1
|
Feigl V, Medgyes-Horváth A, Kari A, Török Á, Bombolya N, Berkl Z, Farkas É, Fekete-Kertész I. The potential of Hungarian bauxite residue isolates for biotechnological applications. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2024; 41:e00825. [PMID: 38225962 PMCID: PMC10788403 DOI: 10.1016/j.btre.2023.e00825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/14/2023] [Accepted: 12/19/2023] [Indexed: 01/17/2024]
Abstract
Bauxite residue (red mud) is considered an extremely alkaline and salty environment for the biota. We present the first attempt to isolate, identify and characterise microbes from Hungarian bauxite residues. Four identified bacterial strains belonged to the Bacilli class, one each to the Actinomycetia, Gammaproteobacteria, and Betaproteobacteria classes, and two to the Alphaproteobacteria class. All three identified fungi strains belonged to the Ascomycota division. Most strains tolerated pH 8-10 and salt content at 5-7% NaCl concentration. Alkalihalobacillus pseudofirmus BRHUB7 and Robertmurraya beringensis BRHUB9 can be considered halophilic and alkalitolerant. Priestia aryabhattai BRHUB2, Penicillium chrysogenum BRHUF1 and Aspergillus sp. BRHUF2 are halo- and alkalitolerant strains. Most strains produced siderophores and extracellular polymeric substances, could mobilise phosphorous, and were cellulose degraders. These strains and their enzymes are possible candidates for biotechnological applications in processes requiring extreme conditions, e.g. bioleaching of critical raw materials and rehabilitation of alkaline waste deposits.
Collapse
Affiliation(s)
- Viktória Feigl
- Budapest University of Technology and Economics, Faculty of Chemical Technology and Biotechnology, Department of Applied Biotechnology and Food Science, Műegyetem Rkp 3., Budapest 1111, Hungary
| | - Anna Medgyes-Horváth
- ELTE Eötvös Loránd University, Department of Physics of Complex Systems, Pázmány P. s. 1A, Budapest 1117, Hungary
| | - András Kari
- ELTE Eötvös Loránd University, Department of Microbiology, Pázmány P. s. 1A, Budapest 1117, Hungary
| | - Ádám Török
- Budapest University of Technology and Economics, Faculty of Chemical Technology and Biotechnology, Department of Applied Biotechnology and Food Science, Műegyetem Rkp 3., Budapest 1111, Hungary
| | - Nelli Bombolya
- Budapest University of Technology and Economics, Faculty of Chemical Technology and Biotechnology, Department of Applied Biotechnology and Food Science, Műegyetem Rkp 3., Budapest 1111, Hungary
| | - Zsófia Berkl
- Budapest University of Technology and Economics, Faculty of Chemical Technology and Biotechnology, Department of Applied Biotechnology and Food Science, Műegyetem Rkp 3., Budapest 1111, Hungary
| | - Éva Farkas
- Budapest University of Technology and Economics, Faculty of Chemical Technology and Biotechnology, Department of Applied Biotechnology and Food Science, Műegyetem Rkp 3., Budapest 1111, Hungary
- Norwegian Institute of Bioeconomy Research (NIBIO), Division of Environment and Natural Resources, Department of Biogeochemistry and Soil Quality, Høgskoleveien 7, 1432 Ås, Norway
| | - Ildikó Fekete-Kertész
- Budapest University of Technology and Economics, Faculty of Chemical Technology and Biotechnology, Department of Applied Biotechnology and Food Science, Műegyetem Rkp 3., Budapest 1111, Hungary
| |
Collapse
|
2
|
Yadav P, Das J, Sundharam SS, Krishnamurthi S. Analysis of Culturable Bacterial Diversity of Pangong Tso Lake via a 16S rRNA Tag Sequencing Approach. Microorganisms 2024; 12:397. [PMID: 38399801 PMCID: PMC10892101 DOI: 10.3390/microorganisms12020397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/01/2024] [Accepted: 01/03/2024] [Indexed: 02/25/2024] Open
Abstract
The Pangong Tso lake is a high-altitude freshwater habitat wherein the resident microbes experience unique selective pressures, i.e., high radiation, low nutrient content, desiccation, and temperature extremes. Our study attempts to analyze the diversity of culturable bacteria by applying a high-throughput amplicon sequencing approach based on long read technology to determine the spectrum of bacterial diversity supported by axenic media. The phyla Pseudomonadota, Bacteriodetes, and Actinomycetota were retrieved as the predominant taxa in both water and sediment samples. The genera Hydrogenophaga and Rheinheimera, Pseudomonas, Loktanella, Marinomonas, and Flavobacterium were abundantly present in the sediment and water samples, respectively. Low nutrient conditions supported the growth of taxa within the phyla Bacteriodetes, Actinomycetota, and Cyanobacteria and were biased towards the selection of Pseudomonas, Hydrogenophaga, Bacillus, and Enterococcus spp. Our study recommends that media formulations can be finalized after analyzing culturable diversity through a high-throughput sequencing effort to retrieve maximum species diversity targeting novel/relevant taxa.
Collapse
Affiliation(s)
- Pooja Yadav
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sec-39A, Chandigarh 160036, India; (P.Y.); (J.D.); (S.S.S.)
| | - Joyasree Das
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sec-39A, Chandigarh 160036, India; (P.Y.); (J.D.); (S.S.S.)
| | - Shiva S. Sundharam
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sec-39A, Chandigarh 160036, India; (P.Y.); (J.D.); (S.S.S.)
- Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Ghaziabad 201002, India
| | - Srinivasan Krishnamurthi
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sec-39A, Chandigarh 160036, India; (P.Y.); (J.D.); (S.S.S.)
- Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Ghaziabad 201002, India
| |
Collapse
|
3
|
Cui S, Du J, Zhu L, Xin D, Xin Y, Zhang J. Analysis of Microbial Diversity in South Shetland Islands and Antarctic Peninsula Soils Based on Illumina High-Throughput Sequencing and Cultivation-Dependent Techniques. Microorganisms 2023; 11:2517. [PMID: 37894176 PMCID: PMC10609098 DOI: 10.3390/microorganisms11102517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/04/2023] [Accepted: 10/06/2023] [Indexed: 10/29/2023] Open
Abstract
To assess the diversity of bacterial taxa in Antarctic soils and obtain novel microbial resources, 15 samples from 3 sampling sites (DIS5, GWS7, FPS10) of South Shetland Islands and 2 sampling sites (APS18, CIS17) of Antarctic Peninsula were collected. High-throughput sequencing (HTS) of 16S rRNA genes within these samples was conducted on an Illumina Miseq platform. A total of 140,303 16S rRNA gene reads comprising 802 operational taxonomic units (OTUs) were obtained. After taxonomic classification, 25 phyla, 196 genera, and a high proportion of unidentified taxa were detected, among which seven phyla and 99 genera were firstly detected in Antarctica. The bacterial communities were dominated by Actinomycetota (40.40%), Pseudomonadota (17.14%), Bacteroidota (10.55%) and Chloroflexota (10.26%). Based on the HTS analyses, cultivation-dependent techniques were optimized to identify the cultivable members. A total of 30 different genera including 91 strains were obtained, the majority of which has previously been reported from Antarctica. However, for the genera Microterricola, Dyadobacter, Filibacter, Duganella, Ensifer, Antarcticirhabdus and Microvirga, this is the first report in Antarctica. In addition, seven strains represented novel taxa, two of which were psychropoilic and could be valuable resources for further research of cold-adaptability and their ecological significance in Antarctica.
Collapse
Affiliation(s)
- Siqi Cui
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing 100081, China; (S.C.); (J.D.); (L.Z.); (D.X.)
| | - Jie Du
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing 100081, China; (S.C.); (J.D.); (L.Z.); (D.X.)
| | - Lin Zhu
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing 100081, China; (S.C.); (J.D.); (L.Z.); (D.X.)
| | - Di Xin
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing 100081, China; (S.C.); (J.D.); (L.Z.); (D.X.)
| | - Yuhua Xin
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China;
| | - Jianli Zhang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing 100081, China; (S.C.); (J.D.); (L.Z.); (D.X.)
| |
Collapse
|
4
|
Chauhan M, Kimothi A, Sharma A, Pandey A. Cold adapted Pseudomonas: ecology to biotechnology. Front Microbiol 2023; 14:1218708. [PMID: 37529326 PMCID: PMC10388556 DOI: 10.3389/fmicb.2023.1218708] [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: 05/08/2023] [Accepted: 06/26/2023] [Indexed: 08/03/2023] Open
Abstract
The cold adapted microorganisms, psychrophiles/psychrotolerants, go through several modifications at cellular and biochemical levels to alleviate the influence of low temperature stress conditions. The low temperature environments depend on these cold adapted microorganisms for various ecological processes. The ability of the microorganisms to function in cold environments depends on the strategies directly associated with cell metabolism, physicochemical constrains, and stress factors. Pseudomonas is one among such group of microorganisms which is predominant in cold environments with a wide range of ecological and biotechnological applications. Bioformulations of Pseudomonas spp., possessing plant growth promotion and biocontrol abilities for application under low temperature environments, are well documented. Further, recent advances in high throughput sequencing provide essential information regarding the prevalence of Pseudomonas in rhizospheres and their role in plant health. Cold adapted species of Pseudomonas are also getting recognition for their potential in biodegradation and bioremediation of environmental contaminants. Production of enzymes and bioactive compounds (primarily as an adaptation mechanism) gives way to their applications in various industries. Exopolysaccharides and various biotechnologically important enzymes, produced by cold adapted species of Pseudomonas, are making their way in food, textiles, and pharmaceuticals. The present review, therefore, aims to summarize the functional versatility of Pseudomonas with particular reference to its peculiarities along with the ecological and biotechnological applications.
Collapse
Affiliation(s)
- Mansi Chauhan
- Department of Microbiology, Graphic Era (Deemed to be University), Dehradun, Uttarakhand, India
| | - Ayushi Kimothi
- Department of Microbiology, Graphic Era (Deemed to be University), Dehradun, Uttarakhand, India
| | - Avinash Sharma
- National Centre for Cell Science, Pune, Maharashtra, India
| | - Anita Pandey
- Department of Biotechnology, Graphic Era (Deemed to be University), Dehradun, Uttarakhand, India
| |
Collapse
|
5
|
Lyng M, Kovács ÁT. Frenemies of the soil: Bacillus and Pseudomonas interspecies interactions. Trends Microbiol 2023:S0966-842X(23)00050-1. [PMID: 36878770 DOI: 10.1016/j.tim.2023.02.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 02/10/2023] [Accepted: 02/13/2023] [Indexed: 03/07/2023]
Abstract
Bacillus and Pseudomonas ubiquitously occur in natural environments and are two of the most intensively studied bacterial genera in the soil. They are often coisolated from environmental samples, and as a result, several studies have experimentally cocultured bacilli and pseudomonads to obtain emergent properties. Even so, the general interaction between members of these genera is virtually unknown. In the past decade, data on interspecies interactions between natural isolates of Bacillus and Pseudomonas has become more detailed, and now, molecular studies permit mapping of the mechanisms behind their pairwise ecology. This review addresses the current knowledge about microbe-microbe interactions between strains of Bacillus and Pseudomonas and discusses how we can attempt to generalize the interaction on a taxonomic and molecular level.
