1
|
Yin Z, Zhang M, Jing C, Cai Y. Organic matter in geothermal springs and its association with the microbial community. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 954:176775. [PMID: 39378948 DOI: 10.1016/j.scitotenv.2024.176775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Revised: 09/08/2024] [Accepted: 10/04/2024] [Indexed: 10/10/2024]
Abstract
Organic matter (OM) plays an important role in the biogeochemical cycles of carbon, nitrogen, and other elements, shaping the structure of the microbiome and vice versa. However, the molecular composition of OM and its impact on the microbial community in terrestrial geothermal environments remain unclear. In this study, we characterized the OM in water and sediment from a typical geothermal field using ultra-high-resolution Fourier transform ion cyclotron resonance mass spectrometry. By combining high-throughput amplicon sequencing and multivariate analyses, we deciphered the association between OM components and microbial community. A surprisingly high chemodiversity of OM was observed in the waters (11,088 compounds) and sediments (7772 compounds) in geothermal springs. Sulfur-containing organic compounds, a characteristic molecular signature of geothermal springs, accounted for 21 % ± 5 % in waters and 33 % ± 4 % in sediments. Multivariate analyses revealed that both labile and recalcitrant fractions of OM (e.g., carbohydrates intensity and tannins chemodiversity) influenced the structure and function of the microbial community. Co-occurrence networks showed that Proteobacteria and Crenarchaeota accounted for most of the connections with OM in waters (33 % and 15 %, respectively) and sediments (15 % and 12 %, respectively), highlighting their key roles in carbon cycling. This study expands our understanding of the molecular compositions of OM in geothermal springs and highlights its potentially important role in global climate change through microbial carbon cycling.
Collapse
Affiliation(s)
- Zhipeng Yin
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, Qingdao 266237, China
| | - Min Zhang
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, Qingdao 266237, China.
| | - Chuanyong Jing
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, Qingdao 266237, China; State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yong Cai
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, Qingdao 266237, China; Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, United States.
| |
Collapse
|
2
|
Burkhardt C, Baruth L, Neele Meyer-Heydecke, Klippel B, Margaryan A, Paloyan A, Panosyan HH, Antranikian G. Mining thermophiles for biotechnologically relevant enzymes: evaluating the potential of European and Caucasian hot springs. Extremophiles 2023; 28:5. [PMID: 37991546 PMCID: PMC10665251 DOI: 10.1007/s00792-023-01321-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 10/06/2023] [Indexed: 11/23/2023]
Abstract
The development of sustainable and environmentally friendly industrial processes is becoming very crucial and demanding for the rapid implementation of innovative bio-based technologies. Natural extreme environments harbor the potential for discovering and utilizing highly specific and efficient biocatalysts that are adapted to harsh conditions. This review focuses on extremophilic microorganisms and their enzymes (extremozymes) from various hot springs, shallow marine vents, and other geothermal habitats in Europe and the Caucasus region. These hot environments have been partially investigated and analyzed for microbial diversity and enzymology. Hotspots like Iceland, Italy, and the Azores harbor unique microorganisms, including bacteria and archaea. The latest results demonstrate a great potential for the discovery of new microbial species and unique enzymes that can be explored for the development of Circular Bioeconomy.Different screening approaches have been used to discover enzymes that are active at extremes of temperature (up 120 °C), pH (0.1 to 11), high salt concentration (up to 30%) as well as activity in the presence of solvents (up to 99%). The majority of published enzymes were revealed from bacterial or archaeal isolates by traditional activity-based screening techniques. However, the latest developments in molecular biology, bioinformatics, and genomics have revolutionized life science technologies. Post-genomic era has contributed to the discovery of millions of sequences coding for a huge number of biocatalysts. Both strategies, activity- and sequence-based screening approaches, are complementary and contribute to the discovery of unique enzymes that have not been extensively utilized so far.
