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Yang S, Sun J, Wang C, Li S, Li Z, Luo W, Wei G, Chen W. Residue quality drives SOC sequestration by altering microbial taxonomic composition and ecophysiological function in desert ecosystem. ENVIRONMENTAL RESEARCH 2024; 250:118518. [PMID: 38382662 DOI: 10.1016/j.envres.2024.118518] [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: 08/16/2023] [Revised: 02/14/2024] [Accepted: 02/16/2024] [Indexed: 02/23/2024]
Abstract
Plant residues are important sources of soil organic carbon in terrestrial ecosystems. The degradation of plant residue by microbes can influence the soil carbon cycle and sequestration. However, little is known about the microbial composition and function, as well as the accumulation of soil organic carbon (SOC) in response to the inputs of different quality plant residues in the desert environment. The present study evaluated the effects of plant residue addition from Pinus sylvestris var. mongolica (Pi), Artemisia desertorum (Ar) and Amorpha fruticosa (Am) on desert soil microbial community composition and function in a field experiment in the Mu Us Desert. The results showed that the addition of the three plant residues with different C/N ratios induced significant variation in soil microbial communities. The Am treatment (low C/N ratio) improved microbial diversity compared with the Ar and Pi treatments (medium and high C/N ratios). The variations in the taxonomic and functional compositions of the dominant phyla Actinobacteria and Proteobacteria were higher than those of the other phyla among the different treatments. Moreover, the network links between Proteobacteria and other phyla and the CAZyme genes abundances from Proteobacteria increased with increasing residue C/N, whereas those decreased for Actinobacteria. The SOC content of the Am, Ar and Pi treatments increased by 45.73%, 66.54% and 107.99%, respectively, as compared to the original soil. The net SOC accumulation was positively correlated with Proteobacteria abundance and negatively correlated with Actinobacteria abundance. These findings showed that changing the initial quality of plant residue from low C/N to high C/N can result in shifts in taxonomic and functional composition from Actinobacteria to Proteobacteria, which favors SOC accumulation. This study elucidates the ecophysiological roles of Actinobacteria and Proteobacteria in the desert carbon cycle, expands our understanding of the potential microbial-mediated mechanisms by which plant residue inputs affect SOC sequestration in desert soils, and provides valuable guidance for species selection in desert vegetation reconstruction.
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Affiliation(s)
- Shanshan Yang
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Shaanxi, China
| | - Jieyu Sun
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Shaanxi, China
| | - Chang Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Shaanxi, China
| | - Shuyue Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Shaanxi, China
| | - Zubing Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Shaanxi, China
| | - Wen Luo
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Shaanxi, China
| | - Gehong Wei
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Shaanxi, China
| | - Weimin Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Shaanxi, China.
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Lu Z, Zhou Y, Li Y, Li C, Lu M, Sun X, Luo Z, Zhao J, Fan M. Effects of partial substitution of chemical fertilizer with organic manure on the activity of enzyme and soil bacterial communities in the mountain red soil. Front Microbiol 2023; 14:1234904. [PMID: 37736094 PMCID: PMC10509364 DOI: 10.3389/fmicb.2023.1234904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 08/24/2023] [Indexed: 09/23/2023] Open
Abstract
Introduction The partial substitution of chemical fertilizer with organic manure takes on a critical significance to enhancing soil quality and boosting sustainable agricultural development. However, rare research has studied the effects of partial substitution of chemical fertilizer with organic manure on soil bacterial community diversity and enzyme activity in maize field in the mountain red soil region of Yunnan. Methods In this study, four treatments were set up in which chemical fertilizer (the application rates of N, P2O5 and K2O were 240, 75 and 75 kg·ha-1, respectively) was substituted by 10% (M10), 20% (M20), 30% (M30) and 40% (M40) of organic manure with equal nitrogen, as well as two control treatments of single application of chemical fertilizer (M0) and no fertilization (CK). The maize (Zea mays L.) crop was sown as a test crop in May 2018. The effects of partial substitution of chemical fertilizer with organic manure on soil physicochemical properties, soil bacterial community diversity and enzyme activity were studied. Results The activities of Cellulase (CBH), Invertase (INV) and β-glucosidase (BG) increased with the increase of organic manure substitution ratio. The activities of β-1,4-N-acetylglucosaminidase (NAG), Urease (URE), and leucine aminopeptidase (LAP) also had the same trend, but the highest activities were 159.92 mg·g-1·h-1, 66.82 mg·g-1·h-1 and 143.90 mg·g-1·h-1 at 30% substitution ratio. Compared with CK and M0 treatments, Shannon index increased notably by 82.91%-116.74% and 92.42%-128.01%, respectively, at the organic manure substitution ratio ranging from 10% to 40%. Chao1 and ACE index increased significantly at the organic manure substitution ratio ranging from 10% to 30%. Proteobacteria was the dominant phylum in all treatments, the relative abundance of Proteobacteria decreased as the organic manure substitution ratio increased. Redundancy analysis showed that microbial biomass C was the main factor affecting the bacterial community composition under partial replacement of chemical fertilizer treatment, while Actinobacteria was the main factor affecting the enzyme activity. In addition, the maize yield of M30 and M40 treatments was significantly higher than that of CK and M0-M20 treatments, and the yield of M30 treatment was the highest, reaching 7652.89 kg·ha-1. Conclusion Therefore, the partial substitution of chemical fertilizer with organic manure can improve soil biological characteristics, while increasing bacterial community diversity and soil enzyme activity. Therefore, a thirty percent organic manure substitution was determined as the optimal substitution ratio for maize farmland in the mountain red soil area of Yunnan, China.
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Affiliation(s)
- Zerang Lu
- College of Resources and Environment, Yunnan Agricultural University, Kunming, China
| | - Yun Zhou
- College of Resources and Environment, Yunnan Agricultural University, Kunming, China
- College of Ecology and Environment, Yunnan University, Kunming, China
| | - Yongmei Li
- College of Resources and Environment, Yunnan Agricultural University, Kunming, China
| | - Chunpei Li
- College of Resources and Environment, Yunnan Agricultural University, Kunming, China
| | - Mei Lu
- College of Resources and Environment, Yunnan Agricultural University, Kunming, China
| | - Xuemei Sun
- College of Resources and Environment, Yunnan Agricultural University, Kunming, China
| | - Zhizhang Luo
- College of Resources and Environment, Yunnan Agricultural University, Kunming, China
| | - Jixia Zhao
- College of Resources and Environment, Yunnan Agricultural University, Kunming, China
| | - Maopan Fan
- College of Resources and Environment, Yunnan Agricultural University, Kunming, China
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Patel A, Sahu KP, Mehta S, Javed M, Balamurugan A, Ashajyothi M, Sheoran N, Ganesan P, Kundu A, Gopalakrishnan S, Gogoi R, Kumar A. New Insights on Endophytic Microbacterium-Assisted Blast Disease Suppression and Growth Promotion in Rice: Revelation by Polyphasic Functional Characterization and Transcriptomics. Microorganisms 2023; 11:microorganisms11020362. [PMID: 36838327 PMCID: PMC9963279 DOI: 10.3390/microorganisms11020362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/24/2022] [Accepted: 01/01/2023] [Indexed: 02/05/2023] Open
Abstract
Plant growth-promoting endophytic microbes have drawn the attention of researchers owing to their ability to confer fitness benefits in many plant species. Here, we report agriculturally beneficial traits of rice-leaf-adapted endophytic Microbacterium testaceum. Our polyphasic taxonomic investigations revealed its identity as M. testaceum. The bacterium displayed typical endophytism in rice leaves, indicated by the green fluorescence of GFP-tagged M. testaceum in confocal laser scanning microscopy. Furthermore, the bacterium showed mineral solubilization and production of IAA, ammonia, and hydrolytic enzymes. Tobacco leaf infiltration assay confirmed its non-pathogenic nature on plants. The bacterium showed antifungal activity on Magnaporthe oryzae, as exemplified by secreted and volatile organic metabolome-mediated mycelial growth inhibition. GC-MS analysis of the volatilome of M. testaceum indicated the abundance of antimicrobial compounds. Bacterization of rice seedlings showed phenotypic traits of MAMP-triggered immunity (MTI), over-expression of OsNPR1 and OsCERK, and the consequent blast suppressive activity. Strikingly, M. testaceum induced the transcriptional tradeoff between physiological growth and host defense pathways as indicated by up- and downregulated DEGs. Coupled with its plant probiotic features and the defense elicitation activity, the present study paves the way for developing Microbacterium testaceum-mediated bioformulation for sustainably managing rice blast disease.
