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Herlemann DPR, Tammert H, Kivistik C, Käiro K, Kisand V. Distinct biogeographical patterns in snail gastrointestinal tract bacterial communities compared with sediment and water. Microbiologyopen 2024; 13:e13. [PMID: 38825966 PMCID: PMC11144953 DOI: 10.1002/mbo3.1413] [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: 01/30/2024] [Revised: 04/16/2024] [Accepted: 04/30/2024] [Indexed: 06/04/2024] Open
Abstract
The factors that influence the distribution of bacterial community composition are not well understood. The role of geographical patterns, which suggest limited dispersal, is still a topic of debate. Bacteria associated with hosts face unique dispersal challenges as they often rely on their hosts, which provide specific environments for their symbionts. In this study, we examined the effect of biogeographic distances on the bacterial diversity and composition of bacterial communities in the gastrointestinal tract of Ampullaceana balthica. We compared the effects on the host-associated bacterial community to those on bacterial communities in water and sediment. This comparison was made using 16S ribosomal RNA gene sequencing. We found that the bacterial communities we sampled in Estonia, Denmark, and Northern Germany varied between water, sediment, and the gastrointestinal tract. They also varied between countries within each substrate. This indicates that the type of substrate is a dominant factor in determining bacterial community composition. We separately analyzed the turnover rates of water, sediment, and gastrointestinal bacterial communities over increasing geographic distances. We observed that the turnover rate was lower for gastrointestinal bacterial communities compared to water bacterial communities. This implies that the composition of gastrointestinal bacteria remains relatively stable over distances, while water bacterial communities exhibit greater variability. However, the gastrointestinal tract had the lowest percentage of country-specific amplicon sequence variants, suggesting bacterial colonization from local bacterial communities. Since the overlap between the water and gastrointestinal tract was highest, it appears that the gastrointestinal bacterial community is colonized by the water bacterial community. Our study confirmed that biogeographical patterns in host-associated communities differ from those in water and sediment bacterial communities. These host-associated communities consist of numerous facultative symbionts derived from the water bacterial community.
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Affiliation(s)
- Daniel P. R. Herlemann
- Centre for Limnology, Institute of Agricultural and Environmental SciencesEstonian University of Life SciencesTartu CountyEstonia
- Department of Biological OceanographyLeibniz Institute for Baltic Sea Research Warnemünde (IOW)RostockGermany
| | - Helen Tammert
- Centre for Limnology, Institute of Agricultural and Environmental SciencesEstonian University of Life SciencesTartu CountyEstonia
- Institute of TechnologyUniversity of TartuTartuEstonia
| | - Carmen Kivistik
- Centre for Limnology, Institute of Agricultural and Environmental SciencesEstonian University of Life SciencesTartu CountyEstonia
| | - Kairi Käiro
- Centre for Limnology, Institute of Agricultural and Environmental SciencesEstonian University of Life SciencesTartu CountyEstonia
| | - Veljo Kisand
- Centre for Limnology, Institute of Agricultural and Environmental SciencesEstonian University of Life SciencesTartu CountyEstonia
- Institute of TechnologyUniversity of TartuTartuEstonia
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2
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Li P, Hong J, Yuan Z, Huang Y, Wu M, Ding T, Wu Z, Sun X, Lin D. Gut microbiota in parasite-transmitting gastropods. Infect Dis Poverty 2023; 12:105. [PMID: 38001502 PMCID: PMC10668521 DOI: 10.1186/s40249-023-01159-z] [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: 08/07/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023] Open
Abstract
BACKGROUND Gastropoda, the largest class within the phylum Mollusca, houses diverse gut microbiota, and some gastropods serve as intermediate hosts for parasites. Studies have revealed that gut bacteria in gastropods are associated with various biological aspects, such as growth, immunity and host-parasite interactions. Here, we summarize our current knowledge of gastropod gut microbiomes and highlight future research priorities and perspectives. METHODS A literature search was undertaken using PubMed, Web of Science and CNKI for the articles on the gut microbiota of gastropods until December 31, 2022. We retrieved a total of 166 articles and identified 73 eligible articles for inclusion in this review based on the inclusion and exclusion criteria. RESULTS Our analysis encompassed freshwater, seawater and land snails, with a specific focus on parasite-transmitting gastropods. We found that most studies on gastropod gut microbiota have primarily utilized 16S rRNA gene sequencing to analyze microbial composition, rather than employing metagenomic, metatranscriptomic, or metabolomic approaches. This comprehensive review provided an overview of the parasites carried by snail species in the context of gut microbiota studies. We presented the gut microbial trends, a comprehensive summary of the diversity and composition, influencing factors, and potential functions of gastropod gut microbiota. Additionally, we discussed the potential applications, research gaps and future perspectives of gut microbiomes in parasite-transmitting gastropods. Furthermore, several strategies for enhancing our comprehension of gut microbiomes in snails were also discussed. CONCLUSIONS This review comprehensively summarizes the current knowledge on the composition, potential function, influencing factors, potential applications, limitations, and challenges of gut microbiomes in gastropods, with a specific emphasis on parasite-transmitting gastropods. These findings provide important insights for future studies aiming to understand the potential role of gastropod gut microbiota in controlling snail populations and snail-borne diseases.
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Affiliation(s)
- Peipei Li
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-Sen University, Guangzhou, China
- Chinese Atomic Energy Agency Center of Excellence on Nuclear Technology Applications for Insect Control, Provincial Engineering Technology Research Center for Diseases-Vectors Control, Sun Yat-Sen University, Guangzhou, China
| | - Jinni Hong
- Department of Traditional Chinese Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, China
| | - Zhanhong Yuan
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-Sen University, Guangzhou, China
| | - Yun Huang
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-Sen University, Guangzhou, China
| | - Mingrou Wu
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-Sen University, Guangzhou, China
| | - Tao Ding
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-Sen University, Guangzhou, China
| | - Zhongdao Wu
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China.
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-Sen University, Guangzhou, China.
- Chinese Atomic Energy Agency Center of Excellence on Nuclear Technology Applications for Insect Control, Provincial Engineering Technology Research Center for Diseases-Vectors Control, Sun Yat-Sen University, Guangzhou, China.
| | - Xi Sun
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China.
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-Sen University, Guangzhou, China.
| | - Datao Lin
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China.
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-Sen University, Guangzhou, China.
- Chinese Atomic Energy Agency Center of Excellence on Nuclear Technology Applications for Insect Control, Provincial Engineering Technology Research Center for Diseases-Vectors Control, Sun Yat-Sen University, Guangzhou, China.
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3
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Li P, Hong J, Wu M, Yuan Z, Li D, Wu Z, Sun X, Lin D. Metagenomic Analysis Reveals Variations in Gut Microbiomes of the Schistosoma mansoni-Transmitting Snails Biomphalaria straminea and Biomphalaria glabrata. Microorganisms 2023; 11:2419. [PMID: 37894077 PMCID: PMC10609589 DOI: 10.3390/microorganisms11102419] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/01/2023] [Accepted: 09/14/2023] [Indexed: 10/29/2023] Open
Abstract
Biomphalaria snails play a crucial role in the transmission of the human blood fluke Schistosoma mansoni. The gut microbiota of intermediate hosts is known to influence their physiological functions, but little is known about its composition and role in Biomphalaria snails. To gain insights into the biological characteristics of these freshwater intermediate hosts, we conducted metagenomic sequencing on Biomphalaria straminea and B. glabrata to investigate variations in their gut microbiota. This study revealed that the dominant members of the gut microbiota in B. glabrata belong to the phyla Bacteroidetes and Proteobacteria, which were also found to be the top two most abundant gut bacteria in B. straminea. We identified Firmicutes, Acidovorax and Bosea as distinctive gut microbes in B. straminea, while Aeromonas, Cloacibacterium and Chryseobacterium were found to be dependent features of the B. glabrata gut microbiota. We observed significant differences in the community structures and bacterial functions of the gut microbiota between the two host species. Notably, we found a distinctive richness of antibiotic resistance genes (ARGs) associated with various classes of antibiotics, including bacitracin, chloramphenicol, tetracycline, sulfonamide, penicillin, cephalosporin_ii and cephalosporin_i, fluoroquinolone, aminoglycoside, beta-lactam, multidrug and trimethoprim, in the digestive tracts of the snails. Furthermore, this study revealed the potential correlations between snail gut microbiota and the infection rate of S. mansoni using Spearman correlation analysis. Through metagenomic analysis, our study provided new insights into the gut microbiota of Biomphalaria snails and how it is influenced by host species, thereby enhancing our understanding of variant patterns of gut microbial communities in intermediate hosts. Our findings may contribute to future studies on gastropod-microbe interactions and may provide valuable knowledge for developing snail control strategies to combat schistosomiasis in the future.
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Affiliation(s)
- Peipei Li
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China (Z.W.)
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-Sen University, Guangzhou 510080, China
- Provincial Engineering Technology Research Center for Diseases-Vectors Control, Sun Yat-Sen University, Guangzhou 510080, China
| | - Jinni Hong
- Department of Traditional Chinese Medicine, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou 510180, China
| | - Mingrou Wu
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China (Z.W.)
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-Sen University, Guangzhou 510080, China
| | - Zhanhong Yuan
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China (Z.W.)
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-Sen University, Guangzhou 510080, China
| | - Dinghao Li
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China (Z.W.)
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-Sen University, Guangzhou 510080, China
| | - Zhongdao Wu
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China (Z.W.)
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-Sen University, Guangzhou 510080, China
- Provincial Engineering Technology Research Center for Diseases-Vectors Control, Sun Yat-Sen University, Guangzhou 510080, China
| | - Xi Sun
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China (Z.W.)
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-Sen University, Guangzhou 510080, China
- Provincial Engineering Technology Research Center for Diseases-Vectors Control, Sun Yat-Sen University, Guangzhou 510080, China
| | - Datao Lin
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China (Z.W.)
