1
|
Dar MA, Xie R, Jing L, Qing X, Ali S, Pandit RS, Shaha CM, Sun J. Elucidating the structure, and composition of bacterial symbionts in the gut regions of wood-feeding termite, Coptotermes formosanus and their functional profile towards lignocellulolytic systems. Front Microbiol 2024; 15:1395568. [PMID: 38846576 PMCID: PMC11155305 DOI: 10.3389/fmicb.2024.1395568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 04/22/2024] [Indexed: 06/09/2024] Open
Abstract
The wood-feeding termite, Coptotermes formosanus, presents an efficient lignocellulolytic system, offering a distinctive model for the exploration of host-microbial symbiosis towards lignocellulose degradation. Despite decades of investigation, understanding the diversity, community structure, and functional profiles of bacterial symbionts within specific gut regions, particularly the foregut and midgut of C. formosanus, remains largely elusive. In light of this knowledge gap, our efforts focused on elucidating the diversity, community composition and functions of symbiotic bacteria inhabiting the foregut, midgut, and hindgut of C. formosanus via metagenomics. The termite harbored a diverse community of bacterial symbionts encompassing 352 genera and 26 known phyla, exhibiting an uneven distribution across gut regions. Notably, the hindgut displayed a higher relative abundance of phyla such as Bacteroidetes (56.9%) and Spirochetes (23.3%). In contrast, the foregut and midgut were predominantly occupied by Proteobacteria (28.9%) and Firmicutes (21.2%) after Bacteroidetes. The foregut harbored unique phyla like Candidate phylum_TM6 and Armatimonadetes. At the family level, Porphyromonadaceae (28.1, 40.6, and 53.5% abundance in foregut, midgut, and hindgut, respectively) and Spirochaetaceae (foregut = 9%, midgut = 16%, hindgut = 21.6%) emerged as dominant families in the termite's gut regions. Enriched operational taxonomic units (OTUs) were most abundant in the foregut (28), followed by the hindgut (14), while the midgut exhibited enrichment of only two OTUs. Furthermore, the functional analyses revealed distinct influences of bacterial symbionts on various metabolic pathways, particularly carbohydrate and energy metabolisms of the host. Overall, these results underscore significant variations in the structure of the bacterial community among different gut regions of C. formosanus, suggesting unique functional roles of specific bacteria, thereby inspiring further investigations to resolve the crosstalk between host and microbiomes in individual gut-regions of the termite.
Collapse
Affiliation(s)
- Mudasir A. Dar
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, China
- Department of Zoology, Savitribai Phule Pune University, Pune, India
| | - Rongrong Xie
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, China
| | - Luohui Jing
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, China
| | - Xu Qing
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, China
| | - Shehbaz Ali
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, China
| | | | - Chaitali M. Shaha
- Department of Zoology, Savitribai Phule Pune University, Pune, India
| | - Jianzhong Sun
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, China
| |
Collapse
|
2
|
Wongfaed N, O-Thong S, Sittijunda S, Reungsang A. Taxonomic and enzymatic basis of the cellulolytic microbial consortium KKU-MC1 and its application in enhancing biomethane production. Sci Rep 2023; 13:2968. [PMID: 36804594 PMCID: PMC9941523 DOI: 10.1038/s41598-023-29895-0] [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: 08/30/2022] [Accepted: 02/13/2023] [Indexed: 02/22/2023] Open
Abstract
Lignocellulosic biomass is a promising substrate for biogas production. However, its recalcitrant structure limits conversion efficiency. This study aims to design a microbial consortium (MC) capable of producing the cellulolytic enzyme and exploring the taxonomic and genetic aspects of lignocellulose degradation. A diverse range of lignocellulolytic bacteria and degrading enzymes from various habitats were enriched for a known KKU-MC1. The KKU-MC1 was found to be abundant in Bacteroidetes (51%), Proteobacteria (29%), Firmicutes (10%), and other phyla (8% unknown, 0.4% unclassified, 0.6% archaea, and the remaining 1% other bacteria with low predominance). Carbohydrate-active enzyme (CAZyme) annotation revealed that the genera Bacteroides, Ruminiclostridium, Enterococcus, and Parabacteroides encoded a diverse set of cellulose and hemicellulose degradation enzymes. Furthermore, the gene families associated with lignin deconstruction were more abundant in the Pseudomonas genera. Subsequently, the effects of MC on methane production from various biomasses were studied in two ways: bioaugmentation and pre-hydrolysis. Methane yield (MY) of pre-hydrolysis cassava bagasse (CB), Napier grass (NG), and sugarcane bagasse (SB) with KKU-MC1 for 5 days improved by 38-56% compared to non-prehydrolysis substrates, while MY of prehydrolysed filter cake (FC) for 15 days improved by 56% compared to raw FC. The MY of CB, NG, and SB (at 4% initial volatile solid concentration (IVC)) with KKU-MC1 augmentation improved by 29-42% compared to the non-augmentation treatment. FC (1% IVC) had 17% higher MY than the non-augmentation treatment. These findings demonstrated that KKU-MC1 released the cellulolytic enzyme capable of decomposing various lignocellulosic biomasses, resulting in increased biogas production.