Collapse
Affiliation(s)
- Christin Burkhardt
- Institute of Technical Biocatalysis, Center for Biobased Solutions, Hamburg University of Technology, Am Schwarzenberg-Campus 4, 21073, Hamburg, Germany
| | - Leon Baruth
- Institute of Technical Biocatalysis, Center for Biobased Solutions, Hamburg University of Technology, Am Schwarzenberg-Campus 4, 21073, Hamburg, Germany
| | - Neele Meyer-Heydecke
- Institute of Technical Biocatalysis, Center for Biobased Solutions, Hamburg University of Technology, Am Schwarzenberg-Campus 4, 21073, Hamburg, Germany
| | - Barbara Klippel
- Institute of Technical Biocatalysis, Center for Biobased Solutions, Hamburg University of Technology, Am Schwarzenberg-Campus 4, 21073, Hamburg, Germany
| | - Armine Margaryan
- Department of Biochemistry, Microbiology and Biotechnology, Yerevan State University, Alex Manoogian 1, 0025, Yerevan, Armenia
- Research Institute of Biology, Yerevan State University, Alex Manoogian 1, 0025, Yerevan, Armenia
| | - Ani Paloyan
- Scientific and Production Center, "Armbiotechnology" NAS RA, 14 Gyurjyan Str. 0056, Yerevan, Armenia
| | - Hovik H Panosyan
- Department of Biochemistry, Microbiology and Biotechnology, Yerevan State University, Alex Manoogian 1, 0025, Yerevan, Armenia
- Research Institute of Biology, Yerevan State University, Alex Manoogian 1, 0025, Yerevan, Armenia
| | - Garabed Antranikian
- Institute of Technical Biocatalysis, Center for Biobased Solutions, Hamburg University of Technology, Am Schwarzenberg-Campus 4, 21073, Hamburg, Germany.
| |
Collapse
|
3
|
Kumari A, Mihooliya KN, Sahoo DK, Bhattacharyya MS, Prasad GS, Pinnaka AK. Description of lipase producing novel yeast species Debaryomyces apis f.a., sp. nov. and a modified pH indicator dye-based method for the screening of lipase producing microorganisms. Sci Rep 2023; 13:11819. [PMID: 37479715 PMCID: PMC10362016 DOI: 10.1038/s41598-023-38241-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 07/05/2023] [Indexed: 07/23/2023] Open
Abstract
Four yeast strains were isolated from the gut of stingless bee, collected in Churdhar, Himachal Pradesh, India. Physiological characterization, morphological examination, and sequence analysis of small subunit ribosomal RNA (18S rRNA) genes, internal transcribed spacer (ITS) region, and D1/D2 domain of the large subunit rRNA gene revealed that the four strains isolated from the gut of stingless bee belonged to the Debaryomyces clade. Strain CIG-23HT showed sequence divergence of 7.5% from Debaryomyces nepalensis JCM 2095T, 7.8% from Debaryomyces udenii JCM 7855T, and Debaryomyces coudertii JCM 2387T in the D1/D2 domain. In the ITS region sequences, strain CIG-23HT showed a 15% sequence divergence from Debaryomyces nepalensis JCM 2095T and Debaryomyces coudertii JCM 2387T. In 18S rRNA gene sequence, the strain CIG-23HT showed 1.14% sequence divergence from Debaryomyces nepalensis JCM 2095 and and Debaryomyces coudertii JCM 2387, and 0.83% sequence divergence from Debaryomyces hansenii NRRL Y-7426. Strain CIG-23HT can utilize more carbon sources than closely related species. The findings suggest that strain CIG-23HT is a novel species of the genus Debaryomyces, and we propose to name it as Debaryomyces apis f.a., sp. nov. The holotype is CBS 16297T, and the isotypes are MTCC 12914T and KCTC 37024T. The MycoBank number of Debaryomyces apis f.a., sp. nov. is MB836065. Additionally, a method using cresol red and Bromothymol blue pH indicator dyes was developed to screen for lipase producers, which is more sensitive and efficient than the currently used phenol red and rhodamine B dye-based screening methods, and avoids the problem of less differentiable zone of hydrolysis.
Collapse
Affiliation(s)
- Alka Kumari
- Microbial Type Culture Collection (MTCC), CSIR-Institute of Microbial Technology, Chandigarh, 160036, India
| | - Kanti N Mihooliya
- Biochemical Engineering Research and Process Development Centre, CSIR-Institute of Microbial Technology, Chandigarh, 160036, India
| | - Debendra K Sahoo
- Biochemical Engineering Research and Process Development Centre, CSIR-Institute of Microbial Technology, Chandigarh, 160036, India
| | - Mani S Bhattacharyya
- Biochemical Engineering Research and Process Development Centre, CSIR-Institute of Microbial Technology, Chandigarh, 160036, India
| | - Gandham S Prasad
- Microbial Type Culture Collection (MTCC), CSIR-Institute of Microbial Technology, Chandigarh, 160036, India.