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-Sen University, Guangzhou 510080, China
- Provincial Engineering Technology Research Center for Diseases-Vectors Control, Sun Yat-Sen University, Guangzhou 510080, China
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Hallmann A, Leszczyńska D, Czumaj A, Świeżak J, Caban M, Michnowska A, Smolarz K. Oxytetracycline-induced inflammatory process without oxidative stress in blue mussels Mytilus trossulus. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:80462-80477. [PMID: 37301807 PMCID: PMC10345040 DOI: 10.1007/s11356-023-28057-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 05/29/2023] [Indexed: 06/12/2023]
Abstract
Potentially harmful compounds including pharmaceuticals are commonly found in marine waters and sediments. Amongst those, antibiotics and their metabolites are detected worldwide in various abiotic (at concentrations as high as µg/L) and biotic matrices at ng/gram of tissue, posing a risk to non-target species exposed to them such as blue mussels. Amongst those, oxytetracycline (OTC) belongs to the most detected antibiotics in the marine environment. In this work, we concentrated on studying the potential induction of oxidative stress, activation of cellular detoxification processes (including Phase I and Phase II xenobiotic biotransformation enzymes) and multixenobiotic resistance pumps (Phase III) as well as changes in the aromatisation efficiency in Mytilus trossulus exposed to 100 μg/L OTC. Our results show that 100 µg/L OTC concentration did not provoke cellular oxidative stress and did not affect the expression of genes involved in detoxification processes in our model. Moreover, no effect of OTC on aromatisation efficiency was found. Instead, phenoloxidase activity measured in haemolymph was significantly higher in OTC exposed mussels than in those from the control (30.95 ± 3.33 U/L and 17.95 ± 2.75 U/L, respectively). OTC exposed mussels were also characterised by a tissue-dependant activation of major vault protein (MVP) gene expression (1.5 times higher in gills and 2.4 times higher in the digestive system) and a decreased expression of the nuclear factor kappa B-a (NF-κB) gene (3.4 times lower in the digestive system) when compared to those from the control. Additionally, an elevated number of regressive changes and inflammatory responses in tissues such as gills, digestive system and mantle (gonads) was observed underlining the worsening of bivalves' general health. Therefore, instead of a free-radical effect of OTC, we for the first time describe the occurrence of typical changes resulting from antibiotic therapy in non-target organisms like M. trossulus exposed to antibiotics such as OTC.
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Affiliation(s)
- Anna Hallmann
- Department of Pharmaceutical Biochemistry, Medical University of Gdańsk, Gdańsk, Poland
| | - Dagmara Leszczyńska
- Department of Pharmaceutical Biochemistry, Medical University of Gdańsk, Gdańsk, Poland
| | - Aleksandra Czumaj
- Department of Pharmaceutical Biochemistry, Medical University of Gdańsk, Gdańsk, Poland
| | - Justyna Świeżak
- Department of Marine Ecosystem Functioning, University of Gdańsk, Gdynia, Poland
| | - Magda Caban
- Department of Environmental Analysis, Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland
| | - Alicja Michnowska
- Department of Marine Ecosystem Functioning, University of Gdańsk, Gdynia, Poland
| | - Katarzyna Smolarz
- Department of Marine Ecosystem Functioning, University of Gdańsk, Gdynia, Poland.
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Sritongon N, Boonlue S, Mongkolthanaruk W, Jogloy S, Riddech N. The combination of multiple plant growth promotion and hydrolytic enzyme producing rhizobacteria and their effect on Jerusalem artichoke growth improvement. Sci Rep 2023; 13:5917. [PMID: 37041302 PMCID: PMC10090049 DOI: 10.1038/s41598-023-33099-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 04/07/2023] [Indexed: 04/13/2023] Open
Abstract
Rhizobacteria are well recognized for their beneficial multifunctions as key promoters of plant development, suppressing pathogens, and improving soil health. In this study, experiments focused on characterizing the plant growth promotion (PGP) and extracellular hydrolase production traits of rhizobacteria, and their impact on Jerusalem artichoke growth. A total of 50 isolates proved capable of either direct PGP or hydrolase-producing traits. Two promising strains (Enterobacter cloacae S81 and Pseudomonas azotoformans C2-114) showed potential on phosphate and potassium solubilization, IAA production, and 1-aminocyclopropane-1-carboxylic acid deaminase activity and hydrolase production. A hydrolase-producing strain (Bacillus subtilis S42) was able to generate cellulase, protease, amylase, β-glucosidase, and phosphatase. These three selected strains also gave positive results for indirect PGP traits such as siderophore, ammonia, oxalate oxidase, polyamine, exopolysaccharide, biofilm, motility, and tolerance to salinity and drought stress. Colonization was observed using a scanning electron microscope and rhizobacteria appeared at the root surface. Interestingly, inoculation with consortia strains (S42, S81, and C2-114) significantly increased all plant parameters, including height, biomass, root (length, surface, diameter, and volume), and tuber fresh weight. Therefore, we recommend that potential consortia of PGP and hydrolase-producing rhizobacteria be employed as a biofertilizer to improve soil and boost crop productivity.
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Affiliation(s)
- Natthawat Sritongon
- Department of Microbiology, Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Sophon Boonlue
- Department of Microbiology, Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Wiyada Mongkolthanaruk
- Department of Microbiology, Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Sanun Jogloy
- Department of Agronomy, Faculty of Agriculture, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Nuntavun Riddech
- Department of Microbiology, Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand.
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Detomasi TC, Rico-Ramírez AM, Sayler RI, Gonçalves AP, Marletta MA, Glass NL. A moonlighting function of a chitin polysaccharide monooxygenase, CWR-1, in Neurospora crassa allorecognition. eLife 2022; 11:e80459. [PMID: 36040303 PMCID: PMC9550227 DOI: 10.7554/elife.80459] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 08/29/2022] [Indexed: 11/13/2022] Open
Abstract
Organisms require the ability to differentiate themselves from organisms of different or even the same species. Allorecognition processes in filamentous fungi are essential to ensure identity of an interconnected syncytial colony to protect it from exploitation and disease. Neurospora crassa has three cell fusion checkpoints controlling formation of an interconnected mycelial network. The locus that controls the second checkpoint, which allows for cell wall dissolution and subsequent fusion between cells/hyphae, cwr (cell wall remodeling), encodes two linked genes, cwr-1 and cwr-2. Previously, it was shown that cwr-1 and cwr-2 show severe linkage disequilibrium with six different haplogroups present in N. crassa populations. Isolates from an identical cwr haplogroup show robust fusion, while somatic cell fusion between isolates of different haplogroups is significantly blocked in cell wall dissolution. The cwr-1 gene encodes a putative polysaccharide monooxygenase (PMO). Herein we confirm that CWR-1 is a C1-oxidizing chitin PMO. We show that the catalytic (PMO) domain of CWR-1 was sufficient for checkpoint function and cell fusion blockage; however, through analysis of active-site, histidine-brace mutants, the catalytic activity of CWR-1 was ruled out as a major factor for allorecognition. Swapping a portion of the PMO domain (V86 to T130) did not switch cwr haplogroup specificity, but rather cells containing this chimera exhibited a novel haplogroup specificity. Allorecognition to mediate cell fusion blockage is likely occurring through a protein-protein interaction between CWR-1 with CWR-2. These data highlight a moonlighting role in allorecognition of the CWR-1 PMO domain.
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Affiliation(s)
- Tyler C Detomasi
- Department of Chemistry, University of California, BerkeleyBerkeleyUnited States
| | - Adriana M Rico-Ramírez
- Department of Plant and Microbial Biology, University of California, BerkeleyBerkeleyUnited States
| | - Richard I Sayler
- California Institute for Quantitative Biosciences, University of California, BerkeleyBerkeleyUnited States
| | - A Pedro Gonçalves
- Department of Plant and Microbial Biology, University of California, BerkeleyBerkeleyUnited States
| | - Michael A Marletta
- Department of Chemistry, University of California, BerkeleyBerkeleyUnited States
- California Institute for Quantitative Biosciences, University of California, BerkeleyBerkeleyUnited States
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - N Louise Glass
- Department of Plant and Microbial Biology, University of California, BerkeleyBerkeleyUnited States
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Escuder-Rodríguez JJ, DeCastro ME, Saavedra-Bouza A, González-Siso MI, Becerra M. Bioprospecting for Thermozymes and Characterization of a Novel Lipolytic Thermozyme Belonging to the SGNH/GDSL Family of Hydrolases. Int J Mol Sci 2022; 23:5733. [PMID: 35628544 PMCID: PMC9145741 DOI: 10.3390/ijms23105733] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/16/2022] [Accepted: 05/18/2022] [Indexed: 01/27/2023] Open
Abstract
Functional screenings were conducted on two metagenomic libraries from hot springs in order to find novel thermozymes with potential biotechnological applications. These included enzymes acting on plant cell walls such as endoglucanases and exoglucanases, β-glucosidases, xylanases, and β-xylosidases, and broad application enzymes such as proteases and lipolytic hydrolases. Of all the enzymes found by this bioprospection, we selected a novel lipolytic enzyme for further characterization. The protein was found to belong to the SGNH/GDSL family of hydrolases. It was purified and its biochemical parameters determined. We found that the enzyme was most active at 60 °C and pH 9 using pNP-laurate as substrate and was highly thermostable. It also showed preference for short-chained substrates and activation with temperature and with certain detergents such as Tween 80. Proteins of this family of hydrolases are relevant for their broad substrate specificity, that coupled with this protein's high temperature optima, broad pH range, and thermostability further highlights its biotechnological potential.
