51
|
Swierts T, Cleary DFR, de Voogd NJ. Prokaryotic communities of Indo-Pacific giant barrel sponges are more strongly influenced by geography than host phylogeny. FEMS Microbiol Ecol 2019; 94:5115559. [PMID: 30289448 PMCID: PMC6196991 DOI: 10.1093/femsec/fiy194] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 10/04/2018] [Indexed: 12/19/2022] Open
Abstract
Sponges harbor complex communities of microorganisms that carry out essential roles for the functioning and survival of their hosts. In some cases, genetically related sponges from different geographic regions share microbes, while in other cases microbial communities are more similar in unrelated sponges collected from the same location. To better understand how geography and host phylogeny cause variation in the prokaryotic community of sponges, we compared the prokaryotic community of 44 giant barrel sponges (Xestospongia spp.). These sponges belonged to six reproductively isolated genetic groups from eight areas throughout the Indo-Pacific region. Using Illumina sequencing, we obtained 440 000 sequences of the 16S rRNA gene V3V4 variable region that were assigned to 3795 operational taxonomic units (OTUs). The prokaryotic community of giant barrel sponges was characterized by 71 core OTUs (i.e. OTUs present in each specimen) that represented 57.5% of the total number of sequences. The relative abundance of these core OTUs varied significantly among samples, and this variation was predominantly related to the geographic origin of the sample. These results show that in giant barrel sponges, the variation in the prokaryotic community is primarily associated with geography as opposed to phylogenetic relatedness.
Collapse
Affiliation(s)
- T Swierts
- Marine Biodiversity, Naturalis Biodiversity Center, PO Box 9517, 2300 RA, Leiden, the Netherlands.,Institute of Environmental Sciences, Leiden University, PO Box 9518, 2300 RA, Leiden, the Netherlands
| | - D F R Cleary
- Departamento de Biologia CESAM, Centro de Estudos do Ambiente e do Mar, Universidade de Aveiro, Aveiro, Portugal
| | - N J de Voogd
- Marine Biodiversity, Naturalis Biodiversity Center, PO Box 9517, 2300 RA, Leiden, the Netherlands.,Institute of Environmental Sciences, Leiden University, PO Box 9518, 2300 RA, Leiden, the Netherlands
| |
Collapse
|
52
|
Schnorr SL, Hofman CA, Netshifhefhe SR, Duncan FD, Honap TP, Lesnik J, Lewis CM. Taxonomic features and comparisons of the gut microbiome from two edible fungus-farming termites (Macrotermes falciger; M. natalensis) harvested in the Vhembe district of Limpopo, South Africa. BMC Microbiol 2019; 19:164. [PMID: 31315576 PMCID: PMC6637627 DOI: 10.1186/s12866-019-1540-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 07/05/2019] [Indexed: 12/12/2022] Open
Abstract
Background Termites are an important food resource for many human populations around the world, and are a good supply of nutrients. The fungus-farming ‘higher’ termite members of Macrotermitinae are also consumed by modern great apes and are implicated as critical dietary resources for early hominins. While the chemical nutritional composition of edible termites is well known, their microbiomes are unexplored in the context of human health. Here we sequenced the V4 region of the 16S rRNA gene of gut microbiota extracted from the whole intestinal tract of two Macrotermes sp. soldiers collected from the Limpopo region of South Africa. Results Major and minor soldier subcastes of M. falciger exhibit consistent differences in taxonomic representation, and are variable in microbial presence and abundance patterns when compared to another edible but less preferred species, M. natalensis. Subcaste differences include alternate patterns in sulfate-reducing bacteria and methanogenic Euryarchaeota abundance, and differences in abundance between Alistipes and Ruminococcaceae. M. falciger minor soldiers and M. natalensis soldiers have similar microbial profiles, likely from close proximity to the termite worker castes, particularly during foraging and fungus garden cultivation. Compared with previously published termite and cockroach gut microbiome data, the taxonomic representation was generally split between termites that directly digest lignocellulose and humic substrates and those that consume a more distilled form of nutrition as with the omnivorous cockroaches and fungus-farming termites. Lastly, to determine if edible termites may point to a shared reservoir for rare bacterial taxa found in the gut microbiome of humans, we focused on the genus Treponema. The majority of Treponema sequences from edible termite gut microbiota most closely relate to species recovered from other termites or from environmental samples, except for one novel OTU strain, which clustered separately with Treponema found in hunter-gatherer human groups. Conclusions Macrotermes consumed by humans display special gut microbial arrangements that are atypical for a lignocellulose digesting invertebrate, but are instead suited to the simplified nutrition in the fungus-farmer diet. Our work brings to light the particular termite microbiome features that should be explored further as avenues in human health, agricultural sustainability, and evolutionary research. Electronic supplementary material The online version of this article (10.1186/s12866-019-1540-5) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Stephanie L Schnorr
- Konrad Lorenz Institute for Evolution and Cognition Research, Klosterneuburg, Austria. .,Department of Anthropology, University of Oklahoma, Norman, OK, USA. .,Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, OK, USA. .,Department of Anthropology, University of Nevada, Las Vegas, Las Vegas, NV, USA.
| | - Courtney A Hofman
- Department of Anthropology, University of Oklahoma, Norman, OK, USA.,Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, OK, USA
| | - Shandukani R Netshifhefhe
- School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Gauteng Department of Agriculture and Rural Development, Johannesburg, South Africa
| | - Frances D Duncan
- School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Tanvi P Honap
- Department of Anthropology, University of Oklahoma, Norman, OK, USA.,Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, OK, USA
| | - Julie Lesnik
- Department of Anthropology, Wayne State University, Detroit, MI, USA
| | - Cecil M Lewis
- Department of Anthropology, University of Oklahoma, Norman, OK, USA. .,Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, OK, USA.
| |
Collapse
|
53
|
Hu H, da Costa RR, Pilgaard B, Schiøtt M, Lange L, Poulsen M. Fungiculture in Termites Is Associated with a Mycolytic Gut Bacterial Community. mSphere 2019; 4:e00165-19. [PMID: 31092601 PMCID: PMC6520439 DOI: 10.1128/msphere.00165-19] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 04/09/2019] [Indexed: 11/20/2022] Open
Abstract
Termites forage on a range of substrates, and it has been suggested that diet shapes the composition and function of termite gut bacterial communities. Through comparative analyses of gut metagenomes in nine termite species with distinct diets, we characterize bacterial community compositions and use peptide-based functional annotation method to determine biomass-degrading enzymes and the bacterial taxa that encode them. We find that fungus-growing termite guts have relatively more fungal cell wall-degrading enzyme genes, while wood-feeding termite gut communities have relatively more plant cell wall-degrading enzyme genes. Interestingly, wood-feeding termite gut bacterial genes code for abundant chitinolytic enzymes, suggesting that fungal biomass within the decaying wood likely contributes to gut bacterial or termite host nutrition. Across diets, the dominant biomass-degrading enzymes are predominantly coded for by the most abundant bacterial taxa, suggesting tight links between diet and gut community composition, with the most marked difference being the communities coding for the mycolytic capacity of the fungus-growing termite gut.IMPORTANCE Understanding functional capacities of gut microbiomes is important to improve our understanding of symbiotic associations. Here, we use peptide-based functional annotation to show that the gut microbiomes of fungus-farming termites code for a wealth of enzymes that likely target the fungal diet the termites eat. Comparisons to other termites showed that fungus-growing termite guts have relatively more fungal cell wall-degrading enzyme genes, whereas wood-feeding termite gut communities have relatively more plant cell wall-degrading enzyme genes. Across termites with different diets, the dominant biomass-degrading enzymes are predominantly coded for by the most abundant bacterial taxa, suggesting tight links between diet and gut community compositions.
Collapse
Affiliation(s)
- Haofu Hu
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Rafael Rodrigues da Costa
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Bo Pilgaard
- Department of Bioengineering, Technical University of Denmark, Lyngby, Denmark
| | - Morten Schiøtt
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Lene Lange
- Department of Bioengineering, Technical University of Denmark, Lyngby, Denmark
| | - Michael Poulsen
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
54
|
Ju H, Zhu D, Qiao M. Effects of polyethylene microplastics on the gut microbial community, reproduction and avoidance behaviors of the soil springtail, Folsomia candida. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 247:890-897. [PMID: 30735918 DOI: 10.1016/j.envpol.2019.01.097] [Citation(s) in RCA: 147] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 01/23/2019] [Accepted: 01/23/2019] [Indexed: 06/09/2023]
Abstract
Microplastics (MPs) are an emerging contaminant and are confirmed to be ubiquitous in the environment. Adverse effects of MPs on aquatic organisms have been widely studied, whereas little research has focused on soil invertebrates. We exposed the soil springtail Folsomia candida to artificial soils contaminated with polyethylene MPs (<500 μm) for 28 d to explore the effects of MPs on avoidance, reproduction, and gut microbiota. Springtails exhibited avoidance behaviors at 0.5% and 1% MPs (w/w in dry soil), and the avoidance rate was 59% and 69%, respectively. Reproduction was inhibited when the concentration of MPs reached 0.1% and was reduced by 70.2% at the highest concentration of 1% MPs compared to control. The half-maximal effective concentration (EC50) value based on reproduction for F. candida was 0.29% MPs. At concentrations of 0.5% dry weight in the soil, MPs significantly altered the microbial community and decreased bacterial diversity in the springtail gut. Specifically, the relative abundance of Wolbachia significantly decreased while the relative abundance of Bradyrhizobiaceae, Ensifer and Stenotrophomonas significantly increased. Our results demonstrated that MPs exerted a significant toxic effect on springtails and can change their gut microbial community. This can provide useful information for risk assessment of MPs in terrestrial ecosystems.
Collapse
Affiliation(s)
- Hui Ju
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dong Zhu
- University of Chinese Academy of Sciences, Beijing, 100049, China; Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China
| | - Min Qiao
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| |
Collapse
|
55
|
da Costa RR, Vreeburg SM, Shik JZ, Aanen DK, Poulsen M. Can interaction specificity in the fungus-farming termite symbiosis be explained by nutritional requirements of the fungal crop? FUNGAL ECOL 2019. [DOI: 10.1016/j.funeco.2018.08.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
56
|
Ding J, Zhu D, Li H, Ding K, Chen QL, Lassen SB, Ke X, O'Connor P, Zhu YG. The gut microbiota of soil organisms show species-specific responses to liming. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 659:715-723. [PMID: 31096401 DOI: 10.1016/j.scitotenv.2018.12.445] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Revised: 12/26/2018] [Accepted: 12/29/2018] [Indexed: 06/09/2023]
Abstract
Liming is a common agronomic practice used for alleviating soil acidification to improve plant growth. However, it is still unclear how liming can affect the gut microbiota composition of soil fauna, and subsequently the nutrient cycling and litter decomposition mediated by soil fauna. In the present study the effect of liming on the gut microbiota of two types of soil fauna, Folsomia candida, and Enchytraeus crypticus was investigated by using 16S rRNA gene high-throughput sequencing. The results revealed that there are differences between the gut microbial communities of the two types of soil fauna as well as between the gut microbiome of the soil fauna and the surrounding soil. Enterobacteriaceae and Bacillaceae were the predominant families in the gut microbiota of E. crypticus, while Rickettsiaceae and Moraxellaceae were the predominant families in the gut microbiota of F. candida. Liming affected the gut microbiota of E. crypticus at both the taxonomical and core microbiota level. The gut microbiota of F. candida was not affected by liming. Structural equation models suggest that 97% of the variation in the E. crypticus gut microbiota could be explained by liming-induced changes in soil properties and the soil microbial community. The indirect effects of liming, caused by a shift in the soil microbial community, contributed more in reshaping the gut microbiota of E. crypticus than the direct effects of the changed soil properties did. These findings suggest that the effects of liming on the gut microbiota composition in soil fauna are species-specific and are likely dependent on the response of the host to changes in soil properties and the soil microbial community.
