1
|
Weinhold A, Grüner E, Keller A. Bumble bee microbiota shows temporal succession and increase of lactic acid bacteria when exposed to outdoor environments. Front Cell Infect Microbiol 2024; 14:1342781. [PMID: 38500505 PMCID: PMC10945022 DOI: 10.3389/fcimb.2024.1342781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 02/19/2024] [Indexed: 03/20/2024] Open
Abstract
Question The large earth bumble bee (Bombus terrestris) maintains a social core gut-microbiota, similar as known from the honey bee, which plays an important role for host health and resistance. Experiments under laboratory conditions with commercial hives are limited to vertically transmitted microbes and neglect influences of environmental factors or external acquisition of microbes. Various environmental and landscape-level factors may have an impact on the gut-microbiota of pollinating insects, with consequences for pollinator health and fitness in agroecosystems. Still, it is not fully clear whether access to different flower diversities will have a significant influence on the bumble bee microbiota. Here, we tested in a semi-field experiment if the bumble bee microbiota changes over time when exposed to different flower diversities within outdoor flight cages. We used commercial hives to distinguish between vertically and horizontally transmitted bacteria, respectively from the nest environment or the exposed outside environment. Result The sequential sampling of foraging workers over a period of 35 days indicated a temporal progression of the bumble bee microbiota when placed outside. The microbiota increased in diversity and changed in composition and variability over time. We observed a major increase in relative abundance of the families Lactobacillaceae, Bifidobacteriaceae and Weeksellaceae. In contrast, major core-taxa like Snodgrassella and Gilliamella declined in their relative abundance over time. The genus Lactobacillus showed a high diversity and strain specific turnover, so that only specific ASVs showed an increase over time, while others had a more erratic occurrence pattern. Exposure to different flower diversities had no significant influence on the progression of the bumble bee microbiota. Conclusion The bumble bee microbiota showed a dynamic temporal succession with distinct compositional changes and diversification over time when placed outdoor. The exposure of bumble bees to environmental conditions, or environmental microbes, increases dissimilarity and changes the gut-community composition. This shows the importance of environmental influences on the temporal dynamic and progression of the bumble bee microbiota.
Collapse
Affiliation(s)
- Arne Weinhold
- Cellular and Organismic Networks, Faculty of Biology, Center for Organismic Adaptation, Ludwig-Maximilians-Universität München, Munich, Germany
| | | | | |
Collapse
|
2
|
Steffan SA, Dharampal PS, Kueneman JG, Keller A, Argueta-Guzmán MP, McFrederick QS, Buchmann SL, Vannette RL, Edlund AF, Mezera CC, Amon N, Danforth BN. Microbes, the 'silent third partners' of bee-angiosperm mutualisms. Trends Ecol Evol 2024; 39:65-77. [PMID: 37940503 DOI: 10.1016/j.tree.2023.09.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 08/30/2023] [Accepted: 09/01/2023] [Indexed: 11/10/2023]
Abstract
While bee-angiosperm mutualisms are widely recognized as foundational partnerships that have shaped the diversity and structure of terrestrial ecosystems, these ancient mutualisms have been underpinned by 'silent third partners': microbes. Here, we propose reframing the canonical bee-angiosperm partnership as a three-way mutualism between bees, microbes, and angiosperms. This new conceptualization casts microbes as active symbionts, processing and protecting pollen-nectar provisions, consolidating nutrients for bee larvae, enhancing floral attractancy, facilitating plant fertilization, and defending bees and plants from pathogens. In exchange, bees and angiosperms provide their microbial associates with food, shelter, and transportation. Such microbial communities represent co-equal partners in tripartite mutualisms with bees and angiosperms, facilitating one of the most important ecological partnerships on land.
Collapse
Affiliation(s)
- Shawn A Steffan
- US Department of Agriculture, Agricultural Research Service, 1575 Linden Drive, Madison, WI 53706, USA; Department of Entomology, University of Wisconsin, 1630 Linden Drive, Madison, WI 53706, USA.
| | - Prarthana S Dharampal
- Department of Entomology, University of Wisconsin, 1630 Linden Drive, Madison, WI 53706, USA; Biology Department, McHenry County College, 8900 Northwest Hwy #14, Crystal Lake, IL 60012, USA
| | - Jordan G Kueneman
- Department of Entomology, Cornell University, Comstock Hall, 2126, Ithaca, NY 14853, USA
| | - Alexander Keller
- Cellular and Organismic Networks, Faculty of Biology, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | | | - Quinn S McFrederick
- Department of Entomology, University of California Riverside, Riverside, CA 92521, USA
| | - Stephen L Buchmann
- Department of Entomology, University of Arizona, Tucson, AZ 85721, USA; Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Rachel L Vannette
- Department of Entomology and Nematology, University of California, Davis, Davis, CA 95616, USA
| | - Anna F Edlund
- Department of Biology, Bethany College, 31 E Campus Drive, Bethany, WV 26032, USA
| | - Celeste C Mezera
- Department of Entomology, University of Wisconsin, 1630 Linden Drive, Madison, WI 53706, USA
| | - Nolan Amon
- Department of Entomology, University of Wisconsin, 1630 Linden Drive, Madison, WI 53706, USA
| | - Bryan N Danforth
- Department of Entomology, Cornell University, Comstock Hall, 2126, Ithaca, NY 14853, USA
| |
Collapse
|
3
|
Balasubramanian VK, Muthuramalingam JB, Chen YP, Chou JY. Recent trends in lactic acid-producing microorganisms through microbial fermentation for the synthesis of polylactic acid. Arch Microbiol 2023; 206:31. [PMID: 38127148 DOI: 10.1007/s00203-023-03745-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 11/13/2023] [Accepted: 11/13/2023] [Indexed: 12/23/2023]
Abstract
Polylactic acid (PLA) is a range of unique bioplastics that are bio-based and biodegradable. PLA is currently driving market expansion for lactic acid (LA) due to its high demand as a building block in production. One of the most practical and environmentally benign techniques for synthesising PLA is through enzymatic polymerisation of microbial LA monomers. However, microbial LA fermentation does have some limitations. Firstly, it requires the use of a nutritionally rich medium. Secondly, LA production can be disrupted by bacteriophage infection or other microorganisms. Lastly, the yield can be low due to the formation of by-products through heterofermentative pathway. Considering the potential use of PLA as a replacement for conventional petrochemical-based polymers in industrial applications, researchers are focused on exploring the diversity of LA-producing microorganisms from various niches. Their goal is to study the functional properties of these microorganisms and their ability to produce industrially valuable metabolites. This review highlights the advantages and disadvantages of lactic acid-producing microorganisms used in microbial fermentation for PLA synthesis.