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Affiliation(s)
| | | | | | - María-Isabel González-Siso
- EXPRELA Group, Advanced Scientific Research Center (CICA), Department of Biology, Faculty of Sciences, Universidade da Coruña, 15071 A Coruña, Spain; (J.-J.E.-R.); (M.-E.D.); (A.S.-B.)
| | - Manuel Becerra
- EXPRELA Group, Advanced Scientific Research Center (CICA), Department of Biology, Faculty of Sciences, Universidade da Coruña, 15071 A Coruña, Spain; (J.-J.E.-R.); (M.-E.D.); (A.S.-B.)
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Zhou Z, Wu H, Li D, Zeng W, Huang J, Wu Z. Comparison of gut microbiome in the Chinese mud snail ( Cipangopaludina chinensis) and the invasive golden apple snail ( Pomacea canaliculata). PeerJ 2022; 10:e13245. [PMID: 35402093 PMCID: PMC8992660 DOI: 10.7717/peerj.13245] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 03/18/2022] [Indexed: 01/13/2023] Open
Abstract
Background Gut microbiota play a critical role in nutrition absorption and environmental adaptation and can affect the biological characteristics of host animals. The invasive golden apple snail (Pomacea canaliculata) and native Chinese mud snail (Cipangopaludina chinensis) are two sympatric freshwater snails with similar ecological niche in southern China. However, gut microbiota comparison of interspecies remains unclear. Comparing the difference of gut microbiota between the invasive snail P. canaliculata and native snail C. chinensis could provide new insight into the invasion mechanism of P.canaliculata at the microbial level. Methods Gut samples from 20 golden apple snails and 20 Chinese mud snails from wild freshwater habitats were collected and isolated. The 16S rRNA gene V3-V4 region of the gut microbiota was analyzed using high throughput Illumina sequencing. Results The gut microbiota dominantly composed of Proteobacteria, Bacteroidetes, Firmicutes and Epsilonbacteraeota at phylum level in golden apple snail. Only Proteobacteria was the dominant phylum in Chinese mud snail. Alpha diversity analysis (Shannon and Simpson indices) showed there were no significant differences in gut microbial diversity, but relative abundances of the two groups differed significantly (P < 0.05). Beta diversity analysis (Bray Curtis and weighted UniFrac distance) showed marked differences in the gut microbiota structure (P < 0.05). Unique or high abundance microbial taxa were more abundant in the invasive snail compared to the native form. Functional prediction analysis indicated that the relative abundances of functions differed significantly regarding cofactor prosthetic group electron carrier and vitamin biosynthesis, amino acid biosynthesis, and nucleoside and nucleotide biosynthesis (P < 0.05). These results suggest an enhanced potential to adapt to new habitats in the invasive snail.
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Affiliation(s)
- Zihao Zhou
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, Guangxi, China,Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, Guangxi, China,Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin Institute for Sustainable Development and Innovation, Guangxi Normal University, Guilin, Guangxi, China
| | - Hongying Wu
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin Institute for Sustainable Development and Innovation, Guangxi Normal University, Guilin, Guangxi, China
| | - Dinghong Li
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin Institute for Sustainable Development and Innovation, Guangxi Normal University, Guilin, Guangxi, China
| | - Wenlong Zeng
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin Institute for Sustainable Development and Innovation, Guangxi Normal University, Guilin, Guangxi, China
| | - Jinlong Huang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, Guangxi, China,Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, Guangxi, China,Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin Institute for Sustainable Development and Innovation, Guangxi Normal University, Guilin, Guangxi, China,College of Life Sciences, Guangxi Normal University, Guilin, Guangxi, China
| | - Zhengjun Wu
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, Guangxi, China,Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, Guangxi, China,Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin Institute for Sustainable Development and Innovation, Guangxi Normal University, Guilin, Guangxi, China
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9
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Belouhova M, Daskalova E, Yotinov I, Topalova Y, Velkova L, Dolashki A, Dolashka P. Microbial diversity of garden snail mucus. Microbiologyopen 2022; 11:e1263. [PMID: 35212476 PMCID: PMC8822593 DOI: 10.1002/mbo3.1263] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 01/07/2022] [Indexed: 01/04/2023] Open
Abstract
The search for new natural compounds for application in medicine and cosmetics is a trend in biotechnology. One of the sources of such active compounds is the snail mucus. Snail physiology and the biological activity of their fluids (especially the mucus) are still poorly studied. Only a few previous studies explored the relationship between snails and their microbiome. The present study was focused on the biodiversity of the snail mucus used in the creation of cosmetic products, therapeutics, and nutraceuticals. The commonly used cultivation techniques were applied for the determination of the number of major bacterial groups. Fluorescence in situ hybridization for key taxa was performed. The obtained images were subjected to digital image analysis. Sequencing of the 16S rRNA gene was also done. The results showed that the mucus harbors a rich bacterial community (10.78 × 1010 CFU/ml). Among the dominant bacteria, some are known for their ability to metabolize complex polysaccharides or are usually found in soil and plants (Rhizobiaceae, Shewanella, Pedobacter, Acinetobacter, Alcaligenes). The obtained data demonstrated that the snail mucus creates a unique environment for the development of the microbial community that differs from other parts of the animal and which resulted from the combined contribution of the microbiomes derived from the soil, plants, and the snails.
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Affiliation(s)
- Mihaela Belouhova
- Faculty of BiologySofia University “St. Kliment Ohridski”SofiaBulgaria
| | - Elmira Daskalova
- Faculty of BiologySofia University “St. Kliment Ohridski”SofiaBulgaria
| | - Ivaylo Yotinov
- Faculty of BiologySofia University “St. Kliment Ohridski”SofiaBulgaria
| | - Yana Topalova
- Faculty of BiologySofia University “St. Kliment Ohridski”SofiaBulgaria
| | - Lyudmila Velkova
- Institute of Organic Chemistry with Centre of PhytochemistryBulgarian Academy of SciencesSofiaBulgaria
| | - Aleksander Dolashki
- Institute of Organic Chemistry with Centre of PhytochemistryBulgarian Academy of SciencesSofiaBulgaria
| | - Pavlina Dolashka
- Institute of Organic Chemistry with Centre of PhytochemistryBulgarian Academy of SciencesSofiaBulgaria
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10
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Makowski K, Leszczewicz M, Broncel N, Lipińska-Zubrycka L, Głębski A, Komorowski P, Walkowiak B. Isolation, Biochemical Characterisation and Identification of Thermotolerant and Cellulolytic Paenibacillus lactis and Bacillus licheniformis. Food Technol Biotechnol 2021; 59:325-336. [PMID: 34759764 PMCID: PMC8542176 DOI: 10.17113/ftb.59.03.21.7096] [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: 12/10/2020] [Accepted: 06/24/2021] [Indexed: 11/12/2022] Open
Abstract
Research background Cellulose is an ingredient of waste materials that can be converted to other valuable substances. This is possible provided that the polymer molecule is degraded to smaller particles and used as a carbon source by microorganisms. Because of the frequently applied methods of pretreatment of lignocellulosic materials, the cellulases derived from thermophilic microorganisms are particularly desirable. Experimental approach We were looking for cellulolytic microorganisms able to grow at 50 °C and we described their morphological features and biochemical characteristics based on carboxymethyl cellulase (CMCase) activity and the API® ZYM system. The growth curves during incubation at 50 °C were examined using the BioLector® microbioreactor. Results and conclusions Forty bacterial strains were isolated from fermenting hay, geothermal karst spring, hot spring and geothermal pond at 50 °C. The vast majority of the bacteria were Gram-positive and rod-shaped with the maximum growth temperature of at least 50 °C. We also demonstrated a large diversity of biochemical characteristics among the microorganisms. The CMCase activity was confirmed in 27 strains. Hydrolysis capacities were significant in bacterial strains: BBLN1, BSO6, BSO10, BSO13 and BSO14, and reached 2.74, 1.62, 1.30, 1.38 and 8.02 respectively. Rapid and stable growth was observed, among others, for BBLN1, BSO10, BSO13 and BSO14. The strains fulfilled the selection conditions and were identified based on the 16S rDNA sequences. BBLN1, BSO10, BSO13 were classified as Bacillus licheniformis, whereas BSO14 as Paenibacillus lactis. Novelty and scientific contribution We described cellulolytic activity and biochemical characteristics of many bacteria isolated from hot environments. We are also the first to report the cellulolytic activity of thermotolerant P. lactis. Described strains can be a source of new thermostable cellulases, which are extremely desirable in various branches of circular bioeconomy.
