the possibilities of these microorganisms in the synthesis of different substances.
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Affiliation(s)
- Willian G Birolli
- Laboratory of Organic Chemistry and Biocatalysis, São Carlos Institute of Chemistry, University of São Paulo, São Carlos, Brazil.,Center of Exact Sciences and Technology, Department of Chemistry, Federal University of São Carlos, São Carlos, Brazil
| | - Rafaely N Lima
- Laboratory of Organic Chemistry and Biocatalysis, São Carlos Institute of Chemistry, University of São Paulo, São Carlos, Brazil.,Center of Exact Sciences and Technology, Department of Chemistry, Federal University of São Carlos, São Carlos, Brazil
| | - André L M Porto
- Laboratory of Organic Chemistry and Biocatalysis, São Carlos Institute of Chemistry, University of São Paulo, São Carlos, Brazil
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143
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De novo genome assembly and comparative annotation reveals metabolic versatility in cellulolytic bacteria from cropland and forest soils. Funct Integr Genomics 2019; 20:89-101. [PMID: 31378834 DOI: 10.1007/s10142-019-00704-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 07/09/2019] [Accepted: 07/24/2019] [Indexed: 10/26/2022]
Abstract
Cellulose, the most abundant polysaccharide in nature, is a rich source of renewable energy and sustains soil nutrients. Among the microorganisms known to degrade cellulose, bacteria are less studied compared to fungi. In the present work, we have investigated the culturable bacteria actively involved in cellulose degradation in forest and crop field soils. Based on clear zone formation and enzyme activity assay, we identified 7 bacterial strains positive for cellulose degradation. Of these, two most efficient strains (Bacillus cereus strains BHU1 and BHU2) were selected for whole genome sequencing, annotation, and information regarding GC content, number of genes, total subsystems, starch, and cellulose degradation pathways. Average nucleotide identity (ANI) showed more than 90% similarity between both the strains (BHU1 and BHU2) and with B. cereus ATCC 14579. Both the strains have genes and enzyme families like endoglucanase and β-glucosidase as evident from whole genome sequence. Cellulase containing gene families (GH5, GH8, GH1), and many other carbohydrate-degrading enzymes, were present in both the bacterial strains. Taken together, the results suggest that the strains were efficient in cellulose degradation, and can be used for energy generation and production of value-added product.
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144
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Arnal G, Stogios PJ, Asohan J, Attia MA, Skarina T, Viborg AH, Henrissat B, Savchenko A, Brumer H. Substrate specificity, regiospecificity, and processivity in glycoside hydrolase family 74. J Biol Chem 2019; 294:13233-13247. [PMID: 31324716 DOI: 10.1074/jbc.ra119.009861] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 07/16/2019] [Indexed: 12/11/2022] Open
Abstract
Glycoside hydrolase family 74 (GH74) is a historically important family of endo-β-glucanases. On the basis of early reports of detectable activity on cellulose and soluble cellulose derivatives, GH74 was originally considered to be a "cellulase" family, although more recent studies have generally indicated a high specificity toward the ubiquitous plant cell wall matrix glycan xyloglucan. Previous studies have indicated that GH74 xyloglucanases differ in backbone cleavage regiospecificities and can adopt three distinct hydrolytic modes of action: exo, endo-dissociative, and endo-processive. To improve functional predictions within GH74, here we coupled in-depth biochemical characterization of 17 recombinant proteins with structural biology-based investigations in the context of a comprehensive molecular phylogeny, including all previously characterized family members. Elucidation of four new GH74 tertiary structures, as well as one distantly related dual seven-bladed β-propeller protein from a marine bacterium, highlighted key structure-function relationships along protein evolutionary trajectories. We could define five phylogenetic groups, which delineated the mode of action and the regiospecificity of GH74 members. At the extremes, a major group of enzymes diverged to hydrolyze the backbone of xyloglucan nonspecifically with a dissociative mode of action and relaxed backbone regiospecificity. In contrast, a sister group of GH74 enzymes has evolved a large hydrophobic platform comprising 10 subsites, which facilitates processivity. Overall, the findings of our study refine our understanding of catalysis in GH74, providing a framework for future experimentation as well as for bioinformatics predictions of sequences emerging from (meta)genomic studies.