- Centre for Knowledge Culture and Innovation Studies, Technology Industrial Liaison and Entrepreneurship Unit, University of Hyderabad, Prof. C R Rao Road, Gachibowli, Hyderabad, Telangana, 500046, India.
| | - Anil Kumar Pinnaka
- Microbial Type Culture Collection (MTCC), CSIR-Institute of Microbial Technology, Chandigarh, 160036, India.
| |
Collapse
|
4
|
Masi C, Tebiso A, Selva Kumar K. Isolation and characterization of potential multiple extracellular enzyme-producing bacteria from waste dumping area in Addis Ababa. Heliyon 2023; 9:e12645. [PMID: 36793964 PMCID: PMC9922826 DOI: 10.1016/j.heliyon.2022.e12645] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 11/01/2022] [Accepted: 12/20/2022] [Indexed: 01/06/2023] Open
Abstract
Extremozymes are innovative and robust biocatalysts produced by various microorganisms from harsh environments. As thermophilic organisms can only develop in a few places, studying them in geothermal environments has provided new insights into the origins and evolution of early life and access to significant bio-resources with potential biotechnology applications. The work aimed to isolate and identify likely multiple extracellular enzyme-producing thermophilic bacteria from an Addis Ababa landfill (Qoshe). The streaking approach was used to purify 102 isolates acquired by serial dilution and spread plate method. The isolates were morphologically and biochemically characterized. Thirty-five cellulases, 22 amylase, 17 protease, and nine lipase-producing bacteria were identified using primary screening methods. Further secondary screening using Strain safety evaluation; two bacterial strains (TQ11 and TQ46) were identified. Based on morphological and biochemical tests, they were found to be gram-positive and rod-shaped. Furthermore, molecular identification and phylogenic analysis of selected promising isolates confirmed the identity of the isolates, Paenibacillus dendritiformis (TQ11) and Anoxybacillus flavithermus (TQ46). The results indicated that, multiple extracellular enzyme-producing thermophilic bacteria isolated from a waste dumping area in Addis Ababa offer useful features for environmental sustainability in a wide range of industrial applications due to their biodegradability and specialized stability under extreme conditions, increased raw material utilization, and decreased waste.
Collapse
Affiliation(s)
- Chandran Masi
- Department of Biotechnology, College of Biological and Chemical Engineering, Addis Ababa Science and Technology University, P.O. Box 16417, Addis Ababa, Ethiopia,Bioprocess and Biotechnology Center of Excellence, Addis Ababa Science and Technology University, P.O. Box 16417, Addis Ababa, Ethiopia,Corresponding author. Department of Biotechnology, College of Biological and Chemical Engineering, Addis Ababa Science and Technology University, P.O. Box 16417, Addis Ababa, Ethiopia.