Collapse
Affiliation(s)
- Mark Lyng
- Bacterial Interactions and Evolution group, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby 2800, Denmark
| | - Ákos T Kovács
- Bacterial Interactions and Evolution group, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby 2800, Denmark; Institute of Biology, Leiden University, Leiden, The Netherlands.
| |
Collapse
|
6
|
Cold-Active Enzymes and Their Potential Industrial Applications-A Review. Molecules 2022; 27:molecules27185885. [PMID: 36144621 PMCID: PMC9501442 DOI: 10.3390/molecules27185885] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/07/2022] [Accepted: 09/08/2022] [Indexed: 11/17/2022] Open
Abstract
More than 70% of our planet is covered by extremely cold environments, nourishing a broad diversity of microbial life. Temperature is the most significant parameter that plays a key role in the distribution of microorganisms on our planet. Psychrophilic microorganisms are the most prominent inhabitants of the cold ecosystems, and they possess potential cold-active enzymes with diverse uses in the research and commercial sectors. Psychrophiles are modified to nurture, replicate, and retain their active metabolic activities in low temperatures. Their enzymes possess characteristics of maximal activity at low to adequate temperatures; this feature makes them more appealing and attractive in biotechnology. The high enzymatic activity of psychrozymes at low temperatures implies an important feature for energy saving. These enzymes have proven more advantageous than their mesophilic and thermophilic counterparts. Therefore, it is very important to explore the efficiency and utility of different psychrozymes in food processing, pharmaceuticals, brewing, bioremediation, and molecular biology. In this review, we focused on the properties of cold-active enzymes and their diverse uses in different industries and research areas. This review will provide insight into the areas and characteristics to be improved in cold-active enzymes so that potential and desired enzymes can be made available for commercial purposes.
Collapse
|
7
|
Das S, Verma S, Choudhary P, Singh R, Saxena AK. Deciphering the genetic and functional diversity of cultivable bacteria from chasmophytic pigweed ( Chenopodium album) from Tsomoriri, Ladakh, India. 3 Biotech 2022; 12:242. [PMID: 36032512 PMCID: PMC9399335 DOI: 10.1007/s13205-022-03278-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 07/26/2022] [Indexed: 11/01/2022] Open
Abstract
Chasmophytes are a group of diverse plants growing on cracks and crevices of rocks. They survive under nutrient and water-limited conditions. Microorganisms associated with chasmophytes may play a critical role in their survival. In the present study, 263 bacterial isolates were obtained from chasmophytic wild Chenopodium collected from Tsomoriri, Ladakh. Members of Enterobacter, Pseudomonas, Pantoea, and Alcaligenes comprised ~ 90% of the Gram-negative bacteria, while among Gram-positive, Bacillus, Solibacillus, Fictibacillus, Microbacterium, and Micrococcus were most abundant. When evaluated for various plant growth-promoting traits, 36 bacteria could solubilize insoluble phosphate, 10 bacteria could release potassium from silicate minerals, and 25 bacteria could solubilize ZnO, while 124 bacteria produced siderophores. ACC deaminase activity was present in 31 isolates, while 46 bacteria could produce IAA (10.40-232.0 μg/mL). Furthermore, more than 64% of the isolates could grow at 50 °C, while ~ 60% could grow at 4 °C. Similarly, ~ 50% isolates were able to grow with > 1.7 M NaCl and ~ 70% could grow under high osmolarity (~ 67 mOsmol/L). The ability of these microorganisms to grow under such a wide range of temperature, salinity, and osmolarity offers adaptive advantage to colonize plants surviving under harsh environmental conditions. A large number (30-49%) of these isolates could produce acids from various sugars and sugar alcohols which is crucial to release mineral nutrients trapped in the rocks. The results indicated that genetically and functionally diverse microflora associated with wild Chenopodium might be helping these plants to effectively mine nutrients and water under extreme conditions. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03278-0.
Collapse
Affiliation(s)
- Sudipta Das
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Mau, Uttar Pradesh India
- Amity Institute of Microbial Technology, Amity University, Noida, Uttar Pradesh India
| | - Shaloo Verma
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Mau, Uttar Pradesh India
| | - Prassan Choudhary
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Mau, Uttar Pradesh India
| | - Rajni Singh
- Amity Institute of Microbial Technology, Amity University, Noida, Uttar Pradesh India
| | - Anil Kumar Saxena
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Mau, Uttar Pradesh India
| |
Collapse
|
8
|
Cozorici D, Măciucă RA, Stancu C, Tihăuan BM, Uță RB, Codrea CI, Matache R, Pop CE, Wolff R, Fendrihan S. Microbial Contamination and Survival Rate on Different Types of Banknotes. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19074310. [PMID: 35409990 PMCID: PMC8998619 DOI: 10.3390/ijerph19074310] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 03/28/2022] [Accepted: 03/29/2022] [Indexed: 12/19/2022]
Abstract
In the COVID-19 pandemic context, numerous concerns have been raised regarding the hygienic status of certain objects we interact with on a daily basis, and especially cash money and their potential to harbor and transmit pathogenic bacteria. Therefore, in the present study, we analyzed different currency bills represented by British pounds (5 £, 10 £ and 20 £), Romanian lei (1 leu, 5 lei and 10 lei), U.S. dollars (1 $, 5 $ and 10 $) and Euros (5 €, 10 € and 20 €) in order to evaluate the bacterial survival rate and bacterial adherence. We used five reference microorganisms by American Type Culture Collection (ATCC, Manassas, VA, USA): Staphylococcus aureus ATCC 6538, Escherichia coli ATCC 8739, Enterococcus sp. ATCC 19952, Salmonella enterica subsp. enterica serovar Typhi ATCC 6539, and Listeria monocytogenes ATCC 7644. Microorganisms were selected in accordance with the criteria of prevalence, pathogenicity, opportunism, and incidence. However, Maldi-TOF analysis from samples taken from the banknotes revealed only a few of the common pathogens that are traditionally thought to be found on banknotes. Some of the most important factors for the survival of pathogenic agents on surfaces are the presence of organic matter, temperature and humidity. Our data showed that Salmonella enterica survived 72 h on every banknote tested, while L. monocytogenes tended to improve persistence in humid conditions. Survival rate is also influenced by the substrate composition, being lower for polymer-based banknotes especially for Salmonella enterica, Listeria monocytogenes and Enterococcus sp. The adherence of bacterial strains was lower for polymer-based banknotes British pounds and Romanian Leu, in contrast to the cotton-based U.S dollars and Euro banknotes. The risk of bacterial contamination from the banknote bills is high as indicated by both a strong survival capacity and low adherence of tested bacteria with differences between the two types of materials used for the tested banknotes.
Collapse
Affiliation(s)
- Derniza Cozorici
- Non-Governmental Research Organization Biologic, 14 Schitului Str., 032044 Bucharest, Romania or (C.S.); (R.B.U.); (S.F.)
- Department of Bioengineering and Biotechnologies, Faculty of Medical Engineering, University Politehnica of Bucharest, 011061 Bucharest, Romania;
| | - Roxana-Alexandra Măciucă
- Non-Governmental Research Organization Biologic, 14 Schitului Str., 032044 Bucharest, Romania or (C.S.); (R.B.U.); (S.F.)
- Faculty of Biology, University of Bucharest, 91–95 Splaiul Independenței, 050095 Bucharest, Romania;
| | - Costel Stancu
- Non-Governmental Research Organization Biologic, 14 Schitului Str., 032044 Bucharest, Romania or (C.S.); (R.B.U.); (S.F.)
| | - Bianca-Maria Tihăuan
- Research Institute of the University of Bucharest—ICUB, 91-95 Splaiul Independenței, 050567 Bucharest, Romania;
- Research & Development for Advanced Biotechnologies and Medical Devices, SC Sanimed International Impex SRL, 087040 Călugăreni, Romania
| | - Robert Bogdan Uță
- Non-Governmental Research Organization Biologic, 14 Schitului Str., 032044 Bucharest, Romania or (C.S.); (R.B.U.); (S.F.)
| | - Cosmin Iulian Codrea
- “Ilie Murgulescu” Institute of Physical Chemistry, Romanian Academy, 202 Splaiul Independentei, 060021 Bucharest, Romania;
- Department of Science and Engineering of Oxide Materials and Nanomaterials, Faculty of Applied Chemistry and Materials Science, University Politehnica of Bucharest, 060042 Bucharest, Romania
| | - Răzvan Matache
- National Institute for Research and Development in Environmental Protection, 294 Splaiul Independentei, 060031 Bucharest, Romania;
| | - Cristian-Emilian Pop
- Non-Governmental Research Organization Biologic, 14 Schitului Str., 032044 Bucharest, Romania or (C.S.); (R.B.U.); (S.F.)
- Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Bucharest, 91-95 Splaiul Independenței, 050095 Bucharest, Romania
- Correspondence:
| | - Robert Wolff
- College of Nursing and Public Health, South University, 9 Science Ct., Columbia, SC 29203, USA;
| | - Sergiu Fendrihan
- Non-Governmental Research Organization Biologic, 14 Schitului Str., 032044 Bucharest, Romania or (C.S.); (R.B.U.); (S.F.)
- Faculty of Medicine, “Vasile Goldis” University, Revoluției Blvd. 94, 310025 Arad, Romania
| |
Collapse
|
9
|
Yanti NA. Phenotypic Characterization and Identification of Potential L-Asparaginase-Producing Thermohalophilic Bacteria from Wawolesea Hot Spring, North Konawe, Southeast Sulawesi, Indonesia. Pak J Biol Sci 2022; 25:1021-1032. [PMID: 36591934 DOI: 10.3923/pjbs.2022.1021.1032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
<b>Background and Objective:</b> L-asparaginase-producing thermohalophilic bacteria have the potential of producing an enzyme tolerant to high heat and salt levels. This enzyme, L-asparaginase, can be used as a biological agent for the cancer therapy of acute lymphoblastic leukemia and melanosarcoma as it has a specific ability to inhibit the formation of nutrients for cancer cells. This enzyme is also used effectively in food industries operating at high temperatures due to its ability to reduce acrylamide, a trigger of cancer cells. This study sought to figure out the phenotypic characters of and identify potential L-asparaginase-producing thermohalophilic bacteria from Wawolesea Hot Spring, North Konawe, Southeast Sulawesi. <b>Materials and Methods:</b> The characterization conducted on potential L-asparaginase-producing thermohalophilic bacterial isolates consisted of the following: Colony morphological characterization, covering the shapes, edges, internal structures, elevations and colours of the colonies, cell morphological characterization, covering gram staining, endospore formation and motility, biochemical characterization, covering catalase, Methyl Red and Voges Proskauer (MR-VP), gelatin hydrolysis, citrate, indole and carbohydrate fermentation tests and physiological characterization, covering pH effect, salinity, oxygen demand and temperature effect tests. Bacterial isolate identification was carried out in two stages, namely phenetic identification based on the phenotypic characterization data determine through a preliminary identification and numeric-phenetic identification. <b>Results:</b> The characterization results showed that the bacterial isolates AAT 1.4, AAT 3.2 and CAT 3.4 were <i>bacillus</i>-shaped, Gram-positive, motile, catalase-positive and aerobic. Based on the numeric-phenetic analysis results, the isolates AAT 1.4 and CAT 3.4 had a 92.9% similarity to <i>Bacillus subtilis</i>, while isolate AAT 3.2 had a 92.9% similarity to <i>Brevibacillus limnophilus</i>. <b>Conclusion:</b> According to the numeric-phenetic analysis results, the isolates AAT 1.4 and CAT 3.4 belong to the species <i>Bacillus subtilis</i>, while isolate AAT 3.2 belongs to the species <i>Brevibacillus limnophilus</i>.
