1
|
Choudhary G, Kumari S, Anu K, Devi S. Deciphering the microbial communities of alkaline hot spring in Panamik, Ladakh, India using a high-throughput sequencing approach. Braz J Microbiol 2024; 55:1465-1476. [PMID: 38662153 PMCID: PMC11153388 DOI: 10.1007/s42770-024-01346-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Accepted: 04/15/2024] [Indexed: 04/26/2024] Open
Abstract
Due to their distinctive physicochemical characteristics, hot springs are extremely important. The whole genome metagenomic sequencing technology can be utilized to analyze the diverse microbial community that thrives in this habitat due to the particular selection pressure that prevails there. The current investigation emphasizes on culture-independent metagenomic study of the Panamik hot spring and its nearby areas from Ladakh, India. Based on different diversity indices, sequence analysis of the soil reservoir showed higher species richness and diversity in comparison to water and sediment samples. The mineral content and various physicochemical pameters like temperature, pH had an impact on the composition of the microbial community of the geothermal springs. The phyla Proteobacteria, Cyanobacteria, Bacteroidetes, Actinobacter, Firmicutes, and Verrucomicrobia in bacterial domain dominate the thermos-alkaline spring at Panamik in different concentrations. Economically significant microbes from the genera Actinobacter, Thermosynechoccus, Candidatus Solibacter, Chthoniobacter, Synechoccus, Pseudomonas and Sphingomonas, were prevalent in hot spring. In the archaeal domain, the most dominant phylum and genera were Euryarchaeota and Thermococcus in all the samples. Further, the most abundant species were Methanosarcina barkeri, Nitrospumilus maritimus and Methanosarcina acetivorans. The present study which only examined one of the several thermal springs present in the Himalayan geothermal area, should be regarded as a preliminary investigation of the microbiota that live in the hot springs on these remote areas. These findings suggest that further investigations should be undertaken to characterize the ecosystems of the Panamik hot spring, which serve as a repository for unidentified microbial lineages.
Collapse
Affiliation(s)
- Geetanjli Choudhary
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
| | - Shalini Kumari
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Kumari Anu
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Sarita Devi
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
| |
Collapse
|
2
|
López-González JA, Suárez-Estrella F, Jurado MM, Martínez-Gallardo MR, Toribio A, Estrella-González MJ, López MJ. Development of functional consortia for the pretreatment of compostable lignocellulosic waste: A simple and effective solution to a large-scale problem. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 356:120638. [PMID: 38518496 DOI: 10.1016/j.jenvman.2024.120638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 02/13/2024] [Accepted: 03/10/2024] [Indexed: 03/24/2024]
Abstract
Microorganisms drive the degradation of organic matter thanks to their enzymatic versatility. However, the structure of lignocellulose poses a great challenge for the microbiota inhabiting a compost pile. Our purpose was to increase the biodegradability of vegetable waste in the early stages of the composting process by applying a microbial consortium with lignocelllulolytic capacity. For this, a previous screening was performed among the culturable microbiota from different composting processes to find inoculants with ligninocellulolytic activity. Selected strains were applied as a pure culture and as a microbial consortium. The starting material was composed of tomato plant and pruning remains mixed in a ratio (50:50 v/v), whose humidity was adjusted to around 65%. To determine the ability of both treatments to activate the biodegradation of the mixtures, moisture, organic matter, ash, C/N ratio, 4-day cumulative respirometric index (AT4) and degradation rates of cellulose, hemicellulose and lignin were evaluated. Subsequently, a real composting process was developed in which the performance of the microbial consortium was compared with the composting process without inoculum (control). According to our tests, three microbial strains (Bacillus safensis, Bacillus licheniformis and Fusarium oxysporum) were selected. The results showed that the application of the bacteria strains at low doses (104 CFU g-1 on the complete residual material of the pile) resulted in higher rates of lignocelullose degradation after 10 days of treatment compared to that observed after application of the fungus in pure culture or untreated controls. The implementation of the strategy described in this work resulted in obtaining compost with better agronomic quality than the uninoculated controls. Therefore, the application of this consortium could be considered as an interesting tool for bioactivation of lignocellulosic waste prior to the composting process.
Collapse
Affiliation(s)
- J A López-González
- Department of Biology and Geology, CITE II-B, University of Almería, Agrifood Campus of International Excellence, ceiA3, CIAIMBITAL, 04120, Almería, Spain.
| | - F Suárez-Estrella
- Department of Biology and Geology, CITE II-B, University of Almería, Agrifood Campus of International Excellence, ceiA3, CIAIMBITAL, 04120, Almería, Spain.
| | - M M Jurado
- Department of Biology and Geology, CITE II-B, University of Almería, Agrifood Campus of International Excellence, ceiA3, CIAIMBITAL, 04120, Almería, Spain
| | - M R Martínez-Gallardo
- Department of Biology and Geology, CITE II-B, University of Almería, Agrifood Campus of International Excellence, ceiA3, CIAIMBITAL, 04120, Almería, Spain
| | - A Toribio
- Department of Biology and Geology, CITE II-B, University of Almería, Agrifood Campus of International Excellence, ceiA3, CIAIMBITAL, 04120, Almería, Spain
| | - M J Estrella-González
- Department of Biology and Geology, CITE II-B, University of Almería, Agrifood Campus of International Excellence, ceiA3, CIAIMBITAL, 04120, Almería, Spain
| | - M J López
- Department of Biology and Geology, CITE II-B, University of Almería, Agrifood Campus of International Excellence, ceiA3, CIAIMBITAL, 04120, Almería, Spain
| |
Collapse
|
3
|
Ciric M, Šaraba V, Budin C, de Boer T, Nikodinovic-Runic J. Polyurethane-Degrading Potential of Alkaline Groundwater Bacteria. MICROBIAL ECOLOGY 2023; 87:21. [PMID: 38153543 DOI: 10.1007/s00248-023-02338-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 12/24/2023] [Indexed: 12/29/2023]
Abstract
Plastic waste is a global environmental burden and long-lasting plastic polymers, including ubiquitous and toxic polyurethanes (PUs), rapidly accumulate in the water environments. In this study, samples were collected from the three alkaline groundwater occurrences in the geotectonic regions of the Pannonian basin of northern Serbia (Torda and Slankamen Banja) and Inner Dinarides of western Serbia (Mokra Gora) with aim to isolate and identify bacteria with plastic- and lignocellulose-degrading potential, that could be applied to reduce the burden of environmental plastic pollution. The investigated occurrences belong to cold, mildly alkaline (pH: 7.6-7.9) brackish and hyperalkaline (pH: 11.5) fresh groundwaters of the SO4 - Na + K, Cl - Na + K and OH, Cl - Ca, Na + K genetic type. Full-length 16S rDNA sequencing, using Oxford Nanopore sequencing device, was performed with DNA extracted from colonies obtained by cultivation of all groundwater samples, as well as with DNA extracted directly from one groundwater sample. The most abundant genera belong to Pseudomonas, Acidovorax, Kocuria and Methylotenera. All screened isolates (100%) had the ability to grow on at least 3 of the tested plastic and lignocellulosic substrates, with 53.9% isolates degrading plastic substrate Impranil® DLN-SD (SD), a model compound for PUs degradation. Isolates degrading SD that were identified by partial 16S rDNA sequencing belong to the Stenotrophomonas, Pseudomonas, Paraburkholderia, Aeromonas, Vibrio and Acidovorax genera. Taking into account that plastics, including commonly produced PUs, are widespread in groundwater, identification of PUs-degrading bacteria may have potential applications in bioremediation of groundwater polluted with this polymer.
Collapse
Affiliation(s)
- Milica Ciric
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia.
| | - Vladimir Šaraba
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Clémence Budin
- Microlife Solutions, Science Park 406, 1098XH, Amsterdam, The Netherlands
| | - Tjalf de Boer
- Microlife Solutions, Science Park 406, 1098XH, Amsterdam, The Netherlands
| | | |
Collapse
|
4
|
Xie R, Dong C, Wang S, Danso B, Dar MA, Pandit RS, Pawar KD, Geng A, Zhu D, Li X, Xu Q, Sun J. Host-Specific Diversity of Culturable Bacteria in the Gut Systems of Fungus-Growing Termites and Their Potential Functions towards Lignocellulose Bioconversion. INSECTS 2023; 14:403. [PMID: 37103218 PMCID: PMC10146277 DOI: 10.3390/insects14040403] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 04/16/2023] [Accepted: 04/19/2023] [Indexed: 06/19/2023]
Abstract
Fungus-growing termites are eusocial insects that represent one of the most efficient and unique systems for lignocellulose bioconversion, evolved from a sophisticated symbiosis with lignocellulolytic fungi and gut bacterial communities. Despite a plethora of information generated during the last century, some essential information on gut bacterial profiles and their unique contributions to wood digestion in some fungus-growing termites is still inadequate. Hence, using the culture-dependent approach, the present study aims to assess and compare the diversity of lignocellulose-degrading bacterial symbionts within the gut systems of three fungus-growing termites: Ancistrotermes pakistanicus, Odontotermes longignathus, and Macrotermes sp. A total of 32 bacterial species, belonging to 18 genera and 10 different families, were successfully isolated and identified from three fungus-growing termites using Avicel or xylan as the sole source of carbon. Enterobacteriaceae was the most dominant family represented by 68.1% of the total bacteria, followed by Yersiniaceae (10.6%) and Moraxellaceae (9%). Interestingly, five bacterial genera such as Enterobacter, Citrobacter, Acinetobacter, Trabulsiella, and Kluyvera were common among the tested termites, while the other bacteria demonstrated a termite-specific distribution. Further, the lignocellulolytic potential of selected bacterial strains was tested on agricultural waste to evaluate their capability for lignocellulose bioconversion. The highest substrate degradation was achieved with E. chengduensis MA11 which degraded 45.52% of rice straw. All of the potential strains showed endoglucanase, exoglucanase, and xylanase activities depicting a symbiotic role towards the lignocellulose digestion within the termite gut. The above results indicated that fungus-growing termites harbor a diverse array of bacterial symbionts that differ from species to species, which may play an inevitable role to enhance the degradation efficacy in lignocellulose decomposition. The present study further elaborates our knowledge about the termite-bacteria symbiosis for lignocellulose bioconversion which could be helpful to design a future biorefinery.
Collapse
Affiliation(s)
- Rongrong Xie
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Chenchen Dong
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Shengjie Wang
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Blessing Danso
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Mudasir A. Dar
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
- Department of Zoology, Savitribai Phule Pune University, Pune 411007, India
| | | | - Kiran D. Pawar
- School of Nanoscience and Biotechnology, Shivaji University, Kolhapur 416004, India
| | - Alei Geng
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Daochen Zhu
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Xia Li
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Qing Xu
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Jianzhong Sun
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| |
Collapse
|
5
|
Molina-Peñate E, Del Carmen Vargas-García M, Artola A, Sánchez A. Filling in the gaps in biowaste biorefineries: The use of the solid residue after enzymatic hydrolysis for the production of biopesticides through solid-state fermentation. WASTE MANAGEMENT (NEW YORK, N.Y.) 2023; 161:92-103. [PMID: 36871406 DOI: 10.1016/j.wasman.2023.02.029] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 01/31/2023] [Accepted: 02/23/2023] [Indexed: 06/18/2023]
Abstract
Alternative production processes using waste are necessary to preserve non-renewable resources and prevent scarcity of materials for future generations. Biowaste, the organic fraction of municipal solid waste, is abundant and easily available. It can be fractionated into building blocks for which fermentative processes can be designed. By using solid-state fermentation, this paper proposes a method of valorizing biowaste's residual solid fraction after enzymatic hydrolysis. In a 22 L bioreactor, two digestates from anaerobic digestion processes were evaluated as cosubstrates to modify the acidic pH of the solid residue after enzymatic hydrolysis and promote the growth of the bacterial biopesticide producer Bacillus thuringiensis. Regardless of the cosubstrate used, the final microbial populations were similar indicating microbial specialization. The final product contained 4 × 108 spores per gram of dry matter and also crystal proteins of Bacillus thuringiensis var israelensis, which have insecticidal activity against pests. This method allows for the sustainable use of all materials liberated during the enzymatic hydrolysis of biowaste, including residual solids.
Collapse
Affiliation(s)
- Esther Molina-Peñate
- GICOM Research Group, Department of Chemical, Biological and Environmental Engineering, School of Engineering, Edifici Q, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain; Aeris Tecnologías Ambientales S.L, Carrer Santa Rosa, 38, local, 08290 Cerdanyola del Vallès, Barcelona, Spain
| | - María Del Carmen Vargas-García
- Microbiology Unit, Department of Biology and Geology, University of Almeria, International Excellence Campus of the Sea (CEI·MAR), Crta. Sacramento s/n, La Cañada de San Urbano, 04120 Almería, Spain
| | - Adriana Artola
- GICOM Research Group, Department of Chemical, Biological and Environmental Engineering, School of Engineering, Edifici Q, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain.
| | - Antoni Sánchez
- GICOM Research Group, Department of Chemical, Biological and Environmental Engineering, School of Engineering, Edifici Q, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| |
Collapse
|
6
|
Zhang C, Cai B, Sun Y, Kang J, Pei F, Ge J. Microbial communities that drive the degradation of flax pectin and hemicellulose during dew retting with Bacillus licheniformis HDYM-04 and Bacillus subtilis ZC-01 addition. BIORESOURCE TECHNOLOGY 2023; 371:128516. [PMID: 36563865 DOI: 10.1016/j.biortech.2022.128516] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/16/2022] [Accepted: 12/17/2022] [Indexed: 06/17/2023]
Abstract
In this study, the combined addition of Bacillus licheniformis HDYM-04 and Bacillus subtilis ZC-01 to flax degradation increased the degradation rates of pectin (74.7 %) and pectinic acid (59.3 %) and increased the maximum activities of pectinase (610.66 ± 7.03 U/mL) and mannanase (656.97 ± 13.16 U/mL). 16S rRNA sequencing showed that the added bacterial agent (Bacillus) was the dominant bacterium, and its addition increased the relative abundance (RA) of Firmicutes and decreased the RA of Bacteroidetes. The core bacterial community linked to degradation (Firmicutes) was determined by RDA. Network analysis showed that the number of bacteria related to pectin and hemicellulose degradation increased with the addition of the bacteria combination. SEM analysis showed that Bacillus was positively correlated with the degradation of pectic substances. These results provide new ideas for improving the utilization of agricultural waste resources and promoting sustainable development in modern agriculture.