Collapse
Affiliation(s)
- Jing Ding
- State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Beijing 100085, China
| | - Dong Zhu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; University of the Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Hu Li
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China
| | - Kai Ding
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China
| | - Qing-Lin Chen
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China
| | - Simon Bo Lassen
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
| | - Xin Ke
- Institute of Plant Physiology and Ecology, Shanghai Institute of Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Patrick O'Connor
- Centre for Global Food and Resources, University of Adelaide, Adelaide 5005, Australia
| | - Yong-Guan Zhu
- State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Beijing 100085, China; Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China.
| |
Collapse
|
57
|
Otani S, Zhukova M, Koné NA, da Costa RR, Mikaelyan A, Sapountzis P, Poulsen M. Gut microbial compositions mirror caste-specific diets in a major lineage of social insects. ENVIRONMENTAL MICROBIOLOGY REPORTS 2019; 11:196-205. [PMID: 30556304 PMCID: PMC6850719 DOI: 10.1111/1758-2229.12728] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Accepted: 12/13/2018] [Indexed: 05/10/2023]
Abstract
Social insects owe their ecological success to the division of labour between castes, but associations between microbial community compositions and castes with different tasks and diets have not been extensively explored. Fungus-growing termites associate with fungi to degrade plant material, complemented by diverse gut microbial communities. Here, we explore whether division of labour and accompanying dietary differences between fungus-growing termite castes are linked to gut bacterial community structure. Using amplicon sequencing, we characterize community compositions in sterile (worker and soldier) and reproductive (queen and king) termites and combine this with gut enzyme activities and microscopy to hypothesise sterile caste-specific microbiota roles. Gut bacterial communities are structured primarily according to termite caste and genus and, in contrast to the observed rich and diverse sterile caste microbiotas, royal pair guts are dominated by few bacterial taxa, potentially reflecting their specialized uniform diet and unique lifestyle.
Collapse
Affiliation(s)
- Saria Otani
- Section for Ecology and Evolution, Department of Biology, Universitetsparken 15University of CopenhagenDK‐2100CopenhagenDenmark
| | - Mariya Zhukova
- Section for Ecology and Evolution, Department of Biology, Universitetsparken 15University of CopenhagenDK‐2100CopenhagenDenmark
| | - N'golo Abdoulaye Koné
- Department of Natural Sciences (UFR‐SN)Nangui Abrogoua University28 BP 847, Abidjan28Côte d'Ivoire
| | - Rafael Rodrigues da Costa
- Section for Ecology and Evolution, Department of Biology, Universitetsparken 15University of CopenhagenDK‐2100CopenhagenDenmark
| | - Aram Mikaelyan
- Department of Entomology and Plant PathologyNorth Carolina State UniversityRaleigh, NorthNC27605USA
| | - Panagiotis Sapountzis
- Section for Ecology and Evolution, Department of Biology, Universitetsparken 15University of CopenhagenDK‐2100CopenhagenDenmark
| | - Michael Poulsen
- Section for Ecology and Evolution, Department of Biology, Universitetsparken 15University of CopenhagenDK‐2100CopenhagenDenmark
| |
Collapse
|
58
|
da Costa RR, Hu H, Li H, Poulsen M. Symbiotic Plant Biomass Decomposition in Fungus-Growing Termites. INSECTS 2019; 10:E87. [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] [Grants] [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
|
59
|
Berg M, Monnin D, Cho J, Nelson L, Crits-Christoph A, Shapira M. TGFβ/BMP immune signaling affects abundance and function of C. elegans gut commensals. Nat Commun 2019; 10:604. [PMID: 30723205 PMCID: PMC6363772 DOI: 10.1038/s41467-019-08379-8] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 12/20/2018] [Indexed: 01/12/2023] Open
Abstract
The gut microbiota contributes to host health and fitness, and imbalances in its composition are associated with pathology. However, what shapes microbiota composition is not clear, in particular the role of genetic factors. Previous work in Caenorhabditis elegans defined a characteristic worm gut microbiota significantly influenced by host genetics. The current work explores the role of central regulators of host immunity and stress resistance, employing qPCR and CFU counts to measure abundance of core microbiota taxa in mutants raised on synthetic communities of previously-isolated worm gut commensals. This revealed a bloom, specifically of Enterobacter species, in immune-compromised TGFβ/BMP mutants. Imaging of fluorescently labeled Enterobacter showed that TGFβ/BMP-exerted control operated primarily in the anterior gut and depended on multi-tissue contributions. Enterobacter commensals are common in the worm gut, contributing to infection resistance. However, disruption of TGFβ/BMP signaling turned a normally beneficial Enterobacter commensal to pathogenic. These results demonstrate specificity in gene-microbe interactions underlying gut microbial homeostasis and highlight the pathogenic potential of their disruption.
Collapse
Affiliation(s)
- Maureen Berg
- Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA
| | - David Monnin
- Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA
| | - Juhyun Cho
- Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA
| | - Lydia Nelson
- Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA
| | - Alex Crits-Christoph
- Graduate Group in Microbiology, University of California, Berkeley, CA, 94720, USA
| | - Michael Shapira
- Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA.
- Graduate Group in Microbiology, University of California, Berkeley, CA, 94720, USA.
| |
Collapse
|
60
|
Sapountzis P, Nash DR, Schiøtt M, Boomsma JJ. The evolution of abdominal microbiomes in fungus-growing ants. Mol Ecol 2018; 28:879-899. [PMID: 30411820 PMCID: PMC6446810 DOI: 10.1111/mec.14931] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 02/08/2018] [Accepted: 10/03/2018] [Indexed: 01/01/2023]
Abstract
The attine ants are a monophyletic lineage that switched to fungus farming ca. 55-60 MYA. They have become a model for the study of complex symbioses after additional fungal and bacterial symbionts were discovered, but their abdominal endosymbiotic bacteria remain largely unknown. Here, we present a comparative microbiome analysis of endosymbiotic bacteria spanning the entire phylogenetic tree. We show that, across 17 representative sympatric species from eight genera sampled in Panama, abdominal microbiomes are dominated by Mollicutes, α- and γ-Proteobacteria, and Actinobacteria. Bacterial abundances increase from basal to crown branches in the phylogeny reflecting a shift towards putative specialized and abundant abdominal microbiota after the ants domesticated gongylidia-bearing cultivars, but before the origin of industrial-scale farming based on leaf-cutting herbivory. This transition coincided with the ancestral single colonization event of Central/North America ca. 20 MYA, documented in a recent phylogenomic study showing that almost the entire crown group of the higher attine ants, including the leaf-cutting ants, evolved there and not in South America. Several bacterial species are located in gut tissues or abdominal organs of the evolutionarily derived, but not the basal attine ants. The composition of abdominal microbiomes appears to be affected by the presence/absence of defensive antibiotic-producing actinobacterial biofilms on the worker ants' cuticle, but the significance of this association remains unclear. The patterns of diversity, abundance and sensitivity of the abdominal microbiomes that we obtained explore novel territory in the comparative analysis of attine fungus farming symbioses and raise new questions for further in-depth research.
Collapse
Affiliation(s)
- Panagiotis Sapountzis
- Centre for Social Evolution, Department of Biology, University of Copenhagen, 2100, Copenhagen, Denmark
| | - David R Nash
- Centre for Social Evolution, Department of Biology, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Morten Schiøtt
- Centre for Social Evolution, Department of Biology, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Jacobus J Boomsma
- Centre for Social Evolution, Department of Biology, University of Copenhagen, 2100, Copenhagen, Denmark
| |
Collapse
|
61
|
Duarte S, Nunes L, Borges PAV, Nobre T. A Bridge Too Far? An Integrative Framework Linking Classical Protist Taxonomy and Metabarcoding in Lower Termites. Front Microbiol 2018; 9:2620. [PMID: 30467496 PMCID: PMC6236014 DOI: 10.3389/fmicb.2018.02620] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 10/12/2018] [Indexed: 11/13/2022] Open
Affiliation(s)
- Sónia Duarte
- National Laboratory for Civil Engineering, Department of Structures, Lisbon, Portugal.,Evolution and Environmental Changes/Azorean Biodiversity Group, cE3c-Center for Ecology, Departamento de Ciências e Engenharia do Ambiente, Universidade dos Açores, Açores, Portugal
| | - Lina Nunes
- National Laboratory for Civil Engineering, Department of Structures, Lisbon, Portugal
| | - Paulo A V Borges
- Evolution and Environmental Changes/Azorean Biodiversity Group, cE3c-Center for Ecology, Departamento de Ciências e Engenharia do Ambiente, Universidade dos Açores, Açores, Portugal
| | - Tania Nobre
- Laboratório de Entomologia, Instituto de Ciências Agrárias e Ambientais Mediterrânicas, Universidade de Évora, Évora, Portugal
| |
Collapse
|
62
|
Benndorf R, Guo H, Sommerwerk E, Weigel C, Garcia-Altares M, Martin K, Hu H, Küfner M, de Beer ZW, Poulsen M, Beemelmanns C. Natural Products from Actinobacteria Associated with Fungus-Growing Termites. Antibiotics (Basel) 2018; 7:E83. [PMID: 30217010 PMCID: PMC6165096 DOI: 10.3390/antibiotics7030083] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 09/02/2018] [Accepted: 09/03/2018] [Indexed: 12/03/2022] Open
Abstract
The chemical analysis of insect-associated Actinobacteria has attracted the interest of natural product chemists in the past years as bacterial-produced metabolites are sought to be crucial for sustaining and protecting the insect host. The objective of our study was to evaluate the phylogeny and bioprospecting of Actinobacteria associated with fungus-growing termites. We characterized 97 Actinobacteria from the gut, exoskeleton, and fungus garden (comb) of the fungus-growing termite Macrotermes natalensis and used two different bioassays to assess their general antimicrobial activity. We selected two strains for chemical analysis and investigated the culture broth of the axenic strains and fungus-actinobacterium co-cultures. From these studies, we identified the previously-reported PKS-derived barceloneic acid A and the PKS-derived rubterolones. Analysis of culture broth yielded a new dichlorinated diketopiperazine derivative and two new tetracyclic lanthipeptides, named rubrominins A and B. The discussed natural products highlight that insect-associated Actinobacteria are highly prolific natural product producers yielding important chemical scaffolds urgently needed for future drug development programs.