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Affiliation(s)
- Gregory Arnal
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, British Columbia V6T 1Z4, Canada
| | - Peter J Stogios
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Jathavan Asohan
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, British Columbia V6T 1Z4, Canada
| | - Mohamed A Attia
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, British Columbia V6T 1Z4, Canada; Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Tatiana Skarina
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Alexander Holm Viborg
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, British Columbia V6T 1Z4, Canada
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Aix-Marseille University, 13007 Marseille, France; INRA, USC1408 Architecture et Fonction des Macromolécules Biologiques (AFMB), 13007 Marseille, France
| | - Alexei Savchenko
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada; Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta T2N 4N1, Canada.
| | - Harry Brumer
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, British Columbia V6T 1Z4, Canada; Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada; Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada.
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145
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Dukunde A, Schneider D, Schmidt M, Veldkamp E, Daniel R. Tree Species Shape Soil Bacterial Community Structure and Function in Temperate Deciduous Forests. Front Microbiol 2019; 10:1519. [PMID: 31338079 PMCID: PMC6629791 DOI: 10.3389/fmicb.2019.01519] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 06/18/2019] [Indexed: 01/23/2023] Open
Abstract
Amplicon-based analysis of 16S rRNA genes and transcripts was used to assess the effect of tree species composition on soil bacterial community structure and function in a temperate deciduous forest. Samples were collected from mono and mixed stands of Fagus sylvatica (beech), Carpinus betulus (hornbeam), Tilia sp. (lime), and Quercus sp. (oak) in spring, summer, and autumn. Soil bacterial community exhibited similar taxonomic composition at total (DNA-based) and potentially active community (RNA-based) level, with fewer taxa present at active community level. Members of Rhizobiales dominated at both total and active bacterial community level, followed by members of Acidobacteriales, Solibacterales, Rhodospirillales, and Xanthomonadales. Bacterial communities at total and active community level showed a significant positive correlation with tree species identity (mono stands) and to a lesser extent with tree species richness (mixed stands). Approximately 58 and 64% of indicator operational taxonomic units (OTUs) showed significant association with only one mono stand at total and active community level, respectively, indicating a strong impact of tree species on soil bacterial community composition. Soil C/N ratio, pH, and P content similarly exhibited a significant positive correlation with soil bacterial communities, which was attributed to direct and indirect effects of forest stands. Seasonality was the strongest driver of predicted metabolic functions related to C fixation and degradation, and N metabolism. Carbon and nitrogen metabolic processes were significantly abundant in spring, while C degradation gene abundances increased from summer to autumn, corresponding to increased litterfall and decomposition. The results revealed that in a spatially homogenous forest soil, tree species diversity and richness are dominant drivers of structure and composition in soil bacterial communities.
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Affiliation(s)
- Amélie Dukunde
- Göttingen Genomics Laboratory, Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Dominik Schneider
- Göttingen Genomics Laboratory, Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Marcus Schmidt
- Soil Science of Tropical and Subtropical Ecosystems, Faculty of Forest Sciences and Forest Ecology, Büsgen Institute, Georg-August University of Göttingen, Göttingen, Germany
| | - Edzo Veldkamp
- Soil Science of Tropical and Subtropical Ecosystems, Faculty of Forest Sciences and Forest Ecology, Büsgen Institute, Georg-August University of Göttingen, Göttingen, Germany
| | - Rolf Daniel
- Göttingen Genomics Laboratory, Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
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146
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Domínguez J, Aira M, Kolbe AR, Gómez-Brandón M, Pérez-Losada M. Changes in the composition and function of bacterial communities during vermicomposting may explain beneficial properties of vermicompost. Sci Rep 2019; 9:9657. [PMID: 31273255 PMCID: PMC6609614 DOI: 10.1038/s41598-019-46018-w] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 06/20/2019] [Indexed: 12/16/2022] Open
Abstract
Vermicomposting is the process by which organic waste is broken down through the synergistic actions of earthworms and microbial communities. Although vermicomposting has been shown to effectively reduce organic biomass and generate high-quality fertilizer for plants, little is known about the bacterial communities that are involved in this decomposition process. Since optimization of vermicomposting for commercial use necessitates additional knowledge of the underlying biological processes, this study sought to characterize the bacterial succession involved in the vermicomposting of Scotch broom (Cytisus scoparius), a leguminous shrub that has become invasive around the world with consequences for the dynamics and productivity of the ecosystems they occupy. Scotch broom was processed in a pilot-scale vermireactor for 91 days with the earthworm species Eisenia andrei. Samples were taken at the initiation of vermicomposting, and days 14, 42 and 91, representing both active and mature stages of vermicomposting. Significant changes (P < 0.0001) in the bacterial community composition (richness and evenness) were observed throughout the process. Increases in taxonomic diversity were accompanied by increases in functional diversity of the bacterial community, including metabolic capacity, streptomycin and salicylic acid synthesis, and nitrification. These results highlight the role of bacterial succession during the vermicomposting process and provide evidence of microbial functions that may explain the beneficial effects of vermicompost on soil and plants.