Collapse
|
10
|
Rai A, Jha MN, Singh D, Thapa S, Chaurasia SK, Jha G. Detection of endophytic association between Aeschynomene nodulating Bradyrhizobium sp. and traditional Desariya rice roots under rice-Aeschynomene ecosystem of chaur land, Bihar, India. Biol Futur 2021; 73:95-105. [PMID: 34773605 DOI: 10.1007/s42977-021-00105-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 11/02/2021] [Indexed: 11/27/2022]
Abstract
Engineering diazotrophic rice having either an integral component of diazotrophic microbes or placing microbial origin nif gene to the rice plant is the dream of biotechnologist. Rice-Aeschynomene ecosystem of pristine chaur land provides a suitable niche to search Rhizobium endophytes in rice. Accordingly, the work was initiated to search suitable endophytic Rhizobium strain for artificial symbiosis within the roots of Desariya rice and its source through morphological, biochemical and molecular approaches. Detection of Acetylene reduction assay (ARA) activity in sterilized Desariya rice root confirmed the presence of putative diazotrophic endophytes in rice root. Isolates from Aeschynomene aspera L. nodulating and Desariya rice endophytic Rhizobium were evaluated for growth, IAA, morphological and biochemical features. Carbon profiling pattern of both these isolates indicated that Desariya rice endophytic Rhizobium has its similarity with Aeschynomene aspera L. nodulating Rhizobium. 16S rRNA gene sequencing confirmed the presence of endophytic Bradyrhizobium sp. in Desariya rice roots and its similarity with Aeschynomene aspera L. nodulating Bradyrhizobium. Desariya rice Bradyrhizobium may be an ideal candidate in the future for creating artificial symbiosis in rice due to its similarity with Aeschynomene aspera L. Bradyrhizobium.
Collapse
Affiliation(s)
- Abhilasha Rai
- Department of Microbiology, College of Basic Sciences and Humanities, Dr. Rajendra Prasad Central Agricultural University, Pusa, Samastipur, Bihar, 848125, India
| | - Manindra Nath Jha
- Department of Microbiology, College of Basic Sciences and Humanities, Dr. Rajendra Prasad Central Agricultural University, Pusa, Samastipur, Bihar, 848125, India
| | - Devendra Singh
- Department of Microbiology, College of Basic Sciences and Humanities, Dr. Rajendra Prasad Central Agricultural University, Pusa, Samastipur, Bihar, 848125, India.
- ICAR-Central Arid Zone Research Institute, Jodhpur, Rajasthan, 342003, India.
| | - Shobit Thapa
- ICAR-National Bureau of Agriculturally Important Microorganisms, Kushmaur, MaunathBhanjan, Uttar Pradesh, 275103, India
| | - Sanjeet Kumar Chaurasia
- Department of Microbiology, College of Basic Sciences and Humanities, Dr. Rajendra Prasad Central Agricultural University, Pusa, Samastipur, Bihar, 848125, India
| | - Gopaljee Jha
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| |
Collapse
|
11
|
Thalassobacillus, a genus of extreme to moderate environmental halophiles with biotechnological potential. World J Microbiol Biotechnol 2021; 37:147. [PMID: 34363544 DOI: 10.1007/s11274-021-03116-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 07/29/2021] [Indexed: 01/09/2023]
Abstract
Thalassobacillus is a moderately halophilic genus that has been isolated from several sites worldwide, such as hypersaline lakes, saline soils, salt flats, and volcanic mud. Halophilic bacteria have provided functional stable biomolecules in harsh conditions for industrial purposes. Despite its potential biotechnological applications, Thalassobacillus has not been fully characterized yet. This review describes the Thalassobacillus genus, with the few species reported, pointing out its possible applications in enzymes (amylases, cellulases, xylanases, and others), biosurfactants, bioactive compounds, biofuels production, bioremediation, and plant growth promotion. The Thalassobacillus genus represents a little-explored biological resource but with a high potential.
Collapse
|
12
|
Sami A, Elimairi I, Patangia D, Watkins C, Ryan CA, Ross RP, Stanton C. The ultra-structural, metabolomic and metagenomic characterisation of the sudanese smokeless tobacco 'Toombak'. Toxicol Rep 2021; 8:1498-1512. [PMID: 34401360 PMCID: PMC8355839 DOI: 10.1016/j.toxrep.2021.07.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 06/08/2021] [Accepted: 07/07/2021] [Indexed: 12/04/2022] Open
Abstract
Toombak, a form of moist smokeless tobacco from Sudan is placed as a dip in the oral cavity most commonly used by males. The microbiome of Toombak predominantly consists of the phyla, Firmicutes and Actinobacteria while abundant species include Corynebacterium casei, Atopostipes suicloacalis and Oceanobacillus chironomi. High concentrations of iron, volatile aldehydes and tobacco specific nitrosamines were found in Toombak and can lead to toxicity. Toombak has a non-homogenous abrasive surface with a high sodium level in the ready to buy form that can damage the oral mucosa. New measures must be taken in Sudan to limit harmful compounds in Toombak.
Toombak is a smokeless tobacco produced from the Nicotiana rustica tobacco plant from Sudan. Pre-prepared and ready to buy Toombak samples were analysed using mass spectrometry (heavy metals), gas and liquid chromatography (metabolomics), 16S rRNA metagenomic sequencing (microbiome) and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt), scanning electron microscopy with energy dispersive X-ray spectroscopy (SEM-EDX) and pH analysis. Chromium, cobalt, and copper were high in the pre-prepared form of Toombak while iron, tobacco specific nitrosamines (TSNAs), formaldehyde and acetaldehyde were high in both types. Firmicutes and Actinobacteria dominated Toombak. Samples of ready to buy Toombak showed inter-variational differences depending on place of purchase. We found Virgibacillus were increased in the pre-prepared form while Corynebacterium casei, Atopococus tabaci, Atopostipes suicloacalis, Oceanobacillus chironomi and Staphylococcus gallinarum were the most abundant species in the ready to buy forms. PICRUSt analysis highlighted increased activity of metal transport systems in the ready to buy samples as well as an antibiotic transport system. SEM-EDX highlighted large non-homogenous, irregular particles with increased sodium, while pH of samples was in the alkaline range. The final composition of Toombak is affected by its method of preparation and the end product has the potential to impart many negative consequences on the health of its users. TSNA levels observed in Toombak were some of the highest in the world while the micro-environment of Toombak supports a distinct microbiota profile.
Collapse
Affiliation(s)
- Amel Sami
- APC Microbiome Institute, University College Cork, Cork, T12 YN60, Ireland.,Department of Oral and Maxillofacial Surgery and Oral Medicine, Faculty of Dentistry, National Ribat University, Nile Street, Khartoum, 1111, Sudan
| | - Imad Elimairi
- Department of Oral and Maxillofacial Surgery and Oral Medicine, Faculty of Dentistry, National Ribat University, Nile Street, Khartoum, 1111, Sudan
| | - Dhrati Patangia
- APC Microbiome Institute, University College Cork, Cork, T12 YN60, Ireland
| | - Claire Watkins
- APC Microbiome Institute, University College Cork, Cork, T12 YN60, Ireland
| | - C Anthony Ryan
- Department of Paediatrics and Child Health, University College Cork, Cork, T12 DFK4, Ireland
| | - R Paul Ross
- APC Microbiome Institute, University College Cork, Cork, T12 YN60, Ireland
| | - Catherine Stanton
- APC Microbiome Institute, University College Cork, Cork, T12 YN60, Ireland.,Teagasc Food Research Centre, Moorepark, Fermoy, Cork, P61 C996, Ireland
| |
Collapse
|
13
|
Lyu Q, Shen Y, Li X, Chen G, Li D, Fan C. Early effects of crop tree management on undergrowth plant diversity and soil physicochemical properties in a Pinus massoniana plantation. PeerJ 2021; 9:e11852. [PMID: 34395087 PMCID: PMC8325914 DOI: 10.7717/peerj.11852] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 07/04/2021] [Indexed: 01/23/2023] Open
Abstract
Background Soil and understory vegetation are vital components of forest ecosystems. Identifying the interaction of plantation management to vegetation and soil is crucial for developing sustainable plantation ecosystem management strategies. As one of the main measures of close-to-nature management of forest plantation, few studies have paid attention to the effect of crop tree management on the soil properties and understory vegetation. Methods A 36-year-old Pinus massoniana plantation in Huaying city, Sichuan Province was taken as the research object to analyse the changes in undergrowth plant diversity and soil physicochemical properties under three different crop tree densities (100, 150, and 200 N/ha). Results Our results showed that the contents of available phosphorus, organic matter and hydrolysable nitrogen in the topsoil increased significantly after crop tree management, while content of available potassium decreased. The composition of shrub and herb layer was richer, and the dominant species were obviously replaced after crop tree management. The Shannon-Wiener index and Richness index of shrub layer, and the diversity of herb layer increased significantly after crop tree management. Herb layer diversity indexes and Richness index of shrub layer were closely related to soil organic matter, available phosphorus, hydrolysable nitrogen, available potassium, soil moisture and bulk density. As the main limiting factors for plant growth, nitrogen, phosphorus and potassium were closely related to plant diversity and to the distribution of the dominant species. At the initial stage of crop tree management, each treatment significantly improved the soil physicochemical properties and plant diversity of Pinus massoniana plantation, and the comprehensive evaluation was 200 N/ha >100 N/ha >150 N/ha >CK. Compared with other treatments, 200 N/ha had the best effect on improving the undergrowth environment of the Pinus massoniana plantation in the initial stage of crop tree management.