Collapse
Affiliation(s)
- Vignesh Kumar Balasubramanian
- Department of Botany, Alagappa University, Karaikudi, Tamil Nadu, 630003, India
- Department of Biology, National Changhua University of Education, Changhua, 500, Taiwan
| | | | - Yen-Po Chen
- Department of Animal Science, National Chung Hsing University, 145 Xingda Road, South Dist., Taichung City, 402, Taiwan
- The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung City, 402, Taiwan
| | - Jui-Yu Chou
- Department of Biology, National Changhua University of Education, Changhua, 500, Taiwan.
| |
Collapse
|
4
|
Hettiarachchi A, Cnockaert M, Joossens M, Gekière A, Meeus I, Vereecken NJ, Michez D, Smagghe G, Vandamme P. The wild solitary bees Andrena vaga, Anthophora plumipes, Colletes cunicularius, and Osmia cornuta microbiota are host specific and dominated by endosymbionts and environmental microorganisms. MICROBIAL ECOLOGY 2023; 86:3013-3026. [PMID: 37794084 DOI: 10.1007/s00248-023-02304-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 09/19/2023] [Indexed: 10/06/2023]
Abstract
We characterized the microbial communities of the crop, midgut, hindgut, and ovaries of the wild solitary bees Andrena vaga, Anthophora plumipes, Colletes cunicularius, and Osmia cornuta through 16S rRNA gene and ITS2 amplicon sequencing and a large-scale isolation campaign. The bacterial communities of these bees were dominated by endosymbionts of the genera Wolbachia and Spiroplasma. Bacterial and yeast genera representing the remaining predominant taxa were linked to an environmental origin. While only a single sampling site was examined for Andrena vaga, Anthophora plumipes, and Colletes cunicularius, and two sampling sites for Osmia cornuta, the microbiota appeared to be host specific: bacterial, but not fungal, communities generally differed between the analyzed bee species, gut compartments and ovaries. This may suggest a selective process determined by floral and host traits. Many of the gut symbionts identified in the present study are characterized by metabolic versatility. Whether they exert similar functionalities within the bee gut and thus functional redundancy remains to be elucidated.
Collapse
Affiliation(s)
- Amanda Hettiarachchi
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K.L. Ledeganckstraat 35, 9000, Ghent, Belgium
| | - Margo Cnockaert
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K.L. Ledeganckstraat 35, 9000, Ghent, Belgium
| | - Marie Joossens
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K.L. Ledeganckstraat 35, 9000, Ghent, Belgium
| | - Antoine Gekière
- Laboratory of Zoology, Research Institute for Biosciences, University of Mons, Place du parc 20, 7000, Mons, Belgium
| | - Ivan Meeus
- Laboratory of Agrozoology, Department of Plants of Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000, Gent, Belgium
| | - Nicolas J Vereecken
- Agroecology Lab, Université libre de Bruxelles (ULB), Boulevard du Triomphe CP 264/02, 1050, Brussels, Belgium
| | - Denis Michez
- Laboratory of Zoology, Research Institute for Biosciences, University of Mons, Place du parc 20, 7000, Mons, Belgium
| | - Guy Smagghe
- Laboratory of Agrozoology, Department of Plants of Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000, Gent, Belgium
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K.L. Ledeganckstraat 35, 9000, Ghent, Belgium.
| |
Collapse
|
5
|
Tuerlings T, Hettiarachchi A, Joossens M, Geslin B, Vereecken NJ, Michez D, Smagghe G, Vandamme P. Microbiota and pathogens in an invasive bee: Megachile sculpturalis from native and invaded regions. INSECT MOLECULAR BIOLOGY 2023; 32:544-557. [PMID: 37191302 DOI: 10.1111/imb.12849] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 04/28/2023] [Indexed: 05/17/2023]
Abstract
The present study aimed to characterise the bacterial, fungal and parasite gut community of the invasive bee Megachile sculpturalis sampled from native (Japan) and invaded (USA and France) regions via 16S rRNA and ITS2 amplicon sequencing and PCR detection of bee microparasites. The bacterial and fungal gut microbiota communities in bees from invaded regions were highly similar and differed strongly from those obtained in Japan. Core amplicon sequence variants (ASVs) within each population represented environmental micro-organisms commonly present in bee-associated niches that likely provide beneficial functions to their host. Although the overall bacterial and fungal communities of the invasive M. sculpturalis in France and the co-foraging native bees Anthidium florentinum and Halictus scabiosae, were significantly different, five out of eight core ASVs were shared suggesting common environmental sources and potential transmission. None of the 46 M. sculpturalis bees analysed harboured known bee pathogens, while microparasite infections were common in A. florentinum, and rare in H. scabiosae. A common shift in the gut microbiota of M. sculpturalis in invaded regions as a response to changed environmental conditions, or a founder effect coupled to population re-establishment in the invaded regions may explain the observed microbial community profiles and the absence of parasites. While the role of pathogen pressure in shaping biological invasions is still debated, the absence of natural enemies may contribute to the invasion success of M. sculpturalis.