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Affiliation(s)
- Jorge Domínguez
- Grupo de Ecoloxía Animal (GEA), Universidade de Vigo, E-36310, Vigo, Pontevedra, Spain
| | - Manuel Aira
- Grupo de Ecoloxía Animal (GEA), Universidade de Vigo, E-36310, Vigo, Pontevedra, Spain
| | - Allison R Kolbe
- Computational Biology Institute, Milken Institute School of Public Health, George Washington University, Ashburn, VA, 20147, USA
| | - María Gómez-Brandón
- Grupo de Ecoloxía Animal (GEA), Universidade de Vigo, E-36310, Vigo, Pontevedra, Spain.
| | - Marcos Pérez-Losada
- Computational Biology Institute, Milken Institute School of Public Health, George Washington University, Ashburn, VA, 20147, USA.,CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal.,Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, George Washington University, Washington, DC, 20052, USA
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147
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Giri S, Waschina S, Kaleta C, Kost C. Defining Division of Labor in Microbial Communities. J Mol Biol 2019; 431:4712-4731. [PMID: 31260694 DOI: 10.1016/j.jmb.2019.06.023] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 06/13/2019] [Accepted: 06/19/2019] [Indexed: 11/15/2022]
Abstract
In order to survive and reproduce, organisms must perform a multitude of tasks. However, trade-offs limit their ability to allocate energy and resources to all of these different processes. One strategy to solve this problem is to specialize in some traits and team up with other organisms that can help by providing additional, complementary functions. By reciprocally exchanging metabolites and/or services in this way, both parties benefit from the interaction. This phenomenon, which has been termed functional specialization or division of labor, is very common in nature and exists on all levels of biological organization. Also, microorganisms have evolved different types of synergistic interactions. However, very often, it remains unclear whether or not a given example represents a true case of division of labor. Here we aim at filling this gap by providing a list of criteria that clearly define division of labor in microbial communities. Furthermore, we propose a set of diagnostic experiments to verify whether a given interaction fulfills these conditions. In contrast to the common use of the term, our analysis reveals that both intraspecific and interspecific interactions meet the criteria defining division of labor. Moreover, our analysis identified non-cooperators of intraspecific public goods interactions as growth specialists that divide labor with conspecific producers, rather than being social parasites. By providing a conceptual toolkit, our work will help to unambiguously identify cases of division of labor and stimulate more detailed investigations of this important and widespread type of inter-microbial interaction.
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Affiliation(s)
- Samir Giri
- Department of Ecology, School of Biology/Chemistry, University of Osnabrück, Osnabrück, Germany
| | - Silvio Waschina
- Research Group Medical Systems Biology, Institute for Experimental Medicine, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Christoph Kaleta
- Research Group Medical Systems Biology, Institute for Experimental Medicine, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Christian Kost
- Department of Ecology, School of Biology/Chemistry, University of Osnabrück, Osnabrück, Germany.