| | - Abel Tebiso
- Department of Biotechnology, College of Biological and Chemical Engineering, Addis Ababa Science and Technology University, P.O. Box 16417, Addis Ababa, Ethiopia
| | - K.V. Selva Kumar
- School of Chemical and Bioengineering, Dire Dawa University Institute of Technology, Dire Dawa, Ethiopia
| |
Collapse
|
5
|
Microbial Diversity of Terrestrial Geothermal Springs in Armenia and Nagorno-Karabakh: A Review. Microorganisms 2021; 9:microorganisms9071473. [PMID: 34361908 PMCID: PMC8307006 DOI: 10.3390/microorganisms9071473] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/24/2021] [Accepted: 07/07/2021] [Indexed: 12/25/2022] Open
Abstract
The microbial diversity of high-altitude geothermal springs has been recently assessed to explore their biotechnological potential. However, little is known regarding the microbiota of similar ecosystems located on the Armenian Highland. This review summarizes the known information on the microbiota of nine high-altitude mineralized geothermal springs (temperature range 25.8–70 °C and pH range 6.0–7.5) in Armenia and Nagorno-Karabakh. All these geothermal springs are at altitudes ranging from 960–2090 m above sea level and are located on the Alpide (Alpine–Himalayan) orogenic belt, a seismically active region. A mixed-cation mixed-anion composition, with total mineralization of 0.5 mg/L, has been identified for these thermal springs. The taxonomic diversity of hot spring microbiomes has been examined using culture-independent approaches, including denaturing gradient gel electrophoresis (DGGE), 16S rRNA gene library construction, 454 pyrosequencing, and Illumina HiSeq. The bacterial phyla Proteobacteria, Bacteroidetes, Cyanobacteria, and Firmicutes are the predominant life forms in the studied springs. Archaea mainly include the phyla Euryarchaeota, Crenarchaeota, and Thaumarchaeota, and comprise less than 1% of the prokaryotic community. Comparison of microbial diversity in springs from Karvachar with that described for other terrestrial hot springs revealed that Proteobacteria, Bacteroidetes, Actinobacteria, and Deinococcus–Thermus are the common bacterial groups in terrestrial hot springs. Contemporaneously, specific bacterial and archaeal taxa were observed in different springs. Evaluation of the carbon, sulfur, and nitrogen metabolism in these hot spring communities has revealed diversity in terms of metabolic activity. Temperature seems to be an important factor in shaping the microbial communities of these springs. Overall, the diversity and richness of the microbiota are negatively affected by increasing temperature. Other abiotic factors, including pH, mineralization, and geological history, also impact the structure and function of the microbial community. More than 130 bacterial and archaeal strains (Bacillus, Geobacillus, Parageobacillus, Anoxybacillus, Paenibacillus, Brevibacillus Aeribacillus, Ureibacillus, Thermoactinomyces, Sporosarcina, Thermus, Rhodobacter, Thiospirillum, Thiocapsa, Rhodopseudomonas, Methylocaldum, Desulfomicrobium, Desulfovibrio, Treponema, Arcobacter, Nitropspira, and Methanoculleus) have been reported, some of which may be representative of novel species (sharing 91–97% sequence identity with their closest matches in GenBank) and producers of thermozymes and biomolecules with potential biotechnological applications. Whole-genome shotgun sequencing of T. scotoductus K1, as well as of the potentially new Treponema sp. J25 and Anoxybacillus sp. K1, were performed. Most of the phyla identified by 16S rRNA were also identified using metagenomic approaches. Detailed characterization of thermophilic isolates indicate the potential of the studied springs as a source of biotechnologically valuable microbes and biomolecules.
Collapse
|
6
|
Tailor AJ, Gadhvi RR, Joshi BP. Draft genome sequence of a hot spring bacterial isolate Brevibacillus borstelensis Gp-1 with potential extracellular lipase activity. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2021.101161] [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]
|
7
|
Liu Y, Shao X, Kong D, Li G, Li Q. Immobilization of thermophilic lipase in inorganic hybrid nanoflower through biomimetic mineralization. Colloids Surf B Biointerfaces 2021; 197:111450. [DOI: 10.1016/j.colsurfb.2020.111450] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 10/29/2020] [Accepted: 11/03/2020] [Indexed: 12/12/2022]
|
8
|
Panosyan H, Margaryan A, Birkeland NK. Geothermal springs in Armenia and Nagorno-Karabakh: potential sources of hydrolase-producing thermophilic bacilli. Extremophiles 2020; 24:519-536. [PMID: 32390108 DOI: 10.1007/s00792-020-01173-1] [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: 10/24/2019] [Accepted: 04/27/2020] [Indexed: 02/02/2023]
Abstract
In recent years, scientists have increasingly focused on the microbial diversity of high-altitude hot springs to explore the biotechnological applications of extremophiles. In this regard, a total of 107 thermophilic bacilli were isolated from 9 high-altitude mineralized geothermal springs (of temperatures ranging from 27.5 to 70 °C) located within the territory of Armenia and Nagorno-Karabakh. The isolated bacilli were phylogenetically profiled and studied for their potential to produce extracellular hydrolytic enzymes (protease, amylase, and lipase). The identification of isolates based on 16S rRNA gene sequences revealed their relationship to members of more than 22 distinct species, of 8 different genera, namely Aeribacillus, Anoxybacillus, Bacillus, Brevibacillus, Geobacillus, Parageobacillus, Paenibacillus and Ureibacillus. Bacillus licheniformis, Parageobacillus toebii and Anoxybacillus flavithermus were found to be the most abundant species in the springs that were studied. Some of the isolated bacilli shared less than 91-97% sequence identity with their closest match in GenBank, indicating that Armenian geothermal springs harbor novel bacilli, at least at the species level. 71% of the isolates actively produced at least one or more extracellular proteases, amylases, or lipases. In total, 22 strains (28.6%) were efficient producers of all three types of thermostable enzymes.