Collapse
Affiliation(s)
- René Benndorf
- Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute, Beutenbergstraße 11a, 07745 Jena, Germany.
| | - Huijuan Guo
- Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute, Beutenbergstraße 11a, 07745 Jena, Germany.
| | - Elisabeth Sommerwerk
- Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute, Beutenbergstraße 11a, 07745 Jena, Germany.
| | - Christiane Weigel
- Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute, Beutenbergstraße 11a, 07745 Jena, Germany.
| | - Maria Garcia-Altares
- Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute, Beutenbergstraße 11a, 07745 Jena, Germany.
| | - Karin Martin
- Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute, Beutenbergstraße 11a, 07745 Jena, Germany.
| | - Haofu Hu
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, 2100 Copenhagen East, Denmark.
| | - Michelle Küfner
- Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute, Beutenbergstraße 11a, 07745 Jena, Germany.
| | - Z Wilhelm de Beer
- Department of Microbiology and Plant Pathology, Forestry and Agriculture Biotechnology Institute, University of Pretoria, Pretoria 0001, South Africa.
| | - Michael Poulsen
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, 2100 Copenhagen East, Denmark.
| | - Christine Beemelmanns
- Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute, Beutenbergstraße 11a, 07745 Jena, Germany.
| |
Collapse
|
63
|
Microbial Community Composition Reveals Spatial Variation and Distinctive Core Microbiome of the Weaver Ant Oecophylla smaragdina in Malaysia. Sci Rep 2018; 8:10777. [PMID: 30018403 PMCID: PMC6050294 DOI: 10.1038/s41598-018-29159-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 06/22/2018] [Indexed: 11/20/2022] Open
Abstract
The weaver ant Oecophylla smaragdina is an aggressive predator of other arthropods and has been employed as a biological control agent against many insect pests in plantations. Despite playing important roles in pest management, information about the microbiota of O. smaragdina is limited. In this work, a number of O. smaragdina colonies (n = 12) from Malaysia had been studied on their microbiome profile using Illumina 16S rRNA gene amplicon sequencing. We characterized the core microbiota associated with these O. smaragdina and investigated variation between colonies from different environments. Across all 12 samples, 97.8% of the sequences were assigned to eight bacterial families and most communities were dominated by families Acetobacteraceae and Lactobacillaceae. Comparison among colonies revealed predominance of Acetobacteraceae in O. smaragdina from forest areas but reduced abundance was observed in colonies from urban areas. In addition, our findings also revealed distinctive community composition in O. smaragdina showing little taxonomic overlap with previously reported ant microbiota. In summary, our work provides information regarding microbiome of O. smaragdina which is essential for establishing healthy colonies. This study also forms the basis for further study on microbiome of O. smaragdina from other regions.
Collapse
|
64
|
Varudkar A, Ramakrishnan U. Gut microflora may facilitate adaptation to anthropic habitat: A comparative study in Rattus. Ecol Evol 2018; 8:6463-6472. [PMID: 30038748 PMCID: PMC6053588 DOI: 10.1002/ece3.4040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 02/14/2018] [Accepted: 02/17/2018] [Indexed: 01/14/2023] Open
Abstract
Anthropophilic species ("commensal" species) that are completely dependent upon anthropic habitats experience different selective pressures particularly in terms of food than their noncommensal counterparts. Using a next-generation sequencing approach, we characterized and compared the gut microflora community of 53 commensal Rattus rattus and 59 noncommensal Rattus satarae captured in 10 locations in the Western Ghats, India. We observed that, while species identity was important in characterizing the microflora communities of the two Rattus hosts, environmental factors also had a significant effect. While there was significant geographic variation in the microflora of the noncommensal R. satarae, there was no effect of geographic distance on gut microflora of the commensal R. rattus. Interestingly, host genetic distance did not significantly influence the community in either Rattus hosts. Collectively, these results indicate that a shift in habitat is likely to result in a change in the gut microflora community and imply that the gut microflora is a complex trait, influenced by various parameters in different habitats.
Collapse
|
65
|
Antifungal activity of 3-acetylbenzamide produced by actinomycete WA23-4-4 from the intestinal tract of Periplaneta americana. J Microbiol 2018; 56:516-523. [PMID: 29956124 DOI: 10.1007/s12275-018-7510-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 03/15/2018] [Accepted: 05/01/2018] [Indexed: 10/28/2022]
Abstract
Actinomycetes are well-known for producing numerous bioactive secondary metabolites. In this study, primary screening by antifungal activity assay found one actinomycete strain WA23-4-4 isolated from the intestinal tract of Periplaneta americana that exhibited broad spectrum antifungal activity. 16S rDNA gene analysis of strain WA23-4-4 revealed close similarity to Streptomyces nogalater (AB045886) with 86.6% sequence similarity. Strain WA23-4-4 was considered as a novel Streptomyces and the 16s rDNA sequence has been submitted to GenBank (accession no. KX291006). The maximum antifungal activity of WA23-4-4 was achieved when culture conditions were optimized to pH 8.0, with 12% inoculum concentration and 210 ml ISP2 medium, which remained stable between the 5th and the 9th day. 3-Acetyl benzoyl amide was isolated by ethyl acetate extraction of WA23-4-4 fermentation broth, and its molecular formula was determined as C9H9NO2 based on MS, IR, 1H, and 13C NMR analyses. The compound showed significant antifungal activity against Candida albicans ATCC 10231 (MIC: 31.25 μg/ml) and Aspergillus niger ATCC 16404 (MIC: 31.25 μg/ml). However, the compound had higher MIC values against Trichophyton rubrum ATCC 60836 (MIC: 500 μg/ml) and Aspergillus fumigatus ATCC 96918 (MIC: 1,000 μg/ml). SEM analysis showed damage to the cell membrane of Candida albicans ATCC 10231 and to the mycelium of Aspergillus niger ATCC 16404 after being treatment with 3-acetyl benzoyl amide. In conclusion, this is the first time that 3-acetyl benzoyl amide has been identified from an actinomycete and this compound exhibited antifungal activity against Candida albicans ATCC 10231 and Aspergillus niger ATCC 16404.
Collapse
|
66
|
da Costa RR, Poulsen M. Mixed-Mode Transmission Shapes Termite Gut Community Assemblies. Trends Microbiol 2018; 26:557-559. [PMID: 29752168 DOI: 10.1016/j.tim.2018.04.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 04/24/2018] [Indexed: 11/30/2022]
Abstract
Understanding how microbial symbiont community assemblies are shaped over evolutionary time is challenging. The current state of the art involves exploring similarities and differences in communities within and between host species, often aiming to link these to host ecology and evolution. However, this masks the evolutionary histories of individual bacterial lineages.
Collapse
Affiliation(s)
- Rafael R da Costa
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen East, Denmark
| | - Michael Poulsen
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen East, Denmark.
| |
Collapse
|
67
|
Ng SH, Stat M, Bunce M, Simmons LW. The influence of diet and environment on the gut microbial community of field crickets. Ecol Evol 2018; 8:4704-4720. [PMID: 29760910 PMCID: PMC5938447 DOI: 10.1002/ece3.3977] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 02/07/2018] [Accepted: 02/09/2018] [Indexed: 12/31/2022] Open
Abstract
The extent to which diet and environment influence gut community membership (presence or absence of taxa) and structure (individual taxon abundance) is the subject of growing interest in microbiome research. Here, we examined the gut bacterial communities of three cricket groups: (1) wild caught field crickets, (2) laboratory-reared crickets fed cat chow, and (3) laboratory-reared crickets fed chemically defined diets. We found that both environment and diet greatly altered the structure of the gut bacterial community. Wild crickets had greater gut microbial diversity and higher Firmicutes to Bacteroidetes ratios, in contrast to laboratory-reared crickets. Predictive metagenomes revealed that laboratory-reared crickets were significantly enriched in amino acid degradation pathways, while wild crickets had a higher relative abundance of peptidases that would aid in amino acid release. Although wild and laboratory animals differ greatly in their bacterial communities, we show that the community proportional membership remains stable from Phylum to Family taxonomic levels regardless of differences in environment and diet, suggesting that endogenous factors, such as host genetics, have greater control in shaping gut community membership.
Collapse
Affiliation(s)
- Soon Hwee Ng
- Centre for Evolutionary Biology School of Biological Sciences University of Western Australia Crawley Australia
| | - Michael Stat
- Department of Biological Sciences Macquarie University Sydney Australia.,Trace and Environmental DNA (TrEnD) Laboratory Department of Environment and Agriculture Curtin University Perth Australia
| | - Michael Bunce
- Trace and Environmental DNA (TrEnD) Laboratory Department of Environment and Agriculture Curtin University Perth Australia
| | - Leigh W Simmons
- Centre for Evolutionary Biology School of Biological Sciences University of Western Australia Crawley Australia
| |
Collapse
|
68
|
Enzyme Activities at Different Stages of Plant Biomass Decomposition in Three Species of Fungus-Growing Termites. Appl Environ Microbiol 2018; 84:AEM.01815-17. [PMID: 29269491 PMCID: PMC5812949 DOI: 10.1128/aem.01815-17] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 12/07/2017] [Indexed: 11/20/2022] Open
Abstract
Fungus-growing termites rely on mutualistic fungi of the genus Termitomyces and gut microbes for plant biomass degradation. Due to a certain degree of symbiont complementarity, this tripartite symbiosis has evolved as a complex bioreactor, enabling decomposition of nearly any plant polymer, likely contributing to the success of the termites as one of the main plant decomposers in the Old World. In this study, we evaluated which plant polymers are decomposed and which enzymes are active during the decomposition process in two major genera of fungus-growing termites. We found a diversity of active enzymes at different stages of decomposition and a consistent decrease in plant components during the decomposition process. Furthermore, our findings are consistent with the hypothesis that termites transport enzymes from the older mature parts of the fungus comb through young worker guts to freshly inoculated plant substrate. However, preliminary fungal RNA sequencing (RNA-seq) analyses suggest that this likely transport is supplemented with enzymes produced in situ. Our findings support that the maintenance of an external fungus comb, inoculated with an optimal mixture of plant material, fungal spores, and enzymes, is likely the key to the extraordinarily efficient plant decomposition in fungus-growing termites. IMPORTANCE Fungus-growing termites have a substantial ecological footprint in the Old World (sub)tropics due to their ability to decompose dead plant material. Through the establishment of an elaborate plant biomass inoculation strategy and through fungal and bacterial enzyme contributions, this farming symbiosis has become an efficient and versatile aerobic bioreactor for plant substrate conversion. Since little is known about what enzymes are expressed and where they are active at different stages of the decomposition process, we used enzyme assays, transcriptomics, and plant content measurements to shed light on how this decomposition of plant substrate is so effectively accomplished.
Collapse
|
69
|
Bourguignon T, Lo N, Dietrich C, Šobotník J, Sidek S, Roisin Y, Brune A, Evans TA. Rampant Host Switching Shaped the Termite Gut Microbiome. Curr Biol 2018; 28:649-654.e2. [PMID: 29429621 DOI: 10.1016/j.cub.2018.01.035] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 11/21/2017] [Accepted: 01/11/2018] [Indexed: 10/18/2022]
Abstract
The gut microbiota of animals exert major effects on host biology [1]. Although horizontal transfer is generally considered the prevalent route for the acquisition of gut bacteria in mammals [2], some bacterial lineages have co-speciated with their hosts on timescales of several million years [3]. Termites harbor a complex gut microbiota, and their advanced social behavior provides the potential for long-term vertical symbiont transmission, and co-evolution of gut symbionts and host [4-6]. Despite clear evolutionary patterns in the gut microbiota of termites [7], a consensus on how microbial communities were assembled during termite diversification has yet to be reached. Although some studies have concluded that vertical transmission has played a major role [8, 9], others indicate that diet and gut microenvironment have been the primary determinants shaping microbial communities in termite guts [7, 10]. To address this issue, we examined the gut microbiota of 94 termite species, through 16S rRNA metabarcoding. We analyzed the phylogeny of 211 bacterial lineages obtained from termite guts, including their closest relatives from other environments, which were identified using BLAST. The results provided strong evidence for rampant horizontal transfer of gut bacteria between termite host lineages. Although the majority of termite-derived phylotypes formed large monophyletic groups, indicating high levels of niche specialization, numerous other clades were interspersed with bacterial lineages from the guts of other animals. Our results indicate that "mixed-mode" transmission, which combines colony-to-offspring vertical transmission with horizontal colony-to-colony transfer, has been the primary driving force shaping the gut microbiota of termites.