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Patel A, Sahu KP, Mehta S, Balamurugan A, Kumar M, Sheoran N, Kumar S, Krishnappa C, Ashajyothi M, Kundu A, Goyal T, Narayanasamy P, Kumar A. Rice leaf endophytic Microbacterium testaceum: Antifungal actinobacterium confers immunocompetence against rice blast disease. Front Microbiol 2022; 13:1035602. [PMID: 36619990 PMCID: PMC9810758 DOI: 10.3389/fmicb.2022.1035602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 11/07/2022] [Indexed: 12/24/2022] Open
Abstract
Genetic and functional characteristics of rice leaf endophytic actinobacterial member, Microbacterium are described. Morphotyping, multilocus sequence analysis and transmission electron microscopy indicated the species identity of the endophytic bacterium, OsEnb-ALM-D18, as Microbacterium testaceum. The endophytic Microbacterium showed probiotic solubilization of plant nutrients/minerals, produced hydrolytic enzyme/phytohormones, and showed endophytism in rice seedlings. Further, the endophytic colonization by M. testaceum OsEnb-ALM-D18 was confirmed using reporter gene coding for green fluorescence protein. Microbacterium OsEnb-ALM-D18 showed volatilome-mediated antibiosis (95.5% mycelial inhibition) on Magnaporthe oryzae. Chemical profiling of M. testaceum OsEnb-ALM-D18 volatilome revealed the abundance of 9-Octadecenoic acid, Hexadecanoic acid, 4-Methyl-2-pentanol, and 2,5-Dihydro-thiophene. Upon endobacterization of rice seedlings, M. testaceum altered shoot and root phenotype suggestive of activated defense. Over 80.0% blast disease severity reduction was observed on the susceptible rice cultivar Pusa Basmati-1 upon foliar spray with M. testaceum. qPCR-based gene expression analysis showed induction of OsCERK1, OsPAD4, OsNPR1.3, and OsFMO1 suggestive of endophytic immunocompetence against blast disease. Moreover, M. testaceum OsEnb-ALM-D18 conferred immunocompetence, and antifungal antibiosis can be the future integrated blast management strategy.
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Affiliation(s)
- Asharani Patel
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | - Sahil Mehta
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | - Mukesh Kumar
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Neelam Sheoran
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Shanu Kumar
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | | | - Aditi Kundu
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Tushar Goyal
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | - Aundy Kumar
- ICAR-Indian Agricultural Research Institute, New Delhi, India,*Correspondence: Aundy Kumar, ; ; orcid.org/0000-0002-7401-9885
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Gul B, Khan S, Ahmad I. Extraction of phytochemicals from date palm (Phoenix dactylifera L.) seeds by enzymatic hydrolysis. J FOOD PROCESS PRES 2022. [DOI: 10.1111/jfpp.17007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Banat Gul
- National University of Science and Technology (NUST) Islamabad Pakistan
| | - Shamim Khan
- Department of Physics Islamia College Peshawar Khyber Pakhtunkhwa Pakistan
| | - Iftikhar Ahmad
- Institute of Radiotherapy and Nuclear Medicine (IRNUM) Peshawar Pakistan
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Ma L, Wang X, Zhou J, Lü X. Degradation of switchgrass by Bacillus subtilis 1AJ3 and expression of a beta-glycoside hydrolase. Front Microbiol 2022; 13:922371. [PMID: 35966659 PMCID: PMC9374367 DOI: 10.3389/fmicb.2022.922371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 07/11/2022] [Indexed: 11/13/2022] Open
Abstract
Increasing demand for carbon neutrality has led to the development of new techniques and modes of low carbon production. The utilization of microbiology to convert low-cost renewable resources into more valuable chemicals is particularly important. Here, we investigated the ability of a cellulolytic bacterium, Bacillus subtilis 1AJ3, in switchgrass lignocellulose degradation. After 5 days of culture with the strain under 37°C, cellulose, xylan, and acid-insoluble lignin degradation rates were 16.13, 14.24, and 13.91%, respectively. Gas chromatography-mass spectrometry (GC-MS) analysis and field emission scanning electron microscopy (FE-SEM) indicated that the lignin and surface of switchgrass were degraded after incubation with the bacterial strain. Strain 1AJ3 can grow well below 60°C, which satisfies the optimum temperature (50°C) condition of most cellulases; subsequent results emphasize that acid-heat incubation conditions increase the reducing sugar content in a wide range of cellulosic biomass degraded by B. subtilis 1AJ3. To obtain more reducing sugars, we focused on β-glycoside hydrolase, which plays an important role in last steps of cellulose degradation to oligosaccharides. A β-glycoside hydrolase (Bgl-16A) was characterized by cloning and expression in Escherichia coli BL21 and further determined to belong to glycoside hydrolase (GH) 16 family. The Bgl-16A had an enzymatic activity of 365.29 ± 10.43 U/mg, and the enzyme's mode of action was explained by molecular docking. Moreover, the critical influence on temperature (50°C) of Bgl-16A also explained the high-efficiency degradation of biomass by strain under acid-heat conditions. In terms of potential applications, both the strain and the recombinant enzyme showed that coffee grounds would be a suitable and valuable substrate. This study provides a new understanding of cellulose degradation by B. subtilis 1AJ3 that both the enzyme action mode and optimum temperature limitation by cellulases could impact the degradation. It also gave new sight to unique advantage utilization in the industrial production of green manufacturing.
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Affiliation(s)
- Lingling Ma
- Science Center for Future Foods, Jiangnan University, Wuxi, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, Wuxi, China
- Laboratory of Bioresources, College of Food Science and Engineering, Northwest A&F University, Xianyang, China
| | - Xin Wang
- Laboratory of Bioresources, College of Food Science and Engineering, Northwest A&F University, Xianyang, China
| | - Jingwen Zhou
- Science Center for Future Foods, Jiangnan University, Wuxi, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, Wuxi, China
| | - Xin Lü
- Laboratory of Bioresources, College of Food Science and Engineering, Northwest A&F University, Xianyang, China
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Inoculation of Prickly Pear Litter with Microbial Agents Promotes the Efficiency in Aerobic Composting. SUSTAINABILITY 2022. [DOI: 10.3390/su14084824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
Prickly pear (Rosa roxburghii Tratt), a shrub mainly distributed in South China, is an economically essential plant for helping the local people out of poverty. To efficiently provide sufficient nutrients to the plant in the soil for the ecological cultivation of prickly pear, we studied the aerobic composting of a prickly pear litter with three agents, including AC (Bacillus natto, Bacillus sp., Actinomycetes sp., Saccharomyces sp., Trichoderma sp., Azotobacter sp., and Lactobacillus sp.), BC (Bacillus subtilis, Lactobacillaceae sp., Bacillus licheniformis, Saccharomyces sp., and Enterococcus faecalis), and CC (Bacillus sp., Actinomycetes sp., Lactobacillaceae sp., Saccharomyces sp., and Trichoderma sp.) and a control without microbial agents. The results show that the physicochemical and microbial traits of three resultant prickly pear composts were different after the inoculation with AC, BC, or CC. The pH values of three composts ranged from 8.0 to 8.5, and their conductivity values were between 1.6 and 1.9 mS/cm. The seed germination index of all three composts exceeded 70%. The contents of volatile solids and organic matter of the three composts both decreased significantly. The BC maximally increased the total N (18%) of the compost, whereas the CC maximally increased the total P (48%) and total K (38%) contents. Contents of available P and available K of the three composts increased significantly, and the available N content in compost after BC inoculation increased by 16%. The physicochemical features showed that three composts were non-hazardous to plants, and the microbial agents improved nutrient availability. The richness, Chao1, and Shannon index in the bacterial communities of three composts increased significantly. At the phylum level, Proteobacteria, Bacteroidetes, and Firmicutes bacterium became dominant in the three composts, whereas at the family level, Microscillaceae and A4b (phylum Chloroflexi) became the dominant groups. Abundant cellulose-degrading bacteria existed at the dominant phylum level, which promoted fiber degradation in composts. Organic matter and the available N content regulated the composting bacterium. The inoculants enhanced the efficiency of composting: agents B and C were more suitable exogenous inoculants for the composting of a prickly pear litter.