Collapse
Affiliation(s)
- Hovik Panosyan
- Department of Biochemistry, Microbiology and Biotechnology, Yerevan State University, Alex Manoogian 1, 0025, Yerevan, Armenia.
| | - Armine Margaryan
- Department of Biochemistry, Microbiology and Biotechnology, Yerevan State University, Alex Manoogian 1, 0025, Yerevan, Armenia
| | - Nils-Kåre Birkeland
- Department of Biological Sciences, University of Bergen, P.O. Box 7803, 5020, Bergen, Norway
| |
Collapse
|
9
|
Khan MT, Kaushik AC, Rana QUA, Malik SI, Khan AS, Wei DQ, Sajjad W, Ahmad S, Ali S, Ameenullah, Irfan M. Characterization and synthetic biology of lipase from Bacillus amyloliquefaciens strain. Arch Microbiol 2020; 202:1497-1506. [PMID: 32219482 DOI: 10.1007/s00203-020-01869-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 03/05/2020] [Accepted: 03/12/2020] [Indexed: 10/24/2022]
Abstract
Lipases with high tolerance to temperature play a significant role in industry from food manufacturing to waste management systems. Thus, there is a need to investigate these enzymes from different geographical areas to look out for a more thermo-stable one. Characterization of lipases through experimental approaches is time consuming process and sometimes the results are ambiguous due to errors. However, integration of computational technologies is quite useful for prediction of optimized conditions. Such technologies can be applied as synthetic biology, which has many major applications in engineered biological approaches for accurate prediction of effects of different physical and chemical parameters on the system. In this study, cloning and expression of a lipase gene from Bacillus amyloliquefaciens, isolated from a novel geographical region of Pakistan, in Escherichia coli DH5α cells followed by sequencing was carried out. To isolate thermostable lipase producing strains, all the samples were kept at 50 °C. Genomic DNA was isolated and signal peptide (1-32 residues) sequence was chopped (ΔSPLipase). The ΔSPLipase was amplified and expressed in Linearized p15TV-L vector. The purified lipase appeared as single band of approximately 26 kDa. Suitable conditions of factors required for maximum lipase activity such as temperature, pH, substrate, organic solvent, detergents and metal ions were predicted through synthetic biology approach and further confirmed in wet lab. The predicted suitable factors for enzyme were almost similar to those determined experimentally. The optimum enzyme activity was recorded at pH 8 and 50 °C temperature. Interestingly, the activity of enzyme was found on a number of solvents, metal ions, detergents, and surfactants. The predicted optimum values and their experimental confirmations highlights the importance of integrated synthetic biology approaches in wet lab experiments. The characterized lipase of B. amyloliquefaciens at molecular level from Pakistani strains displayed good activity on a range of factors that implies this strain to be used for application in industrial level production.