Collapse
Affiliation(s)
- Chi Zhang
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Baiyan Cai
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region & Key Laboratory of Molecular Biology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Yangcun Sun
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Jie Kang
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Fangyi Pei
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Jingping Ge
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin 150080, China.
| |
Collapse
|
7
|
Lee JY, Kim MH, Kim JS, Yun BR, Kim DY, Chung CW. Biotransformation of d-Xylose-Rich Rice Husk Hydrolysate by a Rice Paddy Soil Bacterium, Priestia sp. Strain JY310, to Low Molecular Weight Poly(3-hydroxybutyrate). Biomolecules 2023; 13:biom13010131. [PMID: 36671516 PMCID: PMC9855389 DOI: 10.3390/biom13010131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/06/2023] [Accepted: 01/07/2023] [Indexed: 01/10/2023] Open
Abstract
Poly(3-hydroxybutyrate) (PHB) is a versatile thermoplastic with superior biodegradability and biocompatibility that is intracellularly accumulated by numerous bacterial and archaeal species. Priestia sp. strain JY310 that was able to efficiently biotransform reducing sugars in d-xylose-rich rice husk hydrolysate (reducing sugarRHH) to PHB was isolated from the soil of a rice paddy. Reducing sugarRHH including 12.5% d-glucose, 75.3% d-xylose, and 12.2% d-arabinose was simply prepared using thermochemical hydrolysis of 3% H2SO4-treated rice husk for 15 min at 121 °C. When cultured with 20 g/L reducing sugarRHH under optimized culture conditions in a batch bioreactor, Priestia sp. strain JY310 could produce PHB homopolymer up to 50.4% of cell dry weight (6.2 g/L). The melting temperature, heat of fusion, and thermal decomposition temperature of PHB were determined to be 167.9 °C, 92.1 J/g, and 268.1 °C, respectively. The number average and weight average molecular weights of PHB with a broad polydispersity index value (4.73) were estimated to be approximately 16.2 and 76.8 kg/mol, respectively. The findings of the present study suggest that Priestia sp. strain JY310 can be exploited as a good candidate for the low-cost production of low molecular weight PHB with improved biodegradability and reduced brittleness from inexpensive agricultural waste hydrolysates.
Collapse
Affiliation(s)
- Jae-Yeong Lee
- Department of Biological Sciences, Andong National University, Andong 36729, Republic of Korea; (J.-Y.L.); (M.-H.K.); (J.-S.K.)
| | - Min-Hwan Kim
- Department of Biological Sciences, Andong National University, Andong 36729, Republic of Korea; (J.-Y.L.); (M.-H.K.); (J.-S.K.)
| | - Jong-Sik Kim
- Department of Biological Sciences, Andong National University, Andong 36729, Republic of Korea; (J.-Y.L.); (M.-H.K.); (J.-S.K.)
| | - Bo-Ram Yun
- Korea Disease Control and Prevention Agency, Cheongju 28159, Republic of Korea;
| | - Do Young Kim
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology(KRIBB), Daejeon 34141, Republic of Korea
- Correspondence: (D.Y.K.); (C.-W.C.)
| | - Chung-Wook Chung
- Department of Biological Sciences, Andong National University, Andong 36729, Republic of Korea; (J.-Y.L.); (M.-H.K.); (J.-S.K.)
- Correspondence: (D.Y.K.); (C.-W.C.)
| |
Collapse
|
8
|
Becker R, Ulrich K, Behrendt U, Schneck V, Ulrich A. Genomic Characterization of Aureimonas altamirensis C2P003-A Specific Member of the Microbiome of Fraxinus excelsior Trees Tolerant to Ash Dieback. PLANTS (BASEL, SWITZERLAND) 2022; 11:3487. [PMID: 36559599 PMCID: PMC9781493 DOI: 10.3390/plants11243487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/07/2022] [Accepted: 12/09/2022] [Indexed: 06/17/2023]
Abstract
Some European ash trees show tolerance towards dieback caused by the invasive pathogen Hymenoscyphus fraxineus. The microbiome of these trees harbours a range of specific bacterial groups. One of these groups belonging to the species Aureimonas altamirensis was studied in detail by genome analysis and a plant inoculation trial. The strain group was shown to be phylogenetically distinct from clinical isolates by 16S rRNA analysis and phylogenomics. Genome analysis of a representative strain C2P003 resulted in a large number of unique gene sequences in comparison to other well-studied strains of the species. A functional analysis of the genome revealed features associated with the synthesis of exopolysaccharides, protein secretion and biofilm production as well as genes for stress adaptation, suggesting the ability of C2P003 to effectively colonize ash leaves. The inoculation of ash seedlings with C2P003 showed a significant positive effect on the plant health of the seedlings that were exposed to H. fraxineus infection. This effect was maintained over a period of three years and was accompanied by a significant shift in the bacterial microbiome composition one year after inoculation. Overall, the results indicate that C2P003 may suppress H. fraxineus in or on ash leaves via colonization resistance or indirectly by affecting the microbiome.
Collapse
Affiliation(s)
- Regina Becker
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research (ZALF), 15374 Müncheberg, Germany
| | - Kristina Ulrich
- Institute of Forest Genetics, Johann Heinrich von Thünen Institute, 15377 Waldsieversdorf, Germany
| | - Undine Behrendt
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research (ZALF), 15374 Müncheberg, Germany
| | - Volker Schneck
- Institute of Forest Genetics, Johann Heinrich von Thünen Institute, 15377 Waldsieversdorf, Germany
| | - Andreas Ulrich
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research (ZALF), 15374 Müncheberg, Germany
| |
Collapse
|
9
|
Medium for the Production of Bacillus-Based Biocontrol Agent Effective against Aflatoxigenic Aspergillus flavus: Dual Approach for Modelling and Optimization. Microorganisms 2022; 10:microorganisms10061165. [PMID: 35744682 PMCID: PMC9228200 DOI: 10.3390/microorganisms10061165] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 05/27/2022] [Accepted: 05/30/2022] [Indexed: 12/04/2022] Open
Abstract
One of the leading limiting factors for wider industrial production and commercialization of microbial biopesticides refers to the high costs of cultivation media. The selection of alternative sources of macronutrients crucial for the growth and metabolic activity of the producing microorganism is a necessary phase of the bioprocess development. Gaining a better understanding of the influence of the medium composition on the biotechnological production of biocontrol agents is enabled through bioprocess modelling and optimization. In the present study, after the selection of optimal carbon and nitrogen sources, two modelling approaches were applied to mathematically describe the behavior of the examined bioprocess—the production of biocontrol agents effective against aflatoxigenic Aspergillus flavus strains. The modelling was performed using four independent variables: cellulose, urea, ammonium sulfate and dipotassium phosphate, and the selected response was the inhibition-zone diameter. After the comparison of the results generated by the Response Surface Methodology (RSM) and the Artificial Neural Network (ANN) approach, the first model was chosen for the further optimization step due to the better fit of the experimental results. As the final investigation step, the optimal cultivation medium composition was defined (g/L): cellulose 5.0, ammonium sulfate 3.77, dipotassium phosphate 0.3, magnesium sulfate heptahydrate 0.3.
Collapse
|
10
|
Lake microbiome and trophy fluctuations of the ancient hemp rettery. Sci Rep 2022; 12:8846. [PMID: 35614182 PMCID: PMC9132974 DOI: 10.1038/s41598-022-12761-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 05/16/2022] [Indexed: 11/18/2022] Open
Abstract
Lake sediments not only store the long-term ecological information including pollen and microfossils but are also a source of sedimentary DNA (sedDNA). Here, by the combination of traditional multi-proxy paleolimnological methods with the whole-metagenome shotgun-sequencing of sedDNA we were able to paint a comprehensive picture of the fluctuations in trophy and bacterial diversity and metabolism of a small temperate lake in response to hemp retting, across the past 2000 years. Hemp retting (HR), a key step in hemp fibre production, was historically carried out in freshwater reservoirs and had a negative impact on the lake ecosystems. In Lake Slone, we identified two HR events, during the late stage of the Roman and Early Medieval periods and correlated these to the increased trophy and imbalanced lake microbiome. The metagenomic analyses showed a higher abundance of Chloroflexi, Planctomycetes and Bacteroidetes and a functional shift towards anaerobic metabolism, including degradation of complex biopolymers such as pectin and cellulose, during HR episodes. The lake eutrophication during HR was linked to the allochthonous, rather than autochthonous carbon supply—hemp straws. We also showed that the identification of HR based on the palynological analysis of hemp pollen may be inconclusive and we suggest the employment of the fibre count analysis as an additional and independent proxy.
Collapse
|
11
|
Wu N, Wang X, Mao Z, Liang J, Liu X, Xu X. Bioconversion of chicken meat and bone meal by black soldier fly larvae: Effects of straw addition on the quality and microbial profile of larval frass. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 307:114579. [PMID: 35078063 DOI: 10.1016/j.jenvman.2022.114579] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 01/11/2022] [Accepted: 01/19/2022] [Indexed: 06/14/2023]
Abstract
Meat and bone meal (MBM) is a kind of animal waste with high nutritive values. Bioconversion of MBM by black soldier fly larvae (BSFL) has great potential to obtain high-quality organic fertilizers. However, limited information is available on MBM waste manipulation to enhance BSFL frass quality. In the present study, BSFL were fed with chicken MBM containing increasing levels of rice straw (CK (0%), T1 (1%), T2 (1%), and T3 (3%)). The effects of straw addition into MBM on the quality and microbial profile of BSFL frass were evaluated. Results showed that MBM amended with straw did not significantly affect the body weight of BSFL and most of the nutrients (e.g. pH, EC, TN, TP and Na) in larval frass. Compared to other treatments, T1 sample had the highest organic matter (OM) value, implying proper straw addition could increase OM contents in frass. Fourier transform infrared (FTIR) analysis showed that straw addition might enhance the decomposition of aliphatic carbons and polysaccharides during MBM digestion process. Moreover, T1 sample had the highest microbial richness and Shannon diversity indices. It was supposed that proper straw addition in MBM helped build a more balanced diet and contributed to the BSFL gut health, consequently stimulating the gut microbe-mediated substances transformation or decomposition and promoting the microbial diversity in frass. Compared to CK, straw addition had significant influence on the abundances of Firmicutes, Bacteroidetes and Fusobacteria in frass. Elements including OM, TK and Na played important roles in shaping the microbial profile of BSFL frass.
Collapse
Affiliation(s)
- Nan Wu
- College of Engineering and Technology, Tianjin Agricultural University, Tianjin, 300392, China
| | - Xiaobo Wang
- College of Agronomy and Resource and Environment, Tianjin Agricultural University, Tianjin, 300392, China
| | - Zhiyue Mao
- College of Agronomy and Resource and Environment, Tianjin Agricultural University, Tianjin, 300392, China
| | - Jiaqi Liang
- College of Engineering and Technology, Tianjin Agricultural University, Tianjin, 300392, China
| | - Xinyuan Liu
- College of Engineering and Technology, Tianjin Agricultural University, Tianjin, 300392, China
| | - Xiaoyan Xu
- College of Agronomy and Resource and Environment, Tianjin Agricultural University, Tianjin, 300392, China.
| |
Collapse
|
12
|
De Novo Metagenomic Analysis of Microbial Community Contributing in Lignocellulose Degradation in Humus Samples Harvested from Cuc Phuong Tropical Forest in Vietnam. DIVERSITY 2022. [DOI: 10.3390/d14030220] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We aimed to investigate the microbial diversity, mine lignocellulose-degrading enzymes/proteins, and analyze the domain structures of the mined enzymes/proteins in humus samples collected from the Cuc Phuong National Park, Vietnam. Using a high-throughput Illumina sequencer, 52 Gbs of microbial DNA were assembled in 2,611,883 contigs, from which 4,104,872 open reading frames (ORFs) were identified. Among the total microbiome analyzed, bacteria occupied 99.69%; the five ubiquitous bacterial phyla included Proteobacteria, Bacteroidetes, Actinobacteria, Firmicutes, and Acidobacteria, which accounted for 92.59%. Proteobacteria (75.68%), the most dominant, was 5.77 folds higher than the second abundant phylum Bacteroidetes (13.11%). Considering the enzymes/proteins involved in lignocellulose degradation, 22,226 ORFs were obtained from the annotation analysis using a KEGG database. The estimated ratio of Proteobacteria/Bacteroidetes was approximately 1:1 for pretreatment and hemicellulases groups and 2.4:1 for cellulases. Furthermore, analysis of domain structures revealed their diversity in lignocellulose-degrading enzymes. CE and PL were two main families in pretreatment; GH1 and GH3-FN3 were the highest domains in the cellulase group, whereas GH2 and GH43 represented the hemicellulase group. These results validate that natural tropical forest soil could be considered as an important source to explore bacteria and novel enzymes/proteins for the degradation of lignocellulose.