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Hero JS, Pisa JH, Raimondo EE, Martínez MA. Proteomic analysis of secretomes from Bacillus sp. AR03: characterization of enzymatic cocktails active on complex carbohydrates for xylooligosaccharides production. Prep Biochem Biotechnol 2021; 51:871-880. [PMID: 33439095 DOI: 10.1080/10826068.2020.1870136] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Bacillus sp. AR03 have been described as an important producer of carbohydrate-active enzymes (CAZymes) when growing in a peptone-based medium supplemented with simple sugars and/or carboxymethyl cellulose (CMC) as carbon sources. This work aimed to identify the extracellular enzymatic cocktails through shotgun proteomics. The proteomic analysis showed that enzymes involved in cellulose and xylan degradation were among the most abundant proteins. These enzymes included an endo-glucanase GH5_2 and a glucuronoxylanase GH30_8, which were found in all conditions. In addition, several proteins were differentially expressed in the three evaluated culture media, indicating microbial metabolic changes due to the different supplied carbon sources, particularly, in the presence of CMC. Finally, the capability of the crude enzymatic cocktails from culture media to degrade birchwood xylan was assessed, which produced mostly xylooligosaccharides containing among 3-5 xylose units. Consequently, this work shows the potential of the extracellular enzymes from Bacillus sp. AR03 for producing emergent prebiotics.
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Affiliation(s)
- Johan S Hero
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CONICET, Tucumán, Argentina
| | - José H Pisa
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CONICET, Tucumán, Argentina
| | - Enzo E Raimondo
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CONICET, Tucumán, Argentina.,Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, Tucumán, Argentina
| | - M Alejandra Martínez
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CONICET, Tucumán, Argentina.,Facultad de Ciencias Exactas y Tecnología, Universidad Nacional de Tucumán, Tucumán, Argentina
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Long-Term Exposure to Azo Dyes from Textile Wastewater Causes the Abundance of Saccharibacteria Population. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11010379] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Discharge of untreated wastewater is one of the major problems in various countries. The use of azo dyes in textile industries are one of the key xenobiotic compounds which effect both soil and water ecosystems and result in drastic effect on the microbial communities. Orathupalayam dam, which is constructed over Noyyal river in Tamil Nadu, India has become a sink of wastewater from the nearby textile industries. The present study had aimed to characterize the bacterial diversity and community profiles of soil collected from the vicinity of the dam (DS) and allied agricultural field (ALS) nearby the catchment area. The soil dehydrogenase and cellulase activities were significantly lower in DS compared to ALS. Additionally, the long-term exposure to azo dye compounds resulted in higher relative abundance of Saccharibacteria (36.4%) which are important for degradation of azo dyes. On the other hand, the relative abundance of Proteobacteria (25.4%) were higher in ALS. Interestingly, the abundance of Saccharibacteria (15.2%) were also prominent in ALS suggesting that the azo compounds might have deposited in the agricultural field through irrigation. Hence, this study revealed the potential bacterial phyla which can be key drivers for designing viable technologies for degradation of xenobiotic dyes.
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王 浩. Research Progress of Forest Soil Enzyme Dynamics in Different Succession Stages. INTERNATIONAL JOURNAL OF ECOLOGY 2021. [DOI: 10.12677/ije.2021.101006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Starke R, Morais D, Větrovský T, López Mondéjar R, Baldrian P, Brabcová V. Feeding on fungi: genomic and proteomic analysis of the enzymatic machinery of bacteria decomposing fungal biomass. Environ Microbiol 2020; 22:4604-4619. [PMID: 32743948 DOI: 10.1111/1462-2920.15183] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 07/21/2020] [Accepted: 07/31/2020] [Indexed: 11/29/2022]
Abstract
Dead fungal biomass is an abundant source of nutrition in both litter and soil of temperate forests largely decomposed by bacteria. Here, we have examined the utilization of dead fungal biomass by the five dominant bacteria isolated from the in situ decomposition of fungal mycelia using a multiOMIC approach. The genomes of the isolates encoded a broad suite of carbohydrate-active enzymes, peptidases and transporters. In the extracellular proteome, only Ewingella americana expressed chitinases while the two Pseudomonas isolates attacked chitin by lytic chitin monooxygenase, deacetylation and deamination. Variovorax sp. expressed enzymes acting on the side-chains of various glucans and the chitin backbone. Surprisingly, despite its genomic potential, Pedobacter sp. did not produce extracellular proteins to decompose fungal mycelia but presumably feeds on simple substrates. The ecological roles of the five individual strains exhibited complementary features for a fast and efficient decomposition of dead fungal biomass by the entire bacterial community.
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Affiliation(s)
- Robert Starke
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Daniel Morais
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Tomáš Větrovský
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Ruben López Mondéjar
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Vendula Brabcová
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
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Gill AS, Purnell K, Palmer MI, Stein J, McGuire KL. Microbial Composition and Functional Diversity Differ Across Urban Green Infrastructure Types. Front Microbiol 2020; 11:912. [PMID: 32582043 PMCID: PMC7291602 DOI: 10.3389/fmicb.2020.00912] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 04/17/2020] [Indexed: 01/04/2023] Open
Abstract
Functional and biogeographical properties of soil microbial communities in urban ecosystems are poorly understood despite their role in metabolic processes underlying valuable ecosystem services. The worldwide emergence of engineered habitats in urban landscapes-green roofs, bioswales, and other types of soil-based green infrastructure-highlights the importance of understanding how environmental changes affect the community assembly processes that shape urban microbial diversity and function. In this study we investigated (1) whether engineered green roofs and bioswales in New York City had distinct microbial community composition and trait-associated diversity compared to non-engineered soils in parks and tree pits, and (2) if these patterns were consistent with divergent community assembly processes associated with engineered specifications of green infrastructure habitats not present in conventional, non-engineered green infrastructure; specifically, tree pit and park lawn soils. We found that green roofs and bioswales each had distinct bacterial and fungal communities, but that community composition and diversity were not significantly associated with geographic distance, suggesting that the processes structuring these differences are related to aspects of the habitats themselves. Bioswales, and to a lesser extent green roofs, also contained increased functional potential compared to conventional GI soils, based on the diversity and abundance of taxa associated with nitrogen cycling, biodegradation, decomposition, and traits positively associated with plant growth. We discuss these results in the context of community assembly theory, concluding that urban soil microbial community composition and diversity in engineered habitats are driven largely by environmental filtering, whereas stochastic processes are more important among non-engineered soils.