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Affiliation(s)
- Krzysztof Makowski
- Industrial Biotechnology Laboratory, Bionanopark Ltd., Dubois 114/116, 93-465 Lodz, Poland.,Biotechnika, Tymienieckiego 25, 90-350 Lodz, Poland
| | - Martyna Leszczewicz
- Industrial Biotechnology Laboratory, Bionanopark Ltd., Dubois 114/116, 93-465 Lodz, Poland
| | - Natalia Broncel
- Industrial Biotechnology Laboratory, Bionanopark Ltd., Dubois 114/116, 93-465 Lodz, Poland
| | - Lidia Lipińska-Zubrycka
- Industrial Biotechnology Laboratory, Bionanopark Ltd., Dubois 114/116, 93-465 Lodz, Poland.,Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Adrian Głębski
- Industrial Biotechnology Laboratory, Bionanopark Ltd., Dubois 114/116, 93-465 Lodz, Poland
| | - Piotr Komorowski
- Molecular and Nanostructural Biophysics Laboratory, Bionanopark Ltd., Dubois 114/116, 93-465 Lodz, Poland.,Institute of Materials Science and Engineering, Lodz University of Technology, Stefanowskiego 1/15, 90-537 Lodz, Poland
| | - Bogdan Walkowiak
- Molecular and Nanostructural Biophysics Laboratory, Bionanopark Ltd., Dubois 114/116, 93-465 Lodz, Poland.,Institute of Materials Science and Engineering, Lodz University of Technology, Stefanowskiego 1/15, 90-537 Lodz, Poland
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11
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Chalifour B, Li J. Characterization of the gut microbiome in wild rocky mountainsnails (Oreohelix strigosa). Anim Microbiome 2021; 3:49. [PMID: 34274024 PMCID: PMC8285866 DOI: 10.1186/s42523-021-00111-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 07/04/2021] [Indexed: 11/30/2022] Open
Abstract
Background The Rocky Mountainsnail (Oreohelix strigosa) is a terrestrial gastropod of ecological importance in the Rocky Mountains of western United States and Canada. Across the animal kingdom, including in gastropods, gut microbiomes have profound effects on the health of the host. Current knowledge regarding snail gut microbiomes, particularly throughout various life history stages, is limited. Understanding snail gut microbiome composition and dynamics can provide an initial step toward better conservation and management of this species. Results In this study, we employed 16S rRNA gene amplicon sequencing to examine gut bacteria communities in wild-caught O. strigosa populations from the Front Range of Colorado. These included three treatment groups: (1) adult and (2) fetal snails, as well as (3) sub-populations of adult snails that were starved prior to ethanol fixation. Overall, O. strigosa harbors a high diversity of bacteria. We sequenced the V4 region of the 16S rRNA gene on an Illumina MiSeq and obtained 2,714,330 total reads. We identified a total of 7056 unique operational taxonomic units (OTUs) belonging to 36 phyla. The core gut microbiome of four unique OTUs accounts for roughly half of all sequencing reads returned and may aid the snails’ digestive processes. Significant differences in microbial composition, as well as richness, evenness, and Shannon Indices were found across the three treatment groups. Conclusions Comparisons of gut microbiomes in O. strigosa adult, fetal, and starved samples provide evidence that the host internal environments influence bacterial community compositions, and that bacteria may be transmitted vertically from parent to offspring. This work provides the first comprehensive report on the structure and membership of bacterial populations in the gastropod family Oreohelicidae and reveals similarities and differences across varying life history metrics. Strong differentiation between these life history metrics demonstrates the need for wider sampling for studies of dynamics of the snail gut microbiome. Supplementary Information The online version contains supplementary material available at 10.1186/s42523-021-00111-6.
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Affiliation(s)
- Bridget Chalifour
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, 1900 Pleasant Street, 334 UCB, Boulder, CO, 80309, USA.
| | - Jingchun Li
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, 1900 Pleasant Street, 334 UCB, Boulder, CO, 80309, USA.,Museum of Natural History, University of Colorado Boulder, 265 UCB, Boulder, CO, 80309, USA
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12
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Composition and diversity of gut microbiota in Pomacea canaliculata in sexes and between developmental stages. BMC Microbiol 2021; 21:200. [PMID: 34210255 PMCID: PMC8252327 DOI: 10.1186/s12866-021-02259-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 06/10/2021] [Indexed: 01/16/2023] Open
Abstract
Background The apple snail, Pomacea canaliculata, is one of the world’s 100 worst invasive alien species and vector of some pathogens relevant to human health. Methods On account of the importance of gut microbiota to the host animals, we compared the communities of the intestinal microbiota from P. canaliculata collected at different developmental stages (juvenile and adult) and different sexes by using high-throughput sequencing. Results The core bacteria phyla of P. canaliculata gut microbiota included Tenericutes (at an average relative abundance of 45.7 %), Firmicutes (27.85 %), Proteobacteria (11.86 %), Actinobacteria (4.45 %), and Cyanobacteria (3.61 %). The female group possessed the highest richness values, whereas the male group possessed the lowest bacterial richness and diversity compared with the female and juvenile group. Both the developmental stages and sexes had important effects on the composition of the intestinal microbiota of P. canaliculata. By LEfSe analysis, microbes from the phyla Proteobacteria and Actinobacteria were enriched in the female group, phylum Bacteroidetes was enriched in the male group, family Mycoplasmataceae and genus Leuconostoc were enriched in the juvenile group. PICRUSt analysis predicted twenty-four metabolic functions in all samples, including general function prediction, amino acid transport and metabolism, transcription, replication, recombination and repair, carbohydrate transport and metabolism, etc. Conclusions This study provided a general understanding of the diversity characteristics of intestinal microbial communities of P. canaliculata, and indicated that developmental stage and gender could both influence the intestinal microbes of P. canaliculata. Further study may focus on the interaction between the gut microbiota and their host. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02259-2.
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13
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Jackson D, Maltz MR, Freund HL, Borneman J, Aronson E. Environment and Diet Influence the Bacterial Microbiome of Ambigolimax valentianus, an Invasive Slug in California. INSECTS 2021; 12:575. [PMID: 34201881 PMCID: PMC8307491 DOI: 10.3390/insects12070575] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 06/12/2021] [Accepted: 06/15/2021] [Indexed: 12/27/2022]
Abstract
Ambigolimax valentianus is an invasive European terrestrial gastropod distributed throughout California. It is a serious pest of gardens, plant nurseries, and greenhouses. We evaluated the bacterial microbiome of whole slugs to capture a more detailed picture of bacterial diversity and composition in this host. We concentrated on the influences of diet and environment on the Ambigolimax valentianus core bacterial microbiome as a starting point for obtaining valuable information to aid in future slug microbiome studies. Ambigolimax valentianus were collected from two environments (gardens or reared from eggs in a laboratory). DNA from whole slugs were extracted and next-generation 16S rRNA gene sequencing was performed. Slug microbiomes differed between environmental sources (garden- vs. lab-reared) and were influenced by a sterile diet. Lab-reared slugs fed an unsterile diet harbored greater bacterial species than garden-reared slugs. A small core microbiome was present that was shared across all slug treatments. This is consistent with our hypothesis that a core microbiome is present and will not change due to these treatments. Findings from this study will help elucidate the impacts of slug-assisted bacterial dispersal on soils and plants, while providing valuable information about the slug microbiome for potential integrated pest research applications.
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Affiliation(s)
- Denise Jackson
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521, USA; (D.J.); (H.L.F.); (J.B.)
- Natural Science Division, Porterville College, Porterville, CA 93257, USA
| | - Mia R. Maltz
- Center for Conservation Biology, University of California, Riverside, CA 92521, USA;
- Division of Biomedical Sciences, University of California, Riverside, CA 92521, USA
| | - Hannah L. Freund
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521, USA; (D.J.); (H.L.F.); (J.B.)
- Genetics, Genomics, and Bioinformatics Program, University of California, Riverside, CA 92521, USA
| | - James Borneman
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521, USA; (D.J.); (H.L.F.); (J.B.)
| | - Emma Aronson
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521, USA; (D.J.); (H.L.F.); (J.B.)
- Center for Conservation Biology, University of California, Riverside, CA 92521, USA;
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14
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Wang C, Yan C, Qiu J, Liu C, Yan Y, Ji Y, Wang G, Chen H, Li Y, Li A. Food web biomagnification of the neurotoxin β-N-methylamino-L-alanine in a diatom-dominated marine ecosystem in China. JOURNAL OF HAZARDOUS MATERIALS 2021; 404:124217. [PMID: 33129020 DOI: 10.1016/j.jhazmat.2020.124217] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 09/25/2020] [Accepted: 10/05/2020] [Indexed: 06/11/2023]
Abstract
The neurotoxin β-N-methylamino-L-alanine (BMAA) reported in some cyanobacteria and eukaryote microalgae is a cause of concern due to its potential risk of human neurodegenerative diseases. Here, BMAA distribution in phytoplankton, zooplankton, and other marine organisms was investigated in Jiaozhou Bay, China, a diatom-dominated marine ecosystem, during four seasons in 2019. Results showed that BMAA was biomagnified in the food web from phytoplankton to higher trophic levels. Trophic magnification factors (TMFs) for zooplankton, bivalve mollusks, carnivorous crustaceans and carnivorous gastropod mollusks were ca. 4.58, 30.1, 42.5, and 74.4, respectively. Putative identification of β-amino-N-methylalanine (BAMA), an isomer of BMAA, was frequently detected in phytoplankton samples. A total of 56 diatom strains of the genera Pseudo-nitzschia, Thalassiosira, Chaetoceros, Planktoniella, and Minidiscus isolated from the Chinese coast were cultured in the laboratory, among which 21 strains contained BMAA mainly in precipitated bound form at toxin concentrations ranging from 0.11 to 3.95 µg/g dry weight. Only 2,4-diaminobutyric acid (DAB) but not BMAA or BAMA was detected in seven species of bacteria isolated from the gut of gastropod Neverita didyma, suggesting that this benthic vector of BMAA may have accumulated this compound via trophic transfer.
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Affiliation(s)
- Chao Wang
- College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China; Key Laboratory of Marine Environment and Ecology, Ocean University of China, Ministry of Education, Qingdao 266100, China
| | - Chen Yan
- College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China; Key Laboratory of Marine Environment and Ecology, Ocean University of China, Ministry of Education, Qingdao 266100, China
| | - Jiangbing Qiu
- College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China; Key Laboratory of Marine Environment and Ecology, Ocean University of China, Ministry of Education, Qingdao 266100, China
| | - Chao Liu
- College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China; Key Laboratory of Marine Environment and Ecology, Ocean University of China, Ministry of Education, Qingdao 266100, China
| | - Yeju Yan
- College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China; Key Laboratory of Marine Environment and Ecology, Ocean University of China, Ministry of Education, Qingdao 266100, China
| | - Ying Ji
- College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China; Key Laboratory of Marine Environment and Ecology, Ocean University of China, Ministry of Education, Qingdao 266100, China
| | - Guixiang Wang
- College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China; Key Laboratory of Marine Environment and Ecology, Ocean University of China, Ministry of Education, Qingdao 266100, China
| | - Hongju Chen
- College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China; Key Laboratory of Marine Environment and Ecology, Ocean University of China, Ministry of Education, Qingdao 266100, China
| | - Yang Li
- Guangdong Provincial Key Laboratory of Healthy and Safe Aquaculture, College of Life Science, South China Normal University, Guangzhou 510631, China
| | - Aifeng Li
- College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China; Key Laboratory of Marine Environment and Ecology, Ocean University of China, Ministry of Education, Qingdao 266100, China.
