1
|
Gao H, Jiang S, Wang Y, Hu M, Xue Y, Cao B, Dou H, Li R, Yi X, Jiang L, Zhang B, Li Y. Comparison of gut bacterial communities of Hyphantriacunea Drury (Lepidoptera, Arctiidae), based on 16S rRNA full-length sequencing. Biodivers Data J 2023; 11:e98143. [PMID: 38327372 PMCID: PMC10848398 DOI: 10.3897/bdj.11.e98143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 04/14/2023] [Indexed: 02/09/2024] Open
Abstract
There are a large number of microorganisms in the gut of insects, which form a symbiotic relationship with the host during the long-term co-evolution process and have a significant impact on the host's nutrition, physiology, development, immunity, stress tolerance and other aspects. However, the composition of the gut microbes of Hyphantriacunea remains unclear. In order to investigate the difference and diversity of intestinal microbiota of H.cunea larvae feeding on different host plants, we used PacBio sequencing technology for the first time to sequence the 16S rRNA full-length gene of the intestinal microbiota of H.cunea. The species classification, β diversity and function of intestinal microflora of the 5th instar larvae of four species of H.cunea feeding on apricot, plum, redbud and Chinese ash were analysed. The results showed that a total of nine phyla and 65 genera were identified by PacBio sequencing, amongst which Firmicutes was the dominant phylum and Enterococcus was the dominant genus, with an average relative abundance of 59.29% and 52.16%, respectively. PERMANOVA analysis and cluster heat map showed that the intestinal microbiomes of H.cunea larvae, fed on different hosts, were significantly different. LEfSe analysis confirmed the effect of host diet on intestinal community structure and PICRUSt2 analysis showed that most of the predictive functions were closely related to material transport and synthetic, metabolic and cellular processes. The results of this study laid a foundation for revealing the interaction between the intestinal microorganisms of H.cunea and its hosts and provided ideas for exploring new green prevention and control strategies of H.cunea.
Collapse
Affiliation(s)
- Hui Gao
- School of Life Sciences, Qufu Normal University, Qufu, ChinaSchool of Life Sciences, Qufu Normal UniversityQufuChina
- School of Life Sciences, Shandong University, Qingdao, ChinaSchool of Life Sciences, Shandong UniversityQingdaoChina
| | - Sai Jiang
- School of Life Sciences, Qufu Normal University, Qufu, ChinaSchool of Life Sciences, Qufu Normal UniversityQufuChina
| | - Yinan Wang
- School of Life Sciences, Qufu Normal University, Qufu, ChinaSchool of Life Sciences, Qufu Normal UniversityQufuChina
| | - Meng Hu
- Forestry Protection and Development Service Center of Jining City, Jining, ChinaForestry Protection and Development Service Center of Jining CityJiningChina
| | - Yuyan Xue
- Qufu Bureau of Natural Resources and Planning, Qufu, ChinaQufu Bureau of Natural Resources and PlanningQufuChina
| | - Bing Cao
- Animal Husbandry and Fisheries Development Centre of Tengzhou, Tengzhou, ChinaAnimal Husbandry and Fisheries Development Centre of TengzhouTengzhouChina
| | - Hailong Dou
- School of Life Sciences, Qufu Normal University, Qufu, ChinaSchool of Life Sciences, Qufu Normal UniversityQufuChina
| | - Ran Li
- School of Life Sciences, Qufu Normal University, Qufu, ChinaSchool of Life Sciences, Qufu Normal UniversityQufuChina
| | - Xianfeng Yi
- School of Life Sciences, Qufu Normal University, Qufu, ChinaSchool of Life Sciences, Qufu Normal UniversityQufuChina
| | - Lina Jiang
- School of Life Sciences, Qufu Normal University, Qufu, ChinaSchool of Life Sciences, Qufu Normal UniversityQufuChina
| | - Bin Zhang
- College of Life Sciences and Technology, Inner Mongolia Normal University, Hohhot, Inner Mongolia Autonomous Region, ChinaCollege of Life Sciences and Technology, Inner Mongolia Normal UniversityHohhot, Inner Mongolia Autonomous RegionChina
| | - Yujian Li
- School of Life Sciences, Qufu Normal University, Qufu, ChinaSchool of Life Sciences, Qufu Normal UniversityQufuChina
| |
Collapse
|
2
|
Zhou L, Chen C, Wang X. Gut Bacterial Diversity and Community Structure of Spodoptera exigua (Lepidoptera: Noctuidae) in the Welsh Onion-producing Areas of North China. JOURNAL OF ECONOMIC ENTOMOLOGY 2022; 115:1102-1114. [PMID: 35765845 DOI: 10.1093/jee/toac103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Indexed: 06/15/2023]
Abstract
Gut microbiota play an important role in digestion, development, nutritional metabolism, and detoxification in insects. However, scant information exists on the gut bacterial variation, composition, and community structure of the beet armyworm, Spodoptera exigua (Hübner), and how its gut microbiota has adapted to different geographical environments. Using 16S rRNA high-throughput sequencing technology, we detected 3,837,408 high-quality reads and 1,457 operational taxonomic units (OTUs) in 47 gut samples of S. exigua collected from ten sites in northern China. Overall, we identified 697 bacterial genera from 30 phyla, among which Proteobacteria and Firmicutes were the most dominant phyla. Gut bacterial alpha-diversity metrics revealed significant differences among these populations. We detected the highest alpha bacterial diversity in Xinming, northern Liaoning Province, and the lowest bacterial diversity in Zhangwu, western Liaoning Province. Beta diversity indicated that the gut microbial community structure of S. exigua in Liaoning Province was significantly different from that of other populations. There was a similar microbial community structure among populations in the adjacent province, suggesting that the environment influences bacterial succession in this pest. Finally, PICRUSt analysis demonstrated that microbial functions closely associated with the gut microbiomes mainly included membrane transport, carbohydrate metabolism and replication, and amino acid metabolism.