Collapse
Affiliation(s)
- Qian Lyu
- College of Forestry, Sichuan Agricultural University, Cheng Du, China
| | - Yi Shen
- College of Forestry, Sichuan Agricultural University, Cheng Du, China
| | - Xianwei Li
- College of Forestry, Sichuan Agricultural University, Cheng Du, China.,Key Laboratory of National Forestry and Prairie Bureau on Forest Resources Conservation and Ecological Security in the Upper Reaches of Yangtze River, Sichuan Agricultural University, Cheng Du, China
| | - Gang Chen
- College of Forestry, Sichuan Agricultural University, Cheng Du, China.,Key Laboratory of National Forestry and Prairie Bureau on Forest Resources Conservation and Ecological Security in the Upper Reaches of Yangtze River, Sichuan Agricultural University, Cheng Du, China
| | - Dehui Li
- College of Urban and Rural Planning and Construction, Mianyang Normal University, Mian Yang, China
| | - Chuan Fan
- College of Forestry, Sichuan Agricultural University, Cheng Du, China.,Key Laboratory of National Forestry and Prairie Bureau on Forest Resources Conservation and Ecological Security in the Upper Reaches of Yangtze River, Sichuan Agricultural University, Cheng Du, China
| |
Collapse
|
14
|
Yadav AN, Kour D, Kaur T, Devi R, Yadav A, Dikilitas M, Abdel-Azeem AM, Ahluwalia AS, Saxena AK. Biodiversity, and biotechnological contribution of beneficial soil microbiomes for nutrient cycling, plant growth improvement and nutrient uptake. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2021. [DOI: 10.1016/j.bcab.2021.102009] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
|
15
|
Sansupa C, Purahong W, Wubet T, Tiansawat P, Pathom-Aree W, Teaumroong N, Chantawannakul P, Buscot F, Elliott S, Disayathanoowat T. Soil bacterial communities and their associated functions for forest restoration on a limestone mine in northern Thailand. PLoS One 2021; 16:e0248806. [PMID: 33831034 PMCID: PMC8031335 DOI: 10.1371/journal.pone.0248806] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 03/07/2021] [Indexed: 11/19/2022] Open
Abstract
Opencast mining removes topsoil and associated bacterial communities that play crucial roles in soil ecosystem functioning. Understanding the community composition and functioning of these organisms may lead to improve mine-rehabilitation practices. We used a culture-dependent method, combined with Illumina sequencing, to compare the taxonomic richness and composition of living bacterial communities in opencast mine substrates and young mine-rehabilitation plots, with those of soil in adjacent remnant forest at a limestone mine in northern Thailand. We further investigated the effects of soil physico-chemical factors and ground-flora cover on the same. Although, loosened subsoil, brought in to initiate rehabilitation, improved water retention and facilitated plant re-establishment, it did not increase the population density of living microbes substantially within 9 months. Planted trees and sparse ground flora in young rehabilitation plots had not ameliorated the micro-habitat enough to change the taxonomic composition of the soil bacteria compared with non-rehabilitated mine sites. Viable microbes were significantly more abundant in forest soil than in mine substrates. The living bacterial community composition differed significantly, between the forest plots and both the mine and rehabilitation plots. Proteobacteria dominated in forest soil, whereas Firmicutes dominated in samples from both mine and rehabilitation plots. Although, several bacterial taxa could survive in the mine substrate, soil ecosystem functions were greatly reduced. Bacteria, capable of chitinolysis, aromatic compound degradation, ammonification and nitrate reduction were all absent or rare in the mine substrate. Functional redundancy of the bacterial communities in both mine substrate and young mine-rehabilitation soil was substantially reduced, compared with that of forest soil. Promoting the recovery of microbial biomass and functional diversity, early during mine rehabilitation, is recommended, to accelerate soil ecosystem restoration and support vegetation recovery. Moreover, if inoculation is included in mine rehabilitation programs, the genera: Bacillus, Streptomyces and Arthrobacter are likely to be of particular interest, since these genera can be cultivated easily and this study showed that they can survive under the extreme conditions that prevail on opencast mines.
Collapse
Affiliation(s)
- Chakriya Sansupa
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
- Graduate School, Chiang Mai University, Chiang Mai, Thailand
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Halle (Saale), Germany
| | - Witoon Purahong
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Halle (Saale), Germany
- * E-mail: (TD); (WP)
| | - Tesfaye Wubet
- Department of Community Ecology, UFZ-Helmholtz Centre for Environmental Research, Halle (Saale), Germany
- German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Leipzig, Germany
| | - Pimonrat Tiansawat
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
- Environmental Science Research Centre and Forest Restoration Research Unit, Biology Department, Science Faculty, Chiang Mai University, Chiang Mai, Thailand
| | - Wasu Pathom-Aree
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Neung Teaumroong
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | | | - François Buscot
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Halle (Saale), Germany
- German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Leipzig, Germany
| | - Stephen Elliott
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
- Environmental Science Research Centre and Forest Restoration Research Unit, Biology Department, Science Faculty, Chiang Mai University, Chiang Mai, Thailand
| | - Terd Disayathanoowat
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
- Research Center in Bioresources for Agriculture, Industry and Medicine, Chiang Mai University, Chiang Mai, Thailand
- Research Center of Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai, Thailand
- * E-mail: (TD); (WP)
| |
Collapse
|
16
|
Chaudhary T, Gera R, Shukla P. Deciphering the Potential of Rhizobium pusense MB-17a, a Plant Growth-Promoting Root Endophyte, and Functional Annotation of the Genes Involved in the Metabolic Pathway. Front Bioeng Biotechnol 2021; 8:617034. [PMID: 33537293 PMCID: PMC7848175 DOI: 10.3389/fbioe.2020.617034] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 11/30/2020] [Indexed: 11/13/2022] Open
Abstract
Plant growth-promoting rhizobacteria (PGPR) are root endophytic bacteria used for growth promotion, and they have broader applications in enhancing specific crop yield as a whole. In the present study, we have explored the potential of Rhizobium pusense MB-17a as an endophytic bacterium isolated from the roots of the mung bean (Vigna radiata) plant. Furthermore, this bacterium was sequenced and assembled to reveal its genomic potential associated with plant growth-promoting traits. Interestingly, the root endophyte R. pusense MB-17a showed all essential PGPR traits which were determined by biochemical and PGPR tests. It was noted that this root endophytic bacterium significantly produced siderophores, indole acetic acid (IAA), ammonia, and ACC deaminase and efficiently solubilized phosphate. The maximum IAA and ammonia produced were observed to be 110.5 and 81 μg/ml, respectively. Moreover, the PGPR potential of this endophytic bacterium was also confirmed by a pot experiment for mung bean (V. radiata), whose results show a substantial increase in the plant's fresh weight by 76.1% and dry weight by 76.5% on the 60th day after inoculation of R. pusense MB-17a. Also, there is a significant enhancement in the nodule number by 66.1% and nodule fresh weight by 162% at 45th day after inoculation with 100% field capacity after the inoculation of R. pusense MB-17a. Besides this, the functional genomic annotation of R. pusense MB-17a determined the presence of different proteins and transporters that are responsible for its stress tolerance and its plant growth-promoting properties. It was concluded that the unique presence of genes like rpoH, otsAB, and clpB enhances the symbiosis process during adverse conditions in this endophyte. Through Rapid Annotation using Subsystem Technology (RAST) analysis, the key genes involved in the production of siderophores, volatile compounds, indoles, nitrogenases, and amino acids were also predicted. In conclusion, the strain described in this study gives a novel idea of using such type of endophytes for improving plant growth-promoting traits under different stress conditions for sustainable agriculture.
Collapse
Affiliation(s)
- Twinkle Chaudhary
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
| | - Rajesh Gera
- Department of Microbiology, Chaudhary Charan Singh Haryana Agricultural University, Hisar, India
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
| |
Collapse
|
17
|
Piriformospora indica: Biodiversity, Ecological Significances, and Biotechnological Applications for Agriculture and Allied Sectors. Fungal Biol 2021. [DOI: 10.1007/978-3-030-67561-5_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
18
|
Biodiversity of pesticides degrading microbial communities and their environmental impact. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2021. [DOI: 10.1016/j.bcab.2020.101883] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
|
19
|
Extremophilic Fungi and Their Role in Control of Pathogenic Microbes. Fungal Biol 2021. [DOI: 10.1007/978-3-030-60659-6_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
20
|
Plant Growth-Promoting Endophytic Fungi from Different Habitats and Their Potential Applications in Agriculture. Fungal Biol 2021. [DOI: 10.1007/978-3-030-60659-6_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
21
|
Pal S, Biswas R, Misra A, Sar A, Banerjee S, Mukherjee P, Dam B. Poorly known microbial taxa dominate the microbiome of hypersaline Sambhar Lake salterns in India. Extremophiles 2020; 24:875-885. [PMID: 32955600 DOI: 10.1007/s00792-020-01201-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 09/07/2020] [Indexed: 01/21/2023]
Abstract
Inland athalassohaline solar salterns provide unique opportunity to study microbial successions along salinity gradients that resemble transition in natural hypersaline lakes. We analyzed for the first time 16S rRNA gene amplicon sequences of bacteria (V1-V2) and archaea (V4-V5) in saltern brines of India's largest inland hypersaline Sambhar Lake. Brines of the salterns (S1-S4) are alkaline (pH 9.5-10.5) with salinities of 130, 170, 280 and 350 gL-1 respectively. 16S rRNA gene copy-number of archaea outnumbered that of bacteria in all salterns. Their diversity also increased along S1 through S4, while that of bacteria decreased. Brines of S3 and S4 were dominated by specialized extreme halophilic bacterial (Halanaerobiales, Rhodothermaceae) and archaeal (Halobacteriales, Haloferacales) members with recognized salt-in strategy for osmoadaptation. Microbial assemblages positively correlated to saltern pH, total salinity, and ionic composition. Archaea in S1 and S2 were unprecedentedly represented by poorly known as-yet uncultivated groups, Woesearchaeota (90.35-93.51%) and Nanohaloarchaeota that belong to the newly proposed nano-sized superphylum DPANN. In fact, these taxa were identified in archaeal datasets of other athalassohaline salterns after re-analysis using latest RDP database. Thus, microbial compositions in hypersaline lakes are complex and need revisit particularly for their archaeal diversity to understand their hitherto unknown ecological function in extreme environments.