Collapse
Affiliation(s)
- Tina Tuerlings
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Amanda Hettiarachchi
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Marie Joossens
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Benoît Geslin
- Aix Marseille Univ, Avignon Univ, CNRS, IRD, IMBE, Marseille, France
- Université de Rennes (UNIR), UMR 6553 ECOBIO, CNRS, Rennes, France
| | | | - Denis Michez
- Laboratory of Zoology, Research Institute for Biosciences, University of Mons, Mons, Belgium
| | - Guy Smagghe
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| |
Collapse
|
6
|
Kouya T, Ishiyama Y, Ohashi S, Kumakubo R, Yamazaki T, Otaki T. Philodulcilactobacillus myokoensis gen. nov., sp. nov., a fructophilic, acidophilic, and agar-phobic lactic acid bacterium isolated from fermented vegetable extracts. PLoS One 2023; 18:e0286677. [PMID: 37342988 DOI: 10.1371/journal.pone.0286677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 05/21/2023] [Indexed: 06/23/2023] Open
Abstract
Lactic acid bacteria are commonly in the fermentation industry and pose potential positive effects on health. In this study, a new lactic acid bacterium was isolated from fermented vegetable extracts in Myoko, Niigata, Japan. This bacterium is fructophilic, acidophilic, and hard to grow on agar medium. The isolate is Gram-stain-positive, non-spore-forming, non-motile, rod-shaped, and catalase-negative. Growth occurred at pH 3.5-5.5, with optimal growth at pH 4.5-5.0. The cells formed colonies on a solid MRS medium with 20% (w/v) sucrose and 0.8% (w/v) gellan gum under anaerobic conditions. The bacterium was able to grow on up to 50% (w/v) sucrose but not on d-glucose. Moreover, 16S rRNA gene sequence analysis revealed that the strain was most closely related to Apilactobacillus ozensis (93.1% sequence similarity). The values of average nucleotide identity, digital DNA-DNA hybridization, average amino acid sequence identity, and amino acid identity of conserved genes were calculated between the isolated strain (type strain is WR16-4T = NBRC 115064T = DSM 112857T) and its phylogenetically closest type strains. The average nucleotide identity values (73.36-78.28%) and DNA-DNA hybridization values (16.3-32.9%) were significantly lower than the threshold values for species boundaries. The average amino acid sequence identity values (53.96-60.88%) were significantly below the threshold boundary of genus demarcation (68%). The amino acid identity of conserved genes values compared to strain WR16-4T were the genera Apilactobacillus, Nicoliella spurrieriana SGEP1_A5T, Acetilactobacillus jinshanensis HSLZ-75T, and Fructilactobacillus were 62.51-63.79%, 62.87%, 62.03%, and 58.00-61.04%, respectively. The 16S rRNA gene and core genome phylogenetic trees suggested that this novel strain was most closely related to the type strain of A. jinshanensis HSLZ-75T. Based on the physiological, morphological, and phenotypical characteristics of strain WR16-4T, we propose its classification as a novel genus, Philodulcilactobacillus myokoensis gen. nov., sp. nov.
Collapse
Affiliation(s)
- Tomoaki Kouya
- Department of Materials Chemistry and Bioengineering, National Institute of Technology, Oyama College, Oyama, Tochigi, Japan
| | | | - Shota Ohashi
- Department of Materials Chemistry and Bioengineering, National Institute of Technology, Oyama College, Oyama, Tochigi, Japan
| | - Ryota Kumakubo
- Department of Materials Chemistry and Bioengineering, National Institute of Technology, Oyama College, Oyama, Tochigi, Japan
| | - Takeshi Yamazaki
- Department of Materials Chemistry and Bioengineering, National Institute of Technology, Oyama College, Oyama, Tochigi, Japan
| | | |
Collapse
|
7
|
Gu Y, Han W, Wang Y, Liang D, Gao J, Zhong Y, Zhao S, Wang S. Xylocopa caerulea and Xylocopa auripennis harbor a homologous gut microbiome related to that of eusocial bees. Front Microbiol 2023; 14:1124964. [PMID: 37266019 PMCID: PMC10229870 DOI: 10.3389/fmicb.2023.1124964] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 04/20/2023] [Indexed: 06/03/2023] Open
Abstract
Background Eusocial bees, such as bumblebees and honey bees, harbor host-specific gut microbiota through their social behaviors. Conversely, the gut microbiota of solitary bees is erratic owing to their lack of eusocial activities. Carpenter bees (genus Xylocopa) are long-lived bees that do not exhibit advanced eusociality like honey bees. However, they often compete for nests to reproduce. Xylocopa caerulea and Xylocopa auripennis are important pollinators of wild plants on Hainan Island. Whether they have host-specific bacteria in their guts similar to eusocial bees remains unknown. Methods We targeted the bacterial 16S rRNA V3-V4 region to investigate the diversity of bacterial symbionts in the fore-midgut and hindgut of two carpenter bees, X. caerulea and X. auripennis. Results A maximum of 4,429 unique amplicon sequence variants (ASVs) were detected from all samples, belonging to 10 different phyla. X. caerulea and X. auripennis shared similar bacterial community profiles, with Lactobacillaceae, Bifidobacteriaceae, and Orbaceae being dominant in their entire guts. X. caerulea and X. auripennis harbor a highly conserved core set of bacteria, including the genera Candidatus Schmidhempelia and Bombiscardovia. These two bacterial taxa from carpenter bees are closely related to those isolated from bumblebees. The LEfSe analysis showed that Lactobacillaceae, Bifidobacteriaceae, and the genus Bombilactobacillus were significantly enriched in the hindguts of both carpenter bees. Functional prediction suggested that the most enriched pathways were involved in carbohydrate and lipid metabolism. Conclusions Our results revealed the structure of the gut microbiota in two carpenter bees and confirmed the presence of some core bacterial taxa that were previously only found in the guts of social bees.
Collapse
Affiliation(s)
- Yifan Gu
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Sanya Institute of China Agricultural University, Sanya, China
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Wensu Han
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Bee Industry Technology Research Center, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Yuquan Wang
- College of Plant Protection, Hainan University, Haikou, China
| | - Danlei Liang
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Jinglin Gao
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Bee Industry Technology Research Center, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Yihai Zhong
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Bee Industry Technology Research Center, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Shan Zhao
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Bee Industry Technology Research Center, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Shijie Wang
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Bee Industry Technology Research Center, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| |
Collapse
|
8
|
Hammer TJ, Kueneman J, Argueta-Guzmán M, McFrederick QS, Grant L, Wcislo W, Buchmann S, Danforth BN. Bee breweries: The unusually fermentative, lactobacilli-dominated brood cell microbiomes of cellophane bees. Front Microbiol 2023; 14:1114849. [PMID: 37089560 PMCID: PMC10113673 DOI: 10.3389/fmicb.2023.1114849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Accepted: 03/13/2023] [Indexed: 04/09/2023] Open
Abstract
Pathogens and parasites of solitary bees have been studied for decades, but the microbiome as a whole is poorly understood for most taxa. Comparative analyses of microbiome features such as composition, abundance, and specificity, can shed light on bee ecology and the evolution of host–microbe interactions. Here we study microbiomes of ground-nesting cellophane bees (Colletidae: Diphaglossinae). From a microbial point of view, the diphaglossine genus Ptiloglossa is particularly remarkable: their larval provisions are liquid and smell consistently of fermentation. We sampled larval provisions and various life stages from wild nests of Ptiloglossa arizonensis and two species of closely related genera: Caupolicana yarrowi and Crawfordapis luctuosa. We also sampled nectar collected by P. arizonensis. Using 16S rRNA gene sequencing, we find that larval provisions of all three bee species are near-monocultures of lactobacilli. Nectar communities are more diverse, suggesting ecological filtering. Shotgun metagenomic and phylogenetic data indicate that Ptiloglossa culture multiple species and strains of Apilactobacillus, which circulate among bees and flowers. Larval lactobacilli disappear before pupation, and hence are likely not vertically transmitted, but rather reacquired from flowers as adults. Thus, brood cell microbiomes are qualitatively similar between diphaglossine bees and other solitary bees: lactobacilli-dominated, environmentally acquired, and non-species-specific. However, shotgun metagenomes provide evidence of a shift in bacterial abundance. As compared with several other bee species, Ptiloglossa have much higher ratios of bacterial to plant biomass in larval provisions, matching the unusually fermentative smell of their brood cells. Overall, Ptiloglossa illustrate a path by which hosts can evolve quantitatively novel symbioses: not by acquiring or domesticating novel symbionts, but by altering the microenvironment to favor growth of already widespread and generalist microbes.