Collapse
Affiliation(s)
- Thomas Bourguignon
- Okinawa Institute of Science & Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan; School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia; Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Prague, Czech Republic.
| | - Nathan Lo
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia.
| | - Carsten Dietrich
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany; Strategy and Innovation Technology Center, Siemens Healthcare, Erlangen, Germany
| | - Jan Šobotník
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Prague, Czech Republic
| | - Sarah Sidek
- Department of Biological Sciences, National University of Singapore, 117543 Singapore, Singapore
| | - Yves Roisin
- Evolutionary Biology and Ecology, Université Libre de Bruxelles, Bruxelles, Belgium
| | - Andreas Brune
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Theodore A Evans
- Department of Biological Sciences, National University of Singapore, 117543 Singapore, Singapore; School of Animal Biology, University of Western Australia, Perth, WA 6009, Australia
| |
Collapse
|
70
|
Van Arnam EB, Currie CR, Clardy J. Defense contracts: molecular protection in insect-microbe symbioses. Chem Soc Rev 2018; 47:1638-1651. [DOI: 10.1039/c7cs00340d] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Insects frequently host microbes that produce defensive molecules: a successful protective strategy and also an opportunity for antibiotic discovery
Collapse
Affiliation(s)
- Ethan B. Van Arnam
- Keck Science Department
- Claremont McKenna
- Pitzer
- and Scripps Colleges
- Claremont
| | | | - Jon Clardy
- Department of Biological Chemistry and Molecular Pharmacology
- Harvard Medical School
- Boston
- USA
| |
Collapse
|
71
|
Evidence from the gut microbiota of swarming alates of a vertical transmission of the bacterial symbionts in Nasutitermes arborum (Termitidae, Nasutitermitinae). Antonie van Leeuwenhoek 2017; 111:573-587. [DOI: 10.1007/s10482-017-0978-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 11/01/2017] [Indexed: 12/13/2022]
|
72
|
Richards C, Otani S, Mikaelyan A, Poulsen M. Pycnoscelus surinamensis cockroach gut microbiota respond consistently to a fungal diet without mirroring those of fungus-farming termites. PLoS One 2017; 12:e0185745. [PMID: 28973021 PMCID: PMC5626473 DOI: 10.1371/journal.pone.0185745] [Citation(s) in RCA: 10] [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: 05/30/2017] [Accepted: 08/21/2017] [Indexed: 02/07/2023] Open
Abstract
The gut microbiotas of cockroaches and termites play important roles in the symbiotic digestion of dietary components, such as lignocellulose. Diet has been proposed as a primary determinant of community structure within the gut, acting as a selection force to shape the diversity observed within this “bioreactor”, and as a key factor for the divergence of the termite gut microbiota from the omnivorous cockroach ancestor. The gut microbiota in most termites supports primarily the breakdown of lignocellulose, but the fungus-farming sub-family of higher termites has become similar in gut microbiota to the ancestral omnivorous cockroaches. To assess the importance of a fungus diet as a driver of community structure, we compare community compositions in the guts of experimentally manipulated Pycnoscelus surinamensis cockroaches fed on fungus cultivated by fungus-farming termites. MiSeq amplicon analysis of gut microbiotas from 49 gut samples showed a step-wise gradient pattern in community similarity that correlated with an increase in the proportion of fungal material provided to the cockroaches. Comparison of the taxonomic composition of manipulated communities to that of gut communities of a fungus-feeding termite species showed that although some bacteria OTUs shared by P. surinamensis and the farming termites increased in the guts of cockroaches on a fungal diet, cockroach communities remained distinct from those of termites. These results demonstrate that a fungal diet can play a role in structuring gut community composition, but at the same time exemplifies how original community compositions constrain the magnitude of such change.
Collapse
Affiliation(s)
- Callum Richards
- Centre for Social Evolution, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen East, Denmark
| | - Saria Otani
- Centre for Social Evolution, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen East, Denmark
| | - Aram Mikaelyan
- Department of Biological Sciences, Vanderbilt University, VU Station B, Nashville, TN, United States of America
- Department of Pathology, Microbiology, & Immunology, Vanderbilt University, VU Station B, Nashville, TN, United States of America
| | - Michael Poulsen
- Centre for Social Evolution, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen East, Denmark
- * E-mail:
| |
Collapse
|
73
|
Marynowska M, Goux X, Sillam-Dussès D, Rouland-Lefèvre C, Roisin Y, Delfosse P, Calusinska M. Optimization of a metatranscriptomic approach to study the lignocellulolytic potential of the higher termite gut microbiome. BMC Genomics 2017; 18:681. [PMID: 28863779 PMCID: PMC5580439 DOI: 10.1186/s12864-017-4076-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 08/21/2017] [Indexed: 12/19/2022] Open
Abstract
Background Thanks to specific adaptations developed over millions of years, the efficiency of lignin, cellulose and hemicellulose decomposition of higher termite symbiotic system exceeds that of many other lignocellulose utilizing environments. Especially, the examination of its symbiotic microbes should reveal interesting carbohydrate-active enzymes, which are of primary interest for the industry. Previous metatranscriptomic reports (high-throughput mRNA sequencing) highlight the high representation and overexpression of cellulose and hemicelluloses degrading genes in the termite hindgut digestomes, indicating the potential of this technology in search for new enzymes. Nevertheless, several factors associated with the material sampling and library preparation steps make the metatranscriptomic studies of termite gut prokaryotic symbionts challenging. Methods In this study, we first examined the influence of the sampling strategy, including the whole termite gut and luminal fluid, on the diversity and the metatranscriptomic profiles of the higher termite gut symbiotic bacteria. Secondly, we evaluated different commercially available kits combined in two library preparative pipelines for the best bacterial mRNA enrichment strategy. Results We showed that the sampling strategy did not significantly impact the generated results, both in terms of the representation of the microbes and their transcriptomic profiles. Nevertheless collecting luminal fluid reduces the co-amplification of unwanted RNA species of host origin. Furthermore, for the four studied higher termite species, the library preparative pipeline employing Ribo-Zero Gold rRNA Removal Kit “Epidemiology” in combination with Poly(A) Purist MAG kit resulted in a more efficient rRNA and poly-A-mRNAdepletion (up to 98.44% rRNA removed) than the pipeline utilizing MICROBExpress and MICROBEnrich kits. High correlation of both Ribo-Zero and MICROBExpresse depleted gene expression profiles with total non-depleted RNA-seq data has been shown for all studied samples, indicating no systematic skewing of the studied pipelines. Conclusions We have extensively evaluated the impact of the sampling strategy and library preparation steps on the metatranscriptomic profiles of the higher termite gut symbiotic bacteria. The presented methodological approach has great potential to enhance metatranscriptomic studies of the higher termite intestinal flora and to unravel novel carbohydrate-active enzymes. Electronic supplementary material The online version of this article (10.1186/s12864-017-4076-9) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Martyna Marynowska
- Luxembourg Institute of Science and Technology, 41 rue du Brill, L-4422, Belvaux, Luxembourg
| | - Xavier Goux
- Luxembourg Institute of Science and Technology, 41 rue du Brill, L-4422, Belvaux, Luxembourg
| | - David Sillam-Dussès
- Institute of Research for Development - Sorbonne Universités, Institute of Ecology and Environmental Sciences - Paris, U242, 32 avenue Henri Varagnat, F-93140, Bondy, France.,University Paris 13 - Sorbonne Paris Cité, Laboratory of Experimental and Comparative Ethology, EA4443, 99 avenue Jean-Baptiste Clément, F-93430, Villetaneuse, France
| | - Corinne Rouland-Lefèvre
- Institute of Research for Development - Sorbonne Universités, Institute of Ecology and Environmental Sciences - Paris, U242, 32 avenue Henri Varagnat, F-93140, Bondy, France
| | - Yves Roisin
- Université Libre de Bruxelles, 50 Avenue F.D. Roosevelt, B-1050, Brussels, Belgium
| | - Philippe Delfosse
- Luxembourg Institute of Science and Technology, 41 rue du Brill, L-4422, Belvaux, Luxembourg
| | - Magdalena Calusinska
- Luxembourg Institute of Science and Technology, 41 rue du Brill, L-4422, Belvaux, Luxembourg.
| |
Collapse
|
74
|
Kwong WK, Medina LA, Koch H, Sing KW, Soh EJY, Ascher JS, Jaffé R, Moran NA. Dynamic microbiome evolution in social bees. SCIENCE ADVANCES 2017; 3:e1600513. [PMID: 28435856 PMCID: PMC5371421 DOI: 10.1126/sciadv.1600513] [Citation(s) in RCA: 261] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 02/10/2017] [Indexed: 05/18/2023]
Abstract
The highly social (eusocial) corbiculate bees, comprising the honey bees, bumble bees, and stingless bees, are ubiquitous insect pollinators that fulfill critical roles in ecosystem services and human agriculture. Here, we conduct wide sampling across the phylogeny of these corbiculate bees and reveal a dynamic evolutionary history behind their microbiota, marked by multiple gains and losses of gut associates, the presence of generalist as well as host-specific strains, and patterns of diversification driven, in part, by host ecology (for example, colony size). Across four continents, we found that different host species have distinct gut communities, largely independent of geography or sympatry. Nonetheless, their microbiota has a shared heritage: The emergence of the eusocial corbiculate bees from solitary ancestors appears to coincide with the acquisition of five core gut bacterial lineages, supporting the hypothesis that host sociality facilitates the development and maintenance of specialized microbiomes.
Collapse
Affiliation(s)
- Waldan K. Kwong
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511, USA
- Department of Integrative Biology, University of Texas, Austin, Austin, TX 78712, USA
- Corresponding author. (W.K.K.); (N.A.M.)
| | - Luis A. Medina
- Department of Integrative Biology, University of Texas, Austin, Austin, TX 78712, USA
| | - Hauke Koch
- Department of Integrative Biology, University of Texas, Austin, Austin, TX 78712, USA
| | - Kong-Wah Sing
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Eunice Jia Yu Soh
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - John S. Ascher
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Rodolfo Jaffé
- Vale Institute of Technology, Sustainable Development, 66055-090 Belém PA, Brazil
- Department of Ecology, Universidade de São Paulo, Rua do Matão 321, 05508-090 São Paulo SP, Brazil
| | - Nancy A. Moran
- Department of Integrative Biology, University of Texas, Austin, Austin, TX 78712, USA
- Corresponding author. (W.K.K.); (N.A.M.)