Collapse
Affiliation(s)
- Srikanta Pal
- Microbiology Laboratory, Department of Botany (DST-FIST and UGC-DRS Funded), Institute of Science, Visva-Bharati (A Central University), Santiniketan, West Bengal, 731235, India
| | - Raju Biswas
- Microbiology Laboratory, Department of Botany (DST-FIST and UGC-DRS Funded), Institute of Science, Visva-Bharati (A Central University), Santiniketan, West Bengal, 731235, India
| | - Arijit Misra
- Microbiology Laboratory, Department of Botany (DST-FIST and UGC-DRS Funded), Institute of Science, Visva-Bharati (A Central University), Santiniketan, West Bengal, 731235, India
| | - Abhijit Sar
- Microbiology Laboratory, Department of Botany (DST-FIST and UGC-DRS Funded), Institute of Science, Visva-Bharati (A Central University), Santiniketan, West Bengal, 731235, India
| | - Sohini Banerjee
- Microbiology Laboratory, Department of Botany (DST-FIST and UGC-DRS Funded), Institute of Science, Visva-Bharati (A Central University), Santiniketan, West Bengal, 731235, India.,Present address: Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Puja Mukherjee
- Microbiology Laboratory, Department of Botany (DST-FIST and UGC-DRS Funded), Institute of Science, Visva-Bharati (A Central University), Santiniketan, West Bengal, 731235, India
| | - Bomba Dam
- Microbiology Laboratory, Department of Botany (DST-FIST and UGC-DRS Funded), Institute of Science, Visva-Bharati (A Central University), Santiniketan, West Bengal, 731235, India.
| |
Collapse
|
22
|
Torracchi C JE, Morel MA, Tapia-Vázquez I, Castro-Sowinski S, Batista-García RA, Yarzábal R LA. Fighting plant pathogens with cold-active microorganisms: biopesticide development and agriculture intensification in cold climates. Appl Microbiol Biotechnol 2020; 104:8243-8256. [PMID: 32803297 DOI: 10.1007/s00253-020-10812-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 07/27/2020] [Accepted: 08/02/2020] [Indexed: 01/16/2023]
Abstract
Cold-adapted (CA) microorganisms (= psychrophiles or psychrotolerants) are key players of many ecological interactions in natural ecosystems. Some of them can colonize the rhizosphere of plants and cause damage to their hosts; others, on the contrary, protect plants from their pathogens through direct and indirect mechanisms, thus promoting plant growth and development. These "protective" microbes are known as biocontrol agents (BCA). BCA either limit or inhibit the growth of plant pathogens, owing to the excretion of a panoply of secondary metabolites (including soluble and volatile antibiotics, siderophores, quorum sensing interfering agents). BCA can also control plant pathogens through indirect mechanisms, including competence for nutrients and space, or else by interfering with their chemical communication. That explains why some of these BCA have been included in the formulation of commercial biopesticides, which are environmentally friendly products containing live cells used to control plant diseases and pests. At present, the development of biopesticides from mesophilic microorganisms is an established technology. Unfortunately, these biopesticides are not active at low temperatures. On the other hand, the information concerning the potential use of CA-BCA for the same goal is at its infancy. Here, we review the current knowledge concerning the isolation, identification, and characterization of CA microbes which act as antagonists of plant pathogens, including the mechanisms they deploy to antagonize plant pathogens. We also illustrate their biotechnological potential to develop CA biopesticides and discuss their utility in the context of mountainous agriculture. KEY POINTS: • Many naturally occurring cold-active microbes antagonize plant pathogens. • The mechanisms of biocontrol exerted by these microbes are either direct or indirect. • Cold-active biocontrol agents can be used to develop biopesticides. • Cold-active biopesticides are crucial for sustainably intensifying agriculture in cold climates.
Collapse
Affiliation(s)
- José Esteban Torracchi C
- Unidad de Salud y Bienestar, Universidad Católica de Cuenca, Av. Las Américas y Calle Humboldt, Cuenca, Ecuador
- Centro de Investigación, Innovación y Transferencia de Tecnología (CIITT), Universidad Católica de Cuenca, Campus Miracielos, Ricaurte, Ecuador
| | - María A Morel
- Unidad Microbiología Molecular, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Av Italia 3318, 11600, Montevideo, Uruguay
| | - Irán Tapia-Vázquez
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
- Centro de Investigación en Dinámica Celular, Instituto de Investigaciones en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - Susana Castro-Sowinski
- Unidad Microbiología Molecular, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Av Italia 3318, 11600, Montevideo, Uruguay
- Sección Bioquímica y Biología Molecular, Facultad de Ciencias, UdelaR, Iguá 4225, 11400, Montevideo, Uruguay
| | - Ramón Alberto Batista-García
- Centro de Investigación en Dinámica Celular, Instituto de Investigaciones en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - Luis Andrés Yarzábal R
- Unidad de Salud y Bienestar, Universidad Católica de Cuenca, Av. Las Américas y Calle Humboldt, Cuenca, Ecuador.
- Centro de Investigación, Innovación y Transferencia de Tecnología (CIITT), Universidad Católica de Cuenca, Campus Miracielos, Ricaurte, Ecuador.
| |
Collapse
|
23
|
Fadiji AE, Babalola OO. Elucidating Mechanisms of Endophytes Used in Plant Protection and Other Bioactivities With Multifunctional Prospects. Front Bioeng Biotechnol 2020; 8:467. [PMID: 32500068 PMCID: PMC7242734 DOI: 10.3389/fbioe.2020.00467] [Citation(s) in RCA: 147] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 04/22/2020] [Indexed: 01/06/2023] Open
Abstract
Endophytes are abundant in plants and studies are continuously emanating on their ability to protect plants from pathogens that cause diseases especially in the field of agriculture. The advantage that endophytes have over other biocontrol agents is the ability to colonize plant's internal tissues. Despite this attributes, a deep understanding of the mechanism employed by endophytes in protecting the plant from diseases is still required for both effectiveness and commercialization. Also, there are increasing cases of antibiotics resistance among most causative agents of diseases in human beings, which calls for an alternative drug discovery using natural sources. Endophytes present themselves as a storehouse of many bioactive metabolites such as phenolic acids, alkaloids, quinones, steroids, saponins, tannins, and terpenoids which makes them a promising candidate for anticancer, antimalarial, antituberculosis, antiviral, antidiabetic, anti-inflammatory, antiarthritis, and immunosuppressive properties among many others, even though the primary function of bioactive compounds from endophytes is to make the host plants resistant to both abiotic and biotic stresses. Endophytes still present themselves as a peculiar source of possible drugs. This study elucidates the mechanisms employed by endophytes in protecting the plant from diseases and different bioactivities of importance to humans with a focus on endophytic bacteria and fungi.
Collapse
Affiliation(s)
| | - Olubukola Oluranti Babalola
- Food Security and Safety Niche, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, South Africa
| |
Collapse
|
24
|
Rana KL, Kour D, Kaur T, Sheikh I, Yadav AN, Kumar V, Suman A, Dhaliwal HS. Endophytic Microbes from Diverse Wheat Genotypes and Their Potential Biotechnological Applications in Plant Growth Promotion and Nutrient Uptake. ACTA ACUST UNITED AC 2020. [DOI: 10.1007/s40011-020-01168-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
|
25
|
Spatial distribution and identification of bacteria in stressed environments capable to weather potassium aluminosilicate mineral. Braz J Microbiol 2020; 51:751-764. [PMID: 31898251 DOI: 10.1007/s42770-019-00210-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Accepted: 12/07/2019] [Indexed: 10/25/2022] Open
Abstract
In the present study, we studied the distribution of silicate mineral weathering bacteria (SWB) in stressed environments that release potassium from insoluble source of mineral. Out of 972 isolates, 340 isolates were positive and mineral weathering potential ranged from 5.55 to 180.05%. Maximum abundance of SWB occurred 44.71% in saline environment followed by 23.53% in low temperature and 12.35% each in high temperature and moisture deficit. Among isolates, silicate mineral weathering efficiency ranged from 1.9 to 72.8 μg mL-1 available K in liquid medium. The phylogenetic tree of SWB discriminated in three clusters viz. Firmicutes, Proteobacteria and Actinobacteria. This is the first report on SWB in stressed environments and identified 27 genera and 67 species which is not reported earlier. Among them Bacillus was the predominant genera (58.60%) distantly followed by Pseudomonas (6.37%), Staphylococcus (5.10%) and Paenibacillus (4.46%). These bacterial strains could be developed as inoculants for biological replenishment of K in stressed soils. Graphical abstract.
Collapse
|
26
|
Tiwari P, Bajpai M, Singh LK, Mishra S, Yadav AN. Phytohormones Producing Fungal Communities: Metabolic Engineering for Abiotic Stress Tolerance in Crops. Fungal Biol 2020. [DOI: 10.1007/978-3-030-45971-0_8] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
27
|
Kour D, Rana KL, Kaur T, Sheikh I, Yadav AN, Kumar V, Dhaliwal HS, Saxena AK. Microbe-mediated alleviation of drought stress and acquisition of phosphorus in great millet (Sorghum bicolour L.) by drought-adaptive and phosphorus-solubilizing microbes. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2020. [DOI: 10.1016/j.bcab.2020.101501] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
28
|
Subrahmanyam G, Kumar A, Sandilya SP, Chutia M, Yadav AN. Diversity, Plant Growth Promoting Attributes, and Agricultural Applications of Rhizospheric Microbes. SUSTAINABLE DEVELOPMENT AND BIODIVERSITY 2020. [DOI: 10.1007/978-3-030-38453-1_1] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
|
29
|
Abstract
Although volcanoes represent extreme environments for life, they harbour bacterial communities. Vulcano Island (Aeolian Islands, Sicily) presents an intense fumarolic activity and widespread soil degassing, fed by variable amounts of magmatic gases (dominant at La Fossa Crater) and hydrothermal fluids (dominant at Levante Bay). The aim of this study is to analyse the microbial communities from the different environments of Vulcano Island and to evaluate their possible correlation with the composition of the gas emissions. Microbial analyses were carried out on soils and pioneer plants from both La Fossa Crater and Levante Bay. Total DNA has been extracted from all the samples and sequenced through Illumina MiSeq platform. The analysis of microbiome composition and the gases sampled in the same sites could suggest a possible correlation between the two parameters. We can suggest that the ability of different bacterial genera/species to survive in the same area might be due to the selection of particular genetic traits allowing the survival of these microorganisms. On the other side, the finding that microbial communities inhabiting different sites exhibiting different emission profiles are similar might be explained on the basis of a possible sharing of metabolic abilities related to the gas composition.
Collapse
|
30
|
Isolation, functional characterization and efficacy of biofilm-forming rhizobacteria under abiotic stress conditions. Antonie Van Leeuwenhoek 2019; 112:1827-1839. [DOI: 10.1007/s10482-019-01306-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Accepted: 07/24/2019] [Indexed: 10/26/2022]
|
31
|
Biofouling of FeNP-Coated SWRO Membranes with Bacteria Isolated after Pre-Treatment in the Sea of Cortez. COATINGS 2019. [DOI: 10.3390/coatings9070462] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Commercial seawater reverse osmosis (SWRO) membranes were coated with iron nanoparticles (FeNPs) and biofouled with a bacterium strain isolated from the Sea of Cortez, Mexico. This strain was selected and characterized, as it was the only cultivable strain in pretreated seawater. Molecular identification of the strain showed that it belongs to Bacillus halotolerans MCC1. This strain was Gram positive with spore production, and was susceptible to Fe+2 toxicity with a minimum inhibitory concentration of 1.8 g L−1. Its biofouling potential on both uncoated and FeNP coated reverse osmosis (RO) membranes was measured via biofilm layer thickness, total cell count, optical density and organic matter. The FeNP-coated RO membrane presented a significant reduction in biofilm cake layer thickness (>90%), total cells (>67%), optical density (>42%) and organic matter (>92%) with respect to an uncoated commercial membrane. Thus, Bacillus halotolerans MCC1 shows great potential to biofoul RO membranes as it can pass through ultrafiltration membranes due to its spore producing ability; nonetheless, FeNP-coated membranes represent a potential alternative to mitigate RO membrane biofouling.