Collapse
Affiliation(s)
- Tobin J. Hammer
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA, United States
- *Correspondence: Tobin J. Hammer,
| | - Jordan Kueneman
- Department of Entomology, Cornell University, Ithaca, NY, United States
- Smithsonian Tropical Research Institute, Panama City, Panama
| | - Magda Argueta-Guzmán
- Department of Entomology, University of California, Riverside, Riverside, CA, United States
| | - Quinn S. McFrederick
- Department of Entomology, University of California, Riverside, Riverside, CA, United States
| | - Lady Grant
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, United States
| | - William Wcislo
- Smithsonian Tropical Research Institute, Panama City, Panama
| | - Stephen Buchmann
- Department of Entomology, The University of Arizona, Tucson, AZ, United States
- Department of Ecology and Evolutionary Biology, The University of Arizona, Tucson, AZ, United States
| | - Bryan N. Danforth
- Department of Entomology, Cornell University, Ithaca, NY, United States
| |
Collapse
|
9
|
Handy MY, Sbardellati DL, Yu M, Saleh NW, Ostwald MM, Vannette RL. Incipiently social carpenter bees (Xylocopa) host distinctive gut bacterial communities and display geographical structure as revealed by full-length PacBio 16S rRNA sequencing. Mol Ecol 2023; 32:1530-1543. [PMID: 36239475 DOI: 10.1111/mec.16736] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 09/14/2022] [Accepted: 09/28/2022] [Indexed: 11/27/2022]
Abstract
The gut microbiota of bees affects nutrition, immunity and host fitness, yet the roles of diet, sociality and geographical variation in determining microbiome structure, including variant-level diversity and relatedness, remain poorly understood. Here, we use full-length 16S rRNA amplicon sequencing to compare the crop and gut microbiomes of two incipiently social carpenter bee species, Xylocopa sonorina and Xylocopa tabaniformis, from multiple geographical sites within each species' range. We found that Xylocopa species share a set of core taxa consisting of Bombilactobacillus, Bombiscardovia and Lactobacillus, found in >95% of all individual bees sampled, and Gilliamella and Apibacter were also detected in the gut of both species with high frequency. The crop bacterial community of X. sonorina comprised nearly entirely Apilactobacillus with occasionally abundant nectar bacteria. Despite sharing core taxa, Xylocopa species' microbiomes were distinguished by multiple bacterial lineages, including species-specific variants of core taxa. The use of long-read amplicons revealed otherwise cryptic species and population-level differentiation in core microbiome members, which was masked when a shorter fragment of the 16S rRNA (V4) was considered. Of the core taxa, Bombilactobacillus and Bombiscardovia exhibited differentiation in amplicon sequence variants among bee populations, but this was lacking in Lactobacillus, suggesting that some bacterial genera in the gut may be structured by different processes. We conclude that these Xylocopa species host a distinctive microbiome, similar to that of previously characterized social corbiculate apids, which suggests that further investigation to understand the evolution of the bee microbiome and its drivers is warranted.
Collapse
Affiliation(s)
- Madeline Y Handy
- Department of Entomology and Nematology, University of California Davis, Davis, California, USA
| | - Dino L Sbardellati
- Microbiology Graduate Group, University of California Davis, Davis, California, USA
| | - Michael Yu
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, USA
| | - Nicholas W Saleh
- Entomology and Nematology Department, Fort Lauderdale Research and Education Center, University of Florida, Davie, Florida, USA
| | | | - Rachel L Vannette
- Department of Entomology and Nematology, University of California Davis, Davis, California, USA
| |
Collapse
|
10
|
Oliphant SA, Watson-Haigh NS, Sumby KM, Gardner JM, Jiranek V. Fructilactobacillus cliffordii sp. nov. , Fructilactobacillus hinvesii sp. nov., Fructilactobacillus myrtifloralis sp. nov., Fructilactobacillus carniphilus sp. nov. and Fructobacillus americanaquae sp. nov., five novel lactic acid bacteria isolated from insects or flowers of Kangaroo Island, South Australia. Int J Syst Evol Microbiol 2023; 73. [PMID: 36795096 DOI: 10.1099/ijsem.0.005730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023] Open
Abstract
Six strains, KI11_D11T, KI4_B1, KI11_C11T, KI16_H9T, KI4_A6T and KI3_B9T, were isolated from insects and flowers on Kangaroo Island, South Australia. On the basis of 16S rRNA gene phylogeny, strains KI11_D11T, KI4_B1, KI11_C11T, KI16_H9T, KI4_A6T were found to be closely related to Fructilactobacillus ixorae Ru20-1T. Due to the lack of a whole genome sequence for this species, whole genome sequencing of Fructilactobacillus ixorae Ru20-1T was undertaken. KI3_B9T was found to be closely related to Fructobacillus tropaeoli F214-1T. Utilizing core gene phylogenetics and whole genome analyses, such as determination of AAI, ANI and dDDH, we propose that these six isolates represent five novel species with the names Fructilactobacillus cliffordii (KI11_D11T= LMG 32130T = NBRC 114988T), Fructilactobacillus hinvesii (KI11_C11T = LMG 32129T = NBRC 114987T), Fructilactobacillus myrtifloralis (KI16_H9T= LMG 32131T = NBRC 114989T) Fructilactobacillus carniphilus (KI4_A6T = LMG 32127T = NBRC 114985T) and Fructobacillus americanaquae (KI3_B9T = LMG 32124T = NBRC 114983T). Chemotaxonomic analyses detected no fructophilic characters for these strains of member of the genus Fructilactobacillus. KI3_B9T was found to be obligately fructophilic, similarly to its phylogenetic neighbours in the genus Fructobacillus. This study represents the first isolation, to our knowledge, of novel species in the family Lactobacillaceae from the Australian wild.