Collapse
Affiliation(s)
- Nantharat Wongfaed
- grid.9786.00000 0004 0470 0856Department of Biotechnology, Faculty of Technology, Khon Kaen University, Khon Kaen, 40002 Thailand
| | - Sompong O-Thong
- grid.440406.20000 0004 0634 2087International College, Thaksin University, Songkhla, 90000 Thailand
| | - Sureewan Sittijunda
- grid.10223.320000 0004 1937 0490Faculty of Environment and Resource Studies, Mahidol University, Nakhon Pathom, 73170 Thailand
| | - Alissara Reungsang
- Department of Biotechnology, Faculty of Technology, Khon Kaen University, Khon Kaen, 40002, Thailand. .,Research Group for Development of Microbial Hydrogen Production Process from Biomass, Khon Kaen University, Khon Kaen, 40002, Thailand. .,Academy of Science, Royal Society of Thailand, Bangkok, 10300, Thailand.
| |
Collapse
|
3
|
Hindgut microbiota reflects different digestive strategies in dung beetles (Coleoptera: Scarabaeidae: Scarabaeinae). Appl Environ Microbiol 2021; 87:AEM.02100-20. [PMID: 33355113 PMCID: PMC8090880 DOI: 10.1128/aem.02100-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Gut microbes play an important role in the biology and evolution of insects. Australian native dung beetles (Scarabaeinae) present an opportunity to study gut microbiota in an evolutionary context as they come from two distinct phylogenetic lineages and some species in each lineage have secondarily adapted to alternative or broader diets. In this study, we characterised the hindgut bacterial communities found in 21 species of dung beetles across two lineages using 16S rRNA sequencing. We found that gut microbial diversity was more dependent on host phylogeny and gut morphology than specific dietary preferences or environment. In particular, gut microbial diversity was highest in the endemic, flightless genus Cephalodesmius that feeds on a broad range of composted organic matter. The hindgut of Cephalodesmius harbours a highly conserved core set of bacteria suggesting that the bacteria are symbiotic. Symbiosis is supported by the persistence of the core microbiota across isolated beetle populations and between species in the genus. A co-evolutionary relationship is supported by the expansion of the hindgut to form a fermentation chamber and the fermentative nature of the core microbes. In contrast, Australian species of the widespread dung beetle genus Onthophagus, specialise on a single food resource such as dung or fungus, exhibit minimal food processing behaviour, have a short, narrow hindgut and a variable gut microbiota with relatively few core bacterial taxa. A conserved, complex gut microbiota is hypothesised to be unnecessary for this highly mobile genus.IMPORTANCE Dung beetles are a very important part of an ecosystem because of their role in the removal and decomposition of vertebrate dung. It has been suspected that symbiotic gut bacteria facilitate this role, a hypothesis that we have explored with high throughput barcoding. We found that differences in hindgut morphology had the greatest effect on the bacterial community composition. Species with a hindgut fermentation chamber harboured a distinctly different hindgut community compared to those species with a narrow, undifferentiated hindgut. Diet and phylogeny were also associated with differences in gut community. Further understanding of the relationships between dung beetles and their gut microbes will provide insights into the evolution of their behaviours and how gut communities contribute to their fitness.