Collapse
Affiliation(s)
- Lihong Zhou
- Institute of Flower, Liaoning Academy of Agricultural Sciences, Shenyang, Liaoning, 110161, P.R. China
| | - Chen Chen
- College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning, 110866, P.R. China
| | - Xingya Wang
- College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning, 110866, P.R. China
| |
Collapse
|
3
|
Gawande SJ, Anandhan S, Ingle A, Roylawar P, Khandagale K, Gawai T, Jacobson A, Asokan R, Singh M. Microbiome profiling of the onion thrips, Thrips tabaci Lindeman (Thysanoptera: Thripidae). PLoS One 2019; 14:e0223281. [PMID: 31568480 PMCID: PMC6768462 DOI: 10.1371/journal.pone.0223281] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 09/17/2019] [Indexed: 12/21/2022] Open
Abstract
The gut microbial community structure of adult Thrips tabaci collected from 10 different agro-climatically diverse locations of India was characterized by using the Illumina MiSeq platform to amplify the V3 region of the 16S rRNA gene of bacteria present in the sampled insects. Analyses were performed to study the bacterial communities associated with Thrips tabaci in India. The complete bacterial metagenome of T. tabaci was comprised of 1662 OTUs of which 62.25% belong to known and 37.7% of unidentified/unknown bacteria. These OTUs constituted 21 bacterial phyla of 276 identified genera. Phylum Proteobacteria was predominant, followed by Actinobacteria, Firmicutes, Bacteroidetes and Cyanobacteria. Additionally, the occurrence of the reproductive endosymbiont, Wolbachia was detected at two locations (0.56%) of the total known OTUs. There is high variation in diversity and species richness among the different locations. Alpha-diversity metrics indicated the higher gut bacterial diversity at Bangalore and lowest at Rahuri whereas higher bacterial species richness at T. tabaci samples from Imphal and lowest at Jhalawar. Beta diversity analyses comparing bacterial communities between the samples showed distinct differences in bacterial community composition of T. tabaci samples from different locations. This paper also constitutes the first record of detailed bacterial communities associated with T. tabaci. The location-wise variation in microbial metagenome profile of T. tabaci suggests that bacterial diversity might be governed by its population genetic structure, environment and habitat.
Collapse
Affiliation(s)
- Suresh J. Gawande
- ICAR-Directorate of Onion and Garlic Research, Rajgurunagar, Pune, India
| | | | - Ashish Ingle
- ICAR-Directorate of Onion and Garlic Research, Rajgurunagar, Pune, India
| | - Praveen Roylawar
- ICAR-Directorate of Onion and Garlic Research, Rajgurunagar, Pune, India
| | - Kiran Khandagale
- ICAR-Directorate of Onion and Garlic Research, Rajgurunagar, Pune, India
| | - Tushar Gawai
- ICAR-Directorate of Onion and Garlic Research, Rajgurunagar, Pune, India
| | - Alana Jacobson
- Department of Entomology and Plant Pathology, Auburn University, Auburn, Alabama, United States of America
| | - Ramasamy Asokan
- ICAR-Indian Institute of Horticultural Research, Hessarghatta Lake, Bengaluru, India
| | - Major Singh
- ICAR-Directorate of Onion and Garlic Research, Rajgurunagar, Pune, India
| |
Collapse
|
4
|
Harish ER, ManiChellappan, MakeshKumar T, Mathew D, Ranjith MT, Girija D. Next-generation sequencing reveals endosymbiont variability in cassava whitefly, Bemisia tabaci, across the agro-ecological zones of Kerala, India. Genome 2019; 62:571-584. [PMID: 31283888 DOI: 10.1139/gen-2018-0050] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Silverleaf whitefly, Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae), is one of the most notorious invasive insect pests, infesting more than 900 species of plants and spreading more than 200 viral diseases. This polyphagous agricultural pest harbours diverse bacterial communities in its gut, which perform multiple functions in whiteflies, including nutrient provisioning, amino acid biosynthesis, and virus transmission. The present exploratory study compares the bacterial communities associated with silverleaf whitefly infesting cassava, also known as cassava whitefly, collected from two different zones (zone P: plains; zone H: high ranges), from Kerala, India, using next-generation sequencing of 16S rDNA. The data sets for these two regions consisted of 1 321 906 and 690 661 high-quality paired-end sequences with mean length of 150 bp. Highly diverse bacterial communities were present in the sample, containing approximately 3513 operational taxonomic units (OTUs). Sequence analysis showed a marked difference in the relative abundance of bacteria in the populations. A total of 16 bacterial phyla, 27 classes, 56 orders, 91 families, 236 genera, and 409 species were identified from the P population, against 16, 31, 60, 88, 225, and 355, respectively, in the H population. Arsenophonus sp. (Enterobacteriaceae), which is important for virus transmission by whiteflies, was relatively abundant in the P population, whereas in the H population Bacillus sp. was the most dominant group. The association of whitefly biotypes and secondary symbionts suggests a possible contribution of these bacteria to host characteristics such as virus transmission, host range, insecticide resistance, and speciation.
Collapse
Affiliation(s)
- E R Harish
- ICAR-Central Tuber Crops Research Institute, Sreekaryam, Thiruvananthapuram - 695 017, India
| | - ManiChellappan
- Department of Agricultural Entomology, College of Horticulture, Kerala Agricultural University, Thrissur - 680 656, India
| | - T MakeshKumar
- ICAR-Central Tuber Crops Research Institute, Sreekaryam, Thiruvananthapuram - 695 017, India
| | - Deepu Mathew
- Centre for Plant Biotechnology and Molecular Biology, Kerala Agricultural University, Thrissur - 680 656, India
| | - M T Ranjith
- Department of Agricultural Entomology, College of Horticulture, Kerala Agricultural University, Thrissur - 680 656, India
| | - D Girija
- Department of Agricultural Microbiology, College of Horticulture, Kerala Agricultural University, Thrissur - 680 656, India
| |
Collapse
|
5
|
Bapatla KG, Singh A, Yeddula S, Patil RH. Annotation of gut bacterial taxonomic and functional diversity in Spodoptera litura and Spilosoma obliqua. J Basic Microbiol 2018; 58:217-226. [PMID: 29380873 DOI: 10.1002/jobm.201700462] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 12/18/2017] [Accepted: 12/23/2017] [Indexed: 11/05/2022]
Abstract
The insect gut has been the house of many taxonomically and physiologically diverse groups of microbial colonizers as symbionts and commensals, which are evolving to support the physiological requirement of insects. Lepidoptera is one of the important family of class hexapoda, comprising agriculture insect pest Spodoptera litura and Spilosoma obliqua. Information on gut microbiota and their functional role in these insects was meager to elucidate the wide-ranging survivalist mechanisms. In this context, we analyzed the composition, diversity and functional role of gut bacteria in S. litura and S. obliqua collected from soybean and sunflower crops, respectively, using Next Generation Sequencing of 16S rRNA. A total of 3427 and 206 Operation Taxonomic Units (OTUs) were identified in S. litura and S. obliqua gut metagenome, respectively. Highest number of sequences were annotated to unclassified bacteria (34%), followed by Proteobacteria (27%), and Chlorobi (14%) in S. litura, while S. obliqua has significant representation of Firmicutes (48%), followed by Bacteroidetes (20%), and unclassified bacteria (11%). Functionality of both metagenomes revealed, high abundance of ammonia oxidizers (20.1 58.0%) followed by relative abundance of detoxifying processes - dehalogenation (17.4-41.2%) and aromatic hydrocarbons degradation (1.1-3.1%). This study highlights the significance of the inherent microbiome of two defoliators in shaping the metagenome for nutrition and detoxifying the chemical molecules, and opens an avenue for exploring role of insect gut bacteria in host selection, metabolic endurance of insecticides and synergistic or agonistic mechanisms inside gut of insects feeding on insect-resistant biotech crops.