| |
Collapse
|
75
|
Astudillo‐García C, Bell JJ, Webster NS, Glasl B, Jompa J, Montoya JM, Taylor MW. Evaluating the core microbiota in complex communities: A systematic investigation. Environ Microbiol 2017; 19:1450-1462. [DOI: 10.1111/1462-2920.13647] [Citation(s) in RCA: 118] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 12/14/2016] [Accepted: 12/15/2016] [Indexed: 11/30/2022]
Affiliation(s)
- Carmen Astudillo‐García
- School of Biological SciencesUniversity of AucklandAuckland New Zealand
- Institute of Marine Science, University of AucklandAuckland New Zealand
| | - James J. Bell
- School of Biological SciencesVictoria University of WellingtonWellington New Zealand
| | | | - Bettina Glasl
- AIMS@JCU, Australian Institute of Marine Science, College of Science and EngineeringJames Cook UniversityTownsville Australia
| | - Jamaluddin Jompa
- Research and Development Centre on Marine, Coastal and Small IslandsHasanuddin UniversityMakassar Indonesia
| | - Jose M. Montoya
- Ecological Networks and Global Change Group, Experimental and Theoretical Ecology StationCNRS‐University Paul SabatierMoulis France
| | - Michael W. Taylor
- School of Biological SciencesUniversity of AucklandAuckland New Zealand
- Maurice Wilkins Centre for Molecular BiodiscoveryUniversity of AucklandAuckland New Zealand
| |
Collapse
|
76
|
Lifestyle and Horizontal Gene Transfer-Mediated Evolution of Mucispirillum schaedleri, a Core Member of the Murine Gut Microbiota. mSystems 2017; 2:mSystems00171-16. [PMID: 28168224 PMCID: PMC5285517 DOI: 10.1128/msystems.00171-16] [Citation(s) in RCA: 135] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Accepted: 01/04/2017] [Indexed: 01/01/2023] Open
Abstract
Shifts in gut microbiota composition have been associated with intestinal inflammation, but it remains unclear whether inflammation-associated bacteria are commensal or detrimental to their host. Here, we studied the lifestyle of the gut bacterium Mucispirillum schaedleri, which is associated with inflammation in widely used mouse models. We found that M. schaedleri has specialized systems to handle oxidative stress during inflammation. Additionally, it expresses secretion systems and effector proteins and can modify the mucosal gene expression of its host. This suggests that M. schaedleri undergoes intimate interactions with its host and may play a role in inflammation. The insights presented here aid our understanding of how commensal gut bacteria may be involved in altering susceptibility to disease. Mucispirillum schaedleri is an abundant inhabitant of the intestinal mucus layer of rodents and other animals and has been suggested to be a pathobiont, a commensal that plays a role in disease. In order to gain insights into its lifestyle, we analyzed the genome and transcriptome of M. schaedleri ASF 457 and performed physiological experiments to test traits predicted by its genome. Although described as a mucus inhabitant, M. schaedleri has limited capacity for degrading host-derived mucosal glycans and other complex polysaccharides. Additionally, M. schaedleri reduces nitrate and expresses systems for scavenging oxygen and reactive oxygen species in vivo, which may account for its localization close to the mucosal tissue and expansion during inflammation. Also of note, M. schaedleri harbors a type VI secretion system and putative effector proteins and can modify gene expression in mucosal tissue, suggesting intimate interactions with its host and a possible role in inflammation. The M. schaedleri genome has been shaped by extensive horizontal gene transfer, primarily from intestinal Epsilon- and Deltaproteobacteria, indicating that horizontal gene transfer has played a key role in defining its niche in the gut ecosystem. IMPORTANCE Shifts in gut microbiota composition have been associated with intestinal inflammation, but it remains unclear whether inflammation-associated bacteria are commensal or detrimental to their host. Here, we studied the lifestyle of the gut bacterium Mucispirillum schaedleri, which is associated with inflammation in widely used mouse models. We found that M. schaedleri has specialized systems to handle oxidative stress during inflammation. Additionally, it expresses secretion systems and effector proteins and can modify the mucosal gene expression of its host. This suggests that M. schaedleri undergoes intimate interactions with its host and may play a role in inflammation. The insights presented here aid our understanding of how commensal gut bacteria may be involved in altering susceptibility to disease.
Collapse
|
77
|
Rubino F, Carberry C, M Waters S, Kenny D, McCabe MS, Creevey CJ. Divergent functional isoforms drive niche specialisation for nutrient acquisition and use in rumen microbiome. ISME JOURNAL 2017; 11:932-944. [PMID: 28085156 PMCID: PMC5364355 DOI: 10.1038/ismej.2016.172] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Revised: 07/28/2016] [Accepted: 09/21/2016] [Indexed: 01/16/2023]
Abstract
Many microbes in complex competitive environments share genes for acquiring and utilising nutrients, questioning whether niche specialisation exists and if so, how it is maintained. We investigated the genomic signatures of niche specialisation in the rumen microbiome, a highly competitive, anaerobic environment, with limited nutrient availability determined by the biomass consumed by the host. We generated individual metagenomic libraries from 14 cows fed an ad libitum diet of grass silage and calculated functional isoform diversity for each microbial gene identified. The animal replicates were used to calculate confidence intervals to test for differences in diversity of functional isoforms between microbes that may drive niche specialisation. We identified 153 genes with significant differences in functional isoform diversity between the two most abundant bacterial genera in the rumen (Prevotella and Clostridium). We found Prevotella possesses a more diverse range of isoforms capable of degrading hemicellulose, whereas Clostridium for cellulose. Furthermore, significant differences were observed in key metabolic processes indicating that isoform diversity plays an important role in maintaining their niche specialisation. The methods presented represent a novel approach for untangling complex interactions between microorganisms in natural environments and have resulted in an expanded catalogue of gene targets central to rumen cellulosic biomass degradation.
Collapse
Affiliation(s)
- Francesco Rubino
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, UK.,Animal and Bioscience Research Department, Teagasc, Grange, Dunsany, Co., Meath, Ireland
| | - Ciara Carberry
- Animal and Bioscience Research Department, Teagasc, Grange, Dunsany, Co., Meath, Ireland.,School of Agriculture, University College Dublin, Dublin, Ireland
| | - Sinéad M Waters
- Animal and Bioscience Research Department, Teagasc, Grange, Dunsany, Co., Meath, Ireland
| | - David Kenny
- Animal and Bioscience Research Department, Teagasc, Grange, Dunsany, Co., Meath, Ireland
| | - Matthew S McCabe
- Animal and Bioscience Research Department, Teagasc, Grange, Dunsany, Co., Meath, Ireland
| | - Christopher J Creevey
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, UK
| |
Collapse
|
78
|
Ben Guerrero E, Soria M, Salvador R, Ceja-Navarro JA, Campos E, Brodie EL, Talia P. Effect of Different Lignocellulosic Diets on Bacterial Microbiota and Hydrolytic Enzyme Activities in the Gut of the Cotton Boll Weevil ( Anthonomus grandis). Front Microbiol 2016; 7:2093. [PMID: 28082962 PMCID: PMC5186755 DOI: 10.3389/fmicb.2016.02093] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 12/09/2016] [Indexed: 11/13/2022] Open
Abstract
Cotton boll weevils, Anthonomus grandis, are omnivorous coleopteran that can feed on diets with different compositions, including recalcitrant lignocellulosic materials. We characterized the changes in the prokaryotic community structure and the hydrolytic activities of A. grandis larvae fed on different lignocellulosic diets. A. grandis larvae were fed on three different artificial diets: cottonseed meal (CM), Napier grass (NG) and corn stover (CS). Total DNA was extracted from the gut samples for amplification and sequencing of the V3-V4 hypervariable region of the 16S rRNA gene. Proteobacteria and Firmicutes dominated the gut microbiota followed by Actinobacteria, Spirochaetes and a small number of unclassified phyla in CM and NG microbiomes. In the CS feeding group, members of Spirochaetes were the most prevalent, followed by Proteobacteria and Firmicutes. Bray-Curtis distances showed that the samples from the CS community were clearly separated from those samples of the CM and NG diets. Gut extracts from all three diets exhibited endoglucanase, xylanase, β-glucosidase and pectinase activities. These activities were significantly affected by pH and temperature across different diets. We observed that the larvae reared on a CM showed significantly higher activities than larvae reared on NG and CS. We demonstrated that the intestinal bacterial community structure varies depending on diet composition. Diets with more variable and complex compositions, such as CS, showed higher bacterial diversity and richness than the two other diets. In spite of the detected changes in composition and diversity, we identified a core microbiome shared between the three different lignocellulosic diets. These results suggest that feeding with diets of different lignocellulosic composition could be a viable strategy to discover variants of hemicellulose and cellulose breakdown systems.
Collapse
Affiliation(s)
- Emiliano Ben Guerrero
- Instituto de Biotecnología, Centro de Investigación en Ciencias Veterinarias y Agronómicas, Centro Nacional de Investigaciones Agropecuarias - Instituto Nacional de Tecnología Agropecuaria Castelar Hurlingham, Argentina
| | - Marcelo Soria
- Instituto de Investigaciones en Biociencias Agrícolas y Ambientales-Consejo Nacional de Investigaciones Científicas y Técnicas, Cátedra de Microbiología Agrícola, Facultad de Agronomía, Universidad de Buenos Aires Buenos Aires, Argentina
| | - Ricardo Salvador
- Instituto de Microbiología y Zoología Agrícola, Centro de Investigación en Ciencias Veterinarias y Agronómicas, Centro Nacional de Investigaciones Agropecuarias - Instituto Nacional de Tecnología Agropecuaria Castelar Hurlingham, Argentina
| | - Javier A Ceja-Navarro
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Eleonora Campos
- Instituto de Biotecnología, Centro de Investigación en Ciencias Veterinarias y Agronómicas, Centro Nacional de Investigaciones Agropecuarias - Instituto Nacional de Tecnología Agropecuaria CastelarHurlingham, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)Buenos Aires, Argentina
| | - Eoin L Brodie
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Paola Talia
- Instituto de Biotecnología, Centro de Investigación en Ciencias Veterinarias y Agronómicas, Centro Nacional de Investigaciones Agropecuarias - Instituto Nacional de Tecnología Agropecuaria CastelarHurlingham, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)Buenos Aires, Argentina
| |
Collapse
|
79
|
Sapountzis P, de Verges J, Rousk K, Cilliers M, Vorster BJ, Poulsen M. Potential for Nitrogen Fixation in the Fungus-Growing Termite Symbiosis. Front Microbiol 2016; 7:1993. [PMID: 28018322 PMCID: PMC5156715 DOI: 10.3389/fmicb.2016.01993] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 11/28/2016] [Indexed: 11/13/2022] Open
Abstract
Termites host a gut microbiota of diverse and essential symbionts that enable specialization on dead plant material; an abundant, but nutritionally imbalanced food source. To supplement the severe shortage of dietary nitrogen (N), some termite species make use of diazotrophic bacteria to fix atmospheric nitrogen (N2). Fungus-growing termites (subfamily Macrotermitinae) host a fungal exosymbiont (genus Termitomyces) that provides digestive services and the main food source for the termites. This has been thought to obviate the need for N2-fixation by bacterial symbionts. Here, we challenge this notion by performing acetylene reduction assays of live colony material to show that N2 fixation is present in two major genera (Macrotermes and Odontotermes) of fungus-growing termites. We compare and discuss fixation rates in relation to those obtained from other termites, and suggest avenues of research that may lead to a better understanding of N2 fixation in fungus-growing and other termites.
Collapse
Affiliation(s)
- Panagiotis Sapountzis
- Centre for Social Evolution, Section for Ecology and Evolution, Department of Biology, University of CopenhagenCopenhagen, Denmark
| | - Jane de Verges
- Centre for Social Evolution, Section for Ecology and Evolution, Department of Biology, University of CopenhagenCopenhagen, Denmark
| | - Kathrin Rousk
- Section for Terrestrial Ecology, Department of Biology, University of CopenhagenCopenhagen, Denmark
| | - Magdeleen Cilliers
- Department of Plant Production and Soil Science, Forestry and Agricultural Biotechnology Institute, University of PretoriaPretoria, South Africa
| | - Barend J. Vorster
- Department of Plant Production and Soil Science, Forestry and Agricultural Biotechnology Institute, University of PretoriaPretoria, South Africa
| | - Michael Poulsen
- Centre for Social Evolution, Section for Ecology and Evolution, Department of Biology, University of CopenhagenCopenhagen, Denmark
| |
Collapse
|
80
|
Berg M, Zhou XY, Shapira M. Host-Specific Functional Significance of Caenorhabditis Gut Commensals. Front Microbiol 2016; 7:1622. [PMID: 27799924 PMCID: PMC5066524 DOI: 10.3389/fmicb.2016.01622] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 09/29/2016] [Indexed: 12/27/2022] Open
Abstract
The gut microbiota is an important contributor to host health and fitness. Given its importance, microbiota composition should not be left to chance. However, what determines this composition is far from clear, with results supporting contributions of both environmental factors and host genetics. To gauge the relative contributions of host genetics and environment, specifically the microbial diversity, we characterized the gut microbiotas of Caenorhabditis species spanning 200-300 million years of evolution, and raised on different composted soil environments. Comparisons were based on 16S rDNA deep sequencing data, as well as on functional evaluation of gut isolates. Worm microbiotas were distinct from those in their respective soil environment, and included bacteria previously identified as part of the C. elegans core microbiota. Microbiotas differed between experiments initiated with different soil communities, but within each experiment, worm microbiotas clustered according to host identity, demonstrating a dominant contribution of environmental diversity, but also a significant contribution of host genetics. The dominance of environmental contributions hindered identification of host-associated microbial taxa from 16S data. Characterization of gut isolates from C. elegans and C. briggsae, focusing on the core family Enterobacteriaceae, were also unable to expose phylogenetic distinctions between microbiotas of the two species. However, functional evaluation of the isolates revealed host-specific contributions, wherein gut commensals protected their own host from infection, but not a non-host. Identification of commensal host-specificity at the functional level, otherwise overlooked in standard sequence-based analyses, suggests that the contribution of host genetics to shaping of gut microbiotas may be greater than previously realized.