Collapse
|
4
|
Zeng W, Liu B, Zhong J, Li Q, Li Z. A Natural High-Sugar Diet Has Different Effects on the Prokaryotic Community Structures of Lower and Higher Termites (Blattaria). ENVIRONMENTAL ENTOMOLOGY 2020; 49:21-32. [PMID: 31782953 DOI: 10.1093/ee/nvz130] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Indexed: 06/10/2023]
Abstract
The lignocellulosic digestive symbiosis in termites is a dynamic survival adaptation system. While the contribution of hereditary and habitat factors to the development of the symbiotic bacterial community of termites had been confirmed, the manner in which these factors affect functional synergism among different bacterial lineages has still not been fully elucidated. Therefore, the 16S rRNA gene libraries of Odontotermes formosanus Shiraki (Blattodea: Termitidae) and Coptotermes formosanus Shiraki (Blattodea: Rhinotermitidae) sampled from sugarcane fields (high sugar) or pine tree forests (no free sugar) were sequenced. The results verify that the prokaryotic community structures of termites could be significantly reshaped by native dietary isolation within a species. Although the most dominant phyla are convergent in all samples, their relative abundances in these two termite species exhibited a reverse variation pattern when the termite hosts were fed on the high-sugar diet. Furthermore, we showed that the taxonomic composition of the dominant phyla at the family or genus level differentiate depending on the diet and the host phylogeny. We hypothesize that the flexible bacterial assemblages at low taxonomic level might exert variable functional collaboration to accommodate to high-sugar diet. In addition, the functional predictions of Tax4Fun suggest a stable metabolic functional structure of the microbial communities of the termites in both different diet habitats and taxonomy. We propose that the symbiotic bacterial community in different host termites developed a different functional synergistic pattern, which may be essential to maintain the stability of the overall metabolic function for the survival of termites.
Collapse
Affiliation(s)
- Wenhui Zeng
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, China
| | - Bingrong Liu
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, China
| | - Junhong Zhong
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, China
| | - Qiujian Li
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, China
| | - Zhiqiang Li
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, China
| |
Collapse
|
5
|
Diouf M, Miambi E, Mora P, Frechault S, Robert A, Rouland-Lefèvre C, Hervé V. Variations in the relative abundance of Wolbachia in the gut of Nasutitermes arborum across life stages and castes. FEMS Microbiol Lett 2019; 365:4904115. [PMID: 29579215 DOI: 10.1093/femsle/fny046] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 02/22/2018] [Indexed: 12/19/2022] Open
Abstract
There are multiple forms of interactions between termites and bacteria. In addition to their gut microbiota, which has been intensively studied, termites host intracellular symbionts such as Wolbachia. These distinct symbioses have been so far approached independently and mostly in adult termites. We addressed the dynamics of Wolbachia and the microbiota of the eggs and gut for various life stages and castes of the wood-feeding termite, Nasutitermes arborum, using deep-sequencing of the 16S rRNA gene. Wolbachia was dominant in eggs as expected. Unexpectedly, it persisted in the gut of nearly all stages and castes, indicating a wide somatic distribution in termites. Wolbachia-related sequences clustered into few operational taxonomic units, but these were within the same genotype, acquired maternally. Wolbachia was largely dominant in DNA extracts from the guts of larvae and pre-soldiers (59.1%-99.1% of reads) where gut-resident lineages were less represented and less diverse. The reverse was true for the adult castes. This is the first study reporting the age-dependency of the relative abundance of Wolbachia in the termite gut and its negative correlation with the diversity of the microbiota. The possible mechanisms underlying this negative interaction are discussed.