Collapse
Affiliation(s)
- Scott A Oliphant
- Department of Wine Science, School of Agriculture, Food & Wine, The University of Adelaide, Waite Campus, Adelaide, South Australia, 5064, Australia
| | - Nathan S Watson-Haigh
- South Australian Genomics Centre, SAHMRI, North Terrace, Adelaide, SA 5000, Australia.,Australian Genome Research Facility, Victorian Comprehensive Cancer Centre, Melbourne, VIC 3000, Australia
| | - Krista M Sumby
- Department of Wine Science, School of Agriculture, Food & Wine, The University of Adelaide, Waite Campus, Adelaide, South Australia, 5064, Australia.,Australian Research Council Training Centre for Innovative Wine Production, Glen Osmond, South Australia, 5064, Australia
| | - Jennifer M Gardner
- Department of Wine Science, School of Agriculture, Food & Wine, The University of Adelaide, Waite Campus, Adelaide, South Australia, 5064, Australia
| | - Vladimir Jiranek
- Department of Wine Science, School of Agriculture, Food & Wine, The University of Adelaide, Waite Campus, Adelaide, South Australia, 5064, Australia.,Australian Research Council Training Centre for Innovative Wine Production, Glen Osmond, South Australia, 5064, Australia
| |
Collapse
|
11
|
Oliphant SA, Watson-Haigh NS, Sumby KM, Gardner J, Groom S, Jiranek V. Apilactobacillus apisilvae sp. nov., Nicolia spurrieriana gen. nov. sp. nov., Bombilactobacillus folatiphilus sp. nov. and Bombilactobacillus thymidiniphilus sp. nov., four new lactic acid bacterial isolates from stingless bees Tetragonula carbonaria and Austroplebeia australis. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Four strains, SG5_A10T, SGEP1_A5T, SG4_D2T, and SG4_A1T, were isolated from the honey or homogenate of Australian stingless bee species Tetragonula carbonaria and Austroplebeia australis. Based on 16S rRNA gene phylogeny, core gene phylogenetics, whole genome analyses such as determination of amino acid identity (AAI), cAAI of conserved genes, average nucleotide identity (ANI), and digital DNA–DNA hybridization (dDDH), chemotaxonomic analyses, and the novel isolation sources and unique geography, we propose three new species and one genus with the names Apilactobacillus apisilvae sp. nov. (SG5_A10T = LMG 32133T = NBRC 114991T), Bombilactobacillus thymidiniphilus sp. nov. (SG4_A1T = LMG 32125T = NBRC 114984T), Bombilactobacillus folatiphilus sp. nov. (SG4_D2T = LMG 32126T = NBRC 115004T) and Nicolia spurrieriana sp. nov. (SGEP1_A5T = LMG 32134T = NBRC 114992T). Three out of the four strains were found to be fructophilic, where SG5_A10T and SGEP1_A5T belong to obligately fructophilic lactic acid bacteria, and SG4_D2T representing a new type denoted here as kinetically fructophilic. This study represents the first published lactic acid bacterial species associated with the unique niche of Australian stingless bees.
Collapse
Affiliation(s)
- Scott A. Oliphant
- Department of Wine Science, School of Agriculture, Food & Wine, The University of Adelaide, Waite Campus, Urrbrae, SA 5064, Australia
| | - Nathan S. Watson-Haigh
- Australian Genome Research Facility, Victorian Comprehensive Cancer Centre, Melbourne, VIC 3000, Australia
- South Australian Genomics Centre (SAGC), SAHMRI, Adelaide, SA 5000, Australia
| | - Krista M. Sumby
- Australian Research Council Training Centre for Innovative Wine Production, Glen Osmond, SA 5064, Australia
- Department of Wine Science, School of Agriculture, Food & Wine, The University of Adelaide, Waite Campus, Urrbrae, SA 5064, Australia
| | - Jennifer Gardner
- Department of Wine Science, School of Agriculture, Food & Wine, The University of Adelaide, Waite Campus, Urrbrae, SA 5064, Australia
| | - Scott Groom
- Department of Agricultural Science, School of Agriculture, Food & Wine, The University of Adelaide, Waite Campus, Urrbrae, SA 5064, Australia
| | - Vladimir Jiranek
- Australian Research Council Training Centre for Innovative Wine Production, Glen Osmond, SA 5064, Australia
- Department of Wine Science, School of Agriculture, Food & Wine, The University of Adelaide, Waite Campus, Urrbrae, SA 5064, Australia
| |
Collapse
|
12
|
Russell KA, McFrederick QS. Floral nectar microbial communities exhibit seasonal shifts associated with extreme heat: Potential implications for climate change and plant-pollinator interactions. Front Microbiol 2022; 13:931291. [PMID: 36090097 PMCID: PMC9453676 DOI: 10.3389/fmicb.2022.931291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 07/25/2022] [Indexed: 11/13/2022] Open
Abstract
Floral nectar contains vital nutrients for pollinators, including sugars, amino acids, proteins, and secondary compounds. As pollinators forage, they inoculate nectar with bacteria and fungi. These microbes can colonize nectaries and alter nectar properties, including volume and chemistry. Abiotic factors, such as temperature, can influence microbial community structure and nectar traits. Considering current climate change conditions, studying the effects of increased temperature on ecosystem processes like pollination is ever more important. In a manipulative field experiment, we used a passive-heating technique to increase the ambient temperature of a California native plant, Penstemon heterophyllus, to test the hypothesis that temperatures elevated an average of 0.5°C will affect nectar properties and nectar-inhabiting microbial communities. We found that passive-heat treatment did not affect nectar properties or microbial communities. Penstemon heterophyllus fruit set also was not affected by passive-heat treatments, and neither was capsule mass, however plants subjected to heat treatments produced significantly more seeds than control. Although we conducted pollinator surveys, no pollinators were recorded for the duration of our experiment. A naturally occurring extreme temperature event did, however, have large effects on nectar sugars and nectar-inhabiting microbial communities. The initially dominant Lactobacillus sp. was replaced by Sediminibacterium, while Mesorhizobium, and Acinetobacter persisted suggesting that extreme temperatures can interrupt nectar microbiome community assembly. Our study indicates that the quality and attractiveness of nectar under climate change conditions could have implications on plant-pollinator interactions.