Collapse
|
32
|
Seasonal variations in culturable archaea and their plant growth promoting attributes to predict their role in establishment of vegetation in Rann of Kutch. Biologia (Bratisl) 2019. [DOI: 10.2478/s11756-019-00259-2] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
33
|
Neelam DK, Agrawal A, Tomer AK, Bandyopadhayaya S, Sharma A, Jagannadham MV, Mandal CC, Dadheech PK. A Piscibacillus sp. Isolated from A Soda Lake Exhibits Anticancer Activity Against Breast Cancer MDA-MB-231 Cells. Microorganisms 2019; 7:microorganisms7020034. [PMID: 30691094 PMCID: PMC6406920 DOI: 10.3390/microorganisms7020034] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 01/22/2019] [Accepted: 01/23/2019] [Indexed: 01/04/2023] Open
Abstract
Microorganisms thrive in extreme environments and are known for synthesizing valuable metabolites. Salt-loving microorganisms can flourish in saline environments which inhibit the growth of other microbial life, and they possess the potential to produce stable and novel biomolecules for the use in biotechnological applications, including anticancer compounds. Sambhar Lake is the largest inland soda lake in India and is an appropriate habitat for halophilic bacterial and archaeal strains in terms of diversity and potential production of bioactive compounds. In the present study, a moderately halo-alkaliphilic bacterial strain C12A1 was isolated from Sambhar Lake, located in Rajasthan, India. C12A1 was gram-positive, motile, rod-shaped, formed oval endospores, produced carotenoids, and exhibited optimal growth at 37 °C in 10–15% NaCl (pH 8). C12A1 was found to be able to hydrolyze skimmed milk, gelatin, and Tween 80 but unable to hydrolyze starch and carboxymethylcellulose. C12A1 showed 98.87% and 98.50% identity in 16S rRNA gene sequence to P. halophilus and P. salipiscarius, respectively. Nevertheless, C12A1 was clustered within the clade consisting of P. salipiscarius strains, but it showed a distinct lineage. Thus, C12A1 was designated as Piscibacillus sp. Cell proliferation assay results showed that C12A1 broth extract (BEP) decreased cell viability in breast cancer MDA-MB-231 cells, which was confirmed by the MTT (3-(4, 5-dimethylthiazol-2-yl)-2, 5-diphenyltetrazolium bromide) assay. Induction of cell toxicity was visualized by microscopy. Reverse Transcriptase PCR (RT-PCR) analysis demonstrated that BEP inhibited the expression of proliferative B-cell lymphoma-extra large (Bcl-xL) and cell cycle marker Cyclin-dependent kinase 2 (CDK2) at transcript levels. Similarly, cell migration and colony formation along with mesenchymal marker vimentin and stem cell marker BMI transcripts were found to be inhibited when cells were treated with the BEP. The anti-breast cancer potential of C12A1 indicates that microorganisms inhabiting saline-alkaline habitats, with Piscibacillus sp. in particular, are a promising source for discovery of novel bioactive substances.
Collapse
Affiliation(s)
- Deepesh Kumar Neelam
- Department of Microbiology, School of Life Sciences, Central University of Rajasthan, Bandarsindri 305817, Ajmer, India.
| | - Akhil Agrawal
- Department of Microbiology, School of Life Sciences, Central University of Rajasthan, Bandarsindri 305817, Ajmer, India.
| | - Anuj Kumar Tomer
- Department of Microbiology, School of Life Sciences, Central University of Rajasthan, Bandarsindri 305817, Ajmer, India.
| | - Shreetama Bandyopadhayaya
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Bandarsindri 305817, Ajmer, India.
| | - Ankit Sharma
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Bandarsindri 305817, Ajmer, India.
| | | | - Chandi C Mandal
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Bandarsindri 305817, Ajmer, India.
| | - Pawan K Dadheech
- Department of Microbiology, School of Life Sciences, Central University of Rajasthan, Bandarsindri 305817, Ajmer, India.
| |
Collapse
|
34
|
Biodiversity of Endophytic Fungi from Diverse Niches and Their Biotechnological Applications. ADVANCES IN ENDOPHYTIC FUNGAL RESEARCH 2019. [DOI: 10.1007/978-3-030-03589-1_6] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
35
|
Kumar A, Chaturvedi AK, Yadav K, Arunkumar KP, Malyan SK, Raja P, Kumar R, Khan SA, Yadav KK, Rana KL, Kour D, Yadav N, Yadav AN. Fungal Phytoremediation of Heavy Metal-Contaminated Resources: Current Scenario and Future Prospects. RECENT ADVANCEMENT IN WHITE BIOTECHNOLOGY THROUGH FUNGI 2019. [DOI: 10.1007/978-3-030-25506-0_18] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
36
|
Drought-Tolerant Phosphorus-Solubilizing Microbes: Biodiversity and Biotechnological Applications for Alleviation of Drought Stress in Plants. PLANT GROWTH PROMOTING RHIZOBACTERIA FOR SUSTAINABLE STRESS MANAGEMENT 2019. [DOI: 10.1007/978-981-13-6536-2_13] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
37
|
Endophytic Fungi: Biodiversity, Ecological Significance, and Potential Industrial Applications. RECENT ADVANCEMENT IN WHITE BIOTECHNOLOGY THROUGH FUNGI 2019. [DOI: 10.1007/978-3-030-10480-1_1] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
38
|
Kour D, Rana KL, Yadav N, Yadav AN, Singh J, Rastegari AA, Saxena AK. Agriculturally and Industrially Important Fungi: Current Developments and Potential Biotechnological Applications. RECENT ADVANCEMENT IN WHITE BIOTECHNOLOGY THROUGH FUNGI 2019. [DOI: 10.1007/978-3-030-14846-1_1] [Citation(s) in RCA: 118] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
39
|
Helaly SE, Hamad Z, El Sayed MA, Abdel-Motaal FF, Nassar MI, Ito SI, Stadler M. Bacillus methylotrophicus ASWU-C2, a strain inhabiting hot desert soil, a new source for antibacterial bacillopyrone, pyrophen, and cyclopeptides. ACTA ACUST UNITED AC 2018; 74:55-59. [PMID: 30864389 DOI: 10.1515/znc-2018-0093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 11/23/2018] [Indexed: 11/15/2022]
Abstract
A strain of Bacillus methylotrophicus was isolated from a soil sample collected in Aswan eastern desert, which is known for its extremely arid climate. After fermentation of the strain in liquid culture and subsequent extraction, a bioassay-guided isolation procedure yielded five compounds: 2-benzyl-4H-pyran-4-one, named bacillopyrone (1), pyrophen (2), macrolactin A (3) and the cyclopeptides malformin A1 (4), and bacillopeptin A (5). The structures were determined by interpretation of nuclear magnetic resonance (NMR) spectroscopy and high resolution mass spectrometry (HR-MS) data. This is the first report on the isolation of compounds 1 and 2 from Bacillus species; compound 1 was reported previously as synthetic product. Bacillopyrone (1) exhibited moderate activity against the Gram-negative Chromobacterium violaceum with minimum inhibitory concentration 266.6 μg/mL, while macrolactin A (3) and malformin A1 (4) inhibited Staphylococcus aureus (minimum inhibitory concentrations 13.3 and 133.3 μg/mL, respectively).
Collapse
Affiliation(s)
- Soleiman E Helaly
- Department of Chemistry, Faculty of Science, Aswan University, Aswan 81528, Egypt.,Department of Microbial Drugs, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, Braunschweig 38124, Germany, Phone: 0049(0)53161819401
| | - Zainab Hamad
- Department of Chemistry, Faculty of Science, Aswan University, Aswan 81528, Egypt
| | - Magdi A El Sayed
- Department of Botany, Faculty of Science, Aswan University, Aswan 81528, Egypt, Phone: 0020973480450
| | | | - Mahmoud I Nassar
- Department of Chemistry of Natural Compounds, National Research Centre, 33 El-Bohouth St., Dokki, Giza 12622, Egypt
| | - Shin-Ichi Ito
- Laboratory of Molecular Plant Pathology, College of Agriculture, Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Yamaguchi, Japan
| | - Marc Stadler
- Department of Microbial Drugs, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, Braunschweig 38124, Germany
| |
Collapse
|
40
|
Souza V, Moreno-Letelier A, Travisano M, Alcaraz LD, Olmedo G, Eguiarte LE. The lost world of Cuatro Ciénegas Basin, a relictual bacterial niche in a desert oasis. eLife 2018; 7:38278. [PMID: 30457104 PMCID: PMC6245727 DOI: 10.7554/elife.38278] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 10/12/2018] [Indexed: 12/28/2022] Open
Abstract
Barriers to microbial migrations can lead adaptive radiations and increased endemism. We propose that extreme unbalanced nutrient stoichiometry of essential nutrients can be a barrier to microbial immigration over geological timescales. At the oasis in the Cuatro Ciénegas Basin in Mexico, nutrient stoichiometric proportions are skewed given the low phosphorus availability in the ecosystem. We show that this endangered oasis can be a model for a lost world. The ancient niche of extreme unbalanced nutrient stoichiometry favoured survival of ancestral microorganisms. This extreme nutrient imbalance persisted due to environmental stability and low extinction rates, generating a diverse and unique bacterial community. Several endemic clades of Bacillus invaded the Cuatro Cienegas region in two geological times, the late Precambrian and the Jurassic. Other lineages of Bacillus, Clostridium and Bacteroidetes migrated into the basin in isolated events. Cuatro Ciénegas Basin conservation is vital to the understanding of early evolutionary and ecological processes. Water is a rare sight in a barren land, but there are many more reasons that make the Cuatro Cienegas Basin, an oasis in the North Mexican desert, a puzzling environment. With little phosphorous and nutrients but plenty of sulphur and magnesium, the conditions in the turquoise blue lagoons of the Basin mimic the ones found in the ancient seas of the end of the Precambrian. In fact, Cuatro Cienegas is one of the rare sites where we can still find live stromatolites, a bacterial form of life that once dominated the oceans. Many bacteria of marine origin exist alongside these living fossils, prompting scientists to wonder if the Basin could be a true lost world, a safe haven where ancient microorganisms found refuge and have kept evolving until this day. But to confirm whether this is the case would require scientists to hunt for clues within the genetic information of local bacteria. Souza, Moreno-Letelier et al. came across these hints after sampling for bacteria in a small (about 1km2) lagoon named Churince, and analysing the DNA collected. The results yielded an astonishing amount of biodiversity: 5,167 species representing at least two-third of all known major groups of bacteria were identified, nearly as much as what was found in over 2,000 kilometres in the Pearl River in China. This is unusual, as most other extreme environments with little nutrients have low levels of diversity. Closer investigation into the genomes of 2,500 species of Bacillus bacteria revealed that the sample increased by nearly 21% the number of previously known species in the group. Most of these bacteria were only found in the Basin. These native or ‘endemic’ species have evolved from ancestors that came to the area in two waves. The oldest colonization event happened 680 million years ago, as the first animal forms just started to emerge. The most recent one took place while dinosaurs roamed the Earth about 160 million years ago, when geological events opened again the Basin to the ancient Pacific Ocean. Previous experiments have shown that different species of bacteria in the Churince have evolved to form a close-knit community which ferociously competes with microbes from the outside world. Paired with the extreme conditions found in the lagoon, this may have prevented other microorganisms from proliferating in the environment and replacing the ancient lineages. The days of this lost world may now be numbered. Drained by local farming, the wetlands of the Basin have shrunk by 90% over the past five decades. The Churince lagoon, the most diverse and fragile site where the samples were collected, is now completely dry. Human activities also disrupt the delicate and unique balance of nutrients in the oasis. But all may not be lost – yet. Local high school students have become involved in the research effort to describe and protect these unique microbial communities, and to change agricultural traditions in the area. Closing the canals that export spring water out of the Basin could give the site a chance to recover, and the microbes that are now seeking refuge in underground waters could re-emerge. Maybe there will still be time to celebrate, rather than mourn, the unique life forms of the Cuatro Cienegas Basin.