Collapse
Affiliation(s)
- Kiran G Bapatla
- Department of Agricultural Entomology, UAS Dharwad, Karnataka, India
| | - Arjun Singh
- ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath, Uttar Pradesh, India
| | - Srujana Yeddula
- Department of Agricultural Entomology, UAS Dharwad, Karnataka, India
| | | |
Collapse
|
6
|
Schwarz WH, Brunecky R, Broeker J, Liebl W, Zverlov VV. Handling gene and protein names in the age of bioinformatics: the special challenge of secreted multimodular bacterial enzymes such as the cbhA/cbh9A gene of Clostridium thermocellum. World J Microbiol Biotechnol 2018; 34:42. [PMID: 29480332 DOI: 10.1007/s11274-018-2424-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Accepted: 02/20/2018] [Indexed: 01/11/2023]
Abstract
An increasing number of researchers working in biology, biochemistry, biotechnology, bioengineering, bioinformatics and other related fields of science are using biological molecules. As the scientific background of the members of different scientific communities is more diverse than ever before, the number of scientists not familiar with the rules for non-ambiguous designation of genetic elements is increasing. However, with biological molecules gaining importance through biotechnology, their functional and unambiguous designation is vital. Unfortunately, naming genes and proteins is not an easy task. In addition, the traditional concepts of bioinformatics are challenged with the appearance of proteins comprising different modules with a respective function in each module. This article highlights basic rules and novel solutions in designation recently used within the community of bacterial geneticists, and we discuss the present-day handling of gene and protein designations. As an example we will utilize a recent mischaracterization of gene nomenclature. We make suggestions for better handling of names in future literature as well as in databases and annotation projects. Our methodology emphasizes the hydrolytic function of multi-modular genes and extracellular proteins from bacteria.
Collapse
Affiliation(s)
- Wolfgang H Schwarz
- Department of Microbiology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Emil‑Ramann‑Str. 4, 85354, Freising, Germany.
| | - Roman Brunecky
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
| | - Jannis Broeker
- Department of Microbiology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Emil‑Ramann‑Str. 4, 85354, Freising, Germany
| | - Wolfgang Liebl
- Department of Microbiology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Emil‑Ramann‑Str. 4, 85354, Freising, Germany
| | - Vladimir V Zverlov
- Department of Microbiology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Emil‑Ramann‑Str. 4, 85354, Freising, Germany. .,Institute of Molecular Genetics, Russian Academy of Science, Kurchatov Sq. 2, 123182, Moscow, Russia.
| |
Collapse
|
7
|
Kim CC, Kelly WJ, Patchett ML, Tannock GW, Jordens Z, Stoklosinski HM, Taylor JW, Sims IM, Bell TJ, Rosendale DI. Monoglobus pectinilyticus gen. nov., sp. nov., a pectinolytic bacterium isolated from human faeces. Int J Syst Evol Microbiol 2017; 67:4992-4998. [PMID: 29039307 DOI: 10.1099/ijsem.0.002395] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel anaerobic pectinolytic bacterium (strain 14T) was isolated from human faeces. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 14T belonged to the family Ruminococcaceae, but was located separately from known clostridial clusters within the taxon. The closest cultured relative of strain 14T was Acetivibrio cellulolyticus (89.7 % sequence similarity). Strain 14T shared ~99 % sequence similarity with cloned 16S rRNA gene sequences from uncultured bacteria derived from the human gut. Cells were Gram-stain-positive, non-motile cocci approximately 0.6 µm in diameter. Strain 14T fermented pectins from citrus peel, apple, and kiwifruit as well as carbohydrates that are constituents of pectins and hemicellulose, such as galacturonic acid, xylose, and arabinose. TEM images of strain 14T, cultured in association with plant tissues, suggested extracellular fibrolytic activity associated with the bacterial cells, forming zones of degradation in the pectin-rich regions of middle lamella. Phylogenetic and phenotypic analysis supported the differentiation of strain 14T as a novel genus in the family Ruminococcaceae. The name Monoglobus pectinilyticus gen. nov., sp. nov. is proposed; the type strain is 14T (JCM 31914T=DSM 104782T).
Collapse
Affiliation(s)
- Caroline C Kim
- Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand.,The New Zealand Institute for Plant and Food Research, Palmerston North 4474, New Zealand
| | | | - Mark L Patchett
- Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Gerald W Tannock
- Department of Microbiology and Immunology, Microbiome Otago, University of Otago, Dunedin 9016, New Zealand
| | - Z Jordens
- Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Halina M Stoklosinski
- The New Zealand Institute for Plant and Food Research, Palmerston North 4474, New Zealand
| | - Jordan W Taylor
- Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Ian M Sims
- Ferrier Research Institute, Victoria University of Wellington, Gracefield Research Centre, Lower Hutt 5040, New Zealand
| | - Tracey J Bell
- Ferrier Research Institute, Victoria University of Wellington, Gracefield Research Centre, Lower Hutt 5040, New Zealand
| | - Douglas I Rosendale
- The New Zealand Institute for Plant and Food Research, Palmerston North 4474, New Zealand
| |
Collapse
|
8
|
Zhivin O, Dassa B, Moraïs S, Utturkar SM, Brown SD, Henrissat B, Lamed R, Bayer EA. Unique organization and unprecedented diversity of the Bacteroides (Pseudobacteroides) cellulosolvens cellulosome system. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:211. [PMID: 28912832 PMCID: PMC5590126 DOI: 10.1186/s13068-017-0898-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 08/29/2017] [Indexed: 05/23/2023]
Abstract
BACKGROUND (Pseudo) Bacteroides cellulosolvens is an anaerobic, mesophilic, cellulolytic, cellulosome-producing clostridial bacterium capable of utilizing cellulose and cellobiose as carbon sources. Recently, we sequenced the B. cellulosolvens genome, and subsequent comprehensive bioinformatic analysis, herein reported, revealed an unprecedented number of cellulosome-related components, including 78 cohesin modules scattered among 31 scaffoldins and more than 200 dockerin-bearing ORFs. In terms of numbers, the B. cellulosolvens cellulosome system represents the most intricate, compositionally diverse cellulosome system yet known in nature. RESULTS The organization of the B. cellulosolvens cellulosome is unique compared to previously described cellulosome systems. In contrast to all other known cellulosomes, the cohesin types are reversed for all scaffoldins i.e., the type II cohesins are located on the enzyme-integrating primary scaffoldin, whereas the type I cohesins are located on the anchoring scaffoldins. Many of the type II dockerin-bearing ORFs include X60 modules, which are known to stabilize type II cohesin-dockerin interactions. In the present work, we focused on revealing the architectural arrangement of cellulosome structure in this bacterium by examining numerous interactions between the various cohesin and dockerin modules. In total, we cloned and expressed 43 representative cohesins and 27 dockerins. The results revealed various possible architectures of cell-anchored and cell-free cellulosomes, which serve to assemble distinctive cellulosome types via three distinct cohesin-dockerin specificities: type I, type II, and a novel-type designated R (distinct from type III interactions, predominant in ruminococcal cellulosomes). CONCLUSIONS The results of this study provide novel insight into the architecture and function of the most intricate and extensive cellulosomal system known today, thereby extending significantly our overall knowledge base of cellulosome systems and their components. The robust cellulosome system of B. cellulosolvens, with its unique binding specificities and reversal of cohesin-dockerin types, has served to amend our view of the cellulosome paradigm. Revealing new cellulosomal interactions and arrangements is critical for designing high-efficiency artificial cellulosomes for conversion of plant-derived cellulosic biomass towards improved production of biofuels.