Collapse
Affiliation(s)
- Muhammad Tahir Khan
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology, Islamabad, Pakistan.,College of Life Sciences and Biotechnology, The State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Aman Chandra Kaushik
- College of Life Sciences and Biotechnology, The State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Qurrat Ul Ain Rana
- Department of Microbiology, Quaid-I-Azam University, Islamabad, Pakistan
| | - Shaukat Iqbal Malik
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology, Islamabad, Pakistan
| | - Anwar Sheed Khan
- Department of Microbiology, Kohat University of Science and Technology, Khyber Pakhtunkhwa, Pakistan
| | - Dong-Qing Wei
- College of Life Sciences and Biotechnology, The State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Wasim Sajjad
- State Key Laboratory of Cryosphere Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
| | - Shabir Ahmad
- Institute of Biological Sciences, Sarhad University of Science & Information Technology, Hayatabad Link Landi-Akhun Ahmad. Ring Road, Peshawar, 2500, Pakistan
| | - Sajid Ali
- Institute of Biological Sciences, Sarhad University of Science & Information Technology, Hayatabad Link Landi-Akhun Ahmad. Ring Road, Peshawar, 2500, Pakistan.,Provincial TB Reference Laboratory, Peshawar, Pakistan
| | - Ameenullah
- Department of Microbiology, Quaid-I-Azam University, Islamabad, Pakistan
| | - Muhammad Irfan
- Institute of Biological Sciences, Sarhad University of Science & Information Technology, Hayatabad Link Landi-Akhun Ahmad. Ring Road, Peshawar, 2500, Pakistan.
| |
Collapse
|
10
|
Meng F, Bar-Shmuel N, Shavit R, Behar A, Segoli M. Gut bacteria of weevils developing on plant roots under extreme desert conditions. BMC Microbiol 2019; 19:311. [PMID: 31888482 PMCID: PMC6937996 DOI: 10.1186/s12866-019-1690-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 12/18/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Many phytophagous insects, whose diet is generally nitrogen-poor, rely on gut bacteria to compensate for nutritional deficits. Accordingly, we hypothesized that insects in desert environments may evolve associations with gut bacteria to adapt to the extremely low nutrient availability. For this, we conducted a systematic survey of bacterial communities in the guts of weevils developing inside mud chambers affixed to plant roots in the Negev Desert of Israel, based on 16S rRNA gene amplicon sequencing. RESULTS Our analyses revealed that gut bacterial communities in weevil larvae were similar across a wide geographical range, but differed significantly from those of the mud chambers and of the surrounding soils. Nevertheless, a high proportion of bacteria (including all of the core bacteria) found in the weevils were also detected in the mud chambers and soils at low relative abundances. The genus Citrobacter (of the Enterobacteriaceae family) was the predominant group in the guts of all individual weevils. The relative abundance of Citrobacter significantly decreased at the pupal and adult stages, while bacterial diversity increased. A mini literature survey revealed that members of the genus Citrobacter are associated with nitrogen fixation, recycling of uric acid nitrogen, and cellulose degradation in different insects. CONCLUSIONS The results suggest that although weevils could potentially acquire their gut bacteria from the soil, weevil host internal factors, rather than external environmental factors, were more important in shaping their gut bacterial communities, and suggest a major role for Citrobacter in weevil nutrition in this challenging environment. This study highlights the potential involvement of gut bacteria in the adaptation of insects to nutritional deficiencies under extreme desert conditions.
Collapse
Affiliation(s)
- Fengqun Meng
- Mitrani Department of Desert Ecology, The Swiss Institute for Dryland Environmental and Energy Research, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel.
| | - Nitsan Bar-Shmuel
- Mitrani Department of Desert Ecology, The Swiss Institute for Dryland Environmental and Energy Research, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel
| | - Reut Shavit
- French Associates Institute for Agriculture and Biotechnology of Drylands, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel
| | - Adi Behar
- Division of Parasitology, Kimron Veterinary Institute, Bet Dagan, Israel
| | - Michal Segoli
- Mitrani Department of Desert Ecology, The Swiss Institute for Dryland Environmental and Energy Research, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel
| |
Collapse
|
11
|
Le LTHL, Yoo W, Jeon S, Kim KK, Kim TD. Characterization and Immobilization of a Novel SGNH Family Esterase ( LaSGNH1) from Lactobacillus acidophilus NCFM. Int J Mol Sci 2019; 21:ijms21010091. [PMID: 31877740 PMCID: PMC6981805 DOI: 10.3390/ijms21010091] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 12/10/2019] [Accepted: 12/17/2019] [Indexed: 12/20/2022] Open
Abstract
The SGNH family esterases are highly effective biocatalysts due to their strong catalytic efficiencies, great stabilities, relatively small sizes, and ease of immobilization. Here, a novel SGNH family esterase (LaSGNH1) from Lactobacillus acidophilus NCFM, which has homologues in many Lactobacillus species, was identified, characterized, and immobilized. LaSGNH1 is highly active towards acetate- or butyrate-containing compounds, such as p-nitrophenyl acetate or 1-naphthyl acetate. Enzymatic properties of LaSGNH1, including thermal stability, optimum pH, chemical stability, and urea stability, were investigated. Interestingly, LaSGNH1 displayed a wide range of substrate specificity that included glyceryl tributyrate, tert-butyl acetate, and glucose pentaacetate. Furthermore, immobilization of LaSGNH1 by crosslinked enzyme aggregates (CLEAs) showed enhanced thermal stability and efficient recycling property. In summary, this work paves the way for molecular understandings and industrial applications of a novel SGNH family esterase (LaSGNH1) from Lactobacillus acidophilus.