Collapse
|
13
|
New eco-friendly trends to produce biofuel and bioenergy from microorganisms: An updated review. Saudi J Biol Sci 2022. [DOI: 10.1016/j.sjbs.2022.02.024] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
|
14
|
Díaz-García L, Chaparro D, Jiménez H, Gómez-Ramírez LF, Bernal AJ, Burbano-Erazo E, Jiménez DJ. Top-Down Enrichment Strategy to Co-cultivate Lactic Acid and Lignocellulolytic Bacteria From the Megathyrsus maximus Phyllosphere. Front Microbiol 2022; 12:744075. [PMID: 35035382 PMCID: PMC8753987 DOI: 10.3389/fmicb.2021.744075] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 10/11/2021] [Indexed: 12/15/2022] Open
Abstract
Traditionally, starting inoculants have been applied to improve ensiling of forage used for livestock feed. Here, we aimed to build up a bioinoculant composed of lactic acid-producing and lignocellulolytic bacteria (LB) derived from the Megathyrsus maximus (guinea grass) phyllosphere. For this, the dilution-to-stimulation approach was used, including a sequential modification of the starting culture medium [Man, Rogosa, and Sharpe (MRS) broth] by addition of plant biomass (PB) and elimination of labile carbon sources. Along 10 growth-dilution steps (T1–T10), slight differences were observed in terms of bacterial diversity and composition. After the sixth subculture, the consortium started to degrade PB, decreasing its growth rate. The co-existence of Enterobacteriales (fast growers and highly abundance), Actinomycetales, Bacillales, and Lactobacillales species was observed at the end of the selection process. However, a significant structural change was noticed when the mixed consortium was cultivated in higher volume (500ml) for 8days, mainly increasing the proportion of Paenibacillaceae populations. Interestingly, Actinomycetales, Bacillales, and Lactobacillales respond positively to a pH decrease (4–5), suggesting a relevant role within a further silage process. Moreover, gene-centric metagenomic analysis showed an increase of (hemi)cellulose-degrading enzymes (HDEs) during the enrichment strategy. Reconstruction of metagenome-assembled genomes (MAGs) revealed that Paenibacillus, Cellulosimicrobium, and Sphingomonas appear as key (hemi)cellulolytic members (harboring endo-glucanases/xylanases, arabinofuranosidases, and esterases), whereas Enterococcus and Cellulosimicrobium have the potential to degrade oligosaccharides, metabolize xylose and might produce lactic acid through the phosphoketolase (PK) pathway. Based on this evidence, we conclude that our innovative top-down strategy enriched a unique bacterial consortium that could be useful in biotechnological applications, including the development/design of a synthetic bioinoculant to improve silage processes.
Collapse
Affiliation(s)
- Laura Díaz-García
- Microbiomes and Bioenergy Research Group, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Dayanne Chaparro
- Microbiomes and Bioenergy Research Group, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Hugo Jiménez
- Colombian Corporation for Agricultural Research (Agrosavia), Mosquera, Colombia
| | | | - Adriana J Bernal
- Laboratory of Molecular Interactions of Agricultural Microbes, 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
| |
Collapse
|
15
|
Sun L, Long M, Li J, Wu R, Ma L, Tang D, Lu Y, Wang Z. Different Effects of Thermophilic Microbiological Inoculation With and Without Biochar on Physicochemical Characteristics and Bacterial Communities in Pig Manure Composting. Front Microbiol 2021; 12:746718. [PMID: 34899633 PMCID: PMC8660119 DOI: 10.3389/fmicb.2021.746718] [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: 07/24/2021] [Accepted: 10/04/2021] [Indexed: 11/13/2022] Open
Abstract
This study evaluated the effects of thermophilic microbiological inoculation alone (TA) and integrated with biochar (TB) on the physicochemical characteristics and bacterial communities in pig manure (PM) composting with wheat straw. Both TA and TB accelerated the rate of temperature increase during the PM composting. TA significantly reduced total nitrogen loss by 18.03% as opposed to TB which significantly accelerated total organic carbon degradation by 12.21% compared with the control. Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria were the major phyla in composting. Variation of the relative abundance of genera depended on the composting period and treatment. The genera Lactobacillus (26.88-46.71%) and Clostridium_sensu_stricto (9.03-31.69%) occupied a superior position in the temperature rise stage, and Bacillus (30.90-36.19%) was outstanding in the cooling stage. Temperature, total nitrogen (TN), and ammonium nitrogen significantly influenced the bacterial phyla composition. TN, water content, and nitrite nitrogen were the main drivers of the bacterial community genera. Furthermore, our results demonstrated that microbiological consortia were resistant to high temperatures and could fix nitrogen for enriched Pseudomonas; however, when interacted with biochar, total organic carbon (TOC) degradation was accelerated for higher bacterial richness and diversity as well as overrepresented Corynebacterium.
Collapse
Affiliation(s)
- Likun Sun
- College of Animal Science, Gansu Agricultural University, Lanzhou, China.,Gansu Provincial Engineering Research Center for Animal Waste Utilization, Gansu Agricultural University, Lanzhou, China
| | - Min Long
- College of Animal Science, Gansu Agricultural University, Lanzhou, China.,College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, China
| | - Jianshu Li
- College of Animal Science, Gansu Agricultural University, Lanzhou, China
| | - Renfei Wu
- College of Animal Science, Gansu Agricultural University, Lanzhou, China
| | - Lin Ma
- College of Animal Science, Gansu Agricultural University, Lanzhou, China.,Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetic and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
| | - Defu Tang
- College of Animal Science, Gansu Agricultural University, Lanzhou, China
| | - Yongli Lu
- College of Resources and Environmental Sciences, Gansu Agricultural University, Lanzhou, China
| | - Ziyu Wang
- College of Animal Science, Gansu Agricultural University, Lanzhou, China
| |
Collapse
|
16
|
Genome information of the cellulolytic soil actinobacterium Isoptericola dokdonensis DS-3 and comparative genomic analysis of the genus Isoptericola. J Microbiol 2021; 59:1010-1018. [PMID: 34724179 DOI: 10.1007/s12275-021-1452-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/15/2021] [Accepted: 09/15/2021] [Indexed: 10/20/2022]
Abstract
The actinobacterial group is regarded as a reservoir of biologically active natural products and hydrolytic enzymes with the potential for biomedical and industrial applications. Here, we present the complete genome sequence of Isoptericola dokdonensis DS-3 isolated from soil in Dokdo, small islets in the East Sea of Korea. This actinomycete harbors a large number of genes encoding carbohydrate-degrading enzymes, and its activity to degrade carboxymethyl cellulose into glucose was experimentally evaluated. Since the genus Isoptericola was proposed after reclassification based on phylogenetic analysis, strains of Isoptericola have been continuously isolated from diverse environments and the importance of this genus in the ecosystem has been suggested by recent culturomic or metagenomic studies. The phylogenic relationships of the genus tended to be closer among strains that had been isolated from similar habitats. By analyzing the properties of published genome sequences of seven defined species in the genus, a large number of genes for carbohydrate hydrolysis and utilization, as well as several biosynthetic gene clusters for secondary metabolites, were identified. Genomic information of I. dokdonensis DS-3 together with comparative analysis of the genomes of Isoptericola provides insights into understanding this actinobacterial group with a potential for industrial applications.
Collapse
|
17
|
Considerations on the Identity and Diversity of Organisms Affiliated with Sphingobacterium multivorum-Proposal for a New Species, Sphingobacterium paramultivorum. Microorganisms 2021; 9:microorganisms9102057. [PMID: 34683378 PMCID: PMC8540502 DOI: 10.3390/microorganisms9102057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 09/21/2021] [Accepted: 09/24/2021] [Indexed: 11/16/2022] Open
Abstract
Plant biomass offers great potential as a sustainable resource, and microbial consortia are primordial in its bioconversion. The wheat-straw-biodegradative bacterial strain w15 has drawn much attention as a result of its biodegradative potential and superior degradation performance in bacterial-fungal consortia. Strain w15 was originally assigned to the species Sphingobacterium multivorum based on its 16S ribosomal RNA (rRNA) gene sequence. A closer examination of this taxonomic placement revealed that the sequence used has 98.9% identity with the ‘divergent’ 16S rRNA gene sequence of S. multivorum NCTC 11343T, yet lower relatedness with the canonical 16S rRNA sequence. A specific region of the gene, located between positions 186 and 210, was found to be highly variable and determinative for the divergence. To solve the identity of strain w15, genome metrics and analyses of ecophysiological niches were undertaken on a selection of strains assigned to S. multivorum and related species. These analyses separated all strains into three clusters, with strain w15, together with strain BIGb0170, constituting a separate radiation, next to S. multivorum and S. siyangense. Moreover, the strains denoted FDAARGOS 1141 and 1142 were placed inside S. siyangense. We propose the renaming of strains w15 and BIGb0170 as members of the novel species, coined Sphingobacterium paramultivorum.
Collapse
|
18
|
Vela Gurovic MS, Díaz ML, Gallo CA, Dietrich J. Phylogenomics, CAZyome and core secondary metabolome of Streptomyces albus species. Mol Genet Genomics 2021; 296:1299-1311. [PMID: 34564766 DOI: 10.1007/s00438-021-01823-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 09/13/2021] [Indexed: 12/27/2022]
Abstract
A phylogenomic study conducted with different bioinformatic tools such as TYGS, REALPHY and AAI comparisons revealed a high rate of misidentified Streptomyces albus genomes in GenBank. Only 9 of the 18 annotated genomes available in the public database were correctly identified as S. albus species. The pangenome of the nine in silico confirmed S. albus genomes was almost closed. Lignocellulosic agroresidues were a common niche among strains of the S. albus clade while carbohydrate active enzymes (CAZymes) were highly conserved. Relevant enzymes for cellulose degradation such as beta glucosidases belonging to the GH1 family, a GH6 cellulase and a monooxygenase AA10-CBM2 were encoded by all S. albus genomes. Among them, one GH1 glycosidase would be regulated by CebR. However, this regulatory mechanism was not confirmed for other genes related to cellulose degradation. Based on AntiSMASH predictions, the core secondary metabolome of S. albus encompassed a total of 23 biosynthetic gene clusters (BGCs), where 4 were related to common metabolites within Streptomyces genus. Species specific BGCs included those related to pseudouridimycin and xantholipin. Additionally, four BGCs encoded putative derivatives of ibomycin, the lasso peptide SSV-2086, the lanthipeptide SapB and the terpene isorenieratene. Known metabolites could not be assigned to ten BGCs and three clusters did not match with any previously described BGC. The core genome of S. albus retrieved from nine closely related genomes revealed a high potential for the discovery of novel bioactive metabolites and underexplored regulatory genomic elements related to lignocellulose deconstruction.
Collapse
Affiliation(s)
- María Soledad Vela Gurovic
- CERZOS UNS-CONICET CCT-Bahía Blanca, Camino La Carrindanga Km7, B8000FWB, Bahía Blanca, Argentina. .,Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional del Sur, San Juan 670, 8000, Bahía Blanca, Argentina.
| | - Marina Lucía Díaz
- CERZOS UNS-CONICET CCT-Bahía Blanca, Camino La Carrindanga Km7, B8000FWB, Bahía Blanca, Argentina.,Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional del Sur, San Juan 670, 8000, Bahía Blanca, Argentina
| | - Cristian Andres Gallo
- CERZOS UNS-CONICET CCT-Bahía Blanca, Camino La Carrindanga Km7, B8000FWB, Bahía Blanca, Argentina
| | - Julián Dietrich
- Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional del Sur, San Juan 670, 8000, Bahía Blanca, Argentina
| |
Collapse
|
19
|
Becarelli S, Chicca I, La China S, Siracusa G, Bardi A, Gullo M, Petroni G, Levin DB, Di Gregorio S. A New Ciboria sp. for Soil Mycoremediation and the Bacterial Contribution to the Depletion of Total Petroleum Hydrocarbons. Front Microbiol 2021; 12:647373. [PMID: 34177829 PMCID: PMC8221241 DOI: 10.3389/fmicb.2021.647373] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 04/26/2021] [Indexed: 11/24/2022] Open
Abstract
A Ciboria sp. strain (Phylum Ascomycota) was isolated from hydrocarbon-polluted soil of an abandoned oil refinery in Italy. The strain was able to utilize diesel oil as a sole carbon source for growth. Laboratory-scale experiments were designed to evaluate the use of this fungal strain for treatment of the polluted soil. The concentration of total petroleum hydrocarbons (TPH) in the soil was 8,538 mg/kg. Mesocosms containing the contaminated soil were inoculated with the fungal strain at 1 or 7%, on a fresh weight base ratio. After 90 days of incubation, the depletion of TPH contamination was of 78% with the 1% inoculant, and 99% with the 7% inoculant. 16S rDNA and ITS metabarcoding of the bacterial and fungal communities was performed in order to evaluate the potential synergism between fungi and bacteria in the bioremediation process. The functional metagenomic prediction indicated Arthrobacter, Dietzia, Brachybacerium, Brevibacterium, Gordonia, Leucobacter, Lysobacter, and Agrobacterium spp. as generalist saprophytes, essential for the onset of hydrocarbonoclastic specialist bacterial species, identified as Streptomyces, Nocardoides, Pseudonocardia, Solirubrobacter, Parvibaculum, Rhodanobacter, Luteiomonas, Planomicrobium, and Bacillus spp., involved in the TPH depletion. The fungal metabolism accelerated the onset of specialist over generalist bacteria. The capacity of the Ciboria sp. to deplete TPH in the soil in treatment was also ascertained.
Collapse
Affiliation(s)
- Simone Becarelli
- Department of Biology, University of Pisa, Pisa, Italy.,BD Biodigressioni, Pisa, Italy
| | - Ilaria Chicca
- Department of Biology, University of Pisa, Pisa, Italy.,Department of Biosystem Engineering, University of Manitoba, Winnipeg, MB, Canada
| | - Salvatore La China
- Department of Life Sciences, University of Modena and Reggio-Emilia, Reggio Emilia, Italy
| | | | - Alessandra Bardi
- Department of Civil and Environmental Engineering, University of Florence, Florence, Italy
| | - Maria Gullo
- Department of Life Sciences, University of Modena and Reggio-Emilia, Reggio Emilia, Italy
| | | | - David Bernard Levin
- BD Biodigressioni, Pisa, Italy.,Department of Biosystem Engineering, University of Manitoba, Winnipeg, MB, Canada
| | | |
Collapse
|
20
|
Chukwuma OB, Rafatullah M, Tajarudin HA, Ismail N. Bacterial Diversity and Community Structure of a Municipal Solid Waste Landfill: A Source of Lignocellulolytic Potential. Life (Basel) 2021; 11:493. [PMID: 34071172 PMCID: PMC8228822 DOI: 10.3390/life11060493] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/16/2021] [Accepted: 05/24/2021] [Indexed: 11/24/2022] Open
Abstract
Omics have given rise to research on sparsely studied microbial communities such as the landfill, lignocellulolytic microorganisms and enzymes. The bacterial diversity of Municipal Solid Waste sediments was determined using the illumina MiSeq system after DNA extraction and Polymerase chain reactions. Data analysis was used to determine the community's richness, diversity, and correlation with environmental factors. Physicochemical studies revealed sites with mesophilic and thermophilic temperature ranges and a mixture of acidic and alkaline pH values. Temperature and moisture content showed the highest correlation with the bacteria community. The bacterial analysis of the community DNA revealed 357,030 effective sequences and 1891 operational taxonomic units (OTUs) assigned. Forty phyla were found, with the dominant phyla Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidota, while Aerococcus, Stenotrophomonas, and Sporosarcina were the dominant species. PICRUSt provided insight on community's metabolic function, which was narrowed down to search for lignocellulolytic enzymes' function. Cellulase, xylanase, esterase, and peroxidase were gene functions inferred from the data. This article reports on the first phylogenetic analysis of the Pulau Burung landfill bacterial community. These results will help to improve the understanding of organisms dominant in the landfill and the corresponding enzymes that contribute to lignocellulose breakdown.