Collapse
Affiliation(s)
- Michel Diouf
- Faculté des Sciences et Technologie, Université Paris Est Créteil, Département ECOEVO, Institut d'Ecologie et des Sciences de l'Environnement de Paris (IEES, Paris). 61 Avenue du Général de Gaulle, 94010 Créteil Cedex, France
| | - Edouard Miambi
- Faculté des Sciences et Technologie, Université Paris Est Créteil, Département ECOEVO, Institut d'Ecologie et des Sciences de l'Environnement de Paris (IEES, Paris). 61 Avenue du Général de Gaulle, 94010 Créteil Cedex, France
| | - Philippe Mora
- Faculté des Sciences et Technologie, Université Paris Est Créteil, Département ECOEVO, Institut d'Ecologie et des Sciences de l'Environnement de Paris (IEES, Paris). 61 Avenue du Général de Gaulle, 94010 Créteil Cedex, France
| | - Sophie Frechault
- Faculté des Sciences et Technologie, Université Paris Est Créteil, Département ECOEVO, Institut d'Ecologie et des Sciences de l'Environnement de Paris (IEES, Paris). 61 Avenue du Général de Gaulle, 94010 Créteil Cedex, France
| | - Alain Robert
- Département ECOEVO, Institut d'Ecologie et des Sciences de l'Environnement de Paris (IEES, Paris). Centre IRD France Nord, 32 Avenue Henri Varagnat, 93143 Bondy, France
| | - Corinne Rouland-Lefèvre
- Département ECOEVO, Institut d'Ecologie et des Sciences de l'Environnement de Paris (IEES, Paris). Centre IRD France Nord, 32 Avenue Henri Varagnat, 93143 Bondy, France
| | - Vincent Hervé
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 10, 35043 Marburg, Germany
| |
Collapse
|
6
|
da Costa RR, Hu H, Li H, Poulsen M. Symbiotic Plant Biomass Decomposition in Fungus-Growing Termites. INSECTS 2019; 10:insects10040087. [PMID: 30925664 PMCID: PMC6523192 DOI: 10.3390/insects10040087] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 03/05/2019] [Accepted: 03/06/2019] [Indexed: 01/25/2023]
Abstract
Termites are among the most successful animal groups, accomplishing nutrient acquisition through long-term associations and enzyme provisioning from microbial symbionts. Fungus farming has evolved only once in a single termite sub-family: Macrotermitinae. This sub-family has become a dominant decomposer in the Old World; through enzymatic contributions from insects, fungi, and bacteria, managed in an intricate decomposition pathway, the termites obtain near-complete utilisation of essentially any plant substrate. Here we review recent insights into our understanding of the process of plant biomass decomposition in fungus-growing termites. To this end, we outline research avenues that we believe can help shed light on how evolution has shaped the optimisation of plant-biomass decomposition in this complex multipartite symbiosis.
Collapse
Affiliation(s)
- Rafael R da Costa
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen East, Denmark.
| | - Haofu Hu
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen East, Denmark.
| | - Hongjie Li
- Department of Bacteriology, University of Wisconsin⁻Madison, Madison, WI 53706, USA.
| | - Michael Poulsen
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen East, Denmark.