Collapse
Affiliation(s)
- Maureen Berg
- Department of Integrative Biology, University of California, Berkeley Berkeley, CA, USA
| | - Xiao Ying Zhou
- Department of Integrative Biology, University of California, Berkeley Berkeley, CA, USA
| | - Michael Shapira
- Department of Integrative Biology, University of California, BerkeleyBerkeley, CA, USA; Graduate Group in Microbiology, University of California, BerkeleyBerkeley, CA, USA
| |
Collapse
|
81
|
|
82
|
Berlanga M, Llorens C, Comas J, Guerrero R. Gut Bacterial Community of the Xylophagous Cockroaches Cryptocercus punctulatus and Parasphaeria boleiriana. PLoS One 2016; 11:e0152400. [PMID: 27054320 PMCID: PMC4824515 DOI: 10.1371/journal.pone.0152400] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Accepted: 03/14/2016] [Indexed: 12/12/2022] Open
Abstract
Cryptocercus punctulatus and Parasphaeria boleiriana are two distantly related xylophagous and subsocial cockroaches. Cryptocercus is related to termites. Xylophagous cockroaches and termites are excellent model organisms for studying the symbiotic relationship between the insect and their microbiota. In this study, high-throughput 454 pyrosequencing of 16S rRNA was used to investigate the diversity of metagenomic gut communities of C. punctulatus and P. boleiriana, and thereby to identify possible shifts in symbiont allegiances during cockroaches evolution. Our results revealed that the hindgut prokaryotic communities of both xylophagous cockroaches are dominated by members of four Bacteria phyla: Bacteroidetes, Firmicutes, Proteobacteria, and Actinobacteria. Other identified phyla were Spirochaetes, Planctomycetes, candidatus Saccharibacteria (formerly TM7), and Acidobacteria, each of which represented 1–2% of the total population detected. Community similarity based on phylogenetic relatedness by unweighted UniFrac analyses indicated that the composition of the bacterial community in the two species was significantly different (P < 0.05). Phylogenetic analysis based on the characterized clusters of Bacteroidetes, Spirochaetes, and Deltaproteobacteria showed that many OTUs present in both cockroach species clustered with sequences previously described in termites and other cockroaches, but not with those from other animals or environments. These results suggest that, during their evolution, those cockroaches conserved several bacterial communities from the microbiota of a common ancestor. The ecological stability of those microbial communities may imply the important functional role for the survival of the host of providing nutrients in appropriate quantities and balance.
Collapse
Affiliation(s)
- Mercedes Berlanga
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Barcelona, Barcelona, Spain
| | - Carlos Llorens
- Unity of Genomics. Scientific and Technological Centers, University of Barcelona (CCiTUB), Barcelona, Spain.,Biotechvana, Valencia, Spain
| | - Jaume Comas
- Unity of Genomics. Scientific and Technological Centers, University of Barcelona (CCiTUB), Barcelona, Spain
| | - Ricardo Guerrero
- Laboratory of Molecular Microbiology and Antimicrobials, Department of Pathology and Experimental Therapeutics, Faculty of Medicine, University of Barcelona-IDIBELL, Barcelona, Spain.,Barcelona Knowledge Hub, Academia Europaea, Barcelona, Spain
| |
Collapse
|
83
|
Shapira M. Gut Microbiotas and Host Evolution: Scaling Up Symbiosis. Trends Ecol Evol 2016; 31:539-549. [PMID: 27039196 DOI: 10.1016/j.tree.2016.03.006] [Citation(s) in RCA: 232] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 02/18/2016] [Accepted: 03/05/2016] [Indexed: 02/07/2023]
Abstract
Our understanding of species evolution is undergoing restructuring. It is well accepted that host-symbiont coevolution is responsible for fundamental aspects of biology. However, the emerging importance of plant- and animal-associated microbiotas to their hosts suggests a scale of coevolutionary interactions many-fold greater than previously considered. This review builds on current understanding of symbionts and their contributions to host evolution to evaluate recent data demonstrating similar contributions of gut microbiotas. It further considers a multilayered model for microbiota to account for emerging themes in host-microbiota interactions. Drawing on the structure of bacterial genomes, this model distinguishes between a host-adapted core microbiota, and a flexible, environmentally modulated microbial pool, differing in constraints on their maintenance and in their contributions to host adaptation.
Collapse
Affiliation(s)
- Michael Shapira
- University of California, Berkeley, department of Integrative Biology and Graduate Group in Microbiology. Valley Life Sciences Building, room 5155, Berkeley, CA 94720, USA.
| |
Collapse
|
84
|
Palmer M, de Maayer P, Poulsen M, Steenkamp ET, van Zyl E, Coutinho TA, Venter SN. Draft genome sequences of Pantoea agglomerans and Pantoea vagans isolates associated with termites. Stand Genomic Sci 2016; 11:23. [PMID: 26937267 PMCID: PMC4774006 DOI: 10.1186/s40793-016-0144-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 01/20/2016] [Indexed: 02/02/2023] Open
Abstract
The genus Pantoea incorporates many economically and clinically important species. The plant-associated species, Pantoea agglomerans and Pantoea vagans, are closely related and are often isolated from similar environments. Plasmids conferring certain metabolic capabilities are also shared amongst these two species. The genomes of two isolates obtained from fungus-growing termites in South Africa were sequenced, assembled and annotated. A high number of orthologous genes are conserved within and between these species. The difference in genome size between P. agglomerans MP2 (4,733,829 bp) and P. vagans MP7 (4,598,703 bp) can largely be attributed to the differences in plasmid content. The genome sequences of these isolates may shed light on the common traits that enable P. agglomerans and P. vagans to co-occur in plant- and insect-associated niches.
Collapse
Affiliation(s)
- Marike Palmer
- />Department of Microbiology and Plant Pathology and the Genome Research Institute, University of Pretoria, Pretoria, 0002 South Africa
- />DST-NRF Centre of Excellence in Tree Health Biotechnology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, 0002 South Africa
| | - Pieter de Maayer
- />Department of Microbiology and Plant Pathology and the Genome Research Institute, University of Pretoria, Pretoria, 0002 South Africa
- />Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, 0002 South Africa
| | - Michael Poulsen
- />Department of Biology, Centre for Social Evolution, Section for Ecology and Evolution, University of Copenhagen, Univeritetsparken 15, 2100 Copenhagen East, Denmark
| | - Emma T. Steenkamp
- />Department of Microbiology and Plant Pathology and the Genome Research Institute, University of Pretoria, Pretoria, 0002 South Africa
- />DST-NRF Centre of Excellence in Tree Health Biotechnology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, 0002 South Africa
| | - Elritha van Zyl
- />Department of Microbiology and Plant Pathology and the Genome Research Institute, University of Pretoria, Pretoria, 0002 South Africa
- />DST-NRF Centre of Excellence in Tree Health Biotechnology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, 0002 South Africa
| | - Teresa A. Coutinho
- />Department of Microbiology and Plant Pathology and the Genome Research Institute, University of Pretoria, Pretoria, 0002 South Africa
- />DST-NRF Centre of Excellence in Tree Health Biotechnology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, 0002 South Africa
| | - Stephanus N. Venter
- />Department of Microbiology and Plant Pathology and the Genome Research Institute, University of Pretoria, Pretoria, 0002 South Africa
- />DST-NRF Centre of Excellence in Tree Health Biotechnology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, 0002 South Africa
| |
Collapse
|
85
|
Benjamino J, Graf J. Characterization of the Core and Caste-Specific Microbiota in the Termite, Reticulitermes flavipes. Front Microbiol 2016; 7:171. [PMID: 26925043 PMCID: PMC4756164 DOI: 10.3389/fmicb.2016.00171] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 02/01/2016] [Indexed: 02/01/2023] Open
Abstract
The hindgut of the termite Reticulitermes flavipes harbors a complex symbiotic community consisting of protists, bacteria, and archaea. These symbionts aid in the digestion of lignocellulose from the termite’s wood meal. Termite hindguts were sampled and the V4 hyper-variable region of the 16S rRNA gene was sequenced and analyzed from individual termites. The core microbiota of worker termites consisted of 69 OTUs at the 97% identity level, grouped into 16 taxa, and together accounted for 67.05% of the sequences from the bacterial community. The core was dominated by Treponema, which contained 36 different OTUs and accounted for ∼32% of the sequences, which suggests Treponema sp. have an important impact on the overall physiology in the hindgut. Bray–Curtis beta diversity metrics showed that hindgut samples from termites of the same colony were more similar to each other than to samples from other colonies despite possessing a core that accounted for the majority of the sequences. The specific tasks and dietary differences of the termite castes could have an effect on the composition of the microbial community. The hindgut microbiota of termites from the alate castes differed from the worker caste with significantly lower abundances of Treponema and Endomicrobia, which dominated the hindgut microbiota in workers and soldiers. Protist abundances were also quantified in the same samples using qPCR of the 18S rRNA gene. Parabasalia abundances dropped significantly in the winged alates and the Oxymonadida abundances dropped in both alate castes. These data suggest that the changes in diet or overall host physiology affected the protist and bacterial populations in the hindgut. The in-depth bacterial characterization and protist quantification in this study sheds light on the potential community dynamics within the R. flavipes hindgut and identified a large and complex core microbiota in termites obtained from multiple colonies and castes.
Collapse
Affiliation(s)
- Jacquelynn Benjamino
- Department of Molecular and Cell Biology, University of Connecticut, Storrs CT, USA
| | - Joerg Graf
- Department of Molecular and Cell Biology, University of Connecticut, StorrsCT, USA; Institute for Systems Genomics, University of Connecticut, StorrsCT, USA
| |
Collapse
|
86
|
Wang W, Cao J, Yang F, Wang X, Zheng S, Sharshov K, Li L. High-throughput sequencing reveals the core gut microbiome of Bar-headed goose (Anser indicus) in different wintering areas in Tibet. Microbiologyopen 2016; 5:287-95. [PMID: 26842811 PMCID: PMC4831473 DOI: 10.1002/mbo3.327] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 10/31/2015] [Accepted: 11/04/2015] [Indexed: 12/16/2022] Open
Abstract
Elucidating the spatial dynamic and core gut microbiome related to wild bar‐headed goose is of crucial importance for probiotics development that may meet the demands of bar‐headed goose artificial breeding industries and accelerate the domestication of this species. However, the core microbial communities in the wild bar‐headed geese remain totally unknown. Here, for the first time, we present a comprehensive survey of bar‐headed geese gut microbial communities by Illumina high‐throughput sequencing technology using nine individuals from three distinct wintering locations in Tibet. A total of 236,676 sequences were analyzed, and 607 OTUs were identified. We show that the gut microbial communities of bar‐headed geese have representatives of 14 phyla and are dominated by Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes. The additive abundance of these four most dominant phyla was above 96% across all the samples. At the genus level, the sequences represented 150 genera. A set of 19 genera were present in all samples and considered as core gut microbiome. The top seven most abundant core genera were distributed in that four dominant phyla. Among them, four genera (Lactococcus, Bacillus, Solibacillus, and Streptococcus) belonged to Firmicutes, while for other three phyla, each containing one genus, such as Proteobacteria (genus Pseudomonas), Actinobacteria (genus Arthrobacter), and Bacteroidetes (genus Bacteroides). This broad survey represents the most in‐depth assessment, to date, of the gut microbes that associated with bar‐headed geese. These data create a baseline for future bar‐headed goose microbiology research, and make an original contribution to probiotics development for bar‐headed goose artificial breeding industries.