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Affiliation(s)
- Aman S. Gill
- Department of Environmental Science and Policy Management, University of California, Berkeley, Berkeley, CA, United States
| | - Kai Purnell
- Department of Biology, Barnard College, New York, NY, United States
| | - Matthew I. Palmer
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, United States
| | - Jaime Stein
- Programs for Sustainable Planning and Development, School of Architecture, Pratt Institute, Brooklyn, NY, United States
| | - Krista L. McGuire
- Department of Biology, Institute of Ecology and Evolution, University of Oregon, Eugene, OR, United States
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Ma L, Lu Y, Yan H, Wang X, Yi Y, Shan Y, Liu B, Zhou Y, Lü X. Screening of cellulolytic bacteria from rotten wood of Qinling (China) for biomass degradation and cloning of cellulases from Bacillus methylotrophicus. BMC Biotechnol 2020; 20:2. [PMID: 31910834 PMCID: PMC6947901 DOI: 10.1186/s12896-019-0593-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 12/08/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cellulosic biomass degradation still needs to be paid more attentions as bioenergy is the most likely to replace fossil energy in the future, and more evaluable cellulolytic bacteria isolation will lay a foundation for this filed. Qinling Mountains have unique biodiversity, acting as promising source of cellulose-degrading bacteria exhibiting noteworthy properties. Therefore, the aim of this work was to find potential cellulolytic bacteria and verify the possibility of the cloning of cellulases from the selected powerful bacteria. RESULTS In present study, 55 potential cellulolytic bacteria were screened and identified from the rotten wood of Qinling Mountains. Based on the investigation of cellulase activities and degradation effect on different cellulose substrates, Bacillus methylotrophicus 1EJ7, Bacillus subtilis 1AJ3 and Bacillus subtilis 3BJ4 were further applied to hydrolyze wheat straw, corn stover and switchgrass, and the results suggested that B. methylotrophicus 1EJ7 was the most preponderant bacterium, and which also indicated that Bacillus was the main cellulolytic bacteria in rotten wood. Furthermore, scanning electron microscopy (SEM) and X-ray diffraction analysis of micromorphology and crystallinity of wheat straw also verified the significant hydrolyzation. With ascertaining the target sequence of cellulase β-glucosidase (243 aa) and endoglucanase (499 aa) were successfully heterogeneously cloned and expressed from B. methylotrophicus 1EJ7, and which performed a good effect on cellulose degradation with enzyme activity of 1670.15 ± 18.94 U/mL and 0.130 ± 0.002 U/mL, respectively. In addition, based on analysis of amino acid sequence, it found that β-glucosidase were belonged to GH16 family, and endoglucanase was composed of GH5 family catalytic domain and a carbohydrate-binding module of CBM3 family. CONCLUSIONS Based on the screening, identification and cellulose degradation effect evaluation of cellulolytic bacteria from rotten wood of Qinling Mountains, it found that Bacillus were the predominant species among the isolated strains, and B. methylotrophicus 1EJ7 performed best on cellulose degradation. Meanwhile, the β-glucosidase and endoglucanase were successfully cloned and expressed from B. methylotrophicus for the first time, which provided new materials of both strain and the recombinant enzymes for the study of cellulose degradation and its application in industry.
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Affiliation(s)
- Lingling Ma
- Lab of Bioresources, College of Food Science and Engineering, Northwest A&F University, Yangling, 712100, Shaanxi Province, China
| | - Yingying Lu
- Lab of Bioresources, College of Food Science and Engineering, Northwest A&F University, Yangling, 712100, Shaanxi Province, China
| | - Hong Yan
- Lab of Bioresources, College of Food Science and Engineering, Northwest A&F University, Yangling, 712100, Shaanxi Province, China
| | - Xin Wang
- Lab of Bioresources, College of Food Science and Engineering, Northwest A&F University, Yangling, 712100, Shaanxi Province, China
| | - Yanglei Yi
- Lab of Bioresources, College of Food Science and Engineering, Northwest A&F University, Yangling, 712100, Shaanxi Province, China
| | - Yuanyuan Shan
- Lab of Bioresources, College of Food Science and Engineering, Northwest A&F University, Yangling, 712100, Shaanxi Province, China
| | - Bianfang Liu
- Lab of Bioresources, College of Food Science and Engineering, Northwest A&F University, Yangling, 712100, Shaanxi Province, China
| | - Yuan Zhou
- Lab of Bioresources, College of Food Science and Engineering, Northwest A&F University, Yangling, 712100, Shaanxi Province, China
| | - Xin Lü
- Lab of Bioresources, College of Food Science and Engineering, Northwest A&F University, Yangling, 712100, Shaanxi Province, China.
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López-Mondéjar R, Algora C, Baldrian P. Lignocellulolytic systems of soil bacteria: A vast and diverse toolbox for biotechnological conversion processes. Biotechnol Adv 2019; 37:107374. [DOI: 10.1016/j.biotechadv.2019.03.013] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 03/06/2019] [Accepted: 03/21/2019] [Indexed: 12/12/2022]
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15
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Chen Y, Li P, Huang Y, Yu K, Chen H, Cui K, Huang Q, Zhang J, Yew-Hoong Gin K, He Y. Environmental media exert a bottleneck in driving the dynamics of antibiotic resistance genes in modern aquatic environment. WATER RESEARCH 2019; 162:127-138. [PMID: 31260828 DOI: 10.1016/j.watres.2019.06.047] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 06/17/2019] [Accepted: 06/18/2019] [Indexed: 05/26/2023]
Abstract
With the rapid construction of dams worldwide, reservoir system has become a representation of modern aquatic environment. However, the profiles of antibiotic resistance genes (ARGs) and associated factor influencing their dynamics in modern aquatic environment (e.g., water phase, sediment phase, and soil phase) are largely unknown. Here, we comprehensively characterized the diversity, abundance, distribution of ARGs in a large drinking water reservoir using high-throughput quantitative PCR, as well as ranked the factors (e.g., mobile genetic elements (MGEs), bacteria community, bacterial biomass, antibiotics, and basic properties) influencing the profiles of ARGs on the basis of structural equation models (SEMs). Water phase was prone to harbor more diverse ARGs as compared to sediment phase and soil phase, and soil phase in drawdown area was a potential reservoir and hotspot for ARGs. Environmental media partially affected the ARG diversity in modern aquatic environment, while it observably influenced the distributions of ARGs and MGEs and their co-occurrence patterns. The pathways for the proliferation and spread of ARGs in water phase were both the horizontal gene transfer (HGT) and vertical gene transfer (VGT), while the dominant pathways in sediment phase and soil phase were the HGT and VGT, respectively. The SEMs demonstrated that MGEs contributed the most to drive the ARG dynamics in both water phase and sediment phase, while the most dominant factor for this in soil phase was bacterial community. Overall, environmental media exerted a bottleneck in driving the dynamics of ARGs in modern aquatic environment probably via diversifying the MGEs, bacterial community, bacterial biomass, antibiotics and basic properties.
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Affiliation(s)
- Yihan Chen
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China; School of Resources and Environmental Engineering, Hefei University of Technology, Hefei, 230009, China.
| | - Peng Li
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yuansheng Huang
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Kaifeng Yu
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hongjie Chen
- NUS Environmental Research Institute, National University of Singapore, 5A Engineering Drive 1, #02-01, Singapore, 117411, Singapore; Department of Civil and Environmental Engineering, National University of Singapore, 1 Engineering Drive 2, E1A 07-03, Singapore, 117576, Singapore
| | - Kangping Cui
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Qianli Huang
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Junya Zhang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Karina Yew-Hoong Gin
- NUS Environmental Research Institute, National University of Singapore, 5A Engineering Drive 1, #02-01, Singapore, 117411, Singapore; Department of Civil and Environmental Engineering, National University of Singapore, 1 Engineering Drive 2, E1A 07-03, Singapore, 117576, Singapore
| | - Yiliang He
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China; Shanghai Institute of Pollution Control and Ecological Security, 800 Dongchuan Road, Shanghai, 200240, China.
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16
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De novo genome assembly and comparative annotation reveals metabolic versatility in cellulolytic bacteria from cropland and forest soils. Funct Integr Genomics 2019; 20:89-101. [PMID: 31378834 DOI: 10.1007/s10142-019-00704-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 07/09/2019] [Accepted: 07/24/2019] [Indexed: 10/26/2022]
Abstract
Cellulose, the most abundant polysaccharide in nature, is a rich source of renewable energy and sustains soil nutrients. Among the microorganisms known to degrade cellulose, bacteria are less studied compared to fungi. In the present work, we have investigated the culturable bacteria actively involved in cellulose degradation in forest and crop field soils. Based on clear zone formation and enzyme activity assay, we identified 7 bacterial strains positive for cellulose degradation. Of these, two most efficient strains (Bacillus cereus strains BHU1 and BHU2) were selected for whole genome sequencing, annotation, and information regarding GC content, number of genes, total subsystems, starch, and cellulose degradation pathways. Average nucleotide identity (ANI) showed more than 90% similarity between both the strains (BHU1 and BHU2) and with B. cereus ATCC 14579. Both the strains have genes and enzyme families like endoglucanase and β-glucosidase as evident from whole genome sequence. Cellulase containing gene families (GH5, GH8, GH1), and many other carbohydrate-degrading enzymes, were present in both the bacterial strains. Taken together, the results suggest that the strains were efficient in cellulose degradation, and can be used for energy generation and production of value-added product.