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Hu Z, Tong Q, Chang J, Yu J, Li S, Niu H, Ma D. Gut bacterial communities in the freshwater snail Planorbella trivolvis and their modification by a non-herbivorous diet. PeerJ 2021; 9:e10716. [PMID: 33614273 PMCID: PMC7883694 DOI: 10.7717/peerj.10716] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 12/15/2020] [Indexed: 12/19/2022] Open
Abstract
The freshwater pulmonate snail Planorbella trivolvis is a common species in various bodies of water but is not native to China. Planorbella trivolvis usually live on diets with high fiber content, such as water grasses, algae and fallen leaves. These snails can attach to the wall of a water tank or to water grass and can be transported overseas to China through the ornamental fish trade. There are few studies investigating the intestinal microbiota of freshwater snails. In this study, using culture-independent molecular analysis, we assessed for the first time the complexity of bacterial communities in the intestines of reared snails. The intestinal microbiota in the snails fed different diets, that is, herbivorous feed (HV) with high cellulose and non-herbivorous feed (NHV) with low cellulose, were analyzed by Illumina sequencing. The results showed that the NHV-based diet significantly increased the body mass, shell diameter and specific growth rate of the snails after 60 days of rearing (P < 0.05). Histological experiments showed that the fat droplets in the epithelium columnar cells of the intestines of the NHV snails increased, and the cilia on these cells fell off. The sequencing results identified 486 and 195 OTUs in HV and NHV, respectively. Lots of bacteria were not reported previously in snails. The intestinal microbiota diversity index (Shannon, Simpson, Ace and Chao) in the NHV snails was significantly lower than that in the HV snails. The gut microbiota in the HV snails were predominantly Proteobacteria (52.97%) and Bacteroidetes (28.75%), while the gut microbiota in NHV snails were predominantly Proteobacteria (95.23%). At the genus level, Cloacibacterium (24.60%), Pseudomonas (4.47%), OM6ON (6.12%), and Rhodobacter (5.79%) were observed to be abundant in HV snails. However, Aeromonas (85.4%) was determined to be predominant in NHV snails. Functional prediction of the gut microbiome in snails by PICRUSt demonstrated a significant difference between the two groups, and the HV snails exhibited higher lignocellulose enzyme activity than did the NHV snails. This study represents a first step in characterizing the gut microbiota of the freshwater snail. Most of these microbes can process plant biomass and digest cellulose and lignocellulose, and the enzymes of these bacteria may have potential biotechnological applications in a variety of industrial processes.
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Affiliation(s)
- Zongfu Hu
- College of Animal Science and Technology, Inner Mongolia University for Nationalities, Tongliao, People's Republic of China.,College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Qing Tong
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Jie Chang
- College of Animal Science and Technology, Inner Mongolia University for Nationalities, Tongliao, People's Republic of China
| | - Jianhua Yu
- College of Animal Science and Technology, Inner Mongolia University for Nationalities, Tongliao, People's Republic of China
| | - Shuguo Li
- College of Animal Science and Technology, Inner Mongolia University for Nationalities, Tongliao, People's Republic of China
| | - Huaxin Niu
- College of Animal Science and Technology, Inner Mongolia University for Nationalities, Tongliao, People's Republic of China
| | - Deying Ma
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
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Kamusoko R, Jingura RM, Parawira W, Chikwambi Z. Purification and Amplification of DNA from Cellulolytic Bacteria: Application for Biogas Production from Crop Residues. Methods Mol Biol 2021; 2290:187-201. [PMID: 34009591 DOI: 10.1007/978-1-0716-1323-8_13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Polymerase chain reaction (PCR) is a popular molecular tool for detection of bacteria. PCR allows millions of copies of a target segment of DNA to be produced. The DNA is extracted from overnight grown cultures of pure bacterial isolates using either the organo-solvent method or a commercial DNA extraction kit. The quality and purity of the DNA is determined by performing gel electrophoresis on 0.8% agarose gel. The DNA is amplified by performing PCR assay. Bands of approximately 1.5 kb in size are obtained from the amplified products of DNA. The PCR products run on 1.5% agarose gel are visualized with UV light and imaged by gel documentation system. This chapter outlines the protocol for isolation and amplification of DNA from cellulolytic bacteria. Cellulolytic bacteria are considered a potential source of cellulases for pretreatment of crop residues during biogas production. PCR is considered a very powerful, sensitive, specific, fast, and reliable tool in molecular detection and diagnostics.
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Affiliation(s)
- Reckson Kamusoko
- Department of Biotechnology, School of Agricultural Sciences and Technology, Chinhoyi University of Technology, Chinhoyi, Zimbabwe.
| | - Raphael M Jingura
- Department of Animal Production and Technology, School of Agricultural Sciences and Technology, Chinhoyi University of Technology, Chinhoyi, Zimbabwe
| | - Wilson Parawira
- Faculty of Science, Bindura University of Science Education, Bindura, Zimbabwe
| | - Zedias Chikwambi
- Department of Biotechnology, School of Agricultural Sciences and Technology, Chinhoyi University of Technology, Chinhoyi, Zimbabwe
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Safaei N, Mast Y, Steinert M, Huber K, Bunk B, Wink J. Angucycline-like Aromatic Polyketide from a Novel Streptomyces Species Reveals Freshwater Snail Physa acuta as Underexplored Reservoir for Antibiotic-Producing Actinomycetes. Antibiotics (Basel) 2020; 10:antibiotics10010022. [PMID: 33383910 PMCID: PMC7823578 DOI: 10.3390/antibiotics10010022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 12/23/2020] [Accepted: 12/25/2020] [Indexed: 11/16/2022] Open
Abstract
Simple Summary The current study shows that freshwater snails can be considered as new sources for bioactive metabolites, since a novel Streptomyces species 7NS3 produced four active compounds against Gram-positive bacteria. One of the compounds was an angucycline-like aromatic polyketide matched with a known compound, emycin A. Genome mining studies based on the whole-genome sequence of 7NS3 resulted in the identification of a gene cluster potentially coding for emycin A biosynthesis. Abstract Antibiotic producers have mainly been isolated from soil, which often has led to the rediscovery of known compounds. In this study, we identified the freshwater snail Physa acuta as an unexplored source for new antibiotic producers. The bacterial diversity associated with the snail was characterized by a metagenomic approach using cultivation-independent high-throughput sequencing. Although Actinobacteria represented only 2% of the bacterial community, the focus was laid on the isolation of the genus Streptomyces due to its potential to produce antibiotics. Three Streptomyces strains (7NS1, 7NS2 and 7NS3) were isolated from P. acuta, and the antimicrobial activity of the crude extracts were tested against a selection of Gram-positive and Gram-negative bacteria and fungi. 7NS3 showed the strongest activity against Gram-positive bacteria and, thus, was selected for genome sequencing and a phylogenomic analysis. 7NS3 represents a novel Streptomyces species, which was deposited as Streptomyces sp. DSM 110735 at the Leibniz Institute-German Collection of Microorganisms and Cell Cultures (DSMZ). Bioassay-guided high-performance liquid chromatography (HPLC) and high-resolution electrospray ionization-mass spectrometry (HR-ESI-MS) analyses of crude extract fractions resulted in the detection of four compounds, one of which matched the compound characteristics of emycin A, an angucycline-like aromatic polyketide. Genome mining studies based on the whole-genome sequence of 7NS3 resulted in the identification of a gene cluster potentially coding for emycin A biosynthesis. Our study demonstrates that freshwater snails like P. acuta can represent promising reservoirs for the isolation of new antibiotic-producing actinobacterial species.
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Affiliation(s)
- Nasim Safaei
- Helmholtz Centre for Infection Research, Department of microbial Strain Collection, Inhoffenstrasse 7, D-38124 Braunschweig, Germany;
| | - Yvonne Mast
- German Center for Infection Research (DZIF), Leibniz Institute DSMZ, Inhoffenstrasse 7, D-38124 Braunschweig, Germany; (Y.M.); (K.H.); (B.B.)
| | - Michael Steinert
- Technical University of Braunschweig, Spielmannstr. 7, 38106 Braunschweig, Germany;
| | - Katharina Huber
- German Center for Infection Research (DZIF), Leibniz Institute DSMZ, Inhoffenstrasse 7, D-38124 Braunschweig, Germany; (Y.M.); (K.H.); (B.B.)
| | - Boyke Bunk
- German Center for Infection Research (DZIF), Leibniz Institute DSMZ, Inhoffenstrasse 7, D-38124 Braunschweig, Germany; (Y.M.); (K.H.); (B.B.)
| | - Joachim Wink
- Helmholtz Centre for Infection Research, Department of microbial Strain Collection, Inhoffenstrasse 7, D-38124 Braunschweig, Germany;
- Correspondence: ; Tel.: +49-531-6181-4223
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Chen Y, Wang W, Zhou D, Jing T, Li K, Zhao Y, Tang W, Qi D, Zhang M, Zang X, Luo Y, Xie J. Biodegradation of lignocellulosic agricultural residues by a newly isolated Fictibacillus sp. YS-26 improving carbon metabolic properties and functional diversity of the rhizosphere microbial community. BIORESOURCE TECHNOLOGY 2020; 310:123381. [PMID: 32361643 DOI: 10.1016/j.biortech.2020.123381] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 04/11/2020] [Accepted: 04/11/2020] [Indexed: 06/11/2023]
Abstract
A new isolated cellulolytic bacterium from a soft coral was named as Fictibacillus sp YS-26 based on the morphologic and molecular characteristics. It can degrade different lignocellulosic agricultural residues by producing cellulolytic enzymes, α-amylase, protease, pectinase and xylanase. Especially, Fictibacillus sp. YS-26 exhibited the highest cellulolytic activities in the soybean meal medium. By contrast, the fermentation broth of Fictibacillus sp. YS-26 significantly enhanced utilization efficiency of carboxylic acids and polymers by soil microorganisms as well as the microbial metabolism function and community diversity in rhizosphere soil of banana plantlets. The fermentation broth also improved soil characters and increased the growth of banana plantlets. We found that soil total nitrogen and electrical conductivity had a positive relationship with the increase of microbial diversity. Hence, Fictibacillus sp. YS-26 will be a promising candidate for biodegradating lignocellulosic biomass and improving the soil microbial diversity.