Collapse
Affiliation(s)
| | - Quinn S. McFrederick
- Department of Entomology, University of California, Riverside, Riverside, CA, United States
| |
Collapse
|
13
|
Dharampal PS, Danforth BN, Steffan SA. Exosymbiotic microbes within fermented pollen provisions are as important for the development of solitary bees as the pollen itself. Ecol Evol 2022; 12:e8788. [PMID: 35414891 PMCID: PMC8986510 DOI: 10.1002/ece3.8788] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 03/11/2022] [Accepted: 03/14/2022] [Indexed: 11/26/2022] Open
Abstract
Developing bees derive significant benefits from the microbes present within their guts and fermenting pollen provisions. External microbial symbionts (exosymbionts) associated with larval diets may be particularly important for solitary bees that suffer reduced fitness when denied microbe-colonized pollen.To investigate whether this phenomenon is generalizable across foraging strategy, we examined the effects of exosymbiont presence/absence across two solitary bee species, a pollen specialist and generalist. Larvae from each species were reared on either microbe-rich natural or microbe-deficient sterilized pollen provisions allocated by a female forager belonging to their own species (conspecific-sourced pollen) or that of another species (heterospecific-sourced pollen). Our results reveal that the presence of pollen-associated microbes was critical for the survival of both the generalist and specialist larvae, regardless of whether the pollen was sourced from a conspecific or heterospecific forager.Given the positive effects of exosymbiotic microbes for larval fitness, we then examined if the magnitude of this benefit varied based on whether the microbes were provisioned by a conspecific forager (the mother bee) or a heterospecific forager. In this second study, generalist larvae were reared only on microbe-rich pollen provisions, but importantly, the sources (conspecific versus heterospecific) of the microbes and pollen were experimentally manipulated.Bee fitness metrics indicated that microbial and pollen sourcing both had significant impacts on larval performance, and the effect sizes of each were similar. Moreover, the effects of conspecific-sourced microbes and conspecific-sourced pollen were strongly positive, while that of heterospecific-sourced microbes and heterospecific-sourced pollen, strongly negative.Our findings imply that not only is the presence of exosymbionts critical for both specialist and generalist solitary bees, but more notably, that the composition of the specific microbial community within larval pollen provisions may be as critical for bee development as the composition of the pollen itself.
Collapse
Affiliation(s)
| | | | - Shawn A. Steffan
- Department of EntomologyUniversity of WisconsinMadisonWisconsinUSA
- USDA‐ARSVegetable Crops Research UnitMadisonWisconsinUSA
| |
Collapse
|
14
|
Abstract
Fructophilic lactic acid bacteria (FLAB) are heterofermentative and related to the genera Fructilactobacillus, Convivina, Leuconostoc, Oenococcus and Weissella. Although they generally prefer fructose above glucose, obligate heterofermentative species will ferment glucose in the presence of external electron acceptors such as pyruvate and fructose. Little is known about the presence of FLAB in the human gut, let alone probiotic properties. In this review we discuss the possible role FLAB may have in the human gastro-intestinal tract (GIT) and highlight the advantages and disadvantages these bacteria may have in individuals with a diet high in fructose.
Collapse
Affiliation(s)
- L M T Dicks
- Department of Microbiology, University of Stellenbosch, Matieland, Stellenbosch, 7602, South Africa
| | - A Endo
- Department of Food, Aroma and Cosmetic Chemistry, Tokyo University of Agriculture, Hokkaido 099-2493, Japan
| |
Collapse
|
15
|
Li TT, Gu CT. Lactobacillus huangpiensis sp. nov. and Lactobacillus laiwuensis sp. nov., isolated from the gut of honeybee (Apis mellifera). Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005237] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Four Gram-stain-positive bacterial strains were isolated from the gut of honeybee (Apis mellifera) in China. These strains were characterized using a polyphasic taxonomic approach. The data demonstrated that three of the four strains represented two novel species of the genus
Lactobacillus
, strains F306-1T and F551-2T were designated as the type strains. Results of 16S rRNA gene sequence analysis indicated that strains F306-1T, F447 and F551-2T were phylogenetically related to the type strains of
Lactobacillus kimbladii
and
Lactobacillus kullabergensis
, having 99.1–99.7 % 16S rRNA gene sequence (about 1400 bp) similarities. The phylogenetic tree based on concatenated pheS, rpoA, gyrB, hsp60, recA, rpoB and tuf sequences (4114 bp) and the phylogenomic tree based on whole genome sequences indicated that strains F306-1T and F447 were most closely related to
L. kullabergensis
Biut2NT, and strain F551-2T was most closely related to
L. kimbladii
Hma2NT. Strains F306-1T and F447 shared 99.9 % average nucleotide identity (ANI), 99.7 % digital DNA–DNA hybridization (dDDH) and 99.9 % average amino acid identity (AAI) values, indicating that they belong to the same species. Strain F306-1T exhibited the highest ANI (94.4 %), dDDH (56.7 %) and AAI (94.7 %) values to
L. kullabergensis
Biut2NT. Strain F551-2T had the highest ANI (94.0 %), dDDH (54.3 %) and AAI (95.8 %) values with
L. kimbladii
Hma2NT. Acid production from amygdalin, maltose, starch, gentiobiose and turanose, activity of esterase (C4) and α-glucosidase, growth with 3 % NaCl at 37 °C under strict anaerobic condition (on mMRS agar plates), and growth with 1–6% NaCl at 37 °C under aerobic condition (on mMRS agar plates supplemented with 0.05 % cysteine or with 1 % cysteine and 2 % fructose) could differentiate strains F306-1T and F447 from
L. kullabergensis
DSM 26262T. Acid production from d-glucose, arbutin and gentiobiose, growth with 3 % NaCl at 37 °C under strict anaerobic condition (on mMRS agar plates), and growth at 45 °C under strict anaerobic condition (on mMRS agar plates) could differentiate strain F551-2T from
L. kimbladii
DSM 26263T. Based upon the data obtained in the present study, two novel species, Lactobacillus huangpiensis sp. nov. and Lactobacillus laiwuensis sp. nov., are proposed and the type strains are F306-1T (=LMG 32144T=JCM 34361T=CCTCC AB 2020300T) and F551-2T (=JCM 34502T=CCTCC AB 2021027T), respectively.