Collapse
Affiliation(s)
- Valeria Souza
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Coyoacán, Mexico
| | | | - Michael Travisano
- Department of Ecology, Evolution and Behavior, University of Minnesota, Saint Paul, United States
| | - Luis David Alcaraz
- Laboratorio Nacional de la Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Coyoacán, Mexico
| | - Gabriela Olmedo
- Laboratorio de Biología Molecular y Ecología Microbiana, Departamento de Ingeniería Genética, Unidad Irapuato Centro de Investigación y Estudios Avanzados, Guanajuato, Mexico
| | - Luis Enrique Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Coyoacán, Mexico
| |
Collapse
|
41
|
Hernández-González IL, Moreno-Hagelsieb G, Olmedo-Álvarez G. Environmentally-driven gene content convergence and the Bacillus phylogeny. BMC Evol Biol 2018; 18:148. [PMID: 30285626 PMCID: PMC6171248 DOI: 10.1186/s12862-018-1261-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 09/13/2018] [Indexed: 01/28/2023] Open
Abstract
Background Members of the Bacillus genus have been isolated from a variety of environments. However, the relationship between potential metabolism and the niche from which bacteria of this genus have been isolated has not been extensively studied. The existence of a monophyletic aquatic Bacillus group, composed of members isolated from both marine and fresh water has been proposed. Here, we present a phylogenetic/phylogenomic analysis to investigate the potential relationship between the environment from which group members have been isolated and their evolutionary origin. We also carried out hierarchical clustering based on functional content to test for potential environmental effects on the genetic content of these bacteria. Results The phylogenetic reconstruction showed that Bacillus strains classified as aquatic have evolutionary origins in different lineages. Although we observed the presence of a clade consisting exclusively of aquatic Bacillus, it is not comprised of the same strains previously reported. In contrast to phylogeny, clustering based on the functional categories of the encoded proteomes resulted in groups more compatible with the environments from which the organisms were isolated. This evidence suggests a detectable environmental influence on bacterial genetic content, despite their different evolutionary origins. Conclusion Our results suggest that aquatic Bacillus species have polyphyletic origins, but exhibit convergence at the gene content level. Electronic supplementary material The online version of this article (10.1186/s12862-018-1261-7) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Ismael L Hernández-González
- Department of Genetic Engineering, CINVESTAV-Irapuato, Km. 9.6 Libramiento Norte, Carr. Irapuato-Leon, Irapuato, 36824, Guanajuato, Mexico
| | - Gabriel Moreno-Hagelsieb
- Department of Biology, Wilfrid Laurier University, 75 University Ave. W., Waterloo, N2L 3C5, Ontario, Canada.
| | - Gabriela Olmedo-Álvarez
- Department of Genetic Engineering, CINVESTAV-Irapuato, Km. 9.6 Libramiento Norte, Carr. Irapuato-Leon, Irapuato, 36824, Guanajuato, Mexico.
| |
Collapse
|
42
|
Verma JP, Jaiswal DK, Krishna R, Prakash S, Yadav J, Singh V. Characterization and Screening of Thermophilic Bacillus Strains for Developing Plant Growth Promoting Consortium From Hot Spring of Leh and Ladakh Region of India. Front Microbiol 2018; 9:1293. [PMID: 29997578 PMCID: PMC6028593 DOI: 10.3389/fmicb.2018.01293] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 05/28/2018] [Indexed: 11/13/2022] Open
Abstract
In the present investigation, the main aim is to identify and characterize the potential drought tolerant plant growth promoting consortium for agricultural productivity. Three bacterial isolates were isolated from hot spring of Chumathang area of Leh district. Bacillus species (BHUJP-H1, BHUJP-H2, and BHUJP-H3) were done some biochemical tests including catalase, cellulase, amylase, indole-3-acetic acid, phosphate solubilisation, production of ammonia, siderophore, and hydrogen cyanide. Molecular characterization of isolates was done by 16S rDNA sequencing, e.g., Bacillus subtilis BHUJP-H1 (KU312403), Bacillus sp. BHUJP-H2 (KU312404) and B. licheniformis BHUJP-H3 (KU312405). The genetic diversity of the isolates was assessed by seven inter simple sequence repeat, all primer shows high polymorphism. The highest polymorphism efficiency and polymorphism information content showed by UBC-809 and UBC-836 which were 100% and 0.44 respectively, the lowest is by UBC-807 75% and 0.28 respectively. On an average 90.69% polymorphism efficiency and 0.40 polymorphism information contents obtained by used markers. The highest, 11.08 and the lowest, 4.50 effective multiplex ratios obtained for primer UBC-823 and UBC-807, on an average 7.99 effective multiplex ratio obtained. The highest, 4.89 and the lowest, 1.25 marker indexes obtained by UBC-836 and UBC-807 respectively and on an average 3.24 obtained. The UPGMA cluster analysis divided a population into two clusters I and II, in which BHUJP-H1 and BHUJP-H2 grouped under same while BHUJP-H3 grouped under another cluster. The treatment combination of Bacillus subtilis BHUJP-H1, B. subtilis BHUJP-H1+ B. licheniformis BHUJP-H3 and B. subtilis BHUJP-H1+ Bacillus sp. BHUJP-H2+ B. licheniformis BHUJP-H3 were recorded better combination for enhancing plant growth attributes of Vigna radiata as compared to control and others. The plant growth promoting consortium, e.g., Bacillus subtilis BHUJP-H1, Bacillus subtilis BHUJP-H1+ B. licheniformis BHUJP-H3 and B. subtilis BHUJP-H1+ Bacillus sp. BHUJP-H2+ B. licheniformis BHUJP-H3 can be further used as effective microbial inoculant for enhancing the production of mungbean in field conditions. Bacillus sp. BHUJP-H1 and Bacillus sp. BHUJP-H2 may use as drought tolerant plant growth promoting consortium for enhancing the sustainable agricultural productivity.
Collapse
Affiliation(s)
- Jay Prakash Verma
- Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi, India.,Hawkesbury Institute for the Environment, Western Sydney University, Sydney, NSW, Australia
| | - Durgesh Kumar Jaiswal
- Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi, India
| | - Ram Krishna
- Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi, India
| | - Satya Prakash
- Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi, India
| | - Janardan Yadav
- Department of Soil Science and Agricultural Chemistry, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, India
| | - Vijai Singh
- Synthetic Biology Laboratory, Department of Microbiology, School of Biological Sciences and Biotechnology, Institute of Advanced Research, Gandhinagar, India
| |
Collapse
|
43
|
Vijay A, Arora S, Gupta S, Chhabra M. Halophilic starch degrading bacteria isolated from Sambhar Lake, India, as potential anode catalyst in microbial fuel cell: A promising process for saline water treatment. BIORESOURCE TECHNOLOGY 2018; 256:391-398. [PMID: 29475147 DOI: 10.1016/j.biortech.2018.02.044] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 02/07/2018] [Accepted: 02/08/2018] [Indexed: 06/08/2023]
Abstract
In this study, Microbial Fuel Cell (MFC) capable of treating saline starch water was developed. Sodium chloride (NaCl) concentrations ranging from 500 mM to 3000 mM were tested at the anode. Nitrate was used as an electron acceptor at the biocathode. The halophilic bacteria were isolated from Sambhar Lake, India. Results indicated successful removal of starch (1.83 kg/m3-d) and nitrate (0.13 kg/m3-d NO3--N) with concomitant power output of 207.05 mW/m2 at 1000 mM NaCl concentration. An increase in power density from 71.06 mW/m2 to 207.05 mW/m2 (2.92 folds) was observed when NaCl concentration was increased from 500 mM to 1000 mM. A decline in power density was observed when the salt concentrations >1000 mM were used. Concentration of 3000 mM supported power output as well as the highest starch degradation (3.2 kg/m3-d) and amylase activity of 2.26 IU/ml. The halophilic exoelectrogens were isolated and identified. The present study demonstrates the utility of MFC for degrading starch in saline water.
Collapse
Affiliation(s)
- Ankisha Vijay
- Environmental Biotechnology Laboratory, Department of Bioscience and Bioengineering, Indian Institute of Technology Jodhpur (IIT J), Jodhpur, Rajasthan 342037, India
| | - Shivam Arora
- Environmental Biotechnology Laboratory, Department of Bioscience and Bioengineering, Indian Institute of Technology Jodhpur (IIT J), Jodhpur, Rajasthan 342037, India
| | - Sandeep Gupta
- Department of Mechanical Engineering, Indian Institute of Technology Jodhpur (IIT J), Jodhpur, Rajasthan 342037, India
| | - Meenu Chhabra
- Environmental Biotechnology Laboratory, Department of Bioscience and Bioengineering, Indian Institute of Technology Jodhpur (IIT J), Jodhpur, Rajasthan 342037, India.
| |
Collapse
|
44
|
Psychrotrophic Microbiomes: Molecular Diversity and Beneficial Role in Plant Growth Promotion and Soil Health. MICROORGANISMS FOR SUSTAINABILITY 2018. [DOI: 10.1007/978-981-10-7146-1_11] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
45
|
Misra S, Dixit VK, Khan MH, Kumar Mishra S, Dviwedi G, Yadav S, Lehri A, Singh Chauhan P. Exploitation of agro-climatic environment for selection of 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase producing salt tolerant indigenous plant growth promoting rhizobacteria. Microbiol Res 2017; 205:25-34. [DOI: 10.1016/j.micres.2017.08.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Revised: 07/27/2017] [Accepted: 08/12/2017] [Indexed: 10/19/2022]
|
46
|
Goswami G, Deka P, Das P, Bora SS, Samanta R, Boro RC, Barooah M. Diversity and functional properties of acid-tolerant bacteria isolated from tea plantation soil of Assam. 3 Biotech 2017; 7:229. [PMID: 28681289 DOI: 10.1007/s13205-017-0864-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 06/28/2017] [Indexed: 01/22/2023] Open
Abstract
In this study, we report on the bacterial diversity and their functional properties prevalent in tea garden soils of Assam that have low pH (3.8-5.5). Culture-dependent studies and phospholipid fatty acid analysis revealed a high abundance of Gram-positive bacteria. Further, 70 acid-tolerant bacterial isolates characterized using a polyphasic taxonomy approach could be grouped to the genus Bacillus, Lysinibacillus, Staphylococcus, Brevundimonas, Alcaligenes, Enterobacter, Klebsiella, Escherichia, and Aeromonas. Among the 70 isolates, 47 most promising isolates were tested for their plant growth promoting activity based on the production of Indole Acetic Acid (IAA), siderophore, and HCN as well as solubilization of phosphate, zinc, and potassium. Out of the 47 isolates, 10 isolates tested positive for the entire aforesaid plant growth promoting tests and further tested for quantitative analyses for production of IAA, siderophore, and phosphate solubilization at the acidic and neutral condition. Results indicated that IAA and siderophore production, as well as phosphate solubilization efficiency of the isolates decreased significantly (P ≤ 0.05) in the acidic environment. This study revealed that low soil pH influences bacterial community structure and their functional properties.