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Affiliation(s)
- Yufeng Chen
- Institute of Tropical Bioscience and Biotechnology, China Academy of Tropical Agricultural Sciences, Haikou, Hainan, China; College of Plant Protection, Hainan University, Haikou, Hainan, China
| | - Wei Wang
- Institute of Tropical Bioscience and Biotechnology, China Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Dengbo Zhou
- Institute of Tropical Bioscience and Biotechnology, China Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Tao Jing
- Haikou Experimental Station, China Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Kai Li
- Institute of Tropical Bioscience and Biotechnology, China Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Yankun Zhao
- Institute of Tropical Bioscience and Biotechnology, China Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Wen Tang
- Institute of Tropical Bioscience and Biotechnology, China Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Dengfeng Qi
- Institute of Tropical Bioscience and Biotechnology, China Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Miaoyi Zhang
- Institute of Tropical Bioscience and Biotechnology, China Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Xiaoping Zang
- Haikou Experimental Station, China Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Yanping Luo
- College of Plant Protection, Hainan University, Haikou, Hainan, China
| | - Jianghui Xie
- Institute of Tropical Bioscience and Biotechnology, China Academy of Tropical Agricultural Sciences, Haikou, Hainan, China.
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Osório JB, de Mattos Pereira L, Giongo A, Marconatto L, Potriquet J, Candido RRF, Mulvenna J, Jones M, Graeff-Teixeira C, Morassutti AL. Mollusk microbiota shift during Angiostrongylus cantonensis infection in the freshwater snail Biomphalaria glabrata and the terrestrial slug Phillocaulis soleiformis. Parasitol Res 2020; 119:2495-2503. [PMID: 32556501 DOI: 10.1007/s00436-020-06743-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Accepted: 06/01/2020] [Indexed: 02/01/2023]
Abstract
In the present work, we reported for the first time the microbiome from Phyllocaulis soleiformis and Biomphalaria glabrata assessed using high-throughput DNA sequencing pre- and post-infection with the helminth parasite Angiostrongylus cantonensis. B. glabrata and P. soleiformis were experimentally infected with A. cantonensis. Fecal DNAs from control and infected groups were extracted and subjected to 16S rRNA high-throughput sequencing survey. No significant differences were found in the alpha diversity indexes in Phyllocaulis and Biomphalaria experiments independently. PCoA analysis using the unweighted UniFrac measures showed that both microbiotas behaved differently depending on the host. In Biomphalaria microbiota, control and infected groups were significantly different (p = 0.0219), while Phyllocaulis samples were not (p = 0.5190). The microbiome of P. soleiformis infected with A. cantonensis showed a significant decrease of Sphingobacterium and a substantial increase of Cellvibrio when compared to a control group. The microbiome of B. glabrata infected with A. cantonensis showed a significant decline in the abundance of Flavobacterium, Fluviicola, Nitrospira, Vogesella and an OTU belonging to the family Comamonadaceae, and a significant increase of Uliginosibacterium and an OTU belonging to the family Weeksellaceae when compared to a control group. Overall, the microbiome data reported here provided valuable information with regard to the diversity of bacterial communities that comprise the gut microbiome of gastropods. Furthermore, we report here the effect of the infection of the helminth A. cantonensis in the ratio and distribution of the fecal microbiome of the snails. Further studies are highly valuable in order to better understand those interactions by comparing different microbiome profiles and mollusk models. By now, we anticipate that ecological studies will take significant advantage of these advances, particularly concerning improving our understanding of helminth-microbiome-host interactions.
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Affiliation(s)
- Joana Borges Osório
- Laboratório de Biologia Parasitária, Escola de Ciências, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Av. Ipiranga, 6681, Predio 12C, Porto Alegre, RS, 90060-900, Brazil
| | - Leandro de Mattos Pereira
- Laboratório de Biologia Parasitária, Escola de Ciências, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Av. Ipiranga, 6681, Predio 12C, Porto Alegre, RS, 90060-900, Brazil.,Laboratório de Ecologia Microbiana e Molecular, Bloco E - Predio CCS, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, Rio de Janeiro, RJ, 21941-590, Brazil
| | - Adriana Giongo
- Instituto do Petróleo e Recursos Naturais, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Av. Ipiranga, 6681, Predio 96J, Porto Alegre, RS, 90060-900, Brazil
| | - Letícia Marconatto
- Laboratório de Biologia Parasitária, Escola de Ciências, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Av. Ipiranga, 6681, Predio 12C, Porto Alegre, RS, 90060-900, Brazil.,Laboratório de Ecologia Microbiana e Molecular, Bloco E - Predio CCS, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, Rio de Janeiro, RJ, 21941-590, Brazil.,Instituto do Petróleo e Recursos Naturais, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Av. Ipiranga, 6681, Predio 96J, Porto Alegre, RS, 90060-900, Brazil.,QIMR Berghofer Medical Research Institute, University of Queensland, Brisbane, Queensland, 4006, Australia.,Department of Physics, The University of Western Australia, M013, 35 Stirling Hwy, Crawley, 6009, Australia.,School of Veterinary Science, The University of Queensland, Gatton, Queensland, 4343, Australia
| | - Jeremy Potriquet
- QIMR Berghofer Medical Research Institute, University of Queensland, Brisbane, Queensland, 4006, Australia
| | | | - Jason Mulvenna
- Instituto do Petróleo e Recursos Naturais, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Av. Ipiranga, 6681, Predio 96J, Porto Alegre, RS, 90060-900, Brazil
| | - Malcolm Jones
- School of Veterinary Science, The University of Queensland, Gatton, Queensland, 4343, Australia
| | - Carlos Graeff-Teixeira
- Laboratório de Biologia Parasitária, Escola de Ciências, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Av. Ipiranga, 6681, Predio 12C, Porto Alegre, RS, 90060-900, Brazil
| | - Alessandra Loureiro Morassutti
- Laboratório de Biologia Parasitária, Escola de Ciências, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Av. Ipiranga, 6681, Predio 12C, Porto Alegre, RS, 90060-900, Brazil.
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20
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Biodegradation of recalcitrant compounds and phthalates by culturable bacteria isolated from Liometopum apiculatum microbiota. World J Microbiol Biotechnol 2020; 36:73. [PMID: 32385754 DOI: 10.1007/s11274-020-02850-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 05/04/2020] [Indexed: 10/24/2022]
Abstract
Liometopum apiculatum is a species of ants widely distributed in arid and semi-arid ecosystems where there is a relative food shortage compared with tropical ecosystems. L. apiculatum has established an ecological balance involving symbiotic interactions, which have allowed them to survive through mechanisms that are still unknown. Therefore, the aim of this study was to explore the metabolic potential of isolated bacteria from L. apiculatum using enzymatic activity assay and substrate assimilation. Results revealed a complex bacteria consortium belonging to Proteobacteria, Firmicutes, and Actinobacteria phylum. Most of the isolated bacteria showed activities associated with biopolymers degradation, from them Exiguobacterium and B. simplex showed the highest amylolytic activity (27 U/mg protein), while A. johnsonii and B. pumulis showed the highest cellulolytic and xylanolytic activities (1 and 2.9 U/mg protein, respectively). By other hand, some microorganisms such as S. ficaria, E. asburiae, P. agglomerans, A. johnsonii, S. rubidaea, S. marcescens, S. warneri, and M. hydrocarbonoxydans were able to grow up to 1000 mg/L of phthalates esters. These results not only revealed the important contribution of the symbionts in L apiculatum ants feeding habits, but also have shown a promising source of enzymes with potential biotechnological applications such as lignocellulosic biomass hydrolysis and bioremediation processes.
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21
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Kivistik C, Knobloch J, Käiro K, Tammert H, Kisand V, Hildebrandt JP, Herlemann DPR. Impact of Salinity on the Gastrointestinal Bacterial Community of Theodoxus fluviatilis. Front Microbiol 2020; 11:683. [PMID: 32457702 PMCID: PMC7225522 DOI: 10.3389/fmicb.2020.00683] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Accepted: 03/24/2020] [Indexed: 12/21/2022] Open
Abstract
Differences in salinity are boundaries that act as barriers for the dispersal of most aquatic organisms. This creates distinctive biota in freshwater and brackish water (mesohaline) environments. To test how saline boundaries influence the diversity and composition of host-associated microbiota, we analyzed the microbiome within the digestive tract of Theodoxus fluviatilis, an organism able to cross the freshwater and mesohaline boundary. Alpha-diversity measures of the microbiome in freshwater and brackish water were not significantly different. However, the composition of the bacterial community within freshwater T. fluviatilis differed significantly compared with mesohaline T. fluviatilis and typical bacteria could be determined for the freshwater and the mesohaline digestive tract microbiome. An artificial increase in salinity surrounding these freshwater snails resulted in a strong change in the bacterial community and typical marine bacteria became more pronounced in the digestive tract microbiome of freshwater T. fluviatilis. However, the composition of the digestive tract microbiome in freshwater snails did not converge to that found within mesohaline snails. Within mesohaline snails, no cardinal change was found after either an increase or decrease in salinity. In all samples, Pseudomonas, Pirellula, Flavobacterium, Limnohabitans, and Acinetobacter were among the most abundant bacteria. These bacterial genera were largely unaffected by changes in environmental conditions. As permanent residents in T. fluviatilis, they may support the digestion of the algal food in the digestive tract. Our results show that freshwater and mesohaline water host-associated microbiomes respond differently to changes in salinity. Therefore, the salinization of coastal freshwater environments due to a rise in sea level can influence the gut microbiome and its functions with currently unknown consequences for, e.g., nutritional physiology of the host.