Collapse
Affiliation(s)
- Ting Ting Li
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, PR China
| | - Chun Tao Gu
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, PR China
| |
Collapse
|
16
|
Abstract
Diet and gut microbiomes are intricately linked on both short and long timescales. Changes in diet can alter the microbiome, while microbes in turn allow hosts to access novel diets. Bees are wasps that switched to a vegetarian lifestyle, and the vast majority of bees feed on pollen and nectar. Some stingless bee species, however, also collect carrion, and a few have fully reverted to a necrophagous lifestyle, relying on carrion for protein and forgoing flower visitation altogether. These “vulture” bees belong to the corbiculate apid clade, which is known for its ancient association with a small group of core microbiome phylotypes. Here, we investigate the vulture bee microbiome, along with closely related facultatively necrophagous and obligately pollinivorous species, to understand how these diets interact with microbiome structure. Via deep sequencing of the 16S rRNA gene and subsequent community analyses, we find that vulture bees have lost some core microbes, retained others, and entered into novel associations with acidophilic microbes found in the environment and on carrion. The abundance of acidophilic bacteria suggests that an acidic gut is important for vulture bee nutrition and health, as has been found in other carrion-feeding animals. Facultatively necrophagous bees have more variable microbiomes than strictly pollinivorous bees, suggesting that bee diet may interact with microbiomes on both short and long timescales. Further study of vulture bees promises to provide rich insights into the role of the microbiome in extreme diet switches.
Collapse
|
17
|
Nowak A, Szczuka D, Górczyńska A, Motyl I, Kręgiel D. Characterization of Apis mellifera Gastrointestinal Microbiota and Lactic Acid Bacteria for Honeybee Protection-A Review. Cells 2021; 10:cells10030701. [PMID: 33809924 PMCID: PMC8004194 DOI: 10.3390/cells10030701] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/17/2021] [Accepted: 03/19/2021] [Indexed: 12/15/2022] Open
Abstract
Numerous honeybee (Apis mellifera) products, such as honey, propolis, and bee venom, are used in traditional medicine to prevent illness and promote healing. Therefore, this insect has a huge impact on humans’ way of life and the environment. While the population of A. mellifera is large, there is concern that widespread commercialization of beekeeping, combined with environmental pollution and the action of bee pathogens, has caused significant problems for the health of honeybee populations. One of the strategies to preserve the welfare of honeybees is to better understand and protect their natural microbiota. This paper provides a unique overview of the latest research on the features and functioning of A. mellifera. Honeybee microbiome analysis focuses on both the function and numerous factors affecting it. In addition, we present the characteristics of lactic acid bacteria (LAB) as an important part of the gut community and their special beneficial activities for honeybee health. The idea of probiotics for honeybees as a promising tool to improve their health is widely discussed. Knowledge of the natural gut microbiota provides an opportunity to create a broad strategy for honeybee vitality, including the development of modern probiotic preparations to use instead of conventional antibiotics, environmentally friendly biocides, and biological control agents.
Collapse
Affiliation(s)
- Adriana Nowak
- Department of Environmental Biotechnology, Lodz University of Technology, Wólczańska 171/173, 90-924 Łódź, Poland; (D.S.); (I.M.); (D.K.)
- Correspondence:
| | - Daria Szczuka
- Department of Environmental Biotechnology, Lodz University of Technology, Wólczańska 171/173, 90-924 Łódź, Poland; (D.S.); (I.M.); (D.K.)
| | - Anna Górczyńska
- Faculty of Law and Administration, University of Lodz, Kopcińskiego 8/12, 90-232 Łódź, Poland;
| | - Ilona Motyl
- Department of Environmental Biotechnology, Lodz University of Technology, Wólczańska 171/173, 90-924 Łódź, Poland; (D.S.); (I.M.); (D.K.)
| | - Dorota Kręgiel
- Department of Environmental Biotechnology, Lodz University of Technology, Wólczańska 171/173, 90-924 Łódź, Poland; (D.S.); (I.M.); (D.K.)
| |
Collapse
|
18
|
Maeno S, Nishimura H, Tanizawa Y, Dicks L, Arita M, Endo A. Unique niche-specific adaptation of fructophilic lactic acid bacteria and proposal of three Apilactobacillus species as novel members of the group. BMC Microbiol 2021; 21:41. [PMID: 33563209 PMCID: PMC7871557 DOI: 10.1186/s12866-021-02101-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 01/20/2021] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Fructophilic lactic acid bacteria (FLAB) found in D-fructose rich niches prefer D-fructose over D-glucose as a growth substrate. They need electron acceptors for growth on D-glucose. The organisms share carbohydrate metabolic properties. Fructobacillus spp., Apilactobacillus kunkeei, and Apilactobacillus apinorum are members of this unique group. Here we studied the fructophilic characteristics of recently described species Apilactobacillus micheneri, Apilactobacillus quenuiae, and Apilactobacillus timberlakei. RESULTS The three species prefer D-fructose over D-glucose and only metabolize D-glucose in the presence of electron acceptors. The genomic characteristics of the three species, i.e. small genomes and thus a low number of coding DNA sequences, few genes involved in carbohydrate transport and metabolism, and partial deletion of adhE gene, are characteristic of FLAB. The three species thus are novel members of FLAB. Reduction of genes involved in carbohydrate transport and metabolism in accordance with reduction of genome size were the common characteristics of the family Lactobacillaceae, but FLAB markedly reduced the gene numbers more than other species in the family. Pan-genome analysis of genes involved in metabolism displayed a lack of specific carbohydrate metabolic pathways in FLAB, leading to a unique cluster separation. CONCLUSIONS The present study expanded FLAB group. Fructose-rich environments have induced similar evolution in phylogenetically distant FLAB species. These are examples of convergent evolution of LAB.