Collapse
Affiliation(s)
- Wen Wang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xi'ning, 810000, China.,Center of Growth, Metabolism and Aging, College of Life Sciences, Sichuan University, Chengdu, 610000, China
| | - Jian Cao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xi'ning, 810000, China.,University of the Chinese Academy of Sciences, Beijing, 100101,, China
| | - Fang Yang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xi'ning, 810000, China
| | - Xuelian Wang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xi'ning, 810000, China
| | - Sisi Zheng
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xi'ning, 810000, China.,University of the Chinese Academy of Sciences, Beijing, 100101,, China
| | - Kirill Sharshov
- Research Institute of Experimental and Clinical Medicine, Novosibirsk, 630117, Russia
| | - Laixing Li
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xi'ning, 810000, China
| |
Collapse
|
87
|
Assembly of the Caenorhabditis elegans gut microbiota from diverse soil microbial environments. ISME JOURNAL 2016; 10:1998-2009. [PMID: 26800234 PMCID: PMC5029150 DOI: 10.1038/ismej.2015.253] [Citation(s) in RCA: 225] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 11/22/2015] [Accepted: 12/01/2015] [Indexed: 01/15/2023]
Abstract
It is now well accepted that the gut microbiota contributes to our health. However, what determines the microbiota composition is still unclear. Whereas it might be expected that the intestinal niche would be dominant in shaping the microbiota, studies in vertebrates have repeatedly demonstrated dominant effects of external factors such as host diet and environmental microbial diversity. Hypothesizing that genetic variation may interfere with discerning contributions of host factors, we turned to Caenorhabditis elegans as a new model, offering the ability to work with genetically homogenous populations. Deep sequencing of 16S rDNA was used to characterize the (previously unknown) worm gut microbiota as assembled from diverse produce-enriched soil environments under laboratory conditions. Comparisons of worm microbiotas with those in their soil environment revealed that worm microbiotas resembled each other even when assembled from different microbial environments, and enabled defining a shared core gut microbiota. Community analyses indicated that species assortment in the worm gut was non-random and that assembly rules differed from those in their soil habitat, pointing at the importance of competitive interactions between gut-residing taxa. The data presented fills a gap in C. elegans biology. Furthermore, our results demonstrate a dominant contribution of the host niche in shaping the gut microbiota.
Collapse
|
88
|
Rebollar EA, Hughey MC, Medina D, Harris RN, Ibáñez R, Belden LK. Skin bacterial diversity of Panamanian frogs is associated with host susceptibility and presence of Batrachochytrium dendrobatidis. ISME JOURNAL 2016; 10:1682-95. [PMID: 26744810 DOI: 10.1038/ismej.2015.234] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 10/29/2015] [Accepted: 11/06/2015] [Indexed: 01/06/2023]
Abstract
Symbiotic bacteria on amphibian skin can inhibit growth of the fungus Batrachochytrium dendrobatidis (Bd) that has caused dramatic population declines and extinctions of amphibians in the Neotropics. It remains unclear how the amphibians' skin microbiota is influenced by environmental bacterial reservoirs, host-associated factors such as susceptibility to pathogens, and pathogen presence in tropical amphibians. We sampled skin bacteria from five co-occurring frog species that differ in Bd susceptibility at one Bd-naive site, and sampled one of the non-susceptible species from Bd-endemic and Bd-naive sites in Panama. We hypothesized that skin bacterial communities (1) would be distinct from the surrounding environment regardless of the host habitat, (2) would differ between Bd susceptible and non-susceptible species and (3) would differ on hosts in Bd-naive and Bd-endemic sites. We found that skin bacterial communities were enriched in bacterial taxa that had low relative abundances in the environment. Non-susceptible species had very similar skin bacterial communities that were enriched in particular taxa such as the genera Pseudomonas and Acinetobacter. Bacterial communities of Craugastor fitzingeri in Bd-endemic sites were less diverse than in the naive site, and differences in community structure across sites were explained by changes in relative abundance of specific bacterial taxa. Our results indicate that skin microbial structure was associated with host susceptibility to Bd and might be associated to the history of Bd presence at different sites.
Collapse
Affiliation(s)
- Eria A Rebollar
- Department of Biology, James Madison University, Harrisonburg, VA, USA
| | - Myra C Hughey
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Daniel Medina
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Reid N Harris
- Department of Biology, James Madison University, Harrisonburg, VA, USA
| | - Roberto Ibáñez
- Smithsonian Tropical Research Institute, Panama City, Panama
| | - Lisa K Belden
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA.,Smithsonian Tropical Research Institute, Panama City, Panama
| |
Collapse
|
89
|
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
|
90
|
Su L, Yang L, Huang S, Su X, Li Y, Wang F, Wang E, Kang N, Xu J, Song A. Comparative Gut Microbiomes of Four Species Representing the Higher and the Lower Termites. JOURNAL OF INSECT SCIENCE (ONLINE) 2016; 16:iew081. [PMID: 27638955 PMCID: PMC5026480 DOI: 10.1093/jisesa/iew081] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2016] [Accepted: 07/30/2016] [Indexed: 05/12/2023]
Abstract
Aiming at learning the association between the gut microbiota and termites with different diet habits and phylogenetic positions, the gut bacteria of three populations for each of the two higher termites (wood-feeding Mironasutitermes shangchengensis and fungus-feeding Odontotermes formosanus) and two wood-feeding lower termites (Tsaitermes ampliceps and Reticulitermes flaviceps) were analyzed by high-throughput 454 pyrosequencing of 16S V1-V3 amplicons. As results, 132 bacterial genera and some unidentified operational taxonomic units within 29 phyla in the gut bacteria were detected, with Spirochaetes (11-55%), Firmicutes (7-18%), Bacteroidetes (7-31%), and Proteobacteria (8-14%) as the main phyla, and Treponema, TG5, Dysgonomonas, Tannerella, za29, Lactococcus, Pseudomonas, and SJA-88 as the common genera in all the four termites. The diversity of gut bacterial communities in the higher termite guts was significantly greater than that in the lower termites; while the gut microbiota in M. shangchengensis (wood-feeding higher termite) was more similar to those of the wood-feeding lower termites rather than that of O. formosanus (fungus-feeding higher termite), and phylum Spirochaetes and nitrogen-fixing bacteria were super-dominant in the wood-feeding termites, despite of their phylogenetic relations. This study reported for the first time the gut bacterial communities for the termites of M. shangchengensis and T. ampliceps and the comparative analyses showed that the gut microbial communities varied according to the phylogeny and the diet habits of termites.
Collapse
Affiliation(s)
- LiJuan Su
- College of Life Sciences, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - LeLe Yang
- College of Life Sciences, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Shi Huang
- BioEnergy Genome Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China (; )
| | - XiaoQuan Su
- BioEnergy Genome Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China (; )
| | - Yan Li
- College of Life Sciences, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - FengQin Wang
- College of Life Sciences, Henan Agricultural University, Zhengzhou, Henan 450002, China Key Laboratory of Enzyme Engineering of Agricultural Microbiology, Ministry of Agriculture, Zhengzhou, Henan 450002, China
| | - EnTao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, México, DF 11340, México
| | - Ning Kang
- BioEnergy Genome Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China (; )
| | - Jian Xu
- BioEnergy Genome Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China (; )
| | - AnDong Song
- College of Life Sciences, Henan Agricultural University, Zhengzhou, Henan 450002, China Key Laboratory of Enzyme Engineering of Agricultural Microbiology, Ministry of Agriculture, Zhengzhou, Henan 450002, China
| |
Collapse
|
91
|
Deterministic Assembly of Complex Bacterial Communities in Guts of Germ-Free Cockroaches. Appl Environ Microbiol 2015; 82:1256-63. [PMID: 26655763 DOI: 10.1128/aem.03700-15] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 12/03/2015] [Indexed: 01/09/2023] Open
Abstract
The gut microbiota of termites plays important roles in the symbiotic digestion of lignocellulose. However, the factors shaping the microbial community structure remain poorly understood. Because termites cannot be raised under axenic conditions, we established the closely related cockroach Shelfordella lateralis as a germ-free model to study microbial community assembly and host-microbe interactions. In this study, we determined the composition of the bacterial assemblages in cockroaches inoculated with the gut microbiota of termites and mice using pyrosequencing analysis of their 16S rRNA genes. Although the composition of the xenobiotic communities was influenced by the lineages present in the foreign inocula, their structure resembled that of conventional cockroaches. Bacterial taxa abundant in conventional cockroaches but rare in the foreign inocula, such as Dysgonomonas and Parabacteroides spp., were selectively enriched in the xenobiotic communities. Donor-specific taxa, such as endomicrobia or spirochete lineages restricted to the gut microbiota of termites, however, either were unable to colonize germ-free cockroaches or formed only small populations. The exposure of xenobiotic cockroaches to conventional adults restored their normal microbiota, which indicated that autochthonous lineages outcompete foreign ones. Our results provide experimental proof that the assembly of a complex gut microbiota in insects is deterministic.
Collapse
|
92
|
Bai L, Liu C, Guo L, Piao C, Li Z, Li J, Jia F, Wang X, Xiang W. Streptomyces formicae sp. nov., a novel actinomycete isolated from the head of Camponotus japonicus Mayr. Antonie van Leeuwenhoek 2015; 109:253-61. [PMID: 26608172 DOI: 10.1007/s10482-015-0628-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 11/20/2015] [Indexed: 12/25/2022]
Abstract
During a screening for novel and biotechnologically useful actinobacteria in insects, a novel actinomycete with antifungal activity, designated strain 1H-GS9(T), was isolated from the head of a Camponotus japonicus Mayr ant, which were collected from Northeast Agricultural University (Harbin, Heilongjiang, China). Strain 1H-GS9(T) was characterised using a polyphasic approach. The organism was found to have morphological and chemotaxonomic characteristics typical of members of the genus Streptomyces. 16S rRNA gene sequence similarity studies showed that strain 1H-GS9(T) belongs to the genus Streptomyces with high sequence similarities to Streptomyces scopuliridis DSM 41917(T) (98.8 %) and Streptomyces mauvecolor JCM 5002(T) (98.6 %). However, phylogenetic analysis based on the 16S rRNA gene sequence indicated that it forms a monophyletic clade with Streptomyces kurssanovii JCM 4388(T) (98.6 %), Streptomyces xantholiticus JCM 4282(T) (98.6 %) and Streptomyces peucetius JCM 9920(T) (98.5 %). Thus, a combination of DNA-DNA hybridization experiments and phenotypic tests were carried out between strain 1H-GS9(T) and the above-mentioned five strains, which further clarified their relatedness and demonstrated that strain 1H-GS9(T) could be distinguished from these strains. Therefore, the strain is concluded to represent a novel species of the genus Streptomyces, for which the name Streptomyces formicae sp. nov. is proposed. The type strain is 1H-GS9(T) (=CGMCC 4.7277(T) = DSM 100524(T)).