Collapse
Affiliation(s)
- Ly Thi Huong Luu Le
- Department of Chemistry, College of Natural Science, Sookmyung Women’s University, Seoul 04310, Korea; (L.T.H.L.L.); (W.Y.); (S.J.)
| | - Wanki Yoo
- Department of Chemistry, College of Natural Science, Sookmyung Women’s University, Seoul 04310, Korea; (L.T.H.L.L.); (W.Y.); (S.J.)
- Department of Precision Medicine, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, Korea;
| | - Sangeun Jeon
- Department of Chemistry, College of Natural Science, Sookmyung Women’s University, Seoul 04310, Korea; (L.T.H.L.L.); (W.Y.); (S.J.)
| | - Kyeong Kyu Kim
- Department of Precision Medicine, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, Korea;
| | - T. Doohun Kim
- Department of Chemistry, College of Natural Science, Sookmyung Women’s University, Seoul 04310, Korea; (L.T.H.L.L.); (W.Y.); (S.J.)
- Correspondence: ; Tel.: +82-10-2739-6479
| |
Collapse
|
12
|
Thermoactinomycetes isolated from geothermal springs in Armenia capable of producing extracellular hydrolases. ACTA ACUST UNITED AC 2019. [DOI: 10.1007/s42398-019-00066-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
13
|
Abstract
Abstract
Lipases cleaving oils into fatty acids and glycerol are of great interest for the use in increasing the efficiency of fuels. In this work, a novel lipase from Pseudomonas aeruginosa, P. aeruginosa A12, was isolated by ion-exchange and hydrophobic chromatography. The purity of lipase was shown by electrophoresis and its molecular weight was estimated to be ~ 31.6 kDa. The whole amino acid sequence was analyzed by an LC-MS/MS method. Temperature- and pH-dependent optimum of the enzyme compiled 30 °C and 7.5, respectively. The obtained enzyme exhibited 79 % similarity of amino acid sequence to a lipase isolated from the same strain of P. aeruginosa. Thus, the novel lipase was determined to belong to I.1 subfamily of bacterial true lipases. Three dimensional structure of the isolated lipase isoform was modeled based on obtained sequences. Amino acids forming the catalytic domain were shown in the model. Lid domain is suggested to be in the open conformation. These results provide a potential alternative for enzymatic digestion of fuel oils and serve for the development of fundamental knowledge of lipase activity.
Collapse
|
14
|
Mohr T, Aliyu H, Küchlin R, Zwick M, Cowan D, Neumann A, de Maayer P. Comparative genomic analysis of Parageobacillus thermoglucosidasius strains with distinct hydrogenogenic capacities. BMC Genomics 2018; 19:880. [PMID: 30522433 PMCID: PMC6282330 DOI: 10.1186/s12864-018-5302-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 11/21/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The facultatively anaerobic thermophile Parageobacillus thermoglucosidasius produces hydrogen gas (H2) by coupling CO oxidation to proton reduction in the water-gas shift (WGS) reaction via a carbon monoxide dehydrogenase-hydrogenase enzyme complex. Although little is known about the hydrogenogenic capacities of different strains of this species, these organisms offer a potentially viable process for the synthesis of this alternative energy source. RESULTS The WGS-catalyzed H2 production capacities of four distinct P. thermoglucosidasius strains were determined by cultivation and gas analysis. Three strains (DSM 2542T, DSM 2543 and DSM 6285) were hydrogenogenic, while the fourth strain (DSM 21625) was not. Furthermore, in one strain (DSM 6285) H2 production commenced earlier in the cultivation than the other hydrogenogenic strains. Comparative genomic analysis of the four strains identified extensive differences in the protein complement encoded on the genomes, some of which are postulated to contribute to the different hydrogenogenic capacities of the strains. Furthermore, polymorphisms and deletions in the CODH-NiFe hydrogenase loci may also contribute towards this variable phenotype. CONCLUSIONS Disparities in the hydrogenogenic capacities of different P. thermoglucosidasius strains were identified, which may be correlated to variability in their global proteomes and genetic differences in their CODH-NiFe hydrogenase loci. The data from this study may contribute towards an improved understanding of WGS-catalysed hydrogenogenesis by P. thermoglucosidasius.