Collapse
Affiliation(s)
- Shintaro Maeno
- Department of Food, Aroma and Cosmetic Chemistry, Tokyo University of Agriculture, Abashiri, Hokkaido, 099-2493, Japan
| | - Hiroya Nishimura
- Department of Food, Aroma and Cosmetic Chemistry, Tokyo University of Agriculture, Abashiri, Hokkaido, 099-2493, Japan
| | - Yasuhiro Tanizawa
- Department of Informatics, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Leon Dicks
- Department of Microbiology, University of Stellenbosch, Matieland, Stellenbosch, 7602, South Africa
| | - Masanori Arita
- Department of Informatics, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Akihito Endo
- Department of Food, Aroma and Cosmetic Chemistry, Tokyo University of Agriculture, Abashiri, Hokkaido, 099-2493, Japan.
| |
Collapse
|
19
|
Kapheim KM, Johnson MM, Jolley M. Composition and acquisition of the microbiome in solitary, ground-nesting alkali bees. Sci Rep 2021; 11:2993. [PMID: 33542351 PMCID: PMC7862682 DOI: 10.1038/s41598-021-82573-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 01/21/2021] [Indexed: 01/30/2023] Open
Abstract
Increasing evidence suggests the microbiome plays an important role in bee ecology and health. However, the relationship between bees and their bacterial symbionts has only been explored in a handful of species. We characterized the microbiome across the life cycle of solitary, ground-nesting alkali bees (Nomia melanderi). We find that feeding status is a major determinant of microbiome composition. The microbiome of feeding larvae was similar to that of pollen provisions, but the microbiome of post-feeding larvae (pre-pupae) was similar to that of the brood cell walls and newly-emerged females. Feeding larvae and pollen provisions had the lowest beta diversity, suggesting the composition of larval diet is highly uniform. Comparisons between lab-reared, newly-emerged, and nesting adult females suggest that the hindgut bacterial community is largely shaped by the external environment. However, we also identified taxa that are likely acquired in the nest or which increase or decrease in relative abundance with age. Although Lactobacillus micheneri was highly prevalent in pollen provisions, it was only detected in one lab-reared female, suggesting it is primarily acquired from environmental sources. These results provide the foundation for future research on metagenomic function and development of probiotics for these native pollinators.
Collapse
Affiliation(s)
- Karen M. Kapheim
- grid.53857.3c0000 0001 2185 8768Department of Biology, Utah State University, Logan, UT 84322 USA
| | - Makenna M. Johnson
- grid.53857.3c0000 0001 2185 8768Department of Biology, Utah State University, Logan, UT 84322 USA
| | - Maggi Jolley
- grid.53857.3c0000 0001 2185 8768Department of Biology, Utah State University, Logan, UT 84322 USA
| |
Collapse
|
20
|
Li F, Cheng CC, Zheng J, Liu J, Quevedo RM, Li J, Roos S, Gänzle MG, Walter J. Limosilactobacillus balticus sp. nov., Limosilactobacillus agrestis sp. nov., Limosilactobacillus albertensis sp. nov., Limosilactobacillus rudii sp. nov. and Limosilactobacillus fastidiosus sp. nov., five novel Limosilactobacillus species isolated from the vertebrate gastrointestinal tract, and proposal of six subspecies of Limosilactobacillus reuteri adapted to the gastrointestinal tract of specific vertebrate hosts. Int J Syst Evol Microbiol 2021; 71:004644. [PMID: 33533708 PMCID: PMC8346765 DOI: 10.1099/ijsem.0.004644] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 12/20/2020] [Indexed: 01/17/2023] Open
Abstract
Ten strains, BG-AF3-AT, pH52_RY, WF-MT5-AT, BG-MG3-A, Lr3000T, RRLNB_1_1, STM3_1T, STM2_1, WF-MO7-1T and WF-MA3-C, were isolated from intestinal or faecal samples of rodents, pheasant and primate. 16S rRNA gene analysis identified them as Limosilactobacillus reuteri. However, average nucleotide identity and digital DNA-DNA hybridization values based on whole genomes were below 95 and 70 %, respectively, and thus below the threshold levels for bacterial species delineation. Based on genomic, chemotaxonomic and morphological analyses, we propose five novel species with the names Limosilactobacillus balticus sp. nov. (type strain BG-AF3-AT=DSM 110574T=LMG 31633T), Limosilactobacillus agrestis sp. nov. (type strain WF-MT5-AT=DSM 110569T=LMG 31629T), Limosilactobacillus albertensis sp. nov. (type strain Lr3000T=DSM 110573T=LMG 31632T), Limosilactobacillus rudii sp. nov. (type strain STM3_1T=DSM 110572T=LMG 31631T) and Limosilactobacillus fastidiosus sp. nov. (type strain WF-MO7-1T=DSM 110576T=LMG 31630T). Core genome phylogeny and experimental evidence of host adaptation of strains of L. reuteri further provide a strong rationale to consider a number of distinct lineages within this species as subspecies. Here we propose six subspecies of L. reuteri: L. reuteri subsp. kinnaridis subsp. nov. (type strain AP3T=DSM 110703T=LMG 31724T), L. reuteri subsp. porcinus subsp. nov. (type strain 3c6T=DSM 110571T=LMG 31635T), L. reuteri subsp. murium subsp. nov. (type strain lpuph1T=DSM 110570T=LMG 31634T), L. reuteri subsp. reuteri subsp. nov. (type strain F 275T=DSM 20016T=ATCC 23272T), L. reuteri subsp. suis subsp. nov. (type strain 1063T=ATCC 53608T=LMG 31752T) and L. reuteri subsp. rodentium subsp. nov. (type strain 100-23T=DSM 17509T=CIP 109821T).
Collapse
Affiliation(s)
- Fuyong Li
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G 2E1, Canada
| | - Christopher C. Cheng
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, T6G 2E1, Canada
| | - Jinshui Zheng
- Huazhong Agricultural University, State Key Laboratory of Agricultural Microbiology, Hubei Key Laboratory of Agricultural Bioinformatics, Wuhan, Hubei, 430070, PR China
| | - Junhong Liu
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G 2E1, Canada
| | - Rodrigo Margain Quevedo
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G 2E1, Canada
| | - Junjie Li
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G 2E1, Canada
| | - Stefan Roos
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, 750 07, Sweden
| | - Michael G. Gänzle
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G 2E1, Canada
| | - Jens Walter
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G 2E1, Canada
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, T6G 2E1, Canada
- APC Microbiome Ireland, School of Microbiology, and Department of Medicine, University College Cork, Cork, T12 YT20, Ireland
| |
Collapse
|
21
|
Jung JY, Kang HK, Jin HM, Han SS, Kwon YC, Eun JJ, Kim SC, Seo MJ, Ryu BG, Chung EJ. Companilactobacillus pabuli sp. nov., a lactic acid bacterium isolated from animal feed. Int J Syst Evol Microbiol 2021; 71. [PMID: 33502298 DOI: 10.1099/ijsem.0.004670] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-positive, facultative anaerobic, catalase-negative, non-motile, non-spore-forming and rod-shaped lactic acid bacterium strain, denoted as NFFJ11T and isolated from total mixed fermentation feed in the Republic of Korea, was characterized