Collapse
Affiliation(s)
| | - Mohd Rafatullah
- School of Industrial Technology, Universiti Sains Malaysia, Penang 11800, Malaysia; (O.B.C.); (H.A.T.); (N.I.)
| | | | | |
Collapse
|
21
|
Weiss B, Souza ACO, Constancio MTL, Alvarenga DO, Pylro VS, Alves LMC, Varani AM. Unraveling a Lignocellulose-Decomposing Bacterial Consortium from Soil Associated with Dry Sugarcane Straw by Genomic-Centered Metagenomics. Microorganisms 2021; 9:microorganisms9050995. [PMID: 34063014 PMCID: PMC8170896 DOI: 10.3390/microorganisms9050995] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 03/28/2021] [Accepted: 03/30/2021] [Indexed: 12/02/2022] Open
Abstract
Second-generation biofuel production is in high demand, but lignocellulosic biomass’ complexity impairs its use due to the vast diversity of enzymes necessary to execute the complete saccharification. In nature, lignocellulose can be rapidly deconstructed due to the division of biochemical labor effectuated in bacterial communities. Here, we analyzed the lignocellulolytic potential of a bacterial consortium obtained from soil and dry straw leftover from a sugarcane milling plant. This consortium was cultivated for 20 weeks in aerobic conditions using sugarcane bagasse as a sole carbon source. Scanning electron microscopy and chemical analyses registered modification of the sugarcane fiber’s appearance and biochemical composition, indicating that this consortium can deconstruct cellulose and hemicellulose but no lignin. A total of 52 metagenome-assembled genomes from eight bacterial classes (Actinobacteria, Alphaproteobacteria, Bacilli, Bacteroidia, Cytophagia, Gammaproteobacteria, Oligoflexia, and Thermoleophilia) were recovered from the consortium, in which ~46% of species showed no relevant modification in their abundance during the 20 weeks of cultivation, suggesting a mostly stable consortium. Their CAZymes repertoire indicated that many of the most abundant species are known to deconstruct lignin (e.g., Chryseobacterium) and carry sequences related to hemicellulose and cellulose deconstruction (e.g., Chitinophaga, Niastella, Niabella, and Siphonobacter). Taken together, our results unraveled the bacterial diversity, enzymatic potential, and effectiveness of this lignocellulose-decomposing bacterial consortium.
Collapse
Affiliation(s)
- Bruno Weiss
- Departament of Technology, School of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, São Paulo 14884-900, Brazil; (B.W.); (A.C.O.S.); (M.T.L.C.); (D.O.A.)
- Graduate Program in Agricultural and Livestock Microbiology, School of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, São Paulo 14884-900, Brazil
| | - Anna Carolina Oliveira Souza
- Departament of Technology, School of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, São Paulo 14884-900, Brazil; (B.W.); (A.C.O.S.); (M.T.L.C.); (D.O.A.)
- Graduate Program in Agricultural and Livestock Microbiology, School of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, São Paulo 14884-900, Brazil
| | - Milena Tavares Lima Constancio
- Departament of Technology, School of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, São Paulo 14884-900, Brazil; (B.W.); (A.C.O.S.); (M.T.L.C.); (D.O.A.)
- Graduate Program in Agricultural and Livestock Microbiology, School of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, São Paulo 14884-900, Brazil
| | - Danillo Oliveira Alvarenga
- Departament of Technology, School of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, São Paulo 14884-900, Brazil; (B.W.); (A.C.O.S.); (M.T.L.C.); (D.O.A.)
| | - Victor S. Pylro
- Microbial Ecology and Bioinformatics Laboratory, Department of Biology, Federal University of Lavras (UFLA), Lavras, Minas Gerais 37200-000, Brazil;
| | - Lucia M. Carareto Alves
- Departament of Technology, School of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, São Paulo 14884-900, Brazil; (B.W.); (A.C.O.S.); (M.T.L.C.); (D.O.A.)
- Correspondence: (L.M.C.A.); (A.M.V.)
| | - Alessandro M. Varani
- Departament of Technology, School of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, São Paulo 14884-900, Brazil; (B.W.); (A.C.O.S.); (M.T.L.C.); (D.O.A.)
- Correspondence: (L.M.C.A.); (A.M.V.)
| |
Collapse
|
22
|
Guesmi S, Nouioui I, Pujic P, Dubost A, Najjari A, Ghedira K, Igual JM, Cherif A, Klenk HP, Sghaier H, Normand P. Draft genome sequence of Promicromonospora panici sp. nov., a novel ionizing-radiation-resistant actinobacterium isolated from roots of the desert plant Panicum turgidum. Extremophiles 2020; 25:25-38. [PMID: 33104875 DOI: 10.1007/s00792-020-01207-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 10/07/2020] [Indexed: 11/26/2022]
Abstract
A novel strain of the genus Promicromonospora, designated PT9T, was recovered from irradiated roots of the xerophyte Panicum turgidum collected from the Ksar Ghilane oasis in southern Tunisia. Strain PT9T is aerobic, non-spore-forming, Gram- positive actinomycete that produces branched hyphae and forms white to yellowish-white colonies. Chemotaxonomic features, including fatty acids, whole cell sugars and polar lipid profiles, support the assignment of PT9T to the genus Promicromonospora. The genomic relatedness indexes based on DNA-DNA hybridization and average nucleotide identity values revealed a significant genomic divergence between strain PT9T and all sequenced type strains of the taxon. Phylogenomic analysis showed that isolate PT9T was most closely related to Promicromonospora soli CGMCC 4.7398T. Phenotypic and phylogenomic analyses suggest that isolate PT9T represents a novel species of the genus Promicromonospora, for which the name Promicromonospora panici sp. nov. is proposed. The type strain is PT9T (LMG 31103T = DSM 108613T).The isolate PT9T is an ionizing-radiation-resistant actinobacterium (D10 value = 2.6 kGy), with resistance to desiccation and hydrogen peroxide. The complete genome sequence of PT9T consists of 6,582,650 bps with 71.2% G+C content and 6291 protein-coding sequences. This genome will help to decipher the microbial genetic bases for ionizing-radiation resistance mechanisms including the response to oxidative stress.
Collapse
Affiliation(s)
- Sihem Guesmi
- National Agronomy Institute of Tunisia, Avenue Charles Nicolle, 1082, Tunis, Mahrajène, Tunisia
- Laboratory "Energy and Matter for Development of Nuclear Sciences" (LR16CNSTN02), National Center for Nuclear Sciences and Technology, Sidi Thabet Technopark, 2020, Sidi Thabet, Tunisia
| | - Imen Nouioui
- School of Natural and Environmental Sciences, Newcastle University, Ridley Building 2, Newcastle upon Tyne, NE1 7RU, UK
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Petar Pujic
- Université de Lyon, Université Lyon 1, Lyon, France
- CNRS, UMR 5557, Écologie Microbienne, UMR1418, INRA, 69622 Cedex, Villeurbanne, France
| | - Audrey Dubost
- Université de Lyon, Université Lyon 1, Lyon, France
- CNRS, UMR 5557, Écologie Microbienne, UMR1418, INRA, 69622 Cedex, Villeurbanne, France
| | - Afef Najjari
- Université de Tunis el Manar, Faculté des Sciences de Tunis, LR03ES03 Microorganismes et Biomolécules Actives, 2092, Tunis, Tunisia
| | - Kais Ghedira
- Laboratory of Bioinformatics, Biomathematics and Biostatistics-LR16IPT09, Institut Pasteur de Tunis, Université de Tunis El Manar, 1002, Tunis, Tunisia
| | - José M Igual
- Instituto de Recursos Naturales y Agrobiología de Salamanca, Consejo Superior de Investigaciones Científicas (IRNASA-CSIC), c/Cordel de Merinas 40-52, 37008, Salamanca, Spain
| | - Ameur Cherif
- University Manouba, ISBST, BVBGR-LR11ES31,, Biotechpole Sidi Thabet, 2020, Ariana, Tunisia
| | - Hans-Peter Klenk
- School of Natural and Environmental Sciences, Newcastle University, Ridley Building 2, Newcastle upon Tyne, NE1 7RU, UK
| | - Haïtham Sghaier
- Laboratory "Energy and Matter for Development of Nuclear Sciences" (LR16CNSTN02), National Center for Nuclear Sciences and Technology, Sidi Thabet Technopark, 2020, Sidi Thabet, Tunisia
- University Manouba, ISBST, BVBGR-LR11ES31,, Biotechpole Sidi Thabet, 2020, Ariana, Tunisia
| | - Philippe Normand
- Université de Lyon, Université Lyon 1, Lyon, France.
- CNRS, UMR 5557, Écologie Microbienne, UMR1418, INRA, 69622 Cedex, Villeurbanne, France.
| |
Collapse
|
23
|
Ali SS, Al-Tohamy R, Xie R, El-Sheekh MM, Sun J. Construction of a new lipase- and xylanase-producing oleaginous yeast consortium capable of reactive azo dye degradation and detoxification. BIORESOURCE TECHNOLOGY 2020; 313:123631. [PMID: 32540694 DOI: 10.1016/j.biortech.2020.123631] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 05/30/2020] [Accepted: 06/02/2020] [Indexed: 05/07/2023]
Abstract
A new oleaginous yeast consortium Y-BC-SH which stands for molecularly identified species Yarrowia sp., Barnettozyma californica and Sterigmatomyces halophilus was successfully constructed in this study. This multipurpose oleaginous yeast consortium was developed based on its higher ability to accumulate large amounts of lipids in the form of triacylglycerol, grow on xylose, produce lipase and xylanase and it could rapidly decolorize and degrade commonly-used textile reactive azo dyes. The specific enzyme activities of lipase, xylanase, xylan esterase, β-xylosidase, CMCase, β-glucosidase and cellobiohydrolase produced by Y-BC-SH were significantly higher than that of individual strains. As chemical oxygen demand reduction had occurred in the dye mixture solutions, it was evidence of their color removal and mineralization by Y-BC-SH. The significant induction of oxidoreductive enzymes by Y-BC-SH was probably due to the coordinated metabolic interactions of the individual strains. Phytotoxicity assay confirmed that metabolites generated after dye degradation by Y-BC-SH are non-toxic.
Collapse
Affiliation(s)
- Sameh Samir Ali
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China; Botany Department, Faculty of Science, Tanta University, Tanta 31527, Egypt
| | - Rania Al-Tohamy
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Rongrong Xie
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | | | - Jianzhong Sun
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China.
| |
Collapse
|
24
|
Fagnano M, Agrelli D, Pascale A, Adamo P, Fiorentino N, Rocco C, Pepe O, Ventorino V. Copper accumulation in agricultural soils: Risks for the food chain and soil microbial populations. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 734:139434. [PMID: 32454337 DOI: 10.1016/j.scitotenv.2020.139434] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 04/28/2020] [Accepted: 05/12/2020] [Indexed: 05/25/2023]
Abstract
The long-term use of Cu-based fungicides at doses of several kilograms per hectare stimulated a wide debate about the human health and environmental risks of the progressive accumulation of Cu in agricultural soils. Here, the health risks due to copper accumulation in agricultural soils were evaluated with a survey in intensive agricultural land of the Campania region (Italy), aiming to evaluate Cu accumulation in food crops. The health risk due to dietary exposure was estimated by using the Hazard Quotient (HQ), calculated as the ratio between the average daily dose and the reference dose of copper, suggesting that when HQ > 1 there is a potential risk for consumers. According to a survey of soils with a Cu content up to 217 mg kg-1, no foodstuffs showed dietary risks. Nevertheless, the contribution of Cu contained in these foodstuffs to the overall intake of Cu by consumers could increase health risks since such risks must be evaluated on the basis of the whole standard diet by quantifying the Cu content not only in vegetables and fruits but also in other sources, such as cereals, not cultivated in the study area and thus not considered in this paper. The environmental risks due to copper accumulation in agricultural soils were then evaluated with a field experiment in a soil characterized by a very high Cu concentration (up to 1700 mg kg-1), aiming to study the impacts of Cu on native soil microorganisms. The study of the microbiota highlighted that the presence of Cu in soil did not reduce the total richness and diversity of microorganisms, which were not related to increasing concentrations of Cu in the soil. Nevertheless, Cu contamination was found to exert significant selection pressure on the soil microbiota, as shown by beta diversity and correlation analysis between taxa and Cu content.