Collapse
Affiliation(s)
- Olga Zhivin
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Bareket Dassa
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Sarah Moraïs
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Sagar M. Utturkar
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37919 USA
- BioEnergy Science Center, Oak Ridge, TN USA
| | - Steven D. Brown
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37919 USA
- BioEnergy Science Center, Oak Ridge, TN USA
- Biosciences Division, Energy and Environment Directorate, Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille University and CNRS, Marseille, France
| | - Raphael Lamed
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv, Israel
| | - Edward A. Bayer
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| |
Collapse
|
9
|
Choi J, Klingeman DM, Brown SD, Cox CD. The LacI family protein GlyR3 co-regulates the celC operon and manB in Clostridium thermocellum. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:163. [PMID: 28652864 PMCID: PMC5483248 DOI: 10.1186/s13068-017-0849-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 06/16/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND Clostridium thermocellum utilizes a wide variety of free and cellulosomal cellulases and accessory enzymes to hydrolyze polysaccharides present in complex substrates. To date only a few studies have unveiled the details by which the expression of these cellulases are regulated. Recent studies have described the auto regulation of the celC operon and determined that the celC-glyR3-licA gene cluster and nearby manB-celT gene cluster are co-transcribed as polycistronic mRNA. RESULTS In this paper, we demonstrate that the GlyR3 protein mediates the regulation of manB. We first identify putative GlyR3 binding sites within or just upstream of the coding regions of manB and celT. Using an electrophoretic mobility shift assay (EMSA), we determined that a higher concentration of GlyR3 is required to effectively bind to the putative manB site in comparison to the celC site. Neither the putative celT site nor random DNA significantly binds GlyR3. While laminaribiose interfered with GlyR3 binding to the celC binding site, binding to the manB site was unaffected. In the presence of laminaribiose, in vivo transcription of the celC-glyR3-licA gene cluster increases, while manB expression is repressed, compared to in the absence of laminaribiose, consistent with the results from the EMSA. An in vitro transcription assay demonstrated that GlyR3 and laminaribiose interactions were responsible for the observed patters of in vivo transcription. CONCLUSIONS Together these results reveal a mechanism by which manB is expressed at low concentrations of GlyR3 but repressed at high concentrations. In this way, C. thermocellum is able to co-regulate both the celC and manB gene clusters in response to the availability of β-1,3-polysaccharides in its environment.
Collapse
Affiliation(s)
- Jinlyung Choi
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN 37996 USA
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN 37996 USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Dawn M. Klingeman
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Steven D. Brown
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Chris D. Cox
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN 37996 USA
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN 37996 USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Department Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37996 USA
| |
Collapse
|
10
|
Application of Long Sequence Reads To Improve Genomes for Clostridium thermocellum AD2, Clostridium thermocellum LQRI, and Pelosinus fermentans R7. GENOME ANNOUNCEMENTS 2016; 4:4/5/e01043-16. [PMID: 27688341 PMCID: PMC5043559 DOI: 10.1128/genomea.01043-16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
We and others have shown the utility of long sequence reads to improve genome assembly quality. In this study, we generated PacBio DNA sequence data to improve the assemblies of draft genomes for Clostridium thermocellum AD2, Clostridium thermocellum LQRI, and Pelosinus fermentans R7.
Collapse
|
11
|
Zhu N, Yang J, Ji L, Liu J, Yang Y, Yuan H. Metagenomic and metaproteomic analyses of a corn stover-adapted microbial consortium EMSD5 reveal its taxonomic and enzymatic basis for degrading lignocellulose. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:243. [PMID: 27833656 PMCID: PMC5103373 DOI: 10.1186/s13068-016-0658-z] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 10/28/2016] [Indexed: 05/08/2023]
Abstract
BACKGROUND Microbial consortia represent promising candidates for aiding in the development of plant biomass conversion strategies for biofuel production. However, the interaction between different community members and the dynamics of enzyme complements during the lignocellulose deconstruction process remain poorly understood. We present here a comprehensive study on the community structure and enzyme systems of a lignocellulolytic microbial consortium EMSD5 during growth on corn stover, using metagenome sequencing in combination with quantitative metaproteomics. RESULTS The taxonomic affiliation of the metagenomic data showed that EMSD5 was primarily composed of members from the phyla Proteobacteria, Firmicutes and Bacteroidetes. The carbohydrate-active enzyme (CAZyme) annotation revealed that representatives of Firmicutes encoded a broad array of enzymes responsible for hemicellulose and cellulose deconstruction. Extracellular metaproteome analysis further pinpointed the specific role and synergistic interaction of Firmicutes populations in plant polysaccharide breakdown. In particular, a wide range of xylan degradation-related enzymes, including xylanases, β-xylosidases, α-l-arabinofuranosidases, α-glucuronidases and acetyl xylan esterases, were secreted by diverse members from Firmicutes during growth on corn stover. Using label-free quantitative proteomics, we identified the differential secretion pattern of a core subset of enzymes, including xylanases and cellulases with multiple carbohydrate-binding modules (CBMs). In addition, analysis of the coordinate expression patterns indicated that transport proteins and hypothetical proteins may play a role in bacteria processing lignocellulose. Moreover, enzyme preparation from EMSD5 demonstrated synergistic activities in the hydrolysis of pretreated corn stover by commercial cellulases from Trichoderma reesei. CONCLUSIONS These results demonstrate that the corn stover-adapted microbial consortium EMSD5 harbors a variety of lignocellulolytic anaerobic bacteria and degradative enzymes, especially those implicated in hemicellulose decomposition. The data in this study highlight the pivotal role and cooperative relationship of Firmicutes members in the biodegradation of plant lignocellulose by EMSD5. The differential expression patterns of enzymes reveal the strategy of sequential lignocellulose deconstruction by EMSD5. Our findings provide insights into the mechanism by which consortium members orchestrate their array of enzymes to degrade complex lignocellulosic biomass.