| |
Collapse
|
7
|
Chew YM, Lye S, Md. Salleh M, Yahya A. 16S rRNA metagenomic analysis of the symbiotic community structures of bacteria in foregut, midgut, and hindgut of the wood-feeding termite Bulbitermes sp. Symbiosis 2018. [DOI: 10.1007/s13199-018-0544-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
|
8
|
Syntrophic association of termite gut bacterial symbionts with bifunctional characteristics of cellulose degrading and polyhydroxyalkanoate producing bacteria. Int J Biol Macromol 2017; 103:613-620. [DOI: 10.1016/j.ijbiomac.2017.05.100] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 04/17/2017] [Accepted: 05/16/2017] [Indexed: 11/20/2022]
|
9
|
Applying functional metagenomics to search for novel lignocellulosic enzymes in a microbial consortium derived from a thermophilic composting phase of sugarcane bagasse and cow manure. Antonie van Leeuwenhoek 2016; 109:1217-33. [DOI: 10.1007/s10482-016-0723-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 06/07/2016] [Indexed: 10/21/2022]
|
10
|
Otani S, Hansen LH, Sørensen SJ, Poulsen M. Bacterial communities in termite fungus combs are comprised of consistent gut deposits and contributions from the environment. MICROBIAL ECOLOGY 2016; 71:207-20. [PMID: 26518432 PMCID: PMC4686563 DOI: 10.1007/s00248-015-0692-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 10/15/2015] [Indexed: 05/25/2023]
Abstract
Fungus-growing termites (subfamily Macrotermitinae) mix plant forage with asexual spores of their plant-degrading fungal symbiont Termitomyces in their guts and deposit this blend in fungus comb structures, within which the plant matter is degraded. As Termitomyces grows, it produces nodules with asexual spores, which the termites feed on. Since all comb material passes through termite guts, it is inevitable that gut bacteria are also deposited in the comb, but it has remained unknown which bacteria are deposited and whether distinct comb bacterial communities are sustained. Using high-throughput sequencing of the 16S rRNA gene, we explored the bacterial community compositions of 33 fungus comb samples from four termite species (three genera) collected at four South African geographic locations in 2011 and 2013. We identified 33 bacterial phyla, with Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, and Candidate division TM7 jointly accounting for 92 % of the reads. Analyses of gut microbiotas from 25 of the 33 colonies showed that dominant fungus comb taxa originate from the termite gut. While gut communities were consistent between 2011 and 2013, comb community compositions shifted over time. These shifts did not appear to be due to changes in the taxa present, but rather due to differences in the relative abundances of primarily gut-derived bacteria within fungus combs. This indicates that fungus comb microbiotas are largely termite species-specific due to major contributions from gut deposits and also that environment affects which gut bacteria dominate comb communities at a given point in time.
Collapse
Affiliation(s)
- Saria Otani
- Department of Biology, Section for Ecology and Evolution, Centre for Social Evolution, University of Copenhagen, Universitetsparken 15, Building 3, 2100, Copenhagen East, Denmark.
| | - Lars H Hansen
- Department of Biology, Section for Microbiology, University of Copenhagen, Copenhagen, Denmark.
- Department of Environmental Science, Aarhus University, Aarhus, Denmark.
| | - Søren J Sørensen
- Department of Biology, Section for Microbiology, University of Copenhagen, Copenhagen, Denmark.
| | - Michael Poulsen
- Department of Biology, Section for Ecology and Evolution, Centre for Social Evolution, University of Copenhagen, Universitetsparken 15, Building 3, 2100, Copenhagen East, Denmark.
| |
Collapse
|
11
|
Brune A, Dietrich C. The Gut Microbiota of Termites: Digesting the Diversity in the Light of Ecology and Evolution. Annu Rev Microbiol 2015. [DOI: 10.1146/annurev-micro-092412-155715] [Citation(s) in RCA: 231] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Andreas Brune
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany; ,
| | - Carsten Dietrich
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany; ,
| |
Collapse
|
12
|
Classifying the bacterial gut microbiota of termites and cockroaches: A curated phylogenetic reference database (DictDb). Syst Appl Microbiol 2015; 38:472-82. [DOI: 10.1016/j.syapm.2015.07.004] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Revised: 07/13/2015] [Accepted: 07/23/2015] [Indexed: 11/15/2022]
|
13
|
Makonde HM, Mwirichia R, Osiemo Z, Boga HI, Klenk HP. 454 Pyrosequencing-based assessment of bacterial diversity and community structure in termite guts, mounds and surrounding soils. SPRINGERPLUS 2015; 4:471. [PMID: 26355944 PMCID: PMC4556716 DOI: 10.1186/s40064-015-1262-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 08/20/2015] [Indexed: 11/15/2022]