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17
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Chen L, Xiang W, Wu H, Ouyang S, Lei P, Hu Y, Ge T, Ye J, Kuzyakov Y. Contrasting patterns and drivers of soil fungal communities in subtropical deciduous and evergreen broadleaved forests. Appl Microbiol Biotechnol 2019; 103:5421-5433. [PMID: 31073876 DOI: 10.1007/s00253-019-09867-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 04/14/2019] [Accepted: 04/15/2019] [Indexed: 12/24/2022]
Abstract
Subtropical broadleaved forests play a crucial role in supporting terrestrial ecosystem functions, but little is known about their belowground soil fungal communities despite that they have central functions in C, N, and P cycles. This study investigated the structures and identified the drivers of soil fungal communities in subtropical deciduous and evergreen broadleaved forests, using high-throughput sequencing and FUNGuild for fungal identification and assignment to the trophic guild. Fungal richness was much higher in the deciduous than in the evergreen forest. Both forests were dominated by Ascomycota and Basidiomycota phyla, but saprophytic fungi were more abundant in the deciduous forest and ectomycorrhizal fungi predominated in the evergreen forest. Fungal communities had strong links to plant and soil properties. Specifically, plant diversity and litter biomass were the main aboveground drivers of fungal diversity and composition in the deciduous forest, while host effects were prominent in the evergreen forest. The belowground factors, i.e., soil pH, water content, and nutrients especially available P, were identified as the primary drivers of soil fungal communities in the broadleaved forests. Co-occurrence network analysis revealed assembly of fungal composition in broadleaved forest soils was non-random. The smaller modularity of the network in the deciduous forest reflects lower resistance to environment changes. Concluding, these results showed that plant community attributes, soil properties, and potential interactions among fungal functional guilds operate jointly on the divergence of soil fungal community assembly in the two broadleaved forest types.
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Affiliation(s)
- Liang Chen
- Faculty of Life Science and Technology, Central South University of Forestry and Technology, Changsha, 410004, Hunan, China.,Huitong National Station for Scientific Observation and Research of Chinese Fir Plantation Ecosystems in Hunan Province, Huitong, Huaihua, 438107, Hunan, China
| | - Wenhua Xiang
- Faculty of Life Science and Technology, Central South University of Forestry and Technology, Changsha, 410004, Hunan, China. .,Huitong National Station for Scientific Observation and Research of Chinese Fir Plantation Ecosystems in Hunan Province, Huitong, Huaihua, 438107, Hunan, China.
| | - Huili Wu
- Faculty of Life Science and Technology, Central South University of Forestry and Technology, Changsha, 410004, Hunan, China.,Huitong National Station for Scientific Observation and Research of Chinese Fir Plantation Ecosystems in Hunan Province, Huitong, Huaihua, 438107, Hunan, China
| | - Shuai Ouyang
- Faculty of Life Science and Technology, Central South University of Forestry and Technology, Changsha, 410004, Hunan, China.,Huitong National Station for Scientific Observation and Research of Chinese Fir Plantation Ecosystems in Hunan Province, Huitong, Huaihua, 438107, Hunan, China
| | - Pifeng Lei
- Faculty of Life Science and Technology, Central South University of Forestry and Technology, Changsha, 410004, Hunan, China.,Huitong National Station for Scientific Observation and Research of Chinese Fir Plantation Ecosystems in Hunan Province, Huitong, Huaihua, 438107, Hunan, China
| | - Yajun Hu
- Key Laboratory of Agro-ecological Processes in Subtropical Regions, Changsha Research Station for Agricultural & Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, Hunan, China
| | - Tida Ge
- Key Laboratory of Agro-ecological Processes in Subtropical Regions, Changsha Research Station for Agricultural & Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, Hunan, China
| | - Jun Ye
- Australian Centre for Ecogenomics, The University of Queensland, QLD, St. Lucia, 4072, Australia
| | - Yakov Kuzyakov
- Faculty of Life Science and Technology, Central South University of Forestry and Technology, Changsha, 410004, Hunan, China.,Department of Soil Science of Temperate Ecosystems, Department of Agricultural Soil Science, University of Goettingen, 37077, Göttingen, Germany.,Institute of Physicochemical and Biological Problems in Soil Science, Russian Academy of Sciences, Pushchino, 142290, Russia
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18
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Briassoulis D, Mistriotis A. Key parameters in testing biodegradation of bio-based materials in soil. CHEMOSPHERE 2018; 207:18-26. [PMID: 29763763 DOI: 10.1016/j.chemosphere.2018.05.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 04/24/2018] [Accepted: 05/03/2018] [Indexed: 06/08/2023]
Abstract
Biodegradation of plastics in soil is currently tested by international standard testing methods (e.g. ISO 17556-12 or ASTM D5988-12). Although these testing methods have been developed for plastics, it has been shown in project KBBPPS that they can be extended also to lubricants with small modifications. Reproducibility is a critical issue regarding biodegradation tests in the laboratory. Among the main testing variables are the soil types and nutrients available (mainly nitrogen). For this reason, the effect of the soil type on the biodegradation rates of various bio-based materials (cellulose and lubricants) was tested for five different natural soil types (loam, loamy sand, clay, clay-loam, and silt-loam organic). It was shown that use of samples containing 1 g of C in a substrate of 300 g of soil with the addition of 0.1 g of N as nutrient strongly improves the reproducibility of the test making the results practically independent of the soil type with the exception of the organic soil. The sandy soil was found to need addition of higher amount of nutrients to exhibit similar biodegradation rates as those achieved with the other soil types. Therefore, natural soils can be used for Standard biodegradation tests of bio-based materials yielding reproducible results with the addition of appropriate nutrients.
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Affiliation(s)
- D Briassoulis
- Agricultural University of Athens, Natural Resources & Agricultural Engineering Department, 75, Iera Odos Str., 11855 Athens, Greece.
| | - A Mistriotis
- Agricultural University of Athens, Natural Resources & Agricultural Engineering Department, 75, Iera Odos Str., 11855 Athens, Greece.
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19
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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.
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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
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20
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Liu X, Xu Y, Li Z, Jiang S, Yao S, Wu R, An Y. A silica sands-based method for faithful analysis of microbial communities and DNA isolation from a wide range of species. Prep Biochem Biotechnol 2018; 48:378-382. [PMID: 29561226 DOI: 10.1080/10826068.2018.1451885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
A silica sands-based method has been developed to isolate high quality genomic DNAs from cells of animals, plants and microorganisms, such as Hemisalanx prognathus, Spinacia oleracea, Pichia pastoris, Bacillus licheniformis and Escherichia coli. To the best of our knowledge, no DNA isolation method has so wide application until now. In addition, this method and a commercially available kit were compared in analysis of microbial communities using high-throughput 16s rDNA sequencing. As a result, the silica sands-based method was found to be even more efficient in isolating genomic DNA from gram-positive bacteria than the kit, indicating that it would become a very valuable choice to faithfully reflect the composition of microbial communities.