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148
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Männistö M, Vuosku J, Stark S, Saravesi K, Suokas M, Markkola A, Martz F, Rautio P. Bacterial and fungal communities in boreal forest soil are insensitive to changes in snow cover conditions. FEMS Microbiol Ecol 2019; 94:5043222. [PMID: 29939247 DOI: 10.1093/femsec/fiy123] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 06/22/2018] [Indexed: 02/06/2023] Open
Abstract
The northern regions are experiencing considerable changes in winter climate leading to more frequent warm periods, rain-on-snow events and reduced snow pack diminishing the insulation properties of snow cover and increasing soil frost and freeze-thaw cycles. In this study, we investigated how the lack of snow cover, formation of ice encasement and snow compaction affect the size, structure and activities of soil bacterial and fungal communities. Contrary to our hypotheses, snow manipulation treatments over one winter had limited influence on microbial community structure, bacterial or fungal copy numbers or enzyme activities. However, microbial community structure and activities shifted seasonally among soils sampled before snow melt, in early and late growing season and seemed driven by substrate availability. Bacterial and fungal communities were dominated by stress-resistant taxa such as the orders Acidobacteriales, Chaetothyriales and Helotiales that are likely adapted to adverse winter conditions. This study indicated that microbial communities in acidic northern boreal forest soil may be insensitive to direct effects of changing snow cover. However, in long term, the detrimental effects of increased ice and frost to plant roots may alter plant derived carbon and nutrient pools to the soil likely leading to stronger microbial responses.
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Affiliation(s)
- Minna Männistö
- Natural Resources Institute Finland, P.O. Box 16, FI-96301 Rovaniemi, Finland
| | - Jaana Vuosku
- Natural Resources Institute Finland, P.O. Box 16, FI-96301 Rovaniemi, Finland
| | - Sari Stark
- Natural Resources Institute Finland, P.O. Box 16, FI-96301 Rovaniemi, Finland.,Arctic Centre, University of Lapland, P.O. Box 122, FI-96101 Rovaniemi, Finland
| | - Karita Saravesi
- Department of Ecology and Genetics, P.O. Box 3000, FI-90014 University of Oulu, Finland
| | - Marko Suokas
- Department of Ecology and Genetics, P.O. Box 3000, FI-90014 University of Oulu, Finland
| | - Annamari Markkola
- Department of Ecology and Genetics, P.O. Box 3000, FI-90014 University of Oulu, Finland
| | - Françoise Martz
- Natural Resources Institute Finland, P.O. Box 16, FI-96301 Rovaniemi, Finland
| | - Pasi Rautio
- Natural Resources Institute Finland, P.O. Box 16, FI-96301 Rovaniemi, Finland
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149
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Champreda V, Mhuantong W, Lekakarn H, Bunterngsook B, Kanokratana P, Zhao XQ, Zhang F, Inoue H, Fujii T, Eurwilaichitr L. Designing cellulolytic enzyme systems for biorefinery: From nature to application. J Biosci Bioeng 2019; 128:637-654. [PMID: 31204199 DOI: 10.1016/j.jbiosc.2019.05.007] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 05/06/2019] [Accepted: 05/11/2019] [Indexed: 12/14/2022]
Abstract
Cellulolytic enzymes play a key role on conversion of lignocellulosic plant biomass to biofuels and biochemicals in sugar platform biorefineries. In this review, we survey composite carbohydrate-active enzymes (CAZymes) among groups of cellulolytic fungi and bacteria that exist under aerobic and anaerobic conditions. Recent advances in designing effective cellulase mixtures are described, starting from the most complex microbial consortium-based enzyme preparations, to single-origin enzymes derived from intensively studied cellulase producers such as Trichoderma reesei, Talaromyces cellulolyticus, and Penicellium funiculosum, and the simplest minimal enzyme systems comprising selected sets of mono-component enzymes tailor-made for specific lignocellulosic substrates. We provide a comprehensive update on studies in developing high-performance cellulases for biorefineries.
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Affiliation(s)
- Verawat Champreda
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Khlong Luang, Pathumthani 12120, Thailand.