Abstract
Termites constitute part of diverse and economically important termite fauna in Africa, but information on gut microbiota and their associated soil microbiome is still inadequate. In this study, we assessed and compared the bacterial diversity and community structure between termites’ gut, their mounds and surrounding soil using the 454 pyrosequencing-based analysis of 16S rRNA gene sequences. A wood-feeder termite (Microcerotermes sp.), three fungus-cultivating termites (Macrotermes michaelseni, Odontotermes sp. and Microtermes sp.), their associated mounds and corresponding savannah soil samples were analyzed. The pH of the gut homogenates and soil physico-chemical properties were determined. The results indicated significant difference in bacterial community composition and structure between the gut and corresponding soil samples. Soil samples (Chao1 index ranged from 1359 to 2619) had higher species richness than gut samples (Chao1 index ranged from 461 to 1527). The bacterial composition and community structure in the gut of Macrotermes michaelseni and Odontotermes sp. were almost identical but different from that of Microtermes and Microcerotermes species, which had unique community structures. The most predominant bacterial phyla in the gut were Bacteroidetes (40–58 %), Spirochaetes (10–70 %), Firmicutes (17–27 %) and Fibrobacteres (13 %) while in the soil samples were Acidobacteria (28–45 %), Actinobacteria (20–40 %) and Proteobacteria (18–24 %). Some termite gut-specific bacterial lineages belonging to the genera Dysgonomonas, Parabacteroides, Paludibacter, Tannerella, Alistipes, BCf9-17 termite group and Termite Treponema cluster were observed. The results not only demonstrated a high level of bacterial diversity in the gut and surrounding soil environments, but also presence of distinct bacterial communities that are yet to be cultivated. Therefore, combined efforts using both culture and culture-independent methods are suggested to comprehensively characterize the bacterial species and their specific roles in these environments.
Collapse
Affiliation(s)
- Huxley M Makonde
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Brunswick, Germany ; Pure and Applied Sciences, Technical University of Mombasa, P.O.Box 90420-80100, Mombasa, Kenya
| | - Romano Mwirichia
- Department of Biological Sciences, Embu University College, P.O.Box 6-60100, Embu, Kenya
| | - Zipporah Osiemo
- Zoology, Jomo Kenyatta University of Agriculture and Technology, P.O.Box 62000-00200, Nairobi, Kenya
| | - Hamadi I Boga
- Botany, Jomo Kenyatta University of Agriculture and Technology, P.O.Box 62000-00200, Nairobi, Kenya
| | - Hans-Peter Klenk
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Brunswick, Germany ; School of Biology, Newcastle University, Ridley Building, Newcastle upon Tyne, NE1 7RU UK
| |
Collapse
|
14
|
The Enterobacterium Trabulsiella odontotermitis Presents Novel Adaptations Related to Its Association with Fungus-Growing Termites. Appl Environ Microbiol 2015; 81:6577-88. [PMID: 26162887 PMCID: PMC4561680 DOI: 10.1128/aem.01844-15] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 07/07/2015] [Indexed: 12/13/2022] Open
Abstract
Fungus-growing termites rely on symbiotic microorganisms to help break down plant material and to obtain nutrients. Their fungal cultivar, Termitomyces, is the main plant degrader and food source for the termites, while gut bacteria complement Termitomyces in the degradation of foodstuffs, fixation of nitrogen, and metabolism of amino acids and sugars. Due to the community complexity and because these typically anaerobic bacteria can rarely be cultured, little is known about the physiological capabilities of individual bacterial members of the gut communities and their associations with the termite host. The bacterium Trabulsiella odontotermitis is associated with fungus-growing termites, but this genus is generally understudied, with only two described species. Taking diverse approaches, we obtained a solid phylogenetic placement of T. odontotermitis among the Enterobacteriaceae, investigated the physiology and enzymatic profiles of T. odontotermitis isolates, determined the localization of the bacterium in the termite gut, compared draft genomes of two T. odontotermitis isolates to those of their close relatives, and examined the expression of genes relevant to host colonization and putative symbiont functions. Our findings support the hypothesis that T. odontotermitis is a facultative symbiont mainly located in the paunch compartment of the gut, with possible roles in carbohydrate metabolism and aflatoxin degradation, while displaying adaptations to association with the termite host, such as expressing genes for a type VI secretion system which has been demonstrated to assist bacterial competition, colonization, and survival within hosts.