Collapse
Affiliation(s)
- Massimo Fagnano
- Department of Agricultural Sciences, Division of Plant Biology and Crop Science, University of Naples Federico II, Via Università 100, Portici 80055, Naples, Italy
| | - Diana Agrelli
- Department of Agricultural Sciences, Division of Agricultural Chemistry and Pedology, University of Naples Federico II, Via Università 100, Portici 80055, Naples, Italy
| | - Alberto Pascale
- Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, Via Università 100, Portici 80055, Naples, Italy
| | - Paola Adamo
- Department of Agricultural Sciences, Division of Agricultural Chemistry and Pedology, University of Naples Federico II, Via Università 100, Portici 80055, Naples, Italy
| | - Nunzio Fiorentino
- Department of Agricultural Sciences, Division of Plant Biology and Crop Science, University of Naples Federico II, Via Università 100, Portici 80055, Naples, Italy
| | - Claudia Rocco
- Department of Agricultural Sciences, Division of Agricultural Chemistry and Pedology, University of Naples Federico II, Via Università 100, Portici 80055, Naples, Italy
| | - Olimpia Pepe
- Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, Via Università 100, Portici 80055, Naples, Italy; Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
| | - Valeria Ventorino
- Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, Via Università 100, Portici 80055, Naples, Italy; Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy.
| |
Collapse
|
25
|
Sirohi R, Prakash Pandey J, Kumar Gaur V, Gnansounou E, Sindhu R. Critical overview of biomass feedstocks as sustainable substrates for the production of polyhydroxybutyrate (PHB). BIORESOURCE TECHNOLOGY 2020; 311:123536. [PMID: 32448640 DOI: 10.1016/j.biortech.2020.123536] [Citation(s) in RCA: 92] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 05/09/2020] [Accepted: 05/12/2020] [Indexed: 05/23/2023]
Abstract
Polyhydroxybutyrates (PHBs) are a class of biopolymers produced by different microbial species and are biodegradable and biocompatible in nature as opposed to petrochemically derived plastics. PHBs have advanced applications in medical sector, packaging industries, nanotechnology and agriculture, among others. PHB is produced using various feedstocks such as glycerol, dairy wastes, agro-industrial wastes, food industry waste and sugars. Current focus on PHB research has been primarily on reducing the cost of production and, on downstream processing to isolate PHB from cells. Recent advancements to improve the productivity and quality of PHB include genetic modification of producer strain and modification of PHB by blending to develop desirable properties suited to diversified applications. Selection of feedstock plays a critical role in determining the economic feasibility and sustainability of the process. This review provides a bird's eye view of the suitability of different waste resources for producing polyhydroxybutyrate; providing state-of the art information and analysis.
Collapse
Affiliation(s)
- Ranjna Sirohi
- Department of Post Harvest Process and Food Engineering, G.B. Pant University of Agriculture and Technology, Pantnagar 263 145, India.
| | - Jai Prakash Pandey
- Department of Post Harvest Process and Food Engineering, G.B. Pant University of Agriculture and Technology, Pantnagar 263 145, India
| | - Vivek Kumar Gaur
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, Lucknow 226010, India
| | - Edgard Gnansounou
- Bioenergy and Energy Planning Research Group, Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne, Switzerland
| | - Raveendran Sindhu
- Microbial Processes and Technology Division, CSIR-National Institute of Interdisciplinary Science and Technology (CSIR-NIIST), Trivandrum 695 019, India
| |
Collapse
|
26
|
Callegari M, Jucker C, Fusi M, Leonardi MG, Daffonchio D, Borin S, Savoldelli S, Crotti E. Hydrolytic Profile of the Culturable Gut Bacterial Community Associated With Hermetia illucens. Front Microbiol 2020; 11:1965. [PMID: 32903451 PMCID: PMC7434986 DOI: 10.3389/fmicb.2020.01965] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 07/24/2020] [Indexed: 12/22/2022] Open
Abstract
Larvae of the black soldier fly (BSF) Hermetia illucens (L.) convert organic waste into high valuable insect biomass that can be used as alternative protein source for animal nutrition or as feedstock for biodiesel production. Since insect biology and physiology are influenced by the gut microbiome, knowledge about the functional role of BSF-associated microorganisms could be exploited to enhance the insect performance and growth. Although an increasing number of culture-independent studies are unveiling the microbiota structure and composition of the BSF gut microbiota, a knowledge gap remains on the experimental validation of the contribution of the microorganisms to the insect growth and development. We aimed at assessing if BSF gut-associated bacteria potentially involved in the breakdown of diet components are able to improve host nutrition. A total of 193 bacterial strains were obtained from guts of BSF larvae reared on a nutritious diet using selective and enrichment media. Most of the bacterial isolates are typically found in the insect gut, with major representatives belonging to the Gammaproteobacteria and Bacilli classes. The hydrolytic profile of the bacterial collection was assessed on compounds typically present in the diet. Finally, we tested the hypothesis that the addition to a nutritionally poor diet of the two isolates Bacillus licheniformis HI169 and Stenotrophomonas maltophilia HI121, selected for their complementary metabolic activities, could enhance BSF growth. B. licheniformis HI169 positively influenced the larval final weight and growth rate when compared to the control. Conversely, the addition of S. maltophilia HI121 to the nutritionally poor diet did not result in a growth enhancement in terms of larval weight and pupal weight and length in comparison to the control, whereas the combination of the two strains positively affected the larval final weight and the pupal weight and length. In conclusion, we isolated BSF-associated bacterial strains with potential positive properties for the host nutrition and we showed that selected isolates may enhance BSF growth, suggesting the importance to evaluate the effect of the bacterial administration on the insect performance.
Collapse
Affiliation(s)
- Matteo Callegari
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l’Ambiente (DeFENS), Università degli Studi di Milano, Milan, Italy
- Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Costanza Jucker
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l’Ambiente (DeFENS), Università degli Studi di Milano, Milan, Italy
| | - Marco Fusi
- Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- School of Applied Sciences, Edinburgh Napier University, Edinburgh, United Kingdom
| | - Maria Giovanna Leonardi
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l’Ambiente (DeFENS), Università degli Studi di Milano, Milan, Italy
| | - Daniele Daffonchio
- Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Sara Borin
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l’Ambiente (DeFENS), Università degli Studi di Milano, Milan, Italy
| | - Sara Savoldelli
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l’Ambiente (DeFENS), Università degli Studi di Milano, Milan, Italy
| | - Elena Crotti
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l’Ambiente (DeFENS), Università degli Studi di Milano, Milan, Italy
| |
Collapse
|
27
|
Mei J, Shen X, Gang L, Xu H, Wu F, Sheng L. A novel lignin degradation bacteria-Bacillus amyloliquefaciens SL-7 used to degrade straw lignin efficiently. BIORESOURCE TECHNOLOGY 2020; 310:123445. [PMID: 32361649 DOI: 10.1016/j.biortech.2020.123445] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 04/22/2020] [Accepted: 04/23/2020] [Indexed: 06/11/2023]
Abstract
Using tobacco straw (Ts) and lignin as the sole carbon source, a strain was isolated from Ts and identified as Bacillus amyloliquefaciens SL-7 by 16S rDNA gene-sequencing technology.7-day incubation of Bacillus amyloliquefaciens SL-7 can reduce the chemical oxygen demand (COD) by 69.35% in lignin mineral salt medium. The activity of Manganese peroxidase (MnP) reached maximum level 258.57 U L-1, and Lignin peroxidase (Lip) was 422.68 U L-1 at 4th day. The highest Laccase (Lac) activity (55.95 U L-1) was observed at 3th day. After straw-liquid fermentation degradation of 15 days, the bacterial could degrade 28.55% lignin of the straw which was close to that of fungi. Compared with the control group and effective microorganisms (EM) group, the lignin degradation rate in Bacillus amyloliquefaciens SL-7 group increased by 22.26% and 11.70% at 41-day compost fermentation of tobacco straw. These show the strain has strong lignin degradation performance.
Collapse
Affiliation(s)
- Jinfei Mei
- Engineering Research Centre of Biomass Conversion and Pollution Prevention Control of Anhui Provincial Department of Education, Fuyang 236037, PR China; School of Chemistry and Materials Engineering, Fuyang Normal University, Fuyang 236037, PR China
| | - Xiaobao Shen
- Engineering Research Centre of Biomass Conversion and Pollution Prevention Control of Anhui Provincial Department of Education, Fuyang 236037, PR China
| | - Liping Gang
- Engineering Research Centre of Biomass Conversion and Pollution Prevention Control of Anhui Provincial Department of Education, Fuyang 236037, PR China
| | - Huajie Xu
- Engineering Research Centre of Biomass Conversion and Pollution Prevention Control of Anhui Provincial Department of Education, Fuyang 236037, PR China; School of Chemistry and Materials Engineering, Fuyang Normal University, Fuyang 236037, PR China
| | - Fufang Wu
- Engineering Research Centre of Biomass Conversion and Pollution Prevention Control of Anhui Provincial Department of Education, Fuyang 236037, PR China; School of Chemistry and Materials Engineering, Fuyang Normal University, Fuyang 236037, PR China
| | - Liangquan Sheng
- Engineering Research Centre of Biomass Conversion and Pollution Prevention Control of Anhui Provincial Department of Education, Fuyang 236037, PR China; School of Chemistry and Materials Engineering, Fuyang Normal University, Fuyang 236037, PR China.
| |
Collapse
|
28
|
Hinsu AT, Patel AB, Pandit RJ, Thakkar JR, Shah RK, Jakhesara SJ, Koringa PG, Joshi CG. MetaRNAseq analysis of surti buffalo rumen content reveals that transcriptionally active microorganisms need not be abundant. Mol Biol Rep 2020; 47:5101-5114. [PMID: 32557173 DOI: 10.1007/s11033-020-05581-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 06/10/2020] [Indexed: 11/26/2022]
Abstract
The present study describes rumen microbiota composition and their functional profiles in Indian Surti buffaloes by metagenomic (MG) and metatranscriptomic (MT) approaches. The study compares samples from buffaloes fed three different proportion of roughages; green and dry type of roughage; and different rumen liquor fractions. Irrespective of sample, Bacteroidetes and Firmicutes were the most predominant bacterial phyla, followed by Proteobacteria, Fibrobacteres and Actinobacteria while, Prevotella, Bacteroides, Ruminococcus and Clostridium were the most abundant genera. Different proportions of taxa were observed in both MG and MT approaches indicating the differences in organisms present and organisms active in the rumen. Higher proportions of fungal taxa were observed in MT while important organisms like Fibrobacter and Butyrivibrio and abundant organisms like Bacteroides and Prevotella were underrepresented in MT data. Functionally, higher proportions of genes involved in Carbohydrate metabolism, Amino acid metabolism and Translation were observed in both data. Genes involved in Metabolism were observed to be underrepresented in MT data while, those involved in Genetic information processing were overrepresented in MT data. Further, genes involved in Carbohydrate metabolism were overexpressed compared to genes involved in Amino acid metabolism in MT data compared to MG data which had higher proportion of genes involved in Amino acid metabolism than Carbohydrate metabolism. In all significant differences were observed between both approaches, different fractions of rumen liquor (liquid and solid) and different proportions of roughage in diet.
Collapse
Affiliation(s)
- Ankit T Hinsu
- Department of Animal Genetics & Breeding, College of Veterinary Sciences & A.H, Anand Agricultural University, Anand, Gujarat, India
| | - Avani B Patel
- Department of Animal Genetics & Breeding, College of Veterinary Sciences & A.H, Anand Agricultural University, Anand, Gujarat, India
| | - Ramesh J Pandit
- Department of Animal Biotechnology, College of Veterinary Sciences & A.H, Anand Agricultural University, Anand, Gujarat, India
| | - Jalpa R Thakkar
- Department of Animal Biotechnology, College of Veterinary Sciences & A.H, Anand Agricultural University, Anand, Gujarat, India
| | - Ravi K Shah
- Department of Animal Biotechnology, College of Veterinary Sciences & A.H, Anand Agricultural University, Anand, Gujarat, India
| | - Subhash J Jakhesara
- Department of Animal Biotechnology, College of Veterinary Sciences & A.H, Anand Agricultural University, Anand, Gujarat, India
| | - Prakash G Koringa
- Department of Animal Biotechnology, College of Veterinary Sciences & A.H, Anand Agricultural University, Anand, Gujarat, India
| | - Chaitanya G Joshi
- Department of Animal Biotechnology, College of Veterinary Sciences & A.H, Anand Agricultural University, Anand, Gujarat, India.
| |
Collapse
|
29
|
Exploiting strain diversity and rational engineering strategies to enhance recombinant cellulase secretion by Saccharomyces cerevisiae. Appl Microbiol Biotechnol 2020; 104:5163-5184. [PMID: 32337628 DOI: 10.1007/s00253-020-10602-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 03/26/2020] [Accepted: 03/31/2020] [Indexed: 12/14/2022]
Abstract
Consolidated bioprocessing (CBP) of lignocellulosic material into bioethanol has progressed in the past decades; however, several challenges still exist which impede the industrial application of this technology. Identifying the challenges that exist in all unit operations is crucial and needs to be optimised, but only the barriers related to the secretion of recombinant cellulolytic enzymes in Saccharomyces cerevisiae will be addressed in this review. Fundamental principles surrounding CBP as a biomass conversion platform have been established through the successful expression of core cellulolytic enzymes, namely β-glucosidases, endoglucanases, and exoglucanases (cellobiohydrolases) in S. cerevisiae. This review will briefly address the challenges involved in the construction of an efficient cellulolytic yeast, with particular focus on the secretion efficiency of cellulases from this host. Additionally, strategies for studying enhanced cellulolytic enzyme secretion, which include both rational and reverse engineering approaches, will be discussed. One such technique includes bio-engineering within genetically diverse strains, combining the strengths of both natural strain diversity and rational strain development. Furthermore, with the advancement in next-generation sequencing, studies that utilise this method of exploiting intra-strain diversity for industrially relevant traits will be reviewed. Finally, future prospects are discussed for the creation of ideal CBP strains with high enzyme production levels.Key Points• Several challenges are involved in the construction of efficient cellulolytic yeast, in particular, the secretion efficiency of cellulases from the hosts.• Strategies for enhancing cellulolytic enzyme secretion, a core requirement for CBP host microorganism development, include both rational and reverse engineering approaches.• One such technique includes bio-engineering within genetically diverse strains, combining the strengths of both natural strain diversity and rational strain development.