| | - Wuttichai Mhuantong
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Khlong Luang, Pathumthani 12120, Thailand
| | - Hataikarn Lekakarn
- Department of Biotechnology, Faculty of Science and Technology, Thammasat University, Rangsit Campus, Phahonyothin Road, Khlong Luang, Pathumthani 12120, Thailand
| | - Benjarat Bunterngsook
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Khlong Luang, Pathumthani 12120, Thailand
| | - Pattanop Kanokratana
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Khlong Luang, Pathumthani 12120, Thailand
| | - Xin-Qing Zhao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Fei Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hiroyuki Inoue
- Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology, 3-11-32 Kagamiyama, Hiroshima 739-0046, Japan
| | - Tatsuya Fujii
- Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology, 3-11-32 Kagamiyama, Hiroshima 739-0046, Japan
| | - Lily Eurwilaichitr
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Khlong Luang, Pathumthani 12120, Thailand
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150
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Bredon M, Herran B, Lheraud B, Bertaux J, Grève P, Moumen B, Bouchon D. Lignocellulose degradation in isopods: new insights into the adaptation to terrestrial life. BMC Genomics 2019; 20:462. [PMID: 31174468 PMCID: PMC6555040 DOI: 10.1186/s12864-019-5825-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 05/23/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Isopods constitute a particular group of crustaceans that has successfully colonized all environments including marine, freshwater and terrestrial habitats. Their ability to use various food sources, especially plant biomass, might be one of the reasons of their successful spread. All isopods, which feed on plants and their by-products, must be capable of lignocellulose degradation. This complex composite is the main component of plants and is therefore an important nutrient source for many living organisms. Its degradation requires a large repertoire of highly specialized Carbohydrate-Active enZymes (called CAZymes) which are produced by the organism itself and in some cases, by its associated microbiota. The acquisition of highly diversified CAZymes could have helped isopods to adapt to their diet and to their environment, especially during land colonization. RESULTS To test this hypothesis, isopod host CAZomes (i.e. the entire CAZyme repertoire) were characterized in marine, freshwater and terrestrial species through a transcriptomic approach. Many CAZymes were identified in 64 isopod transcriptomes, comprising 27 de novo datasets. Our results show that marine, freshwater and terrestrial isopods exhibit different CAZomes, illustrating different strategies for lignocellulose degradation. The analysis of variations of the size of CAZy families shows these are expanded in terrestrial isopods while they are contracted in aquatic isopods; this pattern is probably resulting from the evolution of the host CAZomes during the terrestrial adaptation of isopods. We show that CAZyme gene duplications and horizontal transfers can be involved in adaptive divergence between isopod CAZomes. CONCLUSIONS Our characterization of the CAZomes in 64 isopods species provides new insights into the evolutionary processes that enabled isopods to conquer various environments, especially terrestrial ones.
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Affiliation(s)
- Marius Bredon
- Laboratoire Ecologie et Biologie des Interactions - UMR CNRS 7267, Equipe Ecologie Evolution Symbiose - Bâtiment B8-B35, Université de Poitiers, 5 rue Albert Turpain, TSA 51106, F-86073, Poitiers Cedex 9, France
| | - Benjamin Herran
- Laboratoire Ecologie et Biologie des Interactions - UMR CNRS 7267, Equipe Ecologie Evolution Symbiose - Bâtiment B8-B35, Université de Poitiers, 5 rue Albert Turpain, TSA 51106, F-86073, Poitiers Cedex 9, France
| | - Baptiste Lheraud
- Laboratoire Ecologie et Biologie des Interactions - UMR CNRS 7267, Equipe Ecologie Evolution Symbiose - Bâtiment B8-B35, Université de Poitiers, 5 rue Albert Turpain, TSA 51106, F-86073, Poitiers Cedex 9, France
| | - Joanne Bertaux
- Laboratoire Ecologie et Biologie des Interactions - UMR CNRS 7267, Equipe Ecologie Evolution Symbiose - Bâtiment B8-B35, Université de Poitiers, 5 rue Albert Turpain, TSA 51106, F-86073, Poitiers Cedex 9, France
| | - Pierre Grève
- Laboratoire Ecologie et Biologie des Interactions - UMR CNRS 7267, Equipe Ecologie Evolution Symbiose - Bâtiment B8-B35, Université de Poitiers, 5 rue Albert Turpain, TSA 51106, F-86073, Poitiers Cedex 9, France
| | - Bouziane Moumen
- Laboratoire Ecologie et Biologie des Interactions - UMR CNRS 7267, Equipe Ecologie Evolution Symbiose - Bâtiment B8-B35, Université de Poitiers, 5 rue Albert Turpain, TSA 51106, F-86073, Poitiers Cedex 9, France
| | - Didier Bouchon
- Laboratoire Ecologie et Biologie des Interactions - UMR CNRS 7267, Equipe Ecologie Evolution Symbiose - Bâtiment B8-B35, Université de Poitiers, 5 rue Albert Turpain, TSA 51106, F-86073, Poitiers Cedex 9, France.
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