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Kimeklis AK, Gladkov GV, Orlova OV, Afonin AM, Gribchenko ES, Aksenova TS, Kichko AA, Pinaev AG, Andronov EE. The Succession of the Cellulolytic Microbial Community from the Soil during Oat Straw Decomposition. Int J Mol Sci 2023; 24:ijms24076342. [PMID: 37047311 PMCID: PMC10094526 DOI: 10.3390/ijms24076342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 03/24/2023] [Accepted: 03/27/2023] [Indexed: 03/30/2023] Open
Abstract
The process of straw decomposition is dynamic and is accompanied by the succession of the microbial decomposing community, which is driven by poorly understood interactions between microorganisms. Soil is a complex ecological niche, and the soil microbiome can serve as a source of potentially active cellulolytic microorganisms. Here, we performed an experiment on the de novo colonization of oat straw by the soil microbial community by placing nylon bags with sterilized oat straw in the pots filled with chernozem soil and incubating them for 6 months. The aim was to investigate the changes in decomposer microbiota during this process using conventional sequencing techniques. The bacterial succession during straw decomposition occurred in three phases: the early phase (first month) was characterized by high microbial activity and low diversity, the middle phase (second to third month) was characterized by low activity and low diversity, and the late phase (fourth to sixth months) was characterized by low activity and high diversity. Analysis of amplicon sequencing data revealed three groups of co-changing phylotypes corresponding to these phases. The early active phase was abundant in the cellulolytic members from Pseudomonadota, Bacteroidota, Bacillota, and Actinobacteriota for bacteria and Ascomycota for fungi, and most of the primary phylotypes were gone by the end of the phase. The second intermediate phase was marked by the set of phylotypes from the same phyla persisting in the community. In the mature community of the late phase, apart from the core phylotypes, non-cellulolytic members from Bdellovibrionota, Myxococcota, Chloroflexota, and Thermoproteota appeared. Full metagenome sequencing of the microbial community from the end of the middle phase confirmed that major bacterial and fungal members of this consortium had genes of glycoside hydrolases (GH) connected to cellulose and chitin degradation. The real-time analysis of the selection of these genes showed that their representation varied between phases, and this occurred under the influence of the host, and not the GH family factor. Our findings demonstrate that soil microbial community may act as an efficient source of cellulolytic microorganisms and that colonization of the cellulolytic substrate occurs in several phases, each characterized by its own taxonomic and functional profile.
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Affiliation(s)
- Anastasiia K. Kimeklis
- All-Russian Research Institute of Agricultural Microbiology, 196608 Saint Petersburg, Russia
- Department of Applied Ecology, Saint-Petersburg State University, 199034 Saint Petersburg, Russia
- Correspondence: (A.K.K.); (E.E.A.)
| | - Grigory V. Gladkov
- All-Russian Research Institute of Agricultural Microbiology, 196608 Saint Petersburg, Russia
| | - Olga V. Orlova
- All-Russian Research Institute of Agricultural Microbiology, 196608 Saint Petersburg, Russia
| | - Alexey M. Afonin
- All-Russian Research Institute of Agricultural Microbiology, 196608 Saint Petersburg, Russia
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, FI-70211 Kuopio, Finland
| | - Emma S. Gribchenko
- All-Russian Research Institute of Agricultural Microbiology, 196608 Saint Petersburg, Russia
| | - Tatiana S. Aksenova
- All-Russian Research Institute of Agricultural Microbiology, 196608 Saint Petersburg, Russia
| | - Arina A. Kichko
- All-Russian Research Institute of Agricultural Microbiology, 196608 Saint Petersburg, Russia
| | - Alexander G. Pinaev
- All-Russian Research Institute of Agricultural Microbiology, 196608 Saint Petersburg, Russia
| | - Evgeny E. Andronov
- All-Russian Research Institute of Agricultural Microbiology, 196608 Saint Petersburg, Russia
- Dokuchaev Soil Science Institute, 119017 Moscow, Russia
- Correspondence: (A.K.K.); (E.E.A.)