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Affiliation(s)
- Carmen Kivistik
- Centre for Limnology, Estonian University of Life Sciences, Tartu, Estonia
| | - Jan Knobloch
- Zoological Institute and Museum, University of Greifswald, Greifswald, Germany
| | - Kairi Käiro
- Centre for Limnology, Estonian University of Life Sciences, Tartu, Estonia
| | - Helen Tammert
- Centre for Limnology, Estonian University of Life Sciences, Tartu, Estonia
| | - Veljo Kisand
- Centre for Limnology, Estonian University of Life Sciences, Tartu, Estonia
- Institute of Technology, University of Tartu, Tartu, Estonia
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22
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Mioduchowska M, Zając K, Bartoszek K, Madanecki P, Kur J, Zając T. 16S rRNA
gene‐based metagenomic analysis of the gut microbial community associated with the DUI species
Unio crassus
(Bivalvia: Unionidae). J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12377] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Monika Mioduchowska
- Department of Genetics and Biosystematics Faculty of Biology University of Gdańsk Gdańsk Poland
| | - Katarzyna Zając
- Institute of Nature Conservation Polish Academy of Sciences Kraków Poland
| | - Krzysztof Bartoszek
- Department of Computer and Information Science Division of Statistics and Machine Learning Linköping University Linköping Sweden
| | - Piotr Madanecki
- Department of Biology and Pharmaceutical Botany Faculty of Pharmacy Medical University of Gdańsk Gdańsk Poland
| | | | - Tadeusz Zając
- Institute of Nature Conservation Polish Academy of Sciences Kraków Poland
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Kurniawati M, Purkan, Sumarsih S, Baktir A. A Novel 1,3-Β-Glucanase Gene from the Metagenomic Expression Library of Achatina Fulica's Digestive Gland. IRANIAN JOURNAL OF PHARMACEUTICAL RESEARCH : IJPR 2020; 19:483-493. [PMID: 33680046 PMCID: PMC7757977 DOI: 10.22037/ijpr.2020.1101172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
1,3-β-glucanase enzyme has been proved as antibiofilm by hydrolyzing the main component of extracellular matrix of C. albicans polymicrobial biofilm, to prevent resistancy during the use of antibiotics. The aim of this study is to construct a metagenomic expression library from Achatina fulica's digestive gland and to screen for a novel 1,3-β-glucanase genes by using its specific substrate of laminarin. A cDNA expression library was constructed using the λTriplEx2 vector in the E. coli strain XL1-Blue. Cre-recombinase circularization was used to convert λTriplEx2 to pTriplEx2 in the E. coli strain BM 25.8;then IPTG induction was used to express 1,3-β-glucanase. High-efficiency cDNA library of A. fulica's digestive gland was constructed, from where we obtained seventeen halo positive plaques, among them is a novel 1,3-β-glucanase gene designated MkafGlu1. Its nucleotide sequence has similarities to the endo-1,3-β-glucanase from Gossypium hirsutum, as well as the β-glucanases from Paenibacillus mucilaginosus, Verticillium alfalfa, and Cryptopygus antarcticus of 45%, 40%, 38% and 37%, respectively. An open reading frame of 717 bp encoded a protein of 239 amino acids. A novel 1,3-β-glucanase gene called MkafGlu1 was successfully expressed in E.coli BM 25.8 with activity of 1.07 U mL-1.
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Affiliation(s)
- Maris Kurniawati
- Department of Chemistry, Faculty of Science and Technology, Airlangga University, Surabaya, Indonesia. ,Faculty of Science and Technology, Universitas Kanjuruhan, Malang, Indonesia.
| | - Purkan
- Department of Chemistry, Faculty of Science and Technology, Airlangga University, Surabaya, Indonesia.
| | - Sri Sumarsih
- Department of Chemistry, Faculty of Science and Technology, Airlangga University, Surabaya, Indonesia.
| | - Afaf Baktir
- Department of Chemistry, Faculty of Science and Technology, Airlangga University, Surabaya, Indonesia. ,Corresponding author: E-mail:
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24
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Exploring the gut of Helicoverpa armigera for cellulose degrading bacteria and evaluation of a potential strain for lignocellulosic biomass deconstruction. Process Biochem 2018. [DOI: 10.1016/j.procbio.2018.08.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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25
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Liu C, Zhang Y, Ren Y, Wang H, Li S, Jiang F, Yin L, Qiao X, Zhang G, Qian W, Liu B, Fan W. The genome of the golden apple snail Pomacea canaliculata provides insight into stress tolerance and invasive adaptation. Gigascience 2018; 7:5069392. [PMID: 30107526 PMCID: PMC6129957 DOI: 10.1093/gigascience/giy101] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 08/03/2018] [Indexed: 12/22/2022] Open
Abstract
Background The golden apple snail (Pomacea canaliculata) is a freshwater snail listed among the top 100 worst invasive species worldwide and a noted agricultural and quarantine pest that causes great economic losses. It is characterized by fast growth, strong stress tolerance, a high reproduction rate, and adaptation to a broad range of environments. Results Here, we used long-read sequencing to produce a 440-Mb high-quality, chromosome-level assembly of the P. canaliculata genome. In total, 50 Mb (11.4%) repeat sequences and 21,533 gene models were identified in the genome. The major findings of this study include the recent explosion of DNA/hAT-Charlie transposable elements, the expansion of the P450 gene family, and the constitution of the cellular homeostasis system, which contributes to ecological plasticity in stress adaptation. In addition, the high transcriptional levels of perivitelline genes in the ovary and albumen gland promote the function of nutrient supply and defense ability in eggs. Furthermore, the gut metagenome also contains diverse genes for food digestion and xenobiotic degradation. Conclusions These findings collectively provide novel insights into the molecular mechanisms of the ecological plasticity and high invasiveness.
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Affiliation(s)
- Conghui Liu
- Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Pengfei Road Shenzhen, Guangdong, 518120, China
| | - Yan Zhang
- Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Pengfei Road Shenzhen, Guangdong, 518120, China
| | - Yuwei Ren
- Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Pengfei Road Shenzhen, Guangdong, 518120, China
| | - Hengchao Wang
- Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Pengfei Road Shenzhen, Guangdong, 518120, China
| | - Shuqu Li
- Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Pengfei Road Shenzhen, Guangdong, 518120, China
| | - Fan Jiang
- Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Pengfei Road Shenzhen, Guangdong, 518120, China
| | - Lijuan Yin
- Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Pengfei Road Shenzhen, Guangdong, 518120, China
| | - Xi Qiao
- Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Pengfei Road Shenzhen, Guangdong, 518120, China
| | - Guojie Zhang
- BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
| | - Wanqiang Qian
- Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Pengfei Road Shenzhen, Guangdong, 518120, China
| | - Bo Liu
- Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Pengfei Road Shenzhen, Guangdong, 518120, China
| | - Wei Fan
- Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Pengfei Road Shenzhen, Guangdong, 518120, China
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26
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Hu Z, Chen X, Chang J, Yu J, Tong Q, Li S, Niu H. Compositional and predicted functional analysis of the gut microbiota of Radix auricularia (Linnaeus) via high-throughput Illumina sequencing. PeerJ 2018; 6:e5537. [PMID: 30186698 PMCID: PMC6118204 DOI: 10.7717/peerj.5537] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 08/08/2018] [Indexed: 12/14/2022] Open
Abstract
Due to its wide distribution across the world, the snail Radix auricularia plays a central role in the transferal of energy and biomass by consuming plant biomass in freshwater systems. The gut microbiota are involved in the nutrition, digestion, immunity, and development of snails, particularly for cellulolytic bacteria, which greatly contribute to the digestion of plant fiber. For the first time, this study characterized the gut bacterial communities of R. auricularia, as well as predicted functions, using the Illumina Miseq platform to sequence 16S rRNA amplicons. Both juvenile snails (JS) and adult snails (AS) were sampled. The obtained 251,072 sequences were rarefied to 214,584 sequences and clustered into 1,196 operational taxonomic units (OTUs) with 97% sequence identity. The predominant phyla were Proteobacteria (JS: 36.0%, AS: 31.6%) and Cyanobacteria (JS: 16.3%, AS: 19.5%), followed by Chloroflexi (JS: 9.7%, AS: 13.1%), Firmicutes (JS: 14.4%, AS: 6.7%), Actinobacteria (JS: 8.2%, AS: 12.6%), and Tenericutes (JS: 7.3%, AS: 6.2%). The phylum Cyanobacteria may have originated from the plant diet instead of the gut microbiome. A total of 52 bacterial families and 55 genera were found with >1% abundance in at least one sample. A large number of species could not be successfully identified, which could indicate the detection of novel ribotypes or result from insufficient availability of snail microbiome data. The core microbiome consisted of 469 OTUs, representing 88.4% of all sequences. Furthermore, the predicted function of bacterial community of R. auricularia performed by Phylogenetic Investigation of Communities by Reconstruction of Unobserved States suggests that functions related to metabolism and environmental information processing were enriched. The abundance of carbohydrate suggests a strong capability of the gut microbiome to digest lignin. Our results indicate an abundance of bacteria in both JS and AS, and thus the bacteria in R. auricularia gut form a promising source for novel enzymes, such as cellulolytic enzymes, that may be useful for biofuel production. Furthermore, searching for xenobiotic biodegradation bacteria may be a further important application of these snails.