Collapse
Affiliation(s)
- Teresa Mohr
- Section II: Technical Biology, Institute of Process engineering in Life Science, Karlsruhe Institute of Technology, Kaiserstrasse 12, 76131 Karlsruhe, Germany
| | - Habibu Aliyu
- Section II: Technical Biology, Institute of Process engineering in Life Science, Karlsruhe Institute of Technology, Kaiserstrasse 12, 76131 Karlsruhe, Germany
| | - Raphael Küchlin
- Section II: Technical Biology, Institute of Process engineering in Life Science, Karlsruhe Institute of Technology, Kaiserstrasse 12, 76131 Karlsruhe, Germany
| | - Michaela Zwick
- Section II: Technical Biology, Institute of Process engineering in Life Science, Karlsruhe Institute of Technology, Kaiserstrasse 12, 76131 Karlsruhe, Germany
| | - Don Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, Pretoria, 0028 South Africa
| | - Anke Neumann
- Section II: Technical Biology, Institute of Process engineering in Life Science, Karlsruhe Institute of Technology, Kaiserstrasse 12, 76131 Karlsruhe, Germany
| | - Pieter de Maayer
- School of Molecular & Cell Biology, Faculty of Science, University of the Witwatersrand, WITS, Johannesburg, 2050 South Africa
| |
Collapse
|
15
|
Peculiarities and biotechnological potential of environmental adaptation by Geobacillus species. Appl Microbiol Biotechnol 2018; 102:10425-10437. [PMID: 30310966 DOI: 10.1007/s00253-018-9422-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 09/25/2018] [Accepted: 09/26/2018] [Indexed: 12/21/2022]
Abstract
The genus Geobacillus comprises thermophilic bacilli capable of endospore formation. The members of this genus provide thermostable proteins and can be used in whole cell applications at elevated temperatures; therefore, these organisms are of biotechnological importance. While these applications have been described in previous reviews, the present paper highlights the environmental adaptations and genome diversifications of Geobacillus spp. and their applications in evolutionary-protein engineering. Despite their obligate thermophilic properties, Geobacillus spp. are widely distributed in nature. Because several isolates demonstrate remarkable properties for cell reproduction in their respective niches, they seem to exist not only as endospores but also as vegetative cells in diverse environments. This suggests their excellence in environmental adaptation via genome diversification; in fact, evidence suggests that Geobacillus spp. were derived from Bacillus spp. while diversifying their genomes via horizontal gene transfer. Moreover, when subjected to an environmental stressor, Geobacillus spp. diversify their genomes using inductive mutations and transposable elements to produce derivative cells that are adaptive to the stressor. Notably, inductive mutations in Geobacillus spp. occur more rapidly and frequently than the stress-induced mutagenesis observed in other microorganisms. Owing to this, Geobacillus spp. can efficiently generate mutant genes coding for thermostable enzyme variants from the thermolabile enzyme genes under appropriate selection pressures. This phenomenon provides a new approach to generate thermostable enzymes, termed as thermoadaptation-directed enzyme evolution, thereby expanding the biotechnological potentials of Geobacillus spp. In this review, we have discussed this approach using successful examples and major challenges yet to be addressed.
Collapse
|
16
|
Geobacillus and Anoxybacillus spp. from Terrestrial Geothermal Springs Worldwide: Diversity and Biotechnological Applications. EXTREMOPHILES IN EURASIAN ECOSYSTEMS: ECOLOGY, DIVERSITY, AND APPLICATIONS 2018. [DOI: 10.1007/978-981-13-0329-6_5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
|