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Sinha D, Banerjee S, Mandal S, Basu A, Banerjee A, Balachandran S, Chandra Mandal N, Chaudhury S. Enhanced biogas production from Lantana camara via bioaugmentation of cellulolytic bacteria. BIORESOURCE TECHNOLOGY 2021; 340:125652. [PMID: 34332446 DOI: 10.1016/j.biortech.2021.125652] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 07/19/2021] [Accepted: 07/21/2021] [Indexed: 06/13/2023]
Abstract
A study was designed to isolate cellulolytic bacteria from termite-gut and soil, optimizing their cellulase production to enhance biogas generation, using Lantana camara as a substrate. Out of 57 bacteria screened, two isolates DSB1 and DSB12, showed significant cellulolytic activity. 16S rRNA based methods identified these isolates as Microbacterium sp. and Arthrobacter sp. respectively. Maximum cellulase activity of 1.26 ± 0.044 U/ml and 1.31 ± 0.052 U/ml for DSB1 and DSB12 was observed at pH 7 and 7.2 under 35⁰C and 37⁰C, respectively. The L. camara biomass substrate with cow dung as an inoculum, bioaugmented with DSB1 and DSB12 separately, was tested for biogas production, producing 950 l/kg and 980 l/kg VS biogas with 57% and 60% methane, respectively. DSB1 and DSB12 revealed as potent cellulase producers that can be harnessed in the anaerobic digester for biomass conversion practices for enhanced biogas production.
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Affiliation(s)
- Debasree Sinha
- Department of Environmental Studies, Siksha -Bhavana, Visva-Bharati, Santiniketan, West Bengal, 731235, India
| | - Sandipan Banerjee
- Mycology and Plant Pathology Laboratory, Department of Botany, Siksha-Bhavana, Visva-Bharati, Santiniketan, West Bengal, 731235, India
| | - Subhrangshu Mandal
- Department of Botany, Siksha-Bhavana, Visva-Bharati, Santiniketan, Birbhum, West Bengal, 731235, India
| | - Aman Basu
- Department of Environmental Studies, Siksha -Bhavana, Visva-Bharati, Santiniketan, West Bengal, 731235, India; Department of Biology, York University, Toronto, Ontario, Canada
| | - Aishiki Banerjee
- Department of Environmental Studies, Siksha -Bhavana, Visva-Bharati, Santiniketan, West Bengal, 731235, India
| | - Srinivasan Balachandran
- Department of Environmental Studies, Siksha -Bhavana, Visva-Bharati, Santiniketan, West Bengal, 731235, India
| | - Narayan Chandra Mandal
- Mycology and Plant Pathology Laboratory, Department of Botany, Siksha-Bhavana, Visva-Bharati, Santiniketan, West Bengal, 731235, India
| | - Shibani Chaudhury
- Department of Environmental Studies, Siksha -Bhavana, Visva-Bharati, Santiniketan, West Bengal, 731235, India.
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Droplet-based microfluidic platform for high-throughput screening of Streptomyces. Commun Biol 2021; 4:647. [PMID: 34059751 PMCID: PMC8166820 DOI: 10.1038/s42003-021-02186-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 05/05/2021] [Indexed: 12/20/2022] Open
Abstract
Streptomyces are one of the most important industrial microorganisms for the production of proteins and small-molecule drugs. Previously reported flow cytometry-based screening methods can only screen spores or protoplasts released from mycelium, which do not represent the filamentous stationary phase Streptomyces used in industrial cultivation. Here we show a droplet-based microfluidic platform to facilitate more relevant, reliable and rapid screening of Streptomyces mycelium, and achieved an enrichment ratio of up to 334.2. Using this platform, we rapidly characterized a series of native and heterologous constitutive promoters in Streptomyces lividans 66 in droplets, and efficiently screened out a set of engineered promoter variants with desired strengths from two synthetic promoter libraries. We also successfully screened out several hyperproducers of cellulases from a random S. lividans 66 mutant library, which had 69.2–111.4% greater cellulase production than the wild type. Our method provides a fast, simple, and powerful solution for the industrial engineering and screening of Streptomyces in more industry-relevant conditions. Streptomyces are an important filamentous bacterium genus in industry, but most of the high-throughput techniques so far can only separate spores or protoplasts. Tu et al. develop an encapsulating method that allows screening of Streptomyces in the filamentous, stationary phase.
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Han R, Ma Y, Xiao J, You L, Pedisić S, Liao L. The possible mechanism of the protective effect of a sulfated polysaccharide from Gracilaria Lemaneiformis against colitis induced by dextran sulfate sodium in mice. Food Chem Toxicol 2021; 149:112001. [PMID: 33482260 DOI: 10.1016/j.fct.2021.112001] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 11/02/2020] [Accepted: 01/14/2021] [Indexed: 02/05/2023]
Abstract
This study aimed to investigate the possible mechanism of the protective effect of a sulfated polysaccharide (SP) from Gracilaria Lemaneiformis against colitis induced by dextran sulfate sodium (DSS). Balb/c mice were gavaged with SP for four weeks, then colon tissue, cecal contents and feces were collected for further analysis. Results showed that SP was effective for inhibiting colon shortening and oedema forming. It could alleviate colonic inflammation via down-regulating the expression of tumor necrosis factor-α (TNF-α), interleukin (IL-6, IL-1β). Besides, it enhanced the intestinal barrier by up-regulating the expression of tight junction proteins Claudin-1 and Zonula occludens-1 (ZO-1) as well as Mucin (MUC-2). The increased expression of short chain fatty acid (SCFA) receptors including G protein-coupled receptor (GPR43, GPR109A) and olfactory receptor (Olfr78), and SCFA production in feces indicated that most of SCFA were absorbed in colon, which could play positive roles in ameliorating colitis. Furthermore, the results of gut microbiota showed that Enterorhabdus, Desulfovibrio, Alistipes, Bacteroides acidifaciens had closest correlations with the strongest protective effects against colitis. Therefore, SP could alleviate DSS-induced colitis via enhancing intestinal barrier, reducing inflammation, activating SCFA receptors and regulating gut microbiota. It could be developed as functional foods which is good for gut health.