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Affiliation(s)
- Xia Liu
- a Key Laboratory of Agricultural Biotechnology of Liaoning Province, College of Biosciences and Biotechnology , Shenyang Agricultural University , Shenyang , China
| | - Yongdong Xu
- a Key Laboratory of Agricultural Biotechnology of Liaoning Province, College of Biosciences and Biotechnology , Shenyang Agricultural University , Shenyang , China
| | - Zhi Li
- a Key Laboratory of Agricultural Biotechnology of Liaoning Province, College of Biosciences and Biotechnology , Shenyang Agricultural University , Shenyang , China
| | - Shengwei Jiang
- a Key Laboratory of Agricultural Biotechnology of Liaoning Province, College of Biosciences and Biotechnology , Shenyang Agricultural University , Shenyang , China.,b Qingshan Protection Bureau , Forestry Department of Liaoning Province , Shenyang , China
| | - Shuo Yao
- a Key Laboratory of Agricultural Biotechnology of Liaoning Province, College of Biosciences and Biotechnology , Shenyang Agricultural University , Shenyang , China
| | - Rina Wu
- c College of Food Science , Shenyang Agricultural University , Shenyang , China
| | - Yingfeng An
- a Key Laboratory of Agricultural Biotechnology of Liaoning Province, College of Biosciences and Biotechnology , Shenyang Agricultural University , Shenyang , China
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21
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Lee CR, Chi WJ, Lim JH, Dhakshnamoorthy V, Hong SK. Expression and characterization of the processive exo-β-1,4-cellobiohydrolase SCO6546 from Streptomyces coelicolor
A(3). J Basic Microbiol 2018; 58:310-321. [DOI: 10.1002/jobm.201700436] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 11/13/2017] [Accepted: 11/19/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Chang-Ro Lee
- Department of Bioscience and Bioinformatics; Yongin, Gyeoggido Korea
| | - Won-Jae Chi
- Biological and Genetic Resource Assessment Division; National Institute of Biological Resource; Incheon Korea
| | - Ju-Hyeon Lim
- Department of Bioscience and Bioinformatics; Yongin, Gyeoggido Korea
| | | | - Soon-Kwang Hong
- Department of Bioscience and Bioinformatics; Yongin, Gyeoggido Korea
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22
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Moreira-Soto RD, Sanchez E, Currie CR, Pinto-Tomás AA. Ultrastructural and microbial analyses of cellulose degradation in leaf-cutter ant colonies. MICROBIOLOGY-SGM 2017; 163:1578-1589. [PMID: 29034862 DOI: 10.1099/mic.0.000546] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Leaf-cutter ants (Atta and Acromyrmex) use fresh leaves to cultivate a mutualistic fungus (Leucoagaricus gongylophorus) for food in underground gardens. A new ant queen propagates the cultivar by taking a small fragment of fungus from her parent colony on her nuptial flight and uses it to begin her own colony. Recent research has shown that the ants' fungus gardens are colonized by symbiotic bacteria that perform important functions related to nitrogen fixation and have been implicated in contributing to plant biomass degradation. Here, we combine bacterial culturing in several media for counts and identification using the 16S rRNA gene with electron microscopy to investigate the process of cellulose degradation in the fungus garden and refuse dumps, and to assess the potential role of symbiotic bacteria. We show through electron microscopy that plant cell walls are visibly degraded in the bottom section of fungus gardens and refuse dumps, and that bacteria are more abundant in these sections. We also consistently isolated cellulolytic bacteria from all sections of fungus gardens. Finally, we show by culture-dependent and electron microscopy analysis that the fungus garden pellets carried by recently mated queens are colonized by fungus garden-associated bacteria. Taken together, our results indicate that cellulose is degraded in fungus gardens, and that fungus garden bacteria that may contribute to this deconstruction are vertically transmitted by new queens.
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Affiliation(s)
- Rolando Daniel Moreira-Soto
- Centro de Investigación en Estructuras Microscópicas, Universidad de Costa Rica, San José, Costa Rica.,Centro de Investigación en Enfermedades Tropicales, Universidad de Costa Rica, San José, Costa Rica
| | - Ethel Sanchez
- Centro de Investigación en Estructuras Microscópicas, Universidad de Costa Rica, San José, Costa Rica
| | - Cameron R Currie
- Great Lakes Bioenergy Research Center, Wisconsin, USA.,Department of Bacteriology, University of Wisconsin-Madison, Wisconsin, USA
| | - Adrian A Pinto-Tomás
- Centro de Investigación en Estructuras Microscópicas, Universidad de Costa Rica, San José, Costa Rica.,Departamento de Bioquímica, Facultad de Medicina, Universidad de Costa Rica, Costa Rica.,Centro de Investigación en Biología Celular y Molecular, Universidad de Costa Rica, San José, Costa Rica
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23
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Forest Soil Bacteria: Diversity, Involvement in Ecosystem Processes, and Response to Global Change. Microbiol Mol Biol Rev 2017; 81:81/2/e00063-16. [PMID: 28404790 DOI: 10.1128/mmbr.00063-16] [Citation(s) in RCA: 212] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The ecology of forest soils is an important field of research due to the role of forests as carbon sinks. Consequently, a significant amount of information has been accumulated concerning their ecology, especially for temperate and boreal forests. Although most studies have focused on fungi, forest soil bacteria also play important roles in this environment. In forest soils, bacteria inhabit multiple habitats with specific properties, including bulk soil, rhizosphere, litter, and deadwood habitats, where their communities are shaped by nutrient availability and biotic interactions. Bacteria contribute to a range of essential soil processes involved in the cycling of carbon, nitrogen, and phosphorus. They take part in the decomposition of dead plant biomass and are highly important for the decomposition of dead fungal mycelia. In rhizospheres of forest trees, bacteria interact with plant roots and mycorrhizal fungi as commensalists or mycorrhiza helpers. Bacteria also mediate multiple critical steps in the nitrogen cycle, including N fixation. Bacterial communities in forest soils respond to the effects of global change, such as climate warming, increased levels of carbon dioxide, or anthropogenic nitrogen deposition. This response, however, often reflects the specificities of each studied forest ecosystem, and it is still impossible to fully incorporate bacteria into predictive models. The understanding of bacterial ecology in forest soils has advanced dramatically in recent years, but it is still incomplete. The exact extent of the contribution of bacteria to forest ecosystem processes will be recognized only in the future, when the activities of all soil community members are studied simultaneously.
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Krzyśko-Łupicka T, Kręcidło Ł, Kręcidło M. The Comparison of Cellulolytic Activity of the Modified Soil Treated with Roundup. CHEMISTRY-DIDACTICS-ECOLOGY-METROLOGY 2017. [DOI: 10.1515/cdem-2016-0012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
The activity of soil microorganisms affects soil fertility and structure, what leads to satisfactory crop yields, thanks to changes in the decay of organic matter. Their activity may be impaired as a result of application by farmers both fertilizers and pesticides. The degradation of cellulosic biomass represents an important part of the carbon cycle within the biosphere. Cellulolitic microorganisms are responsible for this decomposition, as they produced the enzymes of the cellulase complex. The aim of the study was to compare the cellulolytic activity of soil with Roundup and modified using urea phosphate and / or manure. The pot experiment was conducted under laboratory conditions. The studied material was brown soil (pH of 5.5) fertilized with manure and/or urea phosphate. To each earthenware vase were fed 0.5 kg of the tested soil supplemented with 1% carboxymethyl cellulose. The cellulolytic activities of soil in different experimental variants were expressed in % of C using a colorimetric Petkov method. Modification of soil cellulolytic activity varied considerably depending on the additive manure and/or urea phosphate and Roundup. The lowest soil cellulolytic activity was observed in the presence of manure and urea phosphate, and the highest in the soil with manure and Roundup. The objects of Roundup independently of the other additives urea phosphate stimulate the activity of the cellulolytic microflora compared to objects containing only urea phosphate. The presence of manure in soil treated with Roundup clearly accelerated degradation of cellulose, what can be used in agriculture in the degradation of crop residues. The study shows that pesticides and fertilizers have a big impact on cellulolytic activity in soil. Changes in cellulolytic activity can be used as an ecological indicator of soil pollution level.