Collapse
|
15
|
Ou Q, Liu Y, Deng J, Chen G, Yang Y, Shen P, Wu B, Jiang C. A novel D-amino acid oxidase from a contaminated agricultural soil metagenome and its characterization. Antonie van Leeuwenhoek 2015; 107:1615-23. [PMID: 25900453 DOI: 10.1007/s10482-015-0457-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Accepted: 04/15/2015] [Indexed: 01/07/2023]
Abstract
A novel D-amino acid oxidase (DAAO) gene designated as daoE was cloned by the sequence-based screening of a plasmid metagenomic library of uncultured microorganisms from contaminated agricultural soil. The deduced amino acid sequence comparison and phylogenetic analysis indicated that daoE and other putative DAAOs are closely related. The putative DAAO gene was subcloned into a pETBlue-2 vector and overexpressed in Escherichia coli Tunner(DE3)pLacI. The recombinant protein was purified to homogeneity. The maximum activity of DaoE protein occurred at pH 8.0 and 37 °C. DaoE recombinant protein had an apparent K m of 2.96 mM, V max of 0.018 mM/min, k cat of 10.9/min, and k cat/K m of 1.16 × 10(4)/mol/min. The identification of this novel DAAO gene demonstrated the importance of metagenomic libraries in exploring new D-amino acid oxidases from environmental microorganisms to optimize their applications.
Collapse
Affiliation(s)
- Qian Ou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, The Key Laboratory of Ministry of Education for Microbial and Plant Genetic Engineering, College of Life Science and Technology, Guangxi University, 100 Daxue East Road, Nanning, 530004, Guangxi, China
| | | | | | | | | | | | | | | |
Collapse
|
16
|
Scharf ME. Omic research in termites: an overview and a roadmap. Front Genet 2015; 6:76. [PMID: 25821456 PMCID: PMC4358217 DOI: 10.3389/fgene.2015.00076] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 02/13/2015] [Indexed: 11/13/2022] Open
Abstract
Many recent breakthroughs in our understanding of termite biology have been facilitated by "omics" research. Omic science seeks to collectively catalog, quantify, and characterize pools of biological molecules that translate into structure, function, and life processes of an organism. Biological molecules in this context include genomic DNA, messenger RNA, proteins, and other biochemicals. Other permutations of omics that apply to termites include sociogenomics, which seeks to define social life in molecular terms (e.g., behavior, sociality, physiology, symbiosis, etc.) and digestomics, which seeks to define the collective pool of host and symbiont genes that collaborate to achieve high-efficiency lignocellulose digestion in the termite gut. This review covers a wide spectrum of termite omic studies from the past 15 years. Topics covered include a summary of terminology, the various kinds of omic efforts that have been undertaken, what has been revealed, and to a degree, what the results mean. Although recent omic efforts have contributed to a better understanding of many facets of termite and symbiont biology, and have created important new resources for many species, significant knowledge gaps still remain. Crossing these gaps can best be done by applying new omic resources within multi-dimensional (i.e., functional, translational, and applied) research programs.
Collapse
Affiliation(s)
- Michael E Scharf
- Department of Entomology, Purdue University, West Lafayette, IN USA
| |
Collapse
|
17
|
Poulsen M. Towards an integrated understanding of the consequences of fungus domestication on the fungus-growing termite gut microbiota. Environ Microbiol 2015; 17:2562-72. [PMID: 25581852 DOI: 10.1111/1462-2920.12765] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2014] [Revised: 12/13/2014] [Accepted: 12/26/2014] [Indexed: 01/08/2023]
Abstract
Approximately 30 million years ago (MYA), the subfamily of higher termites Macrotermitinae domesticated a fungus, Termitomyces, as the main plant decomposer and food source for the termite host. The origin of fungiculture shifted the composition of the termite gut microbiota, and some of the functional implications of this shift have recently been established. I review reports on the composition of the Macrotermitinae gut microbiota, evidence for a subfamily core gut microbiota, and the first insight into functional complementarity between fungal and gut symbionts. In addition, I argue that we need to explore the capacities of all members of the symbiotic communities, including better solidifying Termitomyces role(s) in order to understand putative complementary gut bacterial contributions. Approaches that integrate natural history and sequencing data to elucidate symbiont functions will be powerful, particularly if executed in comparative analyses across the well-established congruent termite-fungus phylogenies. This will allow for testing if gut communities have evolved in parallel with their hosts, with implications for our general understanding of the evolution of gut symbiont communities with hosts.