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Affiliation(s)
- Zongfu Hu
- College of Animal Science and Technology, Inner Mongolia University for Nationalities, Tongliao, People's Republic of China.,College of Animal Science and Technology, Northeast Agricultural University, Harbin, People's Republic of China.,Inner Mongolia Key Laboratory of Toxicant Monitoring and Toxicology, Tongliao, People's Republic of China
| | - Xi Chen
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, People's Republic of China
| | - Jie Chang
- College of Animal Science and Technology, Inner Mongolia University for Nationalities, Tongliao, People's Republic of China
| | - Jianhua Yu
- College of Animal Science and Technology, Inner Mongolia University for Nationalities, Tongliao, People's Republic of China
| | - Qing Tong
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, People's Republic of China
| | - Shuguo Li
- College of Animal Science and Technology, Inner Mongolia University for Nationalities, Tongliao, People's Republic of China
| | - Huaxin Niu
- College of Animal Science and Technology, Inner Mongolia University for Nationalities, Tongliao, People's Republic of China
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27
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Physiological and Molecular Understanding of Bacterial Polysaccharide Monooxygenases. Microbiol Mol Biol Rev 2017; 81:81/3/e00015-17. [PMID: 28659491 DOI: 10.1128/mmbr.00015-17] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacteria have long been known to secrete enzymes that degrade cellulose and chitin. The degradation of these two polymers predominantly involves two enzyme families that work synergistically with one another: glycoside hydrolases (GHs) and polysaccharide monooxygenases (PMOs). Although bacterial PMOs are a relatively recent addition to the known biopolymer degradation machinery, there is an extensive amount of literature implicating PMO in numerous physiological roles. This review focuses on these diverse and physiological aspects of bacterial PMOs, including facilitating endosymbiosis, conferring a nutritional advantage, and enhancing virulence in pathogenic organisms. We also discuss the correlation between the presence of PMOs and bacterial lifestyle and speculate on the advantages conferred by PMOs under these conditions. In addition, the molecular aspects of bacterial PMOs, as well as the mechanisms regulating PMO expression and the function of additional domains associated with PMOs, are described. We anticipate that increasing research efforts in this field will continue to expand our understanding of the molecular and physiological roles of bacterial PMOs.
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28
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Ben Guerrero E, Soria M, Salvador R, Ceja-Navarro JA, Campos E, Brodie EL, Talia P. Effect of Different Lignocellulosic Diets on Bacterial Microbiota and Hydrolytic Enzyme Activities in the Gut of the Cotton Boll Weevil ( Anthonomus grandis). Front Microbiol 2016; 7:2093. [PMID: 28082962 PMCID: PMC5186755 DOI: 10.3389/fmicb.2016.02093] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 12/09/2016] [Indexed: 11/13/2022] Open
Abstract
Cotton boll weevils, Anthonomus grandis, are omnivorous coleopteran that can feed on diets with different compositions, including recalcitrant lignocellulosic materials. We characterized the changes in the prokaryotic community structure and the hydrolytic activities of A. grandis larvae fed on different lignocellulosic diets. A. grandis larvae were fed on three different artificial diets: cottonseed meal (CM), Napier grass (NG) and corn stover (CS). Total DNA was extracted from the gut samples for amplification and sequencing of the V3-V4 hypervariable region of the 16S rRNA gene. Proteobacteria and Firmicutes dominated the gut microbiota followed by Actinobacteria, Spirochaetes and a small number of unclassified phyla in CM and NG microbiomes. In the CS feeding group, members of Spirochaetes were the most prevalent, followed by Proteobacteria and Firmicutes. Bray-Curtis distances showed that the samples from the CS community were clearly separated from those samples of the CM and NG diets. Gut extracts from all three diets exhibited endoglucanase, xylanase, β-glucosidase and pectinase activities. These activities were significantly affected by pH and temperature across different diets. We observed that the larvae reared on a CM showed significantly higher activities than larvae reared on NG and CS. We demonstrated that the intestinal bacterial community structure varies depending on diet composition. Diets with more variable and complex compositions, such as CS, showed higher bacterial diversity and richness than the two other diets. In spite of the detected changes in composition and diversity, we identified a core microbiome shared between the three different lignocellulosic diets. These results suggest that feeding with diets of different lignocellulosic composition could be a viable strategy to discover variants of hemicellulose and cellulose breakdown systems.
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Affiliation(s)
- Emiliano Ben Guerrero
- Instituto de Biotecnología, Centro de Investigación en Ciencias Veterinarias y Agronómicas, Centro Nacional de Investigaciones Agropecuarias - Instituto Nacional de Tecnología Agropecuaria Castelar Hurlingham, Argentina
| | - Marcelo Soria
- Instituto de Investigaciones en Biociencias Agrícolas y Ambientales-Consejo Nacional de Investigaciones Científicas y Técnicas, Cátedra de Microbiología Agrícola, Facultad de Agronomía, Universidad de Buenos Aires Buenos Aires, Argentina
| | - Ricardo Salvador
- Instituto de Microbiología y Zoología Agrícola, Centro de Investigación en Ciencias Veterinarias y Agronómicas, Centro Nacional de Investigaciones Agropecuarias - Instituto Nacional de Tecnología Agropecuaria Castelar Hurlingham, Argentina
| | - Javier A Ceja-Navarro
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Eleonora Campos
- Instituto de Biotecnología, Centro de Investigación en Ciencias Veterinarias y Agronómicas, Centro Nacional de Investigaciones Agropecuarias - Instituto Nacional de Tecnología Agropecuaria CastelarHurlingham, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)Buenos Aires, Argentina
| | - Eoin L Brodie
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Paola Talia
- Instituto de Biotecnología, Centro de Investigación en Ciencias Veterinarias y Agronómicas, Centro Nacional de Investigaciones Agropecuarias - Instituto Nacional de Tecnología Agropecuaria CastelarHurlingham, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)Buenos Aires, Argentina
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29
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Pinheiro GL, de Azevedo-Martins AC, Albano RM, de Souza W, Frases S. Comprehensive analysis of the cellulolytic system reveals its potential for deconstruction of lignocellulosic biomass in a novel Streptomyces sp. Appl Microbiol Biotechnol 2016; 101:301-319. [DOI: 10.1007/s00253-016-7851-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 08/21/2016] [Accepted: 09/07/2016] [Indexed: 12/30/2022]
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30
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Su L, Yang L, Huang S, Li Y, Su X, Wang F, Bo C, Wang ET, Song A. Variation in the Gut Microbiota of Termites (Tsaitermes ampliceps) Against Different Diets. Appl Biochem Biotechnol 2016; 181:32-47. [PMID: 27457759 DOI: 10.1007/s12010-016-2197-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 07/13/2016] [Indexed: 11/29/2022]
Abstract
Termites are well recognized for their thriving on recalcitrant lignocellulosic diets through nutritional symbioses with gut-dwelling microbiota; however, the effects of diet changes on termite gut microbiota are poorly understood, especially for the lower termites. In this study, we employed high-throughput 454 pyrosequencing of 16S V1-V3 amplicons to compare gut microbiotas of Tsaitermes ampliceps fed with lignin-rich and lignin-poor cellulose diets after a 2-week-feeding period. As a result, the majority of bacterial taxa were shared across the treatments with different diets, but their relative abundances were modified. In particular, the relative abundance was reduced for Spirochaetes and it was increased for Proteobacteria and Bacteroides by feeding the lignin-poor diet. The evenness of gut microbiota exhibited a significant difference in response to the diet type (filter paper diets < corn stover diets < wood diets), while their richness was constant, which may be related to the lower recalcitrance of this biomass to degradation. These results have important implications for sampling and analysis strategies to probe the lignocellulose degradation features of termite gut microbiota and suggest that the dietary lignocellulose composition could cause shifting rapidly in the termite gut microbiota.
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Affiliation(s)
- Lijuan Su
- College of Life Sciences, Henan Agricultural University, Zhengzhou, Henan, 450002, China
| | - Lele Yang
- College of Life Sciences, Henan Agricultural University, Zhengzhou, Henan, 450002, China
| | - Shi Huang
- BioEnergy Genome Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
| | - Yan Li
- College of Life Sciences, Henan Agricultural University, Zhengzhou, Henan, 450002, China
| | - Xiaoquan Su
- BioEnergy Genome Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
| | - Fengqin Wang
- College of Life Sciences, Henan Agricultural University, Zhengzhou, Henan, 450002, China
- Key Laboratory of Enzyme Engineering of Agricultural Microbiology, Ministry of Agriculture, Zhengzhou, Henan, 450002, China
| | - Cunpei Bo
- BioEnergy Genome Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
| | - En Tao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340, México D.F., Mexico.
| | - Andong Song
- College of Life Sciences, Henan Agricultural University, Zhengzhou, Henan, 450002, China.
- Key Laboratory of Enzyme Engineering of Agricultural Microbiology, Ministry of Agriculture, Zhengzhou, Henan, 450002, China.
- , No. 93, Nongye Road, Zhengzhou, Henan Province, China.
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Balsingh J, Radhakrishna S, Ulaganathan K. Draft Genome Sequence of Bacillus pumilus ku-bf1 Isolated from the Gut Contents of Wood Boring Mesomorphus sp. Front Microbiol 2016; 7:1037. [PMID: 27446065 PMCID: PMC4927586 DOI: 10.3389/fmicb.2016.01037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 06/20/2016] [Indexed: 11/16/2022] Open
Affiliation(s)
- Jatoth Balsingh
- Center for Plant Molecular Biology, Osmania University Hyderabad, India
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