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Affiliation(s)
- Teresa Krzyśko-Łupicka
- Department of Biotechnology and Molecular Biology, University of Opole, ul. kard. B. Kominka 6a, 45-035 Opole, Poland , phone +48 77 401 60 57
| | - Łukasz Kręcidło
- Department of Biotechnology and Molecular Biology, University of Opole, ul. kard. B. Kominka 6a, 45-035 Opole, Poland , phone +48 77 401 60 57
| | - Magdalena Kręcidło
- Department of Biotechnology and Molecular Biology, University of Opole, ul. kard. B. Kominka 6a, 45-035 Opole, Poland , phone +48 77 401 60 57
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Long-Term Warming Alters Carbohydrate Degradation Potential in Temperate Forest Soils. Appl Environ Microbiol 2016; 82:6518-6530. [PMID: 27590813 PMCID: PMC5086546 DOI: 10.1128/aem.02012-16] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 08/19/2016] [Indexed: 11/20/2022] Open
Abstract
As Earth's climate warms, soil carbon pools and the microbial communities that process them may change, altering the way in which carbon is recycled in soil. In this study, we used a combination of metagenomics and bacterial cultivation to evaluate the hypothesis that experimentally raising soil temperatures by 5°C for 5, 8, or 20 years increased the potential for temperate forest soil microbial communities to degrade carbohydrates. Warming decreased the proportion of carbohydrate-degrading genes in the organic horizon derived from eukaryotes and increased the fraction of genes in the mineral soil associated with Actinobacteria in all studies. Genes associated with carbohydrate degradation increased in the organic horizon after 5 years of warming but had decreased in the organic horizon after warming the soil continuously for 20 years. However, a greater proportion of the 295 bacteria from 6 phyla (10 classes, 14 orders, and 34 families) isolated from heated plots in the 20-year experiment were able to depolymerize cellulose and xylan than bacterial isolates from control soils. Together, these findings indicate that the enrichment of bacteria capable of degrading carbohydrates could be important for accelerated carbon cycling in a warmer world.
IMPORTANCE The massive carbon stocks currently held in soils have been built up over millennia, and while numerous lines of evidence indicate that climate change will accelerate the processing of this carbon, it is unclear whether the genetic repertoire of the microbes responsible for this elevated activity will also change. In this study, we showed that bacteria isolated from plots subject to 20 years of 5°C of warming were more likely to depolymerize the plant polymers xylan and cellulose, but that carbohydrate degradation capacity is not uniformly enriched by warming treatment in the metagenomes of soil microbial communities. This study illustrates the utility of combining culture-dependent and culture-independent surveys of microbial communities to improve our understanding of the role changing microbial communities may play in soil carbon cycling under climate change.
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Cellulose and hemicellulose decomposition by forest soil bacteria proceeds by the action of structurally variable enzymatic systems. Sci Rep 2016; 6:25279. [PMID: 27125755 PMCID: PMC4850484 DOI: 10.1038/srep25279] [Citation(s) in RCA: 192] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 04/14/2016] [Indexed: 12/22/2022] Open
Abstract
Evidence shows that bacteria contribute actively to the decomposition of cellulose and hemicellulose in forest soil; however, their role in this process is still unclear. Here we performed the screening and identification of bacteria showing potential cellulolytic activity from litter and organic soil of a temperate oak forest. The genomes of three cellulolytic isolates previously described as abundant in this ecosystem were sequenced and their proteomes were characterized during the growth on plant biomass and on microcrystalline cellulose. Pedobacter and Mucilaginibacter showed complex enzymatic systems containing highly diverse carbohydrate-active enzymes for the degradation of cellulose and hemicellulose, which were functionally redundant for endoglucanases, β-glucosidases, endoxylanases, β-xylosidases, mannosidases and carbohydrate-binding modules. Luteibacter did not express any glycosyl hydrolases traditionally recognized as cellulases. Instead, cellulose decomposition was likely performed by an expressed GH23 family protein containing a cellulose-binding domain. Interestingly, the presence of plant lignocellulose as well as crystalline cellulose both trigger the production of a wide set of hydrolytic proteins including cellulases, hemicellulases and other glycosyl hydrolases. Our findings highlight the extensive and unexplored structural diversity of enzymatic systems in cellulolytic soil bacteria and indicate the roles of multiple abundant bacterial taxa in the decomposition of cellulose and other plant polysaccharides.
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López-Mondéjar R, Zühlke D, Větrovský T, Becher D, Riedel K, Baldrian P. Decoding the complete arsenal for cellulose and hemicellulose deconstruction in the highly efficient cellulose decomposer Paenibacillus O199. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:104. [PMID: 27186238 PMCID: PMC4867992 DOI: 10.1186/s13068-016-0518-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 05/04/2016] [Indexed: 05/11/2023]
Abstract
BACKGROUND The search for new enzymes and microbial strains to degrade plant biomass is one of the most important strategies for improving the conversion processes in the production of environment-friendly chemicals and biofuels. In this study, we report a new Paenibacillus isolate, O199, which showed the highest efficiency for cellulose deconstruction in a screen of environmental isolates. Here, we provide a detailed description of the complex multi-component O199 enzymatic system involved in the degradation of lignocellulose. RESULTS We examined the genome and the proteome of O199 grown on complex lignocellulose (wheat straw) and on microcrystalline cellulose. The genome contained 476 genes with domains assigned to carbohydrate-active enzyme (CAZyme) families, including 100 genes coding for glycosyl hydrolases (GHs) putatively involved in cellulose and hemicellulose degradation. Moreover, 31 % of these CAZymes were expressed on cellulose and 29 % on wheat straw. Proteomic analyses also revealed a complex and complete set of enzymes for deconstruction of cellulose (at least 22 proteins, including 4 endocellulases, 2 exocellulases, 2 cellobiohydrolases and 2 β-glucosidases) and hemicellulose (at least 28 proteins, including 5 endoxylanases, 1 β-xylosidase, 2 xyloglucanases, 2 endomannanases, 2 licheninases and 1 endo-β-1,3(4)-glucanase). Most of these proteins were secreted extracellularly and had numerous carbohydrate-binding domains (CBMs). In addition, O199 also secreted a high number of substrate-binding proteins (SBPs), including at least 42 proteins binding carbohydrates. Interestingly, both plant lignocellulose and crystalline cellulose triggered the production of a wide array of hydrolytic proteins, including cellulases, hemicellulases, and other GHs. CONCLUSIONS Our data provide an in-depth analysis of the complex and complete set of enzymes and accessory non-catalytic proteins-GHs, CBMs, transporters, and SBPs-implicated in the high cellulolytic capacity shown by this bacterial strain. The large diversity of hydrolytic enzymes and the extracellular secretion of most of them supports the use of Paenibacillus O199 as a candidate for second-generation technologies using paper or lignocellulosic agricultural wastes.
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Affiliation(s)
- Rubén López-Mondéjar
- />Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, v. v. i., Průmyslová 595, 252 42 Vestec, Czech Republic
| | - Daniela Zühlke
- />Institute of Microbiology, Ernst-Moritz-Arndt-University of Greifswald, Friedrich-Ludwig-Jahnstrasse 15, 17487 Greifswald, Germany
| | - Tomáš Větrovský
- />Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, v. v. i., Průmyslová 595, 252 42 Vestec, Czech Republic
| | - Dörte Becher
- />Institute of Microbiology, Ernst-Moritz-Arndt-University of Greifswald, Friedrich-Ludwig-Jahnstrasse 15, 17487 Greifswald, Germany
| | - Katharina Riedel
- />Institute of Microbiology, Ernst-Moritz-Arndt-University of Greifswald, Friedrich-Ludwig-Jahnstrasse 15, 17487 Greifswald, Germany
| | - Petr Baldrian
- />Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, v. v. i., Průmyslová 595, 252 42 Vestec, Czech Republic
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Lim JH, Lee CR, Dhakshnamoorthy V, Park JS, Hong SK. Molecular characterization ofStreptomyces coelicolorA(3) SCO6548 as a cellulose 1,4-β-cellobiosidase. FEMS Microbiol Lett 2015; 363:fnv245. [DOI: 10.1093/femsle/fnv245] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/21/2015] [Indexed: 12/21/2022] Open
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Characterization of Thermotolerant Chitinases Encoded by a Brevibacillus laterosporus Strain Isolated from a Suburban Wetland. Genes (Basel) 2015; 6:1268-82. [PMID: 26690223 PMCID: PMC4690040 DOI: 10.3390/genes6041268] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Revised: 11/20/2015] [Accepted: 11/27/2015] [Indexed: 11/16/2022] Open
Abstract
To isolate and characterize chitinases that can be applied with practical advantages, 57 isolates of chitin-degrading bacteria were isolated from the soil of a suburban wetland. 16S rRNA gene analysis revealed that the majority of these strains belonged to two genera, Paenibacillus and Brevibacillus. Taking thermostability into account, the chitinases (ChiA and ChiC) of a B. laterosporus strain were studied further. Ni-NTA affinity-purified ChiA and ChiC were optimally active at pH 7.0 and 6.0, respectively, and showed high temperature stability up to 55 °C. Kinetic analysis revealed that ChiC has a lower affinity and stronger catalytic activity toward colloidal chitin than ChiA. With their stability in a broad temperature range, ChiA and ChiC can be utilized for the industrial bioconversion of chitin wastes into biologically active products.