Collapse
Affiliation(s)
- Lu Bai
- Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin, 150030, People's Republic of China
| | - Chongxi Liu
- Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin, 150030, People's Republic of China
| | - Lifeng Guo
- Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin, 150030, People's Republic of China
| | - Chenyu Piao
- Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin, 150030, People's Republic of China
| | - Zhilei Li
- Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin, 150030, People's Republic of China
| | - Jiansong Li
- Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin, 150030, People's Republic of China
| | - Feiyu Jia
- Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin, 150030, People's Republic of China
| | - Xiangjing Wang
- Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin, 150030, People's Republic of China.
| | - Wensheng Xiang
- Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin, 150030, People's Republic of China.
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China.
| |
Collapse
|
93
|
Jousselin E, Clamens AL, Galan M, Bernard M, Maman S, Gschloessl B, Duport G, Meseguer AS, Calevro F, Coeur d'acier A. Assessment of a 16S rRNA amplicon Illumina sequencing procedure for studying the microbiome of a symbiont-rich aphid genus. Mol Ecol Resour 2015; 16:628-40. [PMID: 26458227 DOI: 10.1111/1755-0998.12478] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 10/02/2015] [Accepted: 10/06/2015] [Indexed: 02/07/2023]
Abstract
The bacterial communities inhabiting arthropods are generally dominated by a few endosymbionts that play an important role in the ecology of their hosts. Rather than comparing bacterial species richness across samples, ecological studies on arthropod endosymbionts often seek to identify the main bacterial strains associated with each specimen studied. The filtering out of contaminants from the results and the accurate taxonomic assignment of sequences are therefore crucial in arthropod microbiome studies. We aimed here to validate an Illumina 16S rRNA gene sequencing protocol and analytical pipeline for investigating endosymbiotic bacteria associated with aphids. Using replicate DNA samples from 12 species (Aphididae: Lachninae, Cinara) and several controls, we removed individual sequences not meeting a minimum threshold number of reads in each sample and carried out taxonomic assignment for the remaining sequences. With this approach, we show that (i) contaminants accounted for a negligible proportion of the bacteria identified in our samples; (ii) the taxonomic composition of our samples and the relative abundance of reads assigned to a taxon were very similar across PCR and DNA replicates for each aphid sample; in particular, bacterial DNA concentration had no impact on the results. Furthermore, by analysing the distribution of unique sequences across samples rather than aggregating them into operational taxonomic units (OTUs), we gained insight into the specificity of endosymbionts for their hosts. Our results confirm that Serratia symbiotica is often present in Cinara species, in addition to the primary symbiont, Buchnera aphidicola. Furthermore, our findings reveal new symbiotic associations with Erwinia- and Sodalis-related bacteria. We conclude with suggestions for generating and analysing 16S rRNA gene sequences for arthropod-endosymbiont studies.
Collapse
Affiliation(s)
- E Jousselin
- INRA - UMR 1062 CBGP (INRA, IRD, CIRAD, Montpellier SupAgro), 755 avenue du Campus Agropolis CS 30016, F-34 988, Montferrier-sur-Lez, France
| | - A-L Clamens
- INRA - UMR 1062 CBGP (INRA, IRD, CIRAD, Montpellier SupAgro), 755 avenue du Campus Agropolis CS 30016, F-34 988, Montferrier-sur-Lez, France
| | - M Galan
- INRA - UMR 1062 CBGP (INRA, IRD, CIRAD, Montpellier SupAgro), 755 avenue du Campus Agropolis CS 30016, F-34 988, Montferrier-sur-Lez, France
| | - M Bernard
- INRA - UMR 1313 GABI-SIGENAE, INRA de Jouy en Josas, Domaine de Vilvert, 78352, Jouy en Josas, France
| | - S Maman
- INRA, GenPhySE, Sigenae, Chemin de Borde rouge -CS 52627, 31326, Castanet Tolosan, France
| | - B Gschloessl
- INRA - UMR 1062 CBGP (INRA, IRD, CIRAD, Montpellier SupAgro), 755 avenue du Campus Agropolis CS 30016, F-34 988, Montferrier-sur-Lez, France
| | - G Duport
- UMR 203 BF2I, Biologie Fonctionnelle Insectes et Interactions, INRA, INSA de Lyon, Université de Lyon, 20 Avenue Einstein, F-69621, Villeurbanne, France
| | - A S Meseguer
- INRA - UMR 1062 CBGP (INRA, IRD, CIRAD, Montpellier SupAgro), 755 avenue du Campus Agropolis CS 30016, F-34 988, Montferrier-sur-Lez, France
| | - F Calevro
- UMR 203 BF2I, Biologie Fonctionnelle Insectes et Interactions, INRA, INSA de Lyon, Université de Lyon, 20 Avenue Einstein, F-69621, Villeurbanne, France
| | - A Coeur d'acier
- INRA - UMR 1062 CBGP (INRA, IRD, CIRAD, Montpellier SupAgro), 755 avenue du Campus Agropolis CS 30016, F-34 988, Montferrier-sur-Lez, France
| |
Collapse
|
94
|
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
|
95
|
Li H, Dietrich C, Zhu N, Mikaelyan A, Ma B, Pi R, Liu Y, Yang M, Brune A, Mo J. Age polyethism drives community structure of the bacterial gut microbiota in the fungus-cultivating termite Odontotermes formosanus. Environ Microbiol 2015; 18:1440-51. [PMID: 26346907 DOI: 10.1111/1462-2920.13046] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 08/30/2015] [Accepted: 09/02/2015] [Indexed: 11/28/2022]
Abstract
Fungus-cultivating termites (Macrotermitinae) possess an elaborate strategy of lignocellulose digestion. It involves a lignocellulose-degrading fungal symbiont (genus Termitomyces), a diverse gut microbiota and a characteristic labour division in food processing. In this study, using pyrotag sequencing and electron microscopy, we analysed the bacterial microbiota in the hindgut of Odontotermes formosanus and its fungus comb to investigate the spatial organization, establishment and temporal succession of the bacterial communities colonizing specific microhabitats. Our results document strong differences between the communities at the hindgut epithelium and the luminal fluid of newly moulted, young and old worker termites. The differences in community structure were consistent with the density, morphology and spatial distribution of bacterial cells and the pools of microbial metabolites in the hindgut compartment, underlining that both gut development and the age-specific changes in diet affect the composition and functional role of their gut microbiota. These findings provide strong support for the concept that changes in diet and gut environment are important determinants of community structure because they create new niches for microbial symbionts.
Collapse
Affiliation(s)
- Hongjie Li
- Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Carsten Dietrich
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Na Zhu
- Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Aram Mikaelyan
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Bin Ma
- Department of Renewable Resources, University of Alberta, Edmonton, Alberta, Canada
| | - Ruoxi Pi
- Program in the Biological and Biomedical Sciences and Department of Microbial Pathogenesis, Yale University, New Haven, CT, USA
| | - Yu Liu
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Mengyi Yang
- Xiaoshan Institute of Termite Control, Xiaoshan, Zhejiang, China
| | - Andreas Brune
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Jianchu Mo
- Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| |
Collapse
|
96
|
Mikaelyan A, Dietrich C, Köhler T, Poulsen M, Sillam-Dussès D, Brune A. Diet is the primary determinant of bacterial community structure in the guts of higher termites. Mol Ecol 2015; 24:5284-95. [PMID: 26348261 DOI: 10.1111/mec.13376] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 08/20/2015] [Accepted: 09/01/2015] [Indexed: 12/22/2022]
Abstract
The gut microbiota of termites plays critical roles in the symbiotic digestion of lignocellulose. While phylogenetically 'lower termites' are characterized by a unique association with cellulolytic flagellates, higher termites (family Termitidae) harbour exclusively prokaryotic communities in their dilated hindguts. Unlike the more primitive termite families, which primarily feed on wood, they have adapted to a variety of lignocellulosic food sources in different stages of humification, ranging from sound wood to soil organic matter. In this study, we comparatively analysed representatives of different taxonomic lineages and feeding groups of higher termites to identify the major drivers of bacterial community structure in the termite gut, using amplicon libraries of 16S rRNA genes from 18 species of higher termites. In all analyses, the wood-feeding species were clearly separated from humus and soil feeders, irrespective of their taxonomic affiliation, offering compelling evidence that diet is the primary determinant of bacterial community structure. Within each diet group, however, gut communities of termites from the same subfamily were more similar than those of distantly related species. A highly resolved classification using a curated reference database revealed only few genus-level taxa whose distribution patterns indicated specificity for certain host lineages, limiting any possible cospeciation between the gut microbiota and host to short evolutionary timescales. Rather, the observed patterns in the host-specific distribution of the bacterial lineages in termite guts are best explained by diet-related differences in the availability of microhabitats and functional niches.
Collapse
Affiliation(s)
- Aram Mikaelyan
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany.,LOEWE Center for Synthetic Microbiology, SYNMIKRO, Philipps-Universität Marburg, Marburg, Germany
| | - Carsten Dietrich
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany
| | - Tim Köhler
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany
| | - Michael Poulsen
- Section for Ecology and Evolution, Department of Biology, Centre for Social Evolution, University of Copenhagen, Copenhagen East, Denmark
| | - David Sillam-Dussès
- Laboratory of Experimental and Comparative Ethology (LEEC), University of Paris 13, Sorbonne Paris Cité, Villetaneuse, France.,Institute of Ecology and Environmental Sciences - Paris (iEES-Paris), Institute of Research for Development, Sorbonne Universités, Bondy, France
| | - Andreas Brune
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany.,LOEWE Center for Synthetic Microbiology, SYNMIKRO, Philipps-Universität Marburg, Marburg, Germany
| |
Collapse
|
97
|
Profiling the Succession of Bacterial Communities throughout the Life Stages of a Higher Termite Nasutitermes arborum (Termitidae, Nasutitermitinae) Using 16S rRNA Gene Pyrosequencing. PLoS One 2015; 10:e0140014. [PMID: 26444989 PMCID: PMC4596844 DOI: 10.1371/journal.pone.0140014] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 09/21/2015] [Indexed: 01/19/2023] Open
Abstract
Previous surveys of the gut microbiota of termites have been limited to the worker caste. Termite gut microbiota has been well documented over the last decades and consists mainly of lineages specific to the gut microbiome which are maintained across generations. Despite this intimate relationship, little is known of how symbionts are transmitted to each generation of the host, especially in higher termites where proctodeal feeding has never been reported. The bacterial succession across life stages of the wood-feeding higher termite Nasutitermes arborum was characterized by 16S rRNA gene deep sequencing. The microbial community in the eggs, mainly affiliated to Proteobacteria and Actinobacteria, was markedly different from the communities in the following developmental stages. In the first instar and last instar larvae and worker caste termites, Proteobacteria and Actinobacteria were less abundant than Firmicutes, Bacteroidetes, Spirochaetes, Fibrobacteres and the candidate phylum TG3 from the last instar larvae. Most of the representatives of these phyla (except Firmicutes) were identified as termite-gut specific lineages, although their relative abundances differed. The most salient difference between last instar larvae and worker caste termites was the very high proportion of Spirochaetes, most of which were affiliated to the Treponema Ic, Ia and If subclusters, in workers. The results suggest that termite symbionts are not transmitted from mother to offspring but become established by a gradual process allowing the offspring to have access to the bulk of the microbiota prior to the emergence of workers, and, therefore, presumably through social exchanges with nursing workers.
Collapse
|
98
|
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]
|
99
|
Aira M, Bybee S, Pérez-Losada M, Domínguez J. Feeding on microbiomes: effects of detritivory on the taxonomic and phylogenetic bacterial composition of animal manures. FEMS Microbiol Ecol 2015; 91:fiv117. [DOI: 10.1093/femsec/fiv117] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/29/2015] [Indexed: 01/09/2023] Open
|
100
|
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
|