Collapse
Affiliation(s)
- Gunajit Goswami
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India
- Department of Life-Sciences, Dibrugarh University, Dibrugarh, Assam, 786004, India
| | - Priyadarshini Deka
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India
| | - Pompi Das
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India
| | - Sudipta Sankar Bora
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India
| | - Ramkrishna Samanta
- Department of Life-Sciences, Dibrugarh University, Dibrugarh, Assam, 786004, India
| | - Robin Chandra Boro
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India
| | - Madhumita Barooah
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India.
| |
Collapse
|
47
|
Sahay H, Yadav AN, Singh AK, Singh S, Kaushik R, Saxena AK. Hot springs of Indian Himalayas: potential sources of microbial diversity and thermostable hydrolytic enzymes. 3 Biotech 2017; 7:118. [PMID: 28567630 PMCID: PMC5451362 DOI: 10.1007/s13205-017-0762-1] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 02/01/2017] [Indexed: 12/23/2022] Open
Abstract
Microbial communities in hot springs at high elevations have been extensively studied worldwide. In this sense, the Indian Himalaya regions is valuable ecosystems for providing both the extreme 'cold' and 'hot' sites for exploring microbial diversity. In the present study, a total of 140 thermophilic bacteria were isolated from 12 samples collected from Manikaran and Yumthang hot springs of Indian Himalayas. The bacterial isolates were studied for phylogenetic profiling, growth properties at varying conditions and potential sources of extracellular thermostable hydrolytic enzymes such as protease, amylase, xylanase and cellulase. Based on production of extracellular hydrolases, 51 isolates from Manikaran (28) and Yumthang thermal springs (23) were selected and identified using 16S rRNA gene sequencing which included 37 distinct species of 14 different genera namely Anoxybacillus, Bacillus, Brevibacillus, Brevundimonas, Burkholderia, Geobacillus, Paenibacillus, Planococcus, Pseudomonas, Rhodanobacter, Thermoactinomyces, Thermobacillus, Thermonema and Thiobacillus. Out of 51 hydrolase producing bacteria, 24 isolates showed stability at wide range of temperature and pH treatments. In present investigation, three thermotolerant bacteria namely, Thermobacillus sp NBM6, Paenibacillus ehimensis NBM24 and Paenibacillus popilliae NBM68 were found to produced cellulase-free xylanase. These potential extracellular thermostable hydrolytic enzymes producing thermophilic bacteria have a great commercial prospect in various industrial, medical and agriculture applications.
Collapse
Affiliation(s)
- Harmesh Sahay
- Department of Biological Science, Rani Durgavati University, Jabalpur, India
- Department of Research and Development, R-Biopharm Neugen Group, Hyderabad, India
| | - Ajar Nath Yadav
- Department of Biotechnology, Akal College of Agriculture, Eternal University, Baru Sahib, India
| | - Atul Kumar Singh
- Division of Infectious Diseases, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Surendra Singh
- Department of Biological Science, Rani Durgavati University, Jabalpur, India
| | - Rajeev Kaushik
- Division of Microbiology, Indian Agricultural Research Institute, New Delhi, India
| | - Anil Kumar Saxena
- National Bureau of Agriculturally Important Microorganisms, Kushmaur, Mau Nath Bhanjan, Mau, Uttar Pradesh, 275103, India.
| |
Collapse
|
48
|
Characterisation of Pseudomonas spp. and Ochrobactrum sp. isolated from volcanic soil. Antonie van Leeuwenhoek 2016; 110:253-270. [PMID: 27853952 DOI: 10.1007/s10482-016-0796-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 10/24/2016] [Indexed: 10/20/2022]
Abstract
Soil bacteria may have properties of plant growth promotion but not be sufficiently beneficial for plants under stress conditions. This challenge has led researchers to extend their searches into extreme environments for potential soil bacteria with multiple plant beneficial traits as well as abiotic stress tolerance abilities. In the current study, an attempt was made to evaluate soil bacteria from an extreme environment, volcano soils, based on plant growth promoting and abiotic stress mitigating characteristics. The screening led to the isolation of eight (NBRISH4, NBRISH6, NBRISH10, NBRISH11, NBRISH13, NBRISH14, NBRISH16 and NBRISH26) bacterial isolates capable of withstanding stresses, namely temperature (up to 45 °C), salt (up to 2 M NaCl) and drought (up to 60% Poly Ethylene Glycol 6000) in vitro. Further, the selected isolates were notable for their in vitro temporal performance with regards to survival (in terms of colony count), phosphate solubilisation, biofilm formation, auxin, alginate and exo-polysaccharide production abilities under abiotic stresses i.e. 40 °C temperature; 500 mM NaCl salt and drought (PEG) conditions. In vivo seed treatments of individual selected bacteria to maize plants resulted into significant enhancement in root and shoot length, root and shoot fresh and dry weight and number of leaves per plant. Overall, the plant growth promoting and abiotic stress tolerance ability was most evident for bacterial isolate NBRISH6 which was identified as an Ochrobactrum sp. using 16S rRNA based phylogenetic analysis.
Collapse
|
49
|
Liu S, Liu W, Yang M, Zhou L, Liang H. The genetic diversity of soil bacteria affected by phytoremediation in a typical barren rare earth mined site of South China. SPRINGERPLUS 2016; 5:1131. [PMID: 27478748 PMCID: PMC4951393 DOI: 10.1186/s40064-016-2814-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 07/12/2016] [Indexed: 11/10/2022]
Abstract
The soil bacterial diversity is one of the most important indicators to evaluate the effect of phytoremediation. In this study, the technologies of Sequence-Related Amplified Polymorphism (SRAP) and 16S rRNA gene sequence analysis were used to evaluate the soil bacterial diversity after phytoremediation in a barren rare earth mined area. The results showed that the plant density was remarkably increased after the phytoremediation. The SRAP analysis suggested that the soil bacterial diversity declined dramatically after mining, while increased significantly in second and third year of the phytoremediation. A total of eight bacterial genera were identified by using 16S rRNA gene sequence analysis, with Arthrobacter and Bacillus as the dominant species before the mining, and Brevibacillus as the dominant species after the mining and during the first year of the phytoremediation. The Bacillus, which was a dominant type of bacteria before the mining, disappeared after mining and appeared again in the second and third years of the phytoremediation, other bacterial genera present. Principal component analysis and 16S rRNA gene analysis revealed a new bacterial type after phytoremediation that was not existed in the original mined area. The results of the present study indicated that the soil bacterial richness and genetic diversity significantly increased after the phytoremediation in the mined site.
Collapse
Affiliation(s)
- Shenghong Liu
- College of Life Sciences, Zhongkai University of Agriculture and Engineering, NO. 501, Zhongkai Road, Haizhu District, Guangzhou, 510225 China
| | - Wen Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, NO. 483, Wushan Road, Tianhe District, Guangzhou, 510642 China
| | - Miaoxian Yang
- College of Life Sciences, Zhongkai University of Agriculture and Engineering, NO. 501, Zhongkai Road, Haizhu District, Guangzhou, 510225 China
| | - Lingyan Zhou
- College of Life Sciences, Zhongkai University of Agriculture and Engineering, NO. 501, Zhongkai Road, Haizhu District, Guangzhou, 510225 China
| | - Hong Liang
- College of Life Sciences, Zhongkai University of Agriculture and Engineering, NO. 501, Zhongkai Road, Haizhu District, Guangzhou, 510225 China
| |
Collapse
|
50
|
Verma P, Yadav AN, Khannam KS, Mishra S, Kumar S, Saxena AK, Suman A. Appraisal of diversity and functional attributes of thermotolerant wheat associated bacteria from the peninsular zone of India. Saudi J Biol Sci 2016; 26:1882-1895. [PMID: 31762671 PMCID: PMC6864300 DOI: 10.1016/j.sjbs.2016.01.042] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Revised: 01/24/2016] [Accepted: 01/27/2016] [Indexed: 11/09/2022] Open
Abstract
The biodiversity of wheat associated bacteria was deciphered from the peninsular zone of India. A total of 264 isolated bacteria were analyzed through amplified ribosomal DNA restriction analysis (ARDRA, using three restriction enzymes Alu I, Msp I and Hae III, which led to the clustering of these isolates into 12–16 groups for the different sites at >75% similarity index, adding up to 70 groups). 16S rRNA gene based phylogenetic analysis, revealed that all the bacteria belonged to three phyla Proteobacteria, Firmicutes, and Actinobacteria of 32 distinct species of 15 genera namely: Achromobacter, Alcaligenes, Arthrobacter, Bacillus, Delftia, Enterobacter, Exiguobacterium, Klebsiella, Methylobacterium, Micrococcus, Paenibacillus, Pseudomonas, Rhodobacter, Salmonella and Staphylococcus. Representative strains from each cluster were screened in vitro for plant growth promoting traits. Among plant growth promoting activities, siderophore producers were highest (15%), when compared to indole acetic acid producers (13%), Zn-solubilizers (11%), P-solubilizers (11%), ammonia (10%), hydrogen cyanide producers (9%), biocontrol (8%), N2-fixers (7%), 1-aminocyclopropane-1-carboxylate deaminase (6%), GA producers (6%) and K-solubilizers (5%). Among 32 representative strains, Alcaligenes faecalis, Arthrobacter sp., Bacillus siamensis, Bacillus subtilis, Delftia acidovorans, Methylobacterium mesophilicum, Methylobacterium sp., Pseudomonas poae, Pseudomonas putida, and Pseudomonas stutzeri exhibited more than six different plant growth promoting activities at high temperature. Thermotolerant bacterial isolates may have application as inoculants for plant growth promotion and biocontrol agents for crops growing at high temperature conditions.
Collapse
Affiliation(s)
- Priyanka Verma
- Division of Microbiology, Indian Agricultural Research Institute, New Delhi 110012, India.,Department of Biotechnology, National Institute of Technology, Durgapur 713209, India
| | - Ajar Nath Yadav
- Division of Microbiology, Indian Agricultural Research Institute, New Delhi 110012, India.,Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi 835215, India.,Department of Biotechnology, Akal College of Agriculture, Eternal University, Baru Sahib, Sirmour-173101, India
| | - Kazy Sufia Khannam
- Department of Biotechnology, National Institute of Technology, Durgapur 713209, India
| | - Shashank Mishra
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi 835215, India
| | - Sanjay Kumar
- Division of Genetics, Indian Agricultural Research Institute, New Delhi 110012, India
| | - Anil Kumar Saxena
- Division of Microbiology, Indian Agricultural Research Institute, New Delhi 110012, India
| | - Archna Suman
- Division of Microbiology, Indian Agricultural Research Institute, New Delhi 110012, India
| |
Collapse
|