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Affiliation(s)
- Rui Han
- School of Food Science and Engineering, South China University of Technology, 381 Wushan Road, Guangzhou, 510640, Guangdong, China
| | - Yongxuan Ma
- Guangzhou Liheng Clinical Nutrition Co.LTD, 133 Yiheng Road, Guangzhou, 510610, Guangdong, China
| | - Jianbo Xiao
- Institute of Chinese Medical Sciences, State Key Laboratory of Quality Control in Chinese Medicine, University of Macau, Macau SAR, China
| | - Lijun You
- School of Food Science and Engineering, South China University of Technology, 381 Wushan Road, Guangzhou, 510640, Guangdong, China; Overseas Expertise Introduction Center for Discipline Innovation of Food Nutrition and Human Health (111 Center), Guangzhou, 510640, Guangdong, China.
| | - Sandra Pedisić
- Faculty of Food Technology and Biotechnology, University of Zagreb, Prolaz Kasandrića 6, 23000, Zadar, Croatia
| | - Lan Liao
- Department of Food Science, College of Food Science and Technology, Foshan University, Foshan, Guangdong, 528000, China
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Banerjee S, Maiti TK, Roy RN. Production, purification, and characterization of cellulase from Acinetobacter junii GAC 16.2, a novel cellulolytic gut isolate of Gryllotalpa africana, and its effects on cotton fiber and sawdust. ANN MICROBIOL 2020. [DOI: 10.1186/s13213-020-01569-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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Thakur V, Kumar V, Kumar S, Singh D. Diverse culturable bacterial communities with cellulolytic potential revealed from pristine habitat in Indian trans-Himalaya. Can J Microbiol 2018; 64:798-808. [DOI: 10.1139/cjm-2017-0754] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The Pangi–Chamba Himalaya (PCH) region is very pristine, unique, and virgin niche for bioresource exploration. In the current study, for the first time, the bacterial diversity of this region was investigated for potential cellulose degraders. A total of 454 pure bacterial isolates were obtained from diverse sites in the PCH region, and 111 isolates were further selected for 16S rDNA characterization based on ARDRA grouping. The identified bacteria belonged to 28 genera representing four phyla: Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes. Pseudomonas was most abundant genus, followed by Bacillus, Geobacillus, Arthrobacter, Paenibacillus, and Flavobacterium. In addition, six putative novel bacteria (based on 16S rDNA sequence similarity) and thermophiles from non-thermogenic sites were also reported for the first time. Screening for cellulose degradation ability on carboxymethyl cellulose plates revealed that 70.92% of bacteria were cellulolytic. The current study reports diverse bacterial genera (Arthrobacter, Paenibacillus, Chryseobacterium, Pedobacter, Streptomyces, Agromyces, Flavobacterium, and Pseudomonas) with high capacity for cellulose hydrolysis and cellulolytic functionality at wide pH and temperature not previously reported in the literature. Diverse bacterial genera with high cellulolytic activity in broad pH and temperature range provide opportunity to develop a bioprocess for efficient pretreatment of lignocellulosic biomass, which is currently being investigated.