Collapse
|
30
|
Gebbie L, Dam TT, Ainscough R, Palfreyman R, Cao L, Harrison M, O'Hara I, Speight R. A snapshot of microbial diversity and function in an undisturbed sugarcane bagasse pile. BMC Biotechnol 2020; 20:12. [PMID: 32111201 PMCID: PMC7049217 DOI: 10.1186/s12896-020-00609-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 02/24/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Sugarcane bagasse is a major source of lignocellulosic biomass, yet its economic potential is not fully realised. To add value to bagasse, processing is needed to gain access to the embodied recalcitrant biomaterials. When bagasse is stored in piles in the open for long periods it is colonised by microbes originating from the sugarcane, the soil nearby or spores in the environment. For these microorganisms to proliferate they must digest the bagasse to access carbon for growth. The microbial community in bagasse piles is thus a potential resource for the discovery of useful and novel microbes and industrial enzymes. We used culturing and metabarcoding to understand the diversity of microorganisms found in a uniquely undisturbed bagasse storage pile and screened the cultured organisms for fibre-degrading enzymes. RESULTS Samples collected from 60 to 80 cm deep in the bagasse pile showed hemicellulose and partial lignin degradation. One hundred and four microbes were cultured from different layers and included a high proportion of oleaginous yeast and biomass-degrading fungi. Overall, 70, 67, 70 and 57% of the microbes showed carboxy-methyl cellulase, xylanase, laccase and peroxidase activity, respectively. These percentages were higher in microbes selectively cultured from deep layers, with all four activities found for 44% of these organisms. Culturing and amplicon sequencing showed that there was less diversity and therefore more selection in the deeper layers, which were dominated by thermophiles and acid tolerant organisms, compared with the top of pile. Amplicon sequencing indicated that novel fungi were present in the pile. CONCLUSIONS A combination of culture-dependent and independent methods was successful in exploring the diversity in the bagasse pile. The variety of species that was found and that are known for biomass degradation shows that the bagasse pile was a valuable selective environment for the identification of new microbes and enzymes with biotechnological potential. In particular, lignin-modifying activities have not been reported previously for many of the species that were identified, suggesting future studies are warranted.
Collapse
Affiliation(s)
- Leigh Gebbie
- Queensland University of Technology, 2 George St, Brisbane, QLD, 4000, Australia
| | - Tuan Tu Dam
- Queensland University of Technology, 2 George St, Brisbane, QLD, 4000, Australia
| | - Rebecca Ainscough
- Queensland University of Technology, 2 George St, Brisbane, QLD, 4000, Australia
| | - Robin Palfreyman
- Metabolomics Australia, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Li Cao
- Queensland University of Technology, 2 George St, Brisbane, QLD, 4000, Australia
| | - Mark Harrison
- Queensland University of Technology, 2 George St, Brisbane, QLD, 4000, Australia
| | - Ian O'Hara
- Queensland University of Technology, 2 George St, Brisbane, QLD, 4000, Australia
| | - Robert Speight
- Queensland University of Technology, 2 George St, Brisbane, QLD, 4000, Australia.
| |
Collapse
|
31
|
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.
Collapse
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
| |
Collapse
|
32
|
Puentes-Téllez PE, Salles JF. Dynamics of Abundant and Rare Bacteria During Degradation of Lignocellulose from Sugarcane Biomass. MICROBIAL ECOLOGY 2020; 79:312-325. [PMID: 31286170 PMCID: PMC7033055 DOI: 10.1007/s00248-019-01403-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 06/19/2019] [Indexed: 06/02/2023]
Abstract
Microorganisms play a crucial role in lignocellulosic degradation. Many enriched microbial communities have demonstrated to reach functional and structural stability with effective degrading capacities of industrial interest. These microbial communities are typically composed by only few dominant species and a high number of usually overlooked rare species. Here, we used two sources of lignocellulose (sugarcane bagasse and straw) in order to obtain lignocellulose-degrading bacteria through an enriched process, followed the selective trajectory of both abundant and rare bacterial communities by 16S rRNA gene amplification and analyzed the outcomes of selection in terms of capacities and specialization. We verified the importance of pre-selection by using two sources of microbial inoculum: soil samples from a sugarcane field with history of straw addition (St15) and control samples, from the same field, without amendments (St0). We found similitudes in terms of stabilization between the abundant and rare fractions. We also found positive correlations of both abundant and rare taxa (like Caulobacteraceae and Alcaligenaceae) and the degradation of lignocellulosic fractions. Differences in the inocula's initial diversity rapidly decreased during the enrichment resulting in comparable richness levels at the end of the process; however, the legacy of the St15 inoculum and its specialization positively influenced the degradation capacities of the community. Analysis of specialization of the final communities revealed increased straw degradation capacity in the communities enriched in bagasse, which could be potentially used as a strategy for improving lignocellulose waste degradation on the sugarcane fields. This work highlights the importance of including the rare fraction of bacterial communities during investigations involving the screening and assessment of effective degrading communities.
Collapse
Affiliation(s)
- Pilar Eliana Puentes-Téllez
- Microbial Community Ecology, GELIFES, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
- Department of Biology, Institute of Environmental Biology, Ecology and Biodiversity Group, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Joana Falcao Salles
- Microbial Community Ecology, GELIFES, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.
| |
Collapse
|
33
|
Zhang H, Li Q, Zhao Y, Zhang M, Xu D, Wu Z, Zhou Q. Endoglucanase activity of cellulolytic bacteria from lake sediments and its application in hydrophyte degradation. FEMS Microbiol Lett 2020; 367:6029119. [PMID: 33296466 DOI: 10.1093/femsle/fnaa200] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 12/07/2020] [Indexed: 11/14/2022] Open
Abstract
Hydrophytes are plants that grow in or on water. Their overgrowth adversely affects the ecosystem because of crowding out other aquatic organisms and polluting the environment with plant residue. In principle, cellulolytic bacteria can be used to degrade hydrophyte biomass. We here isolated and characterized four cellulolytic bacterial strains from Lake Donghu sediments (Wuhan, China) that are rich in organic matter and plant residues. The isolates (WDHS-01 to 04) represent Bacillus, Micromonospora and Streptomyces genera. The bacteria exhibited pronounced endoglucanase activities (from 0.022 to 0.064 U mL-1). They did not extensively degrade the emerged plant Canna indica L. However, in an Hydrilla verticillata (submerged plant) degradation medium, strain WDHS-02 exhibited a high degradation rate (54.91%), endoglucanase activity of 0.35 U mL-1 and the conversion rate of cellulose to reducing sugars of 7.15%. Correlation analysis revealed that bacterial endoglucanase activity was significantly correlated with the degradation rate, and acid detergent lignin, ash and cellulose content of the residual H. verticillata powder. In conclusion, the identified bacteria efficiently decomposed submerged plants without the need for acid-base pretreatment. They expand the set of known cellulolytic bacteria and can be used for natural degradation of submerged plants.
Collapse
Affiliation(s)
- Hongpei Zhang
- College of Resources and Environmental Engineering, Wuhan University of Technology, Wuhan 430070, No. 122 Luoshi Road, Hongshan District, Wuhan, Hubei Province, P.R. China.,State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, No. 7 Donghu South Road, Wuchang District, Wuhan, Hubei Province, P.R. China
| | - Qianzheng Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, No. 7 Donghu South Road, Wuchang District, Wuhan, Hubei Province, P.R. China.,College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, No.19(A) Yuquan Road, Shijingshan District, Beijing, P.R. China
| | - Yuqing Zhao
- College of Resources and Environmental Engineering, Wuhan University of Technology, Wuhan 430070, No. 122 Luoshi Road, Hongshan District, Wuhan, Hubei Province, P.R. China.,State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, No. 7 Donghu South Road, Wuchang District, Wuhan, Hubei Province, P.R. China
| | - Mingzhen Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, No. 7 Donghu South Road, Wuchang District, Wuhan, Hubei Province, P.R. China.,College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, No.19(A) Yuquan Road, Shijingshan District, Beijing, P.R. China
| | - Dong Xu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, No. 7 Donghu South Road, Wuchang District, Wuhan, Hubei Province, P.R. China
| | - Zhenbin Wu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, No. 7 Donghu South Road, Wuchang District, Wuhan, Hubei Province, P.R. China
| | - Qiaohong Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, No. 7 Donghu South Road, Wuchang District, Wuhan, Hubei Province, P.R. China
| |
Collapse
|
34
|
Romano I, Ventorino V, Pepe O. Effectiveness of Plant Beneficial Microbes: Overview of the Methodological Approaches for the Assessment of Root Colonization and Persistence. FRONTIERS IN PLANT SCIENCE 2020; 11:6. [PMID: 32076431 PMCID: PMC7006617 DOI: 10.3389/fpls.2020.00006] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 01/06/2020] [Indexed: 05/22/2023]
Abstract
Issues concerning the use of harmful chemical fertilizers and pesticides that have large negative impacts on environmental and human health have generated increasing interest in the use of beneficial microorganisms for the development of sustainable agri-food systems. A successful microbial inoculant has to colonize the root system, establish a positive interaction and persist in the environment in competition with native microorganisms living in the soil through rhizocompetence traits. Currently, several approaches based on culture-dependent, microscopic and molecular methods have been developed to follow bioinoculants in the soil and plant surface over time. Although culture-dependent methods are commonly used to estimate the persistence of bioinoculants, it is difficult to differentiate inoculated organisms from native populations based on morphological characteristics. Therefore, these methods should be used complementary to culture-independent approaches. Microscopy-based techniques (bright-field, electron and fluorescence microscopy) allow to obtain a picture of microbial colonization outside and inside plant tissues also at high resolution, but it is not possible to always distinguish living cells from dead cells by direct observation as well as distinguish bioinoculants from indigenous microbial populations living in soils. In addition, the development of metagenomic techniques, including the use of DNA probes, PCR-based methods, next-generation sequencing, whole-genome sequencing and pangenome methods, provides a complementary approach useful to understand plant-soil-microbe interactions. However, to ensure good results in microbiological analysis, the first fundamental prerequisite is correct soil sampling and sample preparation for the different methodological approaches that will be assayed. Here, we provide an overview of the advantages and limitations of the currently used methods and new methodological approaches that could be developed to assess the presence, plant colonization and soil persistence of bioinoculants in the rhizosphere. We further discuss the possibility of integrating multidisciplinary approaches to examine the variations in microbial communities after inoculation and to track the inoculated microbial strains.
Collapse
Affiliation(s)
- Ida Romano
- Department of Agricultural Sciences, University of Naples Federico II, Naples, Italy
| | - Valeria Ventorino
- Department of Agricultural Sciences, University of Naples Federico II, Naples, Italy
- Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
- *Correspondence: Valeria Ventorino,
| | - Olimpia Pepe
- Department of Agricultural Sciences, University of Naples Federico II, Naples, Italy
- Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
| |
Collapse
|
35
|
Stimulation of indigenous microbes by optimizing the water cut in low permeability reservoirs for green and enhanced oil recovery. Sci Rep 2019; 9:15772. [PMID: 31673044 PMCID: PMC6823453 DOI: 10.1038/s41598-019-52330-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 10/13/2019] [Indexed: 01/08/2023] Open
Abstract
Low permeability oil reservoirs are a widespread petroleum reservoir type all over the world. Therefore, methods to recover these reservoirs efficiently are of importance to guarantee energy supply. Here we report our novel stimulation of indigenous microbes by optimizing the water cut in low permeability reservoirs for green and enhanced oil recovery. We aimed to investigate the characteristics of indigenous bacterial communities with changes in water cut in reservoirs by high-throughput sequencing technology, and reveal the mechanism and characteristics of the crude oil biotreatment under different crude oil-water ratio conditions and the optimum activation time of indigenous functional microbial groups in reservoirs. The indigenous microbial metabolism products were characterized by gas chromatography mass spectrometry. Results showed that Acinetobacter (47.1%) and Pseudomones (19.8%) were the main functional genus of crude oil degradation at the optimal activation time, and can reduce the viscosity of crude oil from 8.33 to 5.75 mPa·s. The dominant bacteria genus for oil recovery after activation of the production fluids was similar to those in the reservoirs with water cut of 60-80%. Furthermore seven mechanism pathways of enhancing oil recovery by the synergistic of functional microbial groups and their metabolites under different water cut conditions in low permeability reservoirs have been established.
Collapse
|
36
|
Zealand AM, Mei R, Roskilly AP, Liu W, Graham DW. Molecular microbial ecology of stable versus failing rice straw anaerobic digesters. Microb Biotechnol 2019; 12:879-891. [PMID: 31233284 PMCID: PMC6681398 DOI: 10.1111/1751-7915.13438] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 05/13/2019] [Accepted: 05/14/2019] [Indexed: 12/01/2022] Open
Abstract
Waste rice straw (RS) is generated in massive quantities around the world and is often burned, creating greenhouse gas and air quality problems. Anaerobic digestion (AD) may be a better option for RS management, but RS is presumed to be comparatively refractory under anaerobic conditions without pre-treatment or co-substrates. However, this presumption assumes frequent reactor feeding regimes but less frequent feeding may be better for RS due to slow hydrolysis rates. Here, we assess how feeding frequency (FF) and organic loading rate (OLR) impacts microbial communities and biogas production in RS AD reactors. Using 16S rDNA amplicon sequencing and bioinformatics, microbial communities from five bench-scale bioreactors were characterized. At low OLR (1.0 g VS l-1 day-1 ), infrequently fed units (once every 21 days) had higher specific biogas yields than more frequent feeding (five in 7 days), although microbial community diversities were statistically similar (P > 0.05; ANOVA with Tukey comparison). In contrast, an increase in OLR to 2.0 g VS l-1 day-1 significantly changed Archaeal and fermenting Eubacterial sub-communities and the least frequency fed reactors failed. 'Stable' reactors were dominated by Methanobacterium, Methanosarcina and diverse Bacteroidetes, whereas 'failed' reactors saw shifts towards Clostridia and Christensenellaceae among fermenters and reduced methanogen abundances. Overall, OLR impacted RS AD microbial communities more than FF. However, combining infrequent feeding and lower OLRs may be better for RS AD because of higher specific yields.