Collapse
Affiliation(s)
- Michael Poulsen
- Centre for Social Evolution, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, Copenhagen Ø, DK-2100, Denmark
| |
Collapse
|
18
|
Reid NM, Addison SL, West MA, Lloyd-Jones G. The bacterial microbiota of Stolotermes ruficeps (Stolotermitidae), a phylogenetically basal termite endemic to New Zealand. FEMS Microbiol Ecol 2014; 90:678-88. [PMID: 25196080 DOI: 10.1111/1574-6941.12424] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 08/31/2014] [Accepted: 09/02/2014] [Indexed: 12/01/2022] Open
Abstract
Stolotermes ruficeps is a widespread, primitive, lower termite occupying dead and decaying wood of many tree species in New Zealand's temperate forests. We identified core bacterial taxa involved in gut processes through combined DNA- and RNA (cDNA)-based pyrosequencing analysis of the 16S nucleotide sequence from five S. ruficeps colonies. Most family and many genus-level taxa were common to S. ruficeps colonies despite being sampled from different tree species. Major taxa identified were Spirochaetaceae, Elusimicrobiaceae and Porphyromonadaceae. Others less well known in termite guts were Synergistaceae, Desulfobacteraceae, Rhodocyclaceae, Lachnospiraceae and Ruminococcaceae. Synergistaceae, Lachnospiraceae and Spirochaetaceae were well represented in the RNA data set, indicating a high-protein synthesis potential. Using 130,800 sequences from nine S. ruficeps DNA and RNA data sets, we estimated a high level of bacterial richness (4024 phylotypes at 3% genetic distance). Very few abundant phylotypes were site-specific; almost all (95%) abundant phylotypes, representing 97% of data set sequences, were detected in at least two S. ruficeps colonies. This study of a little-researched phylogenetically basal termite identifies core bacteria taxa. These findings will extend inventories of termite gut microbiota and contribute to the understanding of the specificity of termite gut microbiota.
Collapse
|
19
|
Otani S, Mikaelyan A, Nobre T, Hansen LH, Koné NA, Sørensen SJ, Aanen DK, Boomsma JJ, Brune A, Poulsen M. Identifying the core microbial community in the gut of fungus-growing termites. Mol Ecol 2014; 23:4631-44. [DOI: 10.1111/mec.12874] [Citation(s) in RCA: 119] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Revised: 07/08/2014] [Accepted: 07/11/2014] [Indexed: 12/20/2022]
Affiliation(s)
- Saria Otani
- Section for Ecology and Evolution; Department of Biology; Centre for Social Evolution; University of Copenhagen; Copenhagen Denmark
| | - Aram Mikaelyan
- Department of Biogeochemistry; Max Planck Institute for Terrestrial Microbiology; Marburg Germany
| | - Tânia Nobre
- Laboratory of Genetics; Wageningen University; Wageningen The Netherlands
| | - Lars H. Hansen
- Section for Microbiology; Department of Biology; University of Copenhagen; Copenhagen Denmark
| | - N'Golo A. Koné
- UFR des-Sciences de la Nature; Station d’Écologie de LAMTO; Université Nangui Abrogoua; BP 28 N'Douci Ivory Coast
| | - Søren J. Sørensen
- Section for Microbiology; Department of Biology; University of Copenhagen; Copenhagen Denmark
| | - Duur K. Aanen
- Laboratory of Genetics; Wageningen University; Wageningen The Netherlands
| | - Jacobus J. Boomsma
- Section for Ecology and Evolution; Department of Biology; Centre for Social Evolution; University of Copenhagen; Copenhagen Denmark
| | - Andreas Brune
- Department of Biogeochemistry; Max Planck Institute for Terrestrial Microbiology; Marburg Germany
| | - Michael Poulsen
- Section for Ecology and Evolution; Department of Biology; Centre for Social Evolution; University of Copenhagen; Copenhagen Denmark
| |
Collapse
|