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Affiliation(s)
- Vikas Thakur
- Biotechnology Division, CSIR – Institute of Himalayan Bioresource Technology, Post Box No. 6, Palampur-176 061, Himachal Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR – Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
| | - Vijay Kumar
- Biotechnology Division, CSIR – Institute of Himalayan Bioresource Technology, Post Box No. 6, Palampur-176 061, Himachal Pradesh, India
| | - Sanjay Kumar
- Biotechnology Division, CSIR – Institute of Himalayan Bioresource Technology, Post Box No. 6, Palampur-176 061, Himachal Pradesh, India
| | - Dharam Singh
- Biotechnology Division, CSIR – Institute of Himalayan Bioresource Technology, Post Box No. 6, Palampur-176 061, Himachal Pradesh, India
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Evaluation of wild herbivore faeces from South Africa as a potential source of hydrolytically active microorganisms. SPRINGERPLUS 2016; 5:118. [PMID: 26900540 PMCID: PMC4746204 DOI: 10.1186/s40064-016-1739-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 01/18/2016] [Indexed: 11/10/2022]
Abstract
This study assessed faecal matter from three indigenous South African herbivores-zebra, giraffe and impala-as a potential source for hydrolytically active aerobic and facultatively anaerobic bacteria. Herbivore droppings were collected freshly in a local nature reserve in Pietermaritzburg, South Africa. Soil samples adjacent to faecal collection sites and faeces from a domestic herbivore, the Nguni cow, were included as controls. Hydrolase and dehydrogenase activity in faecal matter and soil samples were measured by the fluorescein diacetate and the triphenyltetrazolium chloride assay. Viable counts and counts for amylase, cellulase, esterase and protease producers were established using plate count agar and solid media containing cellulose, skim milk, starch and Tween 80. Zebra droppings produced the highest hydrolase and dehydrogenase activity. Faecal matter of the three indigenous herbivores generally produced higher hydrolytic activity than Nguni cow faeces and soil controls, thereby confirming that these materials are potential targets for hydrolytic enzyme mining.
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Manfredi AP, Pisa JH, Valdeón DH, Perotti NI, Martínez MA. Synergistic Effect of Simple Sugars and Carboxymethyl Cellulose on the Production of a Cellulolytic Cocktail from Bacillus sp. AR03 and Enzyme Activity Characterization. Appl Biochem Biotechnol 2016; 179:16-32. [DOI: 10.1007/s12010-015-1976-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 12/29/2015] [Indexed: 11/27/2022]
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Paudel YP, Qin W. Characterization of Novel Cellulase-producing Bacteria Isolated From Rotting Wood Samples. Appl Biochem Biotechnol 2015; 177:1186-98. [DOI: 10.1007/s12010-015-1806-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 08/10/2015] [Indexed: 11/30/2022]
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Tun HM, Mauroo NF, Yuen CS, Ho JCW, Wong MT, Leung FCC. Microbial diversity and evidence of novel homoacetogens in the gut of both geriatric and adult giant pandas (Ailuropoda melanoleuca). PLoS One 2014; 9:e79902. [PMID: 24475017 PMCID: PMC3901650 DOI: 10.1371/journal.pone.0079902] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Accepted: 09/25/2013] [Indexed: 12/20/2022] Open
Abstract
Recent studies have described the bacterial community residing in the guts of giant pandas, together with the presence of lignocellulolytic enzymes. However, a more comprehensive understanding of the intestinal microbial composition and its functional capacity in giant pandas remains a major goal. Here, we conducted a comparison of bacterial, fungal and homoacetogenic microbial communities from fecal samples taken from two geriatric and two adult captive giant pandas. 16S rDNA amplicon pyrosequencing revealed that Firmicutes and Proteobacteria are the most abundant microbiota in both geriatric and adult giant pandas. However, members of phylum Actinobacteria found in adult giant pandas were absent in their geriatric counterparts. Similarly, ITS1 amplicon pyrosequencing identified developmental changes in the most abundant fungal classes from Sordariomycetes in adult pandas to Saccharomycetes in geriatric pandas. Geriatric pandas exhibited significantly higher abundance of a potential probiotic fungus (Candida tropicalis) as compared to adult pandas, indicating their importance in the normal digestive physiology of aged pandas. Our study also reported the presence of a lignocellulolytic white-rot fungus, Perenniporia medulla-panis, and the evidence of novel homoacetogens residing in the guts of giant pandas.
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Affiliation(s)
- Hein Min Tun
- School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong SAR
| | - Nathalie France Mauroo
- Department of Pathology, The University of Hong Kong, Hong Kong, Hong Kong SAR
- Hong Kong Wildlife Health Foundation, Hong Kong, Hong Kong SAR
| | - Chan San Yuen
- Clinical Laboratory, Veterinary Center, Ocean Park Corporation, Hong Kong, Hong Kong SAR
| | - John Chi Wang Ho
- School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong SAR
| | - Mabel Ting Wong
- School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong SAR
| | - Frederick Chi-Ching Leung
- School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong SAR
- Bioinformatics Center, Nanjing Agricultural University, Nanjing, China
- * E-mail:
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Sadhu S, Ghosh PK, De TK, Maiti TK. Optimization of Cultural Condition and Synergistic Effect of Lactose with Carboxymethyl Cellulose on Cellulase Production by <i>Bacillus</i> sp. Isolated from Fecal Matter of Elephant (<i>Elephas maximus</i>). ACTA ACUST UNITED AC 2013. [DOI: 10.4236/aim.2013.33040] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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