Collapse
Affiliation(s)
- Andrew M. Zealand
- School of EngineeringNewcastle UniversityNewcastle upon TyneNE1 7RUUK
| | - Ran Mei
- Department of Civil and Environmental EngineeringUniversity of Illinois at Urbana‐Champaign205 North Mathews AveUrbanaIL61801USA
| | - Anthony P. Roskilly
- Sir Joseph Swan Centre for Energy ResearchNewcastle UniversityNewcastle upon TyneNE1 7RUUK
| | - WenTso Liu
- Department of Civil and Environmental EngineeringUniversity of Illinois at Urbana‐Champaign205 North Mathews AveUrbanaIL61801USA
| | - David W. Graham
- School of EngineeringNewcastle UniversityNewcastle upon TyneNE1 7RUUK
| |
Collapse
|
37
|
Bourles A, Guentas L, Chalkiadakis E, Majorel C, Juillot F, Cavaloc Y, Burtet-Sarramegna V, Medevielle V, Jourand P, Amir H. New Caledonian ultramafic conditions structure the features of Curtobacterium citreum strains that play a role in plant adaptation. Can J Microbiol 2019; 65:880-894. [PMID: 31442382 DOI: 10.1139/cjm-2019-0283] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The present study focused on the characterization of 10 Curtobacterium citreum strains isolated from the rhizosphere of pioneer plants growing on ultramafic soils from New Caledonia. Taxonomic status was investigated using a polyphasic approach. Three strains (BE, BB, and AM) were selected in terms of multiple-metal resistance and plant-growth-promoting traits. They were tested on sorghum growing on ultramafic soil and compared with the reference strain C. citreum DSM20528T. To better understand the bacterial mechanisms involved, biosorption, bioaccumulation, and biofilm formation were investigated for the representative strain of the ultramafic cluster (strain BE) versus C. citreum DSM20528T. The polyphasic approach confirmed that all native isolates belong to the same cluster and are C. citreum. The inoculation of sorghum with strains BE and BB significantly reduced Ni content in shoots compared with inoculation with C. citreum DSM20528T and control values. This result was related to the higher Ni tolerance of the ultramafic strains compared with C. citreum DSM20528T. Ni biosorption and bioaccumulation showed that BE exhibited a lower Ni content, which is explained by the ability of this strain to produce exopolysaccharides involved in Ni chelation. We suggested that ultramafic C. citreum strains are more adapted to this substrate than is C. citreum DSM20528T, and their features allow them to enhance plant metal tolerance.
Collapse
Affiliation(s)
- Alexandre Bourles
- Institut des sciences exactes et appliquées, Université de la Nouvelle-Calédonie, B.P. R4, 98851 Nouméa, Nouvelle-Calédonie
| | - Linda Guentas
- Institut des sciences exactes et appliquées, Université de la Nouvelle-Calédonie, B.P. R4, 98851 Nouméa, Nouvelle-Calédonie.,Université de Toulon, Laboratoire MAPIEM EA 4323, SeaTech-Ecole d'ingénieurs, B.P. 20132, 83957 La Garde CEDEX, France
| | | | - Clarisse Majorel
- Institut des sciences exactes et appliquées, Université de la Nouvelle-Calédonie, B.P. R4, 98851 Nouméa, Nouvelle-Calédonie
| | - Farid Juillot
- UMR IRD 206 - Institut de recherche pour le développement, Centre IRD Nouméa, 101 promenade Roger Laroque, B.P. A5, 98848 Nouméa CEDEX, France
| | - Yvon Cavaloc
- Institut des sciences exactes et appliquées, Université de la Nouvelle-Calédonie, B.P. R4, 98851 Nouméa, Nouvelle-Calédonie
| | - Valérie Burtet-Sarramegna
- Institut des sciences exactes et appliquées, Université de la Nouvelle-Calédonie, B.P. R4, 98851 Nouméa, Nouvelle-Calédonie
| | - Valérie Medevielle
- Institut des sciences exactes et appliquées, Université de la Nouvelle-Calédonie, B.P. R4, 98851 Nouméa, Nouvelle-Calédonie
| | - Philippe Jourand
- IRD, Laboratoire des symbioses tropicales et Méditerranéennes (LSTM UMR040), Campus international de Baillarguet, TA A-82/J, F-34398 Montpellier CEDEX 5, France
| | - Hamid Amir
- Institut des sciences exactes et appliquées, Université de la Nouvelle-Calédonie, B.P. R4, 98851 Nouméa, Nouvelle-Calédonie
| |
Collapse
|
38
|
Degradation profile of nixtamalized maize pericarp by the action of the microbial consortium PM-06. AMB Express 2019; 9:85. [PMID: 31197616 PMCID: PMC6565776 DOI: 10.1186/s13568-019-0812-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 06/08/2019] [Indexed: 11/25/2022] Open
Abstract
The nixtamalized maize pericarp (NMP) is a plentiful by-product of the tortilla industry and an important source of fermentable sugars. The aim of this study was to describe the degradation profile of NMP by the action of a consortium (PM-06) obtained from the native microbial community of this residue. The degradation was analyzed in terms of the changes in the community dynamics, production of enzymes (endo-xylanase and endo-cellulase), physicochemical parameters, and substrate chemical and microstructural characteristics, to understand the mechanisms behind the process. The consortium PM-06 degraded 86.8 ± 3.3% of NMP after 192 h of growth. Scanning electron microscopy images, and the composition and weight of the residual solids, showed that degradation was sequential starting with the consumption of hemicellulose. Xylanase was the highest enzyme activity produced, with a maximum value of 12.45 ± 0.03 U mL−1. There were fluctuations in the pH during the NMP degradation, starting with the acidification of the culture media and finishing with a pH close to 8.5. The most abundant species in the consortium, at the moment of maximum degradation activity, were Aneurinibacillus migulanus, Paenibacillus macerans, Bacillus coagulans, Microbacterium sp. LCT-H2, and Bacillus thuringiensis. The diversity of PM-06 provided metabolic abilities that in combination helped to produce an efficient process. The consortium PM-06 generated a set of different tools that worked coordinated to increase the substrate availability through the solubilization of components and elimination of structural diffusion barriers. This is the first report about the degradation of NMP using a microbial consortium.
Collapse
|
39
|
Tahir AA, Mohd Barnoh NF, Yusof N, Mohd Said NN, Utsumi M, Yen AM, Hashim H, Mohd Noor MJM, Akhir FNM, Mohamad SE, Sugiura N, Othman N, Zakaria Z, Hara H. Microbial Diversity in Decaying Oil Palm Empty Fruit Bunches (OPEFB) and Isolation of Lignin-degrading Bacteria from a Tropical Environment. Microbes Environ 2019; 34:161-168. [PMID: 31019143 PMCID: PMC6594733 DOI: 10.1264/jsme2.me18117] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Oil palm empty fruit bunches (OPEFB) are the most abundant, inexpensive, and environmentally friendly lignocellulosic biomass in Malaysia. Investigations on the microbial diversity of decaying OPEFB may reveal microbes with complex enzymes that have the potential to enhance the conversion of lignocellulose into second-generation biofuels as well as the production of other value-added products. In the present study, fungal and bacterial diversities in decaying OPEFB were identified using Illumina MiSeq sequencing of the V3 region of the 16S rRNA gene and V4 region of the 18S rRNA gene. Fungal diversity in decaying OPEFB was dominated by the phylum Ascomycota (14.43%), while most of the bacterial sequences retrieved belonged to Proteobacteria (76.71%). Three bacterial strains isolated from decaying OPEFB, designated as S18, S20, and S36, appeared to grow with extracted OPEFB-lignin and Kraft lignin (KL) as the sole carbon source. 16S rRNA gene sequencing identified the 3 isolates as Paenibacillus sp.. The molecular weight distribution of KL before and after degradation showed significant depolymerization when treated with bacterial strains S18, S20, and S36. The presence of low-molecular-weight lignin-related compounds, such as vanillin and 2-methoxyphenol derivatives, which were detected by a GC-MS analysis, confirmed the KL-degrading activities of isolated Paenibacillus strains.
Collapse
Affiliation(s)
- Analhuda Abdullah Tahir
- Department of Environmental Engineering and Green Technology, Malaysia-Japan International Institute of Technology, Universiti Teknologi Malaysia
| | - Nor Farhana Mohd Barnoh
- Department of Environmental Engineering and Green Technology, Malaysia-Japan International Institute of Technology, Universiti Teknologi Malaysia
| | - Nurtasbiyah Yusof
- Department of Environmental Engineering and Green Technology, Malaysia-Japan International Institute of Technology, Universiti Teknologi Malaysia
| | - Nuurul Nadrah Mohd Said
- Department of Environmental Engineering and Green Technology, Malaysia-Japan International Institute of Technology, Universiti Teknologi Malaysia
| | - Motoo Utsumi
- Graduate School of Life and Environmental Science, University of Tsukuba
| | - Ang May Yen
- Analytical and Scientific Instruments Division, Shimadzu Malaysia Sdn. Bhd
| | - Hazni Hashim
- Analytical and Scientific Instruments Division, Shimadzu Malaysia Sdn. Bhd
| | - Megat Johari Megat Mohd Noor
- Department of Environmental Engineering and Green Technology, Malaysia-Japan International Institute of Technology, Universiti Teknologi Malaysia
| | - Fazrena Nadia Md Akhir
- Department of Environmental Engineering and Green Technology, Malaysia-Japan International Institute of Technology, Universiti Teknologi Malaysia
| | - Shaza Eva Mohamad
- Department of Environmental Engineering and Green Technology, Malaysia-Japan International Institute of Technology, Universiti Teknologi Malaysia
| | - Norio Sugiura
- Department of Environmental Engineering and Green Technology, Malaysia-Japan International Institute of Technology, Universiti Teknologi Malaysia.,Graduate School of Life and Environmental Science, University of Tsukuba
| | - Nor'azizi Othman
- Department of Mechanical Precision Engineering, Malaysia-Japan International Institute of Technology, Universiti Teknologi Malaysia
| | - Zuriati Zakaria
- Department of Environmental Engineering and Green Technology, Malaysia-Japan International Institute of Technology, Universiti Teknologi Malaysia
| | - Hirofumi Hara
- Department of Chemical Process Engineering, Malaysia-Japan International Institute of Technology, Universiti Teknologi Malaysia
| |
Collapse
|
40
|
Gong G, Oh HJ, Cho S, Kim S, Oh MK, Um Y, Lee SM. Complete Genome Sequence of Paenibacillus sp. CAA11: A Promising Microbial Host for Lignocellulosic Biorefinery with Consolidated Processing. Curr Microbiol 2019; 76:732-737. [DOI: 10.1007/s00284-019-01685-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Accepted: 04/08/2019] [Indexed: 11/30/2022]
|
41
|
|
42
|
Pagliano G, Ventorino V, Panico A, Romano I, Pirozzi F, Pepe O. Anaerobic Process for Bioenergy Recovery From Dairy Waste: Meta-Analysis and Enumeration of Microbial Community Related to Intermediates Production. Front Microbiol 2019; 9:3229. [PMID: 30687248 PMCID: PMC6334743 DOI: 10.3389/fmicb.2018.03229] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 12/12/2018] [Indexed: 11/28/2022] Open
Abstract
Dairy wastes are widely studied for the hydrogen and methane production, otherwise the changes in microbial communities related to intermediate valuable products was not deeply investigated. Culture independent techniques are useful tools for exploring microbial communities in engineered system having new insights into their structure and function as well as potential industrial application. The deep knowledge of the microbiota involved in the anaerobic process of specific waste and by-products represents an essential step to better understand the entire process and the relation of each microbial population with biochemical intermediates and final products. Therefore, this study investigated the microbial communities involved in the laboratory-scale anaerobic digestion of a mixture of mozzarella cheese whey and buttermilk amended with 5% w/v of industrial animal manure pellets. Culture-independent methods by employing high-throughput sequencing and microbial enumerations highlighted that lactic acid bacteria, such as Lactobacillaceae and Streptococcaceae dominated the beginning of the process until about day 14 when a relevant increase in hydrogen production (more than 10 ml H2 gVS-1 from days 13 to 14) was observed. Furthermore, during incubation a gradual decrease of lactic acid bacteria was detected with a simultaneous increase of Clostridia, such as Clostridiaceae and Tissierellaceae families. Moreover, archaeal populations in the biosystem were strongly related to inoculum since the non-inoculated samples of the dairy waste mixture had a relative abundance of archaea less than 0.1%; whereas, in the inoculated samples of the same mixture several archaeal genera were identified. Among methanogenic archaea, Methanoculleus was the dominant genus during all the process especially when the methane production occurred, and its relative abundance increased up to 99% at the end of the incubation time highlighting that methane was formed from dairy wastes primarily by the hydrogenotrophic pathway in the reactors.
Collapse
Affiliation(s)
- Giorgia Pagliano
- Department of Agricultural Sciences, University of Naples Federico II, Naples, Italy
| | - Valeria Ventorino
- Department of Agricultural Sciences, University of Naples Federico II, Naples, Italy.,Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
| | | | - Ida Romano
- Department of Agricultural Sciences, University of Naples Federico II, Naples, Italy
| | - Francesco Pirozzi
- Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy.,Department of Civil, Architectural and Environmental Engineering, University of Naples Federico II, Naples, Italy
| | - Olimpia Pepe
- Department of Agricultural Sciences, University of Naples Federico II, Naples, Italy.,Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
| |
Collapse
|
43
|
Isolation and diversity of culturable rhizobacteria associated with economically important crops and uncultivated plants in Québec, Canada. Syst Appl Microbiol 2018; 41:629-640. [DOI: 10.1016/j.syapm.2018.06.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 06/26/2018] [Indexed: 11/19/2022]
|
44
|
Comparative assessment of autochthonous bacterial and fungal communities and microbial biomarkers of polluted agricultural soils of the Terra dei Fuochi. Sci Rep 2018; 8:14281. [PMID: 30250138 PMCID: PMC6155181 DOI: 10.1038/s41598-018-32688-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 09/11/2018] [Indexed: 02/08/2023] Open
Abstract
Organic and inorganic xenobiotic compounds can affect the potential ecological function of the soil, altering its biodiversity. Therefore, the response of microbial communities to environmental pollution is a critical issue in soil ecology. Here, a high-throughput sequencing approach was used to investigate the indigenous bacterial and fungal community structure as well as the impact of pollutants on their diversity and richness in contaminated and noncontaminated soils of a National Interest Priority Site of Campania Region (Italy) called "Terra dei Fuochi". The microbial populations shifted in the polluted soils via their mechanism of adaptation to contamination, establishing a new balance among prokaryotic and eukaryotic populations. Statistical analyses showed that the indigenous microbial communities were most strongly affected by contamination rather than by site of origin. Overabundant taxa and Actinobacteria were identified as sensitive biomarkers for assessing soil pollution and could provide general information on the health of the environment. This study has important implications for microbial ecology in contaminated environments, increasing our knowledge of the capacity of natural ecosystems to develop microbiota adapted to polluted soil in sites with high agricultural potential and providing a possible approach for modeling pollution indicators for bioremediation purposes.