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Ding J, Zhang Y, Wang M, Sun X, Cong J, Deng Y, Lu H, Yuan T, Van Nostrand JD, Li D, Zhou J, Yang Y. Soil organic matter quantity and quality shape microbial community compositions of subtropical broadleaved forests. Mol Ecol 2015; 24:5175-85. [PMID: 26363284 DOI: 10.1111/mec.13384] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 09/05/2015] [Accepted: 09/09/2015] [Indexed: 11/27/2022]
Abstract
As two major forest types in the subtropics, broadleaved evergreen and broadleaved deciduous forests have long interested ecologists. However, little is known about their belowground ecosystems despite their ecological importance in driving biogeochemical cycling. Here, we used Illumina MiSeq sequencing targeting 16S rRNA gene and a microarray named GeoChip targeting functional genes to analyse microbial communities in broadleaved evergreen and deciduous forest soils of Shennongjia Mountain of Central China, a region known as 'The Oriental Botanic Garden' for its extraordinarily rich biodiversity. We observed higher plant diversity and relatively richer nutrients in the broadleaved evergreen forest than the deciduous forest. In odds to our expectation that plant communities shaped soil microbial communities, we found that soil organic matter quantity and quality, but not plant community parameters, were the best predictors of microbial communities. Actinobacteria, a copiotrophic phylum, was more abundant in the broadleaved evergreen forest, while Verrucomicrobia, an oligotrophic phylum, was more abundant in the broadleaved deciduous forest. The density of the correlation network of microbial OTUs was higher in the broadleaved deciduous forest but its modularity was smaller, reflecting lower resistance to environment changes. In addition, keystone OTUs of the broadleaved deciduous forest were mainly oligotrophic. Microbial functional genes associated with recalcitrant carbon degradation were also more abundant in the broadleaved deciduous forests, resulting in low accumulation of organic matters. Collectively, these findings revealed the important role of soil organic matter in shaping microbial taxonomic and functional traits.
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Affiliation(s)
- Junjun Ding
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Yuguang Zhang
- Institute of Forestry Ecology, Environment and Protection and the Key Laboratory of Forest Ecology and Environment of State Forestry Administration, the Chinese Academy of Forestry, Beijing, 100091, China
| | - Mengmeng Wang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Xin Sun
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Jing Cong
- Institute of Forestry Ecology, Environment and Protection and the Key Laboratory of Forest Ecology and Environment of State Forestry Administration, the Chinese Academy of Forestry, Beijing, 100091, China
| | - Ye Deng
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.,Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
| | - Hui Lu
- Institute of Forestry Ecology, Environment and Protection and the Key Laboratory of Forest Ecology and Environment of State Forestry Administration, the Chinese Academy of Forestry, Beijing, 100091, China
| | - Tong Yuan
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
| | - Joy D Van Nostrand
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
| | - Diqiang Li
- Institute of Forestry Ecology, Environment and Protection and the Key Laboratory of Forest Ecology and Environment of State Forestry Administration, the Chinese Academy of Forestry, Beijing, 100091, China
| | - Jizhong Zhou
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China.,Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA.,Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
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Ning C, Wang X, Li L, Zhu Y, Li M, Yu P, Zhou L, Zhou Z, Chen J, Tan G, Zhang Y, Wang Y, Mao C. Concentration ranges of antibacterial cations for showing the highest antibacterial efficacy but the least cytotoxicity against mammalian cells: implications for a new antibacterial mechanism. Chem Res Toxicol 2015; 28:1815-22. [PMID: 26258952 DOI: 10.1021/acs.chemrestox.5b00258] [Citation(s) in RCA: 136] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Antibacterial metal ions, such as Ag(+), Zn(2+) and Cu(2+), have been extensively used in medical implants and devices due to their strong broad spectrum of antibacterial activity. However, it is still a controversial issue as to whether they can show the desired antibacterial activity while being toxic to mammalian cells. It is very important to balance their antibacterial effectiveness with minimal damage to mammalian cells. Toward this end, this study is to identify the suitable concentrations of these three ions at which they can effectively kill two types of clinically relevant bacteria (Staphylococcus aureus (S. aureus) and Escherichia coli (E. coli)) but show no obvious cytotoxicity on fibroblasts. Such concentration ranges are found to be 2.5 × 10(-7) M-10(-6) M, 10(-5) M-10(-4) M, and 10(-5) M-10(-4) M for Ag(+), Zn(2+), and Cu(2+), respectively. Investigation of their antibacterial mechanism shows that these three metal ions all show antibacterial property through a mechanism of damaging bacterial cell membranes by the generation of reactive oxygen species but surprisingly preserving the integrity of bacterial genomic DNA. The encouraging results indicate that antibacterial metal ions with controlled concentrations can bring considerable benefits to biomedical applications.
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Affiliation(s)
- Chengyun Ning
- School of Materials Science and Engineering, South China University of Technology , Guangzhou 510641, China
| | - Xiaolan Wang
- School of Materials Science and Engineering, South China University of Technology , Guangzhou 510641, China
| | - Lihua Li
- Department of Orthopedics, Guangdong Key Lab of Orthopaedic Technology and Implant, Guangzhou General Hospital of Guangzhou Military Command , 111 Liuhua Road, Guangzhou 510010, China
| | - Ye Zhu
- Department of Chemistry & Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma , 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Mei Li
- Department of Orthopedics, Guangdong Key Lab of Orthopaedic Technology and Implant, Guangzhou General Hospital of Guangzhou Military Command , 111 Liuhua Road, Guangzhou 510010, China
| | - Peng Yu
- School of Materials Science and Engineering, South China University of Technology , Guangzhou 510641, China
| | - Lei Zhou
- School of Materials Science and Engineering, South China University of Technology , Guangzhou 510641, China
| | - Zhengnan Zhou
- School of Materials Science and Engineering, South China University of Technology , Guangzhou 510641, China
| | - Junqi Chen
- School of Materials Science and Engineering, South China University of Technology , Guangzhou 510641, China
| | - Guoxin Tan
- Institute of Chemical Engineering and Light Industry, Guangdong University of Technology , Guangzhou 510006, China
| | - Yu Zhang
- Department of Orthopedics, Guangdong Key Lab of Orthopaedic Technology and Implant, Guangzhou General Hospital of Guangzhou Military Command , 111 Liuhua Road, Guangzhou 510010, China
| | - Yingjun Wang
- School of Materials Science and Engineering, South China University of Technology , Guangzhou 510641, China
| | - Chuanbin Mao
- Department of Chemistry & Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma , 101 Stephenson Parkway, Norman, Oklahoma 73019, United States.,School of Materials Science and Engineering, Zhejiang University , Hangzhou, Zhejiang 310027, China
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Cellulolytic Bacteria Associated with the Gut of Dendroctonus armandi Larvae (Coleoptera: Curculionidae: Scolytinae). FORESTS 2014. [DOI: 10.3390/f5030455] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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