Collapse
Affiliation(s)
- Ning Zhu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, Beijing, China
| | - Jinshui Yang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, Beijing, China
| | - Lei Ji
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, Beijing, China
| | - Jiawen Liu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, Beijing, China
| | - Yi Yang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, Beijing, China
| | - Hongli Yuan
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, Beijing, China
- National Energy R & D Center for Non-food Biomass, China Agricultural University, Beijing, 100193 China
| |
Collapse
|
12
|
Stolze Y, Zakrzewski M, Maus I, Eikmeyer F, Jaenicke S, Rottmann N, Siebner C, Pühler A, Schlüter A. Comparative metagenomics of biogas-producing microbial communities from production-scale biogas plants operating under wet or dry fermentation conditions. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:14. [PMID: 25688290 PMCID: PMC4329661 DOI: 10.1186/s13068-014-0193-8] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 12/22/2014] [Indexed: 05/23/2023]
Abstract
BACKGROUND Decomposition of biomass for biogas production can be practiced under wet and dry fermentation conditions. In contrast to the dry fermentation technology, wet fermentation is characterized by a high liquid content and a relatively low total solid content. In this study, the composition and functional potential of a biogas-producing microbial community in an agricultural biogas reactor operating under wet fermentation conditions was analyzed by a metagenomic approach applying 454-pyrosequencing. The obtained metagenomic dataset and corresponding 16S rRNA gene amplicon sequences were compared to the previously sequenced comparable metagenome from a dry fermentation process, meeting explicitly identical boundary conditions regarding sample and community DNA preparation, sequencing technology, processing of sequence reads and data analyses by bioinformatics tools. RESULTS High-throughput metagenome sequencing of community DNA from the wet fermentation process applying the pyrosequencing approach resulted in 1,532,780 reads, with an average read length of 397 bp, accounting for approximately 594 million bases of sequence information in total. Taxonomic comparison of the communities from wet and dry fermentation revealed similar microbial profiles with Bacteria being the predominant superkingdom, while the superkingdom Archaea was less abundant. In both biogas plants, the bacterial phyla Firmicutes, Bacteroidetes, Spirochaetes and Proteobacteria were identified with descending frequencies. Within the archaeal superkingdom, the phylum Euryarchaeota was most abundant with the dominant class Methanomicrobia. Functional profiles of the communities revealed that environmental gene tags representing methanogenesis enzymes were present in both biogas plants in comparable frequencies. 16S rRNA gene amplicon high-throughput sequencing disclosed differences in the sub-communities comprising methanogenic Archaea between both processes. Fragment recruitments of metagenomic reads to the reference genome of the archaeon Methanoculleus bourgensis MS2(T) revealed that dominant methanogens within the dry fermentation process were highly related to the reference. CONCLUSIONS Although process parameters, substrates and technology differ between the wet and dry biogas fermentations analyzed in this study, community profiles are very similar at least at higher taxonomic ranks, illustrating that core community taxa perform key functions in biomass decomposition and methane synthesis. Regarding methanogenesis, Archaea highly related to the type strain M. bourgensis MS2(T) dominate the dry fermentation process, suggesting the adaptation of members belonging to this species to specific fermentation process parameters.
Collapse
Affiliation(s)
- Yvonne Stolze
- />Institute for Genome Research and Systems Biology, CeBiTec, Bielefeld University, Universitätsstraße 25, D-33615 Bielefeld, Germany
| | - Martha Zakrzewski
- />QIMR Berghofer Medical Research Institute Herston, 300 Herston Road, Brisbane, QLD 4006 Australia
| | - Irena Maus
- />Institute for Genome Research and Systems Biology, CeBiTec, Bielefeld University, Universitätsstraße 25, D-33615 Bielefeld, Germany
| | - Felix Eikmeyer
- />Institute for Genome Research and Systems Biology, CeBiTec, Bielefeld University, Universitätsstraße 25, D-33615 Bielefeld, Germany
| | - Sebastian Jaenicke
- />Bioinformatics Resource Facility, CeBiTec, Bielefeld University, Universitätsstraße 25, D-33615 Bielefeld, Germany
| | - Nils Rottmann
- />NORTH-TEC Maschinenbau GmbH, Oldenhörn 1, 25821 Bredstedt, Germany
| | - Clemens Siebner
- />Institute for Genome Research and Systems Biology, CeBiTec, Bielefeld University, Universitätsstraße 25, D-33615 Bielefeld, Germany
| | - Alfred Pühler
- />Institute for Genome Research and Systems Biology, CeBiTec, Bielefeld University, Universitätsstraße 25, D-33615 Bielefeld, Germany
| | - Andreas Schlüter
- />Institute for Genome Research and Systems Biology, CeBiTec, Bielefeld University, Universitätsstraße 25, D-33615 Bielefeld, Germany
| |
Collapse
|
13
|
Akinosho H, Yee K, Close D, Ragauskas A. The emergence of Clostridium thermocellum as a high utility candidate for consolidated bioprocessing applications. Front Chem 2014; 2:66. [PMID: 25207268 PMCID: PMC4143619 DOI: 10.3389/fchem.2014.00066] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Accepted: 07/28/2014] [Indexed: 01/25/2023] Open
Abstract
First isolated in 1926, Clostridium thermocellum has recently received increased attention as a high utility candidate for use in consolidated bioprocessing (CBP) applications. These applications, which seek to process lignocellulosic biomass directly into useful products such as ethanol, are gaining traction as economically feasible routes toward the production of fuel and other high value chemical compounds as the shortcomings of fossil fuels become evident. This review evaluates C. thermocellum's role in this transitory process by highlighting recent discoveries relating to its genomic, transcriptomic, proteomic, and metabolomic responses to varying biomass sources, with a special emphasis placed on providing an overview of its unique, multivariate enzyme cellulosome complex and the role that this structure performs during biomass degradation. Both naturally evolved and genetically engineered strains are examined in light of their unique attributes and responses to various biomass treatment conditions, and the genetic tools that have been employed for their creation are presented. Several future routes for potential industrial usage are presented, and it is concluded that, although there have been many advances to significantly improve C. thermocellum's amenability to industrial use, several hurdles still remain to be overcome as this unique organism enjoys increased attention within the scientific community.
Collapse
Affiliation(s)
- Hannah Akinosho
- School of Chemistry and Biochemistry, Institute of Paper Science and Technology, Georgia Institute of Technology Atlanta, GA, USA ; Oak Ridge National Laboratory, BioEnergy Science Center Oak Ridge, TN, USA
| | - Kelsey Yee
- Oak Ridge National Laboratory, BioEnergy Science Center Oak Ridge, TN, USA ; Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA
| | - Dan Close
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA
| | - Arthur Ragauskas
- Oak Ridge National Laboratory, BioEnergy Science Center Oak Ridge, TN, USA ; Department of Chemical and Biomolecular Engineering and Department of Forestry, Wildlife, and Fisheries, University of Tennessee Knoxville, TN, USA
| |
Collapse
|
14
|
Artzi L, Dassa B, Borovok I, Shamshoum M, Lamed R, Bayer EA. Cellulosomics of the cellulolytic thermophile Clostridium clariflavum. BIOTECHNOLOGY FOR BIOFUELS 2014; 7:100. [PMID: 26413154 PMCID: PMC4582956 DOI: 10.1186/1754-6834-7-100] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 06/12/2014] [Indexed: 05/23/2023]
Abstract
BACKGROUND Clostridium clariflavum is an anaerobic, thermophilic, Gram-positive bacterium, capable of growth on crystalline cellulose as a single carbon source. The genome of C. clariflavum has been sequenced to completion, and numerous cellulosomal genes were identified, including putative scaffoldin and enzyme subunits. RESULTS Bioinformatic analysis of the C. clariflavum genome revealed 49 cohesin modules distributed on 13 different scaffoldins and 79 dockerin-containing proteins, suggesting an abundance of putative cellulosome assemblies. The 13-scaffoldin system of C. clariflavum is highly reminiscent of the proposed cellulosome system of Acetivibrio cellulolyticus. Analysis of the C. clariflavum type I dockerin sequences indicated a very high level of conservation, wherein the putative recognition residues are remarkably similar to those of A. cellulolyticus. The numerous interactions among the cellulosomal components were elucidated using a standardized affinity ELISA-based fusion-protein system. The results revealed a rather simplistic recognition pattern of cohesin-dockerin interaction, whereby the type I and type II cohesins generally recognized the dockerins of the same type. The anticipated exception to this rule was the type I dockerin of the ScaB adaptor scaffoldin which bound selectively to the type I cohesins of ScaC and ScaJ. CONCLUSIONS The findings reveal an intricate picture of predicted cellulosome assemblies in C. clariflavum. The network of cohesin-dockerin pairs provides a thermophilic alternative to those of C. thermocellum and a basis for subsequent utilization of the C. clariflavum cellulosomal system for biotechnological application.
Collapse
Affiliation(s)
- Lior Artzi
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel
| | - Bareket Dassa
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel
| | - Ilya Borovok
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv, Israel
| | - Melina Shamshoum
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel
| | - Raphael Lamed
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv, Israel
| | - Edward A Bayer
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel
| |
Collapse
|
15
|
Blumer-Schuette SE, Brown SD, Sander KB, Bayer EA, Kataeva I, Zurawski JV, Conway JM, Adams MWW, Kelly RM. Thermophilic lignocellulose deconstruction. FEMS Microbiol Rev 2014; 38:393-448. [DOI: 10.1111/1574-6976.12044] [Citation(s) in RCA: 128] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Revised: 08/20/2013] [Accepted: 08/28/2013] [Indexed: 11/28/2022] Open
|
16
|
Wei H, Fu Y, Magnusson L, Baker JO, Maness PC, Xu Q, Yang S, Bowersox A, Bogorad I, Wang W, Tucker MP, Himmel ME, Ding SY. Comparison of transcriptional profiles of Clostridium thermocellum grown on cellobiose and pretreated yellow poplar using RNA-Seq. Front Microbiol 2014; 5:142. [PMID: 24782837 PMCID: PMC3990059 DOI: 10.3389/fmicb.2014.00142] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Accepted: 03/19/2014] [Indexed: 01/01/2023] Open
Abstract
The anaerobic, thermophilic bacterium, Clostridium thermocellum, secretes multi-protein enzyme complexes, termed cellulosomes, which synergistically interact with the microbial cell surface and efficiently disassemble plant cell wall biomass. C. thermocellum has also been considered a potential consolidated bioprocessing (CBP) organism due to its ability to produce the biofuel products, hydrogen, and ethanol. We found that C. thermocellum fermentation of pretreated yellow poplar (PYP) produced 30 and 39% of ethanol and hydrogen product concentrations, respectively, compared to fermentation of cellobiose. RNA-seq was used to analyze the transcriptional profiles of these cells. The PYP-grown cells taken for analysis at the late stationary phase showed 1211 genes up-regulated and 314 down-regulated by more than two-fold compared to the cellobiose-grown cells. These affected genes cover a broad spectrum of specific functional categories. The transcriptional analysis was further validated by sub-proteomics data taken from the literature; as well as by quantitative reverse transcription-PCR (qRT-PCR) analyses of selected genes. Specifically, 47 cellulosomal protein-encoding genes, genes for 4 pairs of SigI-RsgI for polysaccharide sensing, 7 cellodextrin ABC transporter genes, and a set of NAD(P)H hydogenase and alcohol dehydrogenase genes were up-regulated for cells growing on PYP compared to cellobiose. These genes could be potential candidates for future studies aimed at gaining insight into the regulatory mechanism of this organism as well as for improvement of C. thermocellum in its role as a CBP organism.
Collapse
Affiliation(s)
- Hui Wei
- Biosciences Center, National Renewable Energy Laboratory Golden, CO, USA
| | - Yan Fu
- Center for Plant Genomics, Iowa State University Ames, IA, USA
| | - Lauren Magnusson
- Biosciences Center, National Renewable Energy Laboratory Golden, CO, USA
| | - John O Baker
- Biosciences Center, National Renewable Energy Laboratory Golden, CO, USA
| | - Pin-Ching Maness
- Biosciences Center, National Renewable Energy Laboratory Golden, CO, USA
| | - Qi Xu
- Biosciences Center, National Renewable Energy Laboratory Golden, CO, USA
| | - Shihui Yang
- National Bioenergy Center, National Renewable Energy Laboratory Golden, CO, USA
| | - Andrew Bowersox
- Biosciences Center, National Renewable Energy Laboratory Golden, CO, USA ; National Bioenergy Center, National Renewable Energy Laboratory Golden, CO, USA
| | - Igor Bogorad
- Biosciences Center, National Renewable Energy Laboratory Golden, CO, USA
| | - Wei Wang
- Biosciences Center, National Renewable Energy Laboratory Golden, CO, USA
| | - Melvin P Tucker
- National Bioenergy Center, National Renewable Energy Laboratory Golden, CO, USA
| | - Michael E Himmel
- Biosciences Center, National Renewable Energy Laboratory Golden, CO, USA
| | - Shi-You Ding
- Biosciences Center, National Renewable Energy Laboratory Golden, CO, USA
| |
Collapse
|
17
|
Draft Genome Sequence of Clostridium straminisolvens Strain JCM 21531T, Isolated from a Cellulose-Degrading Bacterial Community. GENOME ANNOUNCEMENTS 2014; 2:2/1/e00110-14. [PMID: 24558248 PMCID: PMC3931369 DOI: 10.1128/genomea.00110-14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Here, we report the draft genome sequence of a fibrolytic bacterium, Clostridium straminisolvens JCM 21531(T), isolated from a cellulose-degrading bacterial community. The genome information of this strain will be useful for studies on the degradation enzymes and functional interactions with other members in the community.
Collapse
|
18
|
Brown SD, Nagaraju S, Utturkar S, De Tissera S, Segovia S, Mitchell W, Land ML, Dassanayake A, Köpke M. Comparison of single-molecule sequencing and hybrid approaches for finishing the genome of Clostridium autoethanogenum and analysis of CRISPR systems in industrial relevant Clostridia. BIOTECHNOLOGY FOR BIOFUELS 2014; 7:40. [PMID: 24655715 PMCID: PMC4022347 DOI: 10.1186/1754-6834-7-40] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Accepted: 02/19/2014] [Indexed: 05/04/2023]
Abstract
BACKGROUND Clostridium autoethanogenum strain JA1-1 (DSM 10061) is an acetogen capable of fermenting CO, CO2 and H2 (e.g. from syngas or waste gases) into biofuel ethanol and commodity chemicals such as 2,3-butanediol. A draft genome sequence consisting of 100 contigs has been published. RESULTS A closed, high-quality genome sequence for C. autoethanogenum DSM10061 was generated using only the latest single-molecule DNA sequencing technology and without the need for manual finishing. It is assigned to the most complex genome classification based upon genome features such as repeats, prophage, nine copies of the rRNA gene operons. It has a low G + C content of 31.1%. Illumina, 454, Illumina/454 hybrid assemblies were generated and then compared to the draft and PacBio assemblies using summary statistics, CGAL, QUAST and REAPR bioinformatics tools and comparative genomic approaches. Assemblies based upon shorter read DNA technologies were confounded by the large number repeats and their size, which in the case of the rRNA gene operons were ~5 kb. CRISPR (Clustered Regularly Interspaced Short Paloindromic Repeats) systems among biotechnologically relevant Clostridia were classified and related to plasmid content and prophages. Potential associations between plasmid content and CRISPR systems may have implications for historical industrial scale Acetone-Butanol-Ethanol (ABE) fermentation failures and future large scale bacterial fermentations. While C. autoethanogenum contains an active CRISPR system, no such system is present in the closely related Clostridium ljungdahlii DSM 13528. A common prophage inserted into the Arg-tRNA shared between the strains suggests a common ancestor. However, C. ljungdahlii contains several additional putative prophages and it has more than double the amount of prophage DNA compared to C. autoethanogenum. Other differences include important metabolic genes for central metabolism (as an additional hydrogenase and the absence of a phophoenolpyruvate synthase) and substrate utilization pathway (mannose and aromatics utilization) that might explain phenotypic differences between C. autoethanogenum and C. ljungdahlii. CONCLUSIONS Single molecule sequencing will be increasingly used to produce finished microbial genomes. The complete genome will facilitate comparative genomics and functional genomics and support future comparisons between Clostridia and studies that examine the evolution of plasmids, bacteriophage and CRISPR systems.
Collapse
Affiliation(s)
- Steven D Brown
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37996, USA
| | | | - Sagar Utturkar
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37996, USA
| | | | | | | | - Miriam L Land
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | | | | |
Collapse
|
19
|
Wilson CM, Yang S, Rodriguez M, Ma Q, Johnson CM, Dice L, Xu Y, Brown SD. Clostridium thermocellum transcriptomic profiles after exposure to furfural or heat stress. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:131. [PMID: 24028713 PMCID: PMC3848806 DOI: 10.1186/1754-6834-6-131] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Accepted: 09/04/2013] [Indexed: 05/23/2023]
Abstract
BACKGROUND The thermophilic anaerobe Clostridium thermocellum is a candidate consolidated bioprocessing (CBP) biocatalyst for cellulosic ethanol production. It is capable of both cellulose solubilization and its fermentation to produce lignocellulosic ethanol. Intolerance to stresses routinely encountered during industrial fermentations may hinder the commercial development of this organism. A previous C. thermocellum ethanol stress study showed that the largest transcriptomic response was in genes and proteins related to nitrogen uptake and metabolism. RESULTS In this study, C. thermocellum was grown to mid-exponential phase and treated with furfural or heat to a final concentration of 3 g.L-1 or 68°C respectively to investigate general and specific physiological and regulatory stress responses. Samples were taken at 10, 30, 60 and 120 min post-shock, and from untreated control fermentations, for transcriptomic analyses and fermentation product determinations and compared to a published dataset from an ethanol stress study. Urea uptake genes were induced following furfural stress, but not to the same extent as ethanol stress and transcription from these genes was largely unaffected by heat stress. The largest transcriptomic response to furfural stress was genes for sulfate transporter subunits and enzymes in the sulfate assimilatory pathway, although these genes were also affected late in the heat and ethanol stress responses. Lactate production was higher in furfural treated culture, although the lactate dehydrogenase gene was not differentially expressed under this condition. Other redox related genes such as a copy of the rex gene, a bifunctional acetaldehyde-CoA/alcohol dehydrogenase and adjacent genes did show lower expression after furfural stress compared to the control, heat and ethanol fermentation profiles. Heat stress induced expression from chaperone related genes and overlap was observed with the responses to the other stresses. This study suggests the involvement of C. thermocellum genes with functions in oxidative stress protection, electron transfer, detoxification, sulfur and nitrogen acquisition, and DNA repair mechanisms in its stress responses and the use of different regulatory networks to coordinate and control adaptation. CONCLUSIONS This study has identified C. thermocellum gene regulatory motifs and aspects of physiology and gene regulation for further study. The nexus between future systems biology studies and recently developed genetic tools for C. thermocellum offers the potential for more rapid strain development and for broader insights into this organism's physiology and regulation.
Collapse
Affiliation(s)
- Charlotte M Wilson
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, 37831 TN, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Shihui Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, 37831 TN, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Present address: National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Miguel Rodriguez
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, 37831 TN, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Qin Ma
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Department of Biochemistry and Molecular Biology and Institute of Bioinformatics, Computational Systems Biology Laboratory, University of Georgia, Athens, GA 30602, USA
| | - Courtney M Johnson
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, 37831 TN, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Lezlee Dice
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, 37831 TN, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Ying Xu
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Department of Biochemistry and Molecular Biology and Institute of Bioinformatics, Computational Systems Biology Laboratory, University of Georgia, Athens, GA 30602, USA
- College of Computer Science and Technology, Jilin University, Changchun, Jilin, China
| | - Steven D Brown
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, 37831 TN, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| |
Collapse
|
20
|
Shi W, Xie S, Chen X, Sun S, Zhou X, Liu L, Gao P, Kyrpides NC, No EG, Yuan JS. Comparative genomic analysis of the microbiome [corrected] of herbivorous insects reveals eco-environmental adaptations: biotechnology applications. PLoS Genet 2013; 9:e1003131. [PMID: 23326236 PMCID: PMC3542064 DOI: 10.1371/journal.pgen.1003131] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Accepted: 10/15/2012] [Indexed: 02/01/2023] Open
Abstract
Metagenome analysis of the gut symbionts of three different insects was conducted as a means of comparing taxonomic and metabolic diversity of gut microbiomes to diet and life history of the insect hosts. A second goal was the discovery of novel biocatalysts for biorefinery applications. Grasshopper and cutworm gut symbionts were sequenced and compared with the previously identified metagenome of termite gut microbiota. These insect hosts represent three different insect orders and specialize on different food types. The comparative analysis revealed dramatic differences among the three insect species in the abundance and taxonomic composition of the symbiont populations present in the gut. The composition and abundance of symbionts was correlated with their previously identified capacity to degrade and utilize the different types of food consumed by their hosts. The metabolic reconstruction revealed that the gut metabolome of cutworms and grasshoppers was more enriched for genes involved in carbohydrate metabolism and transport than wood-feeding termite, whereas the termite gut metabolome was enriched for glycosyl hydrolase (GH) enzymes relevant to lignocellulosic biomass degradation. Moreover, termite gut metabolome was more enriched with nitrogen fixation genes than those of grasshopper and cutworm gut, presumably due to the termite's adaptation to the high fiber and less nutritious food types. In order to evaluate and exploit the insect symbionts for biotechnology applications, we cloned and further characterized four biomass-degrading enzymes including one endoglucanase and one xylanase from both the grasshopper and cutworm gut symbionts. The results indicated that the grasshopper symbiont enzymes were generally more efficient in biomass degradation than the homologous enzymes from cutworm symbionts. Together, these results demonstrated a correlation between the composition and putative metabolic functionality of the gut microbiome and host diet, and suggested that this relationship could be exploited for the discovery of symbionts and biocatalysts useful for biorefinery applications.
Collapse
Affiliation(s)
- Weibing Shi
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas, United States of America
- Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, Texas, United States of America
| | - Shangxian Xie
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas, United States of America
- Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, Texas, United States of America
- School of Life Sciences and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xueyan Chen
- Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, Texas, United States of America
- Department of Veterinary Pathology, Texas A&M University, College Station, Texas, United States of America
| | - Su Sun
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas, United States of America
- Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, Texas, United States of America
| | - Xin Zhou
- Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, Texas, United States of America
| | - Lantao Liu
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas, United States of America
- Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, Texas, United States of America
| | - Peng Gao
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas, United States of America
- Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, Texas, United States of America
| | - Nikos C. Kyrpides
- DOE Joint Genomes Institute, Walnut Creek, California, United States of America
| | - En-Gyu No
- Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, Texas, United States of America
| | - Joshua S. Yuan
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas, United States of America
- Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, Texas, United States of America
- * E-mail:
| |
Collapse
|
21
|
Yang S, Giannone RJ, Dice L, Yang ZK, Engle NL, Tschaplinski TJ, Hettich RL, Brown SD. Clostridium thermocellum ATCC27405 transcriptomic, metabolomic and proteomic profiles after ethanol stress. BMC Genomics 2012; 13:336. [PMID: 22823947 PMCID: PMC3478167 DOI: 10.1186/1471-2164-13-336] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Accepted: 07/01/2012] [Indexed: 01/12/2023] Open
Abstract
Background Clostridium thermocellum is a candidate consolidated bioprocessing biocatalyst, which is a microorganism that expresses enzymes for both cellulose hydrolysis and its fermentation to produce fuels such as lignocellulosic ethanol. However, C. thermocellum is relatively sensitive to ethanol compared to ethanologenic microorganisms such as yeast and Zymomonas mobilis that are used in industrial fermentations but do not possess native enzymes for industrial cellulose hydrolysis. Results In this study, C. thermocellum was grown to mid-exponential phase and then treated with ethanol to a final concentration of 3.9 g/L to investigate its physiological and regulatory responses to ethanol stress. Samples were taken pre-shock and 2, 12, 30, 60, 120, and 240 min post-shock, and from untreated control fermentations for systems biology analyses. Cell growth was arrested by ethanol supplementation with intracellular accumulation of carbon sources such as cellobiose, and sugar phosphates, including fructose-6-phosphate and glucose-6-phosphate. The largest response of C. thermocellum to ethanol shock treatment was in genes and proteins related to nitrogen uptake and metabolism, which is likely important for redirecting the cells physiology to overcome inhibition and allow growth to resume. Conclusion This study suggests possible avenues for metabolic engineering and provides comprehensive, integrated systems biology datasets that will be useful for future metabolic modeling and strain development endeavors.
Collapse
Affiliation(s)
- Shihui Yang
- Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, USA
| | | | | | | | | | | | | | | |
Collapse
|
22
|
Genome sequences published outside of Standards in Genomic Sciences, May-June 2012. Stand Genomic Sci 2012. [PMCID: PMC3558956 DOI: 10.4056/sigs.3126494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
The purpose of this table is to provide the community with a citable record of publications of ongoing genome sequencing projects that have led to a publication in the scientific literature. While our goal is to make the list complete, there is no guarantee that we may have omitted one or more publications appearing in this time frame. Readers and authors who wish to have publications added to subsequent versions of this list are invited to provide the bibliographic data for such references to the SIGS editorial office.
Collapse
|