Collapse
|
45
|
Bredon M, Dittmer J, Noël C, Moumen B, Bouchon D. Lignocellulose degradation at the holobiont level: teamwork in a keystone soil invertebrate. MICROBIOME 2018; 6:162. [PMID: 30223906 PMCID: PMC6142342 DOI: 10.1186/s40168-018-0536-y] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Accepted: 08/22/2018] [Indexed: 05/22/2023]
Abstract
BACKGROUND Woodlice are recognized as keystone species in terrestrial ecosystems due to their role in the decomposition of organic matter. Thus, they contribute to lignocellulose degradation and nutrient cycling in the environment together with other macroarthropods. Lignocellulose is the main component of plants and is composed of cellulose, lignin and hemicellulose. Its digestion requires the action of multiple Carbohydrate-Active enZymes (called CAZymes), typically acting together as a cocktail with complementary, synergistic activities and modes of action. Some invertebrates express a few endogenous lignocellulose-degrading enzymes but in most species, an efficient degradation and digestion of lignocellulose can only be achieved through mutualistic associations with endosymbionts. Similar to termites, it has been suspected that several bacterial symbionts may be involved in lignocellulose degradation in terrestrial isopods, by completing the CAZyme repertoire of their hosts. RESULTS To test this hypothesis, host transcriptomic and microbiome shotgun metagenomic datasets were obtained and investigated from the pill bug Armadillidium vulgare. Many genes of bacterial and archaeal origin coding for CAZymes were identified in the metagenomes of several host tissues and the gut content of specimens from both laboratory lineages and a natural population of A. vulgare. Some of them may be involved in the degradation of cellulose, hemicellulose, and lignin. Reconstructing a lignocellulose-degrading microbial community based on the prokaryotic taxa contributing relevant CAZymes revealed two taxonomically distinct but functionally redundant microbial communities depending on host origin. In parallel, endogenous CAZymes were identified from the transcriptome of the host and their expression in digestive tissues was demonstrated by RT-qPCR, demonstrating a complementary enzyme repertoire for lignocellulose degradation from both the host and the microbiome in A. vulgare. CONCLUSIONS Our results provide new insights into the role of the microbiome in the evolution of terrestrial isopods and their adaptive radiation in terrestrial habitats.
Collapse
Affiliation(s)
- Marius Bredon
- Laboratoire Ecologie et Biologie des Interactions-UMR CNRS 7267, Equipe Ecologie Evolution Symbiose-Batiment B8-B35, Université de Poitiers, 5 rue Albert Turpain, TSA 51106, F-86073 Poitiers Cedex 9, France
| | - Jessica Dittmer
- Laboratoire Ecologie et Biologie des Interactions-UMR CNRS 7267, Equipe Ecologie Evolution Symbiose-Batiment B8-B35, Université de Poitiers, 5 rue Albert Turpain, TSA 51106, F-86073 Poitiers Cedex 9, France
- Dipartimento di Biologia e Biotecnologie, Università degli Studi di Pavia, Pavia, Italy
| | - Cyril Noël
- Laboratoire Ecologie et Biologie des Interactions-UMR CNRS 7267, Equipe Ecologie Evolution Symbiose-Batiment 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-Batiment 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-Batiment B8-B35, Université de Poitiers, 5 rue Albert Turpain, TSA 51106, F-86073 Poitiers Cedex 9, France
| |
Collapse
|
46
|
Pennacchio A, Ventorino V, Cimini D, Pepe O, Schiraldi C, Inverso M, Faraco V. Isolation of new cellulase and xylanase producing strains and application to lignocellulosic biomasses hydrolysis and succinic acid production. BIORESOURCE TECHNOLOGY 2018; 259:325-333. [PMID: 29573612 DOI: 10.1016/j.biortech.2018.03.027] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 03/03/2018] [Accepted: 03/05/2018] [Indexed: 05/16/2023]
Abstract
The enzymatic extracellular mixtures of two new microorganisms - Streptomyces flavogriseus AE64X and AE63X - isolated from Eucalyptus camaldulensis and Populus nigra and producing cellulase and xylanase, were characterized and applied to hydrolysis of pretreated Arundo donax, Populus nigra and Panicum virgatum (10% w/v) replacing the commercial enzymes Accelerase 1500 and Accelerase XY (5.4 and 145 U/g of pretreated biomass, respectively). It is worth of noting that the newly developed extracellular enzymatic mixtures, without any purification step and at the same dosage, presented saccharification yields that are higher (86% for S. flavogriseus AE64X) than those of commercial enzymes (81%). Moreover, these enzymatic mixes allowed us to hydrolyse both cellulose and xylan within the different lignocellulose biomasses substituting both the cellulase and xylanase of commercial source. The produced sugars were also fermentable by Basfia succiniciproducens BPP7 into succinic acid with high yield.
Collapse
Affiliation(s)
- Anna Pennacchio
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Valeria Ventorino
- Department of Agricultural Sciences, University of Naples Federico II, Portici (Naples), Italy
| | - Donatella Cimini
- Department of Experimental Medicine, School of Medicine, University of Campania "Luigi Vanvitelli", via L.de Crecchio 7, 80138 Naples, Italy
| | - Olimpia Pepe
- Department of Agricultural Sciences, University of Naples Federico II, Portici (Naples), Italy
| | - Chiara Schiraldi
- Department of Experimental Medicine, School of Medicine, University of Campania "Luigi Vanvitelli", via L.de Crecchio 7, 80138 Naples, Italy
| | - Michela Inverso
- Department of Experimental Medicine, School of Medicine, University of Campania "Luigi Vanvitelli", via L.de Crecchio 7, 80138 Naples, Italy
| | - Vincenza Faraco
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy.
| |
Collapse
|
47
|
Ho JCK, Yin Sze L. Isolation, identification and characterization of enzyme-producing lactic acid bacteria from traditional fermented foods. ACTA ACUST UNITED AC 2018. [DOI: 10.1093/biohorizons/hzy004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Jason Chen Kok Ho
- School of Biosciences, Faculty of Science, University of Nottingham Malaysia Campus, Jalan Broga, Semenyih, Selangor Darul Ehsan, Malaysia
| | - Lim Yin Sze
- School of Biosciences, Faculty of Science, University of Nottingham Malaysia Campus, Jalan Broga, Semenyih, Selangor Darul Ehsan, Malaysia
| |
Collapse
|
48
|
Jones JA, Kerr R, Haltli B, Tinto WF. Temperature and pH effect on glucose production from pretreated bagasse by a novel species of Citrobacter and other bacteria. Heliyon 2018; 4:e00657. [PMID: 29942873 PMCID: PMC6010966 DOI: 10.1016/j.heliyon.2018.e00657] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 05/29/2018] [Accepted: 06/13/2018] [Indexed: 11/29/2022] Open
Abstract
Cellulolytic bacteria that produce cellulases, which are active over a range of pH and temperatures, can be used to catalyze hydrolysis of pretreated lignocellulosic material. This is important in the production of second generation biofuels among other biotechnological applications. In this investigation, bacteria isolated from sugarcane bagasse were identified as strains of Enterobacter xiangfangensis, Serratia rubidaea, Klebsiella pneumoniae and a novel species of Citrobacter designated Citrobacter sp. UWIBGS10. The glucose production potential of these strains was studied on thermally and solvent pretreated sugarcane bagasse. This was performed at 24-hour intervals up to 168 hours in the range of pH 5-9 and temperature range 25-40 °C. Maximal concentrations of glucose for Citrobacter sp. UWIBGS10 occurred at pH 6 and 25 °C. For E. xiangfangensis, S. rubidaea, K. pneumoniae glucose concentrations were consistent across the pH and temperature ranges examined. From these results it could be concluded that the bacteria demonstrated ability for lignocellulolytic hydrolysis for the production of glucose and could be further explored for the characterization of commercial cellulolytic enzymes.
Collapse
Affiliation(s)
- Jamila A.D. Jones
- Department of Biological and Chemical Sciences, Faculty of Science and Technology, University of the West Indies, Cave Hill Campus, St. Michael, Barbados
| | - R.G. Kerr
- Department of Biomedical Sciences, University of Prince Edwards Island, 550 University Avenue, Charlottetown, PE C1A 4P3, Canada
| | - B.A. Haltli
- Department of Biomedical Sciences, University of Prince Edwards Island, 550 University Avenue, Charlottetown, PE C1A 4P3, Canada
| | - Winston F. Tinto
- Department of Biological and Chemical Sciences, Faculty of Science and Technology, University of the West Indies, Cave Hill Campus, St. Michael, Barbados
| |
Collapse
|
49
|
Varriale S, Houbraken J, Granchi Z, Pepe O, Cerullo G, Ventorino V, Chin-A-Woeng T, Meijer M, Riley R, Grigoriev IV, Henrissat B, de Vries RP, Faraco V. Talaromyces borbonicus, sp. nov., a novel fungus from biodegraded Arundo donax with potential abilities in lignocellulose conversion. Mycologia 2018; 110:316-324. [PMID: 29843575 DOI: 10.1080/00275514.2018.1456835] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
A novel fungal species able to synthesize enzymes with potential synergistic actions in lignocellulose conversion was isolated from the biomass of Arundo donax during biodegradation under natural conditions in the Gussone Park of the Royal Palace of Portici (Naples, Italy). In this work, this species was subjected to morphological and phylogenetic analyses. Sequencing of its genome was performed, resulting in 28 scaffolds that were assembled into 27.05 Mb containing 9744 predicted genes, among which 396 belong to carbohydrate-active enzyme (CAZyme)-encoding genes. Here we describe and illustrate this previously unknown species, which was named Talaromyces borbonicus, by a polyphasic approach combining phenotypic, physiological, and sequence data.
Collapse
Affiliation(s)
- Simona Varriale
- a Department of Chemical Sciences , University of Naples Federico II, Complesso Universitario Monte S. Angelo , via Cintia, 4 80126 Naples , Italy
| | - Jos Houbraken
- b Department of Applied and Industrial Mycology , Westerdijk Fungal Biodiversity Institute , Uppsalalaan 8, 3584 CT Utrecht , The Netherlands
| | - Zoraide Granchi
- c GenomeScan B.V., Plesmanlaan 1/D, 2333 BZ Leiden , The Netherlands
| | - Olimpia Pepe
- d Department of Agricultural Sciences , University of Naples Federico II , Via Università 100, 80055 Portici (NA) , Italy
| | - Gabriella Cerullo
- a Department of Chemical Sciences , University of Naples Federico II, Complesso Universitario Monte S. Angelo , via Cintia, 4 80126 Naples , Italy
| | - Valeria Ventorino
- d Department of Agricultural Sciences , University of Naples Federico II , Via Università 100, 80055 Portici (NA) , Italy
| | | | - Martin Meijer
- b Department of Applied and Industrial Mycology , Westerdijk Fungal Biodiversity Institute , Uppsalalaan 8, 3584 CT Utrecht , The Netherlands
| | - Robert Riley
- f US Department of Energy Joint Genome Institute , 2800 Mitchell Drive, Walnut Creek , California 94598
| | - Igor V Grigoriev
- f US Department of Energy Joint Genome Institute , 2800 Mitchell Drive, Walnut Creek , California 94598
| | - Bernard Henrissat
- g Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257 CNRS , Université Aix-Marseille , 163 Avenue de Luminy, 13288 , Marseille , France.,h INRA, USC 1408 AFMB, 13288 , Marseille , France.,i Department of Biological Sciences , King Abdulaziz University , Jeddah , Saudi Arabia
| | - Ronald P de Vries
- j Department of Fungal Physiology , Westerdijk Fungal Biodiversity Institute , Uppsalalaan 8, 3584 CT Utrecht , The Netherlands.,k Department of Fungal Molecular Physiology , Utrecht University , Uppsalalaan 8, 3584 CT Utrecht , The Netherlands
| | - Vincenza Faraco
- a Department of Chemical Sciences , University of Naples Federico II, Complesso Universitario Monte S. Angelo , via Cintia, 4 80126 Naples , Italy
| |
Collapse
|
50
|
Fang X, Li Q, Lin Y, Lin X, Dai Y, Guo Z, Pan D. Screening of a microbial consortium for selective degradation of lignin from tree trimmings. BIORESOURCE TECHNOLOGY 2018; 254:247-255. [PMID: 29413930 DOI: 10.1016/j.biortech.2018.01.058] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 01/10/2018] [Accepted: 01/11/2018] [Indexed: 05/27/2023]
Abstract
To acquire microbial consortia with effectively precedent degradation of lignin, samples obtained from rotten trunks, rotten stumps and soil near it were screened and isolated after generations of subculture. The dynamic change illustrated that their community structures were affected by pH and tended to be stable after 6 days' cultivation. The desired one, named DM-1, was gained through successive cultivation for over 5 generations, whose high selectivity in lignin degradation was observed within 16 days' cultivation (SV = 2.78). Meanwhile, a remarkable reduction in the fiber crystallinity of tree trimmings (10.35%) resulted from the bio-degradation of DM-1, displayed a greater exposure of cellulose by selective removal of lignin. The diversity analysis of DM-1 was investigated by PCR amplification and 16S rDNA sequencing, indicated that mesorhizobium, cellulosimicrobium, pandoraea, achromobacter and stenotrophomones were the predominant genera. Furthermore, fungi (3 strains), bacteria (4 strains) and actinomycetes (5 strains) constituted 12 strains in total were gained by plate isolation from DM-1.
Collapse
Affiliation(s)
- Xiuxiu Fang
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, Guangdong 510642, PR China
| | - Qiumin Li
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, Guangdong 510642, PR China; School of Agriculture and Food Science, Belfield Campus, University College Dublin, Dublin 4, Ireland
| | - Yunqin Lin
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, Guangdong 510642, PR China; Integrate Microbiology Research Center, South China Agricultural University, Guangzhou, Guangdong 510642, PR China.
| | - Xinlei Lin
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, Guangdong 510642, PR China
| | - Yiqi Dai
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, Guangdong 510642, PR China
| | - Zexiang Guo
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, Guangdong 510642, PR China
| | - Dezhao Pan
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, Guangdong 510642, PR China
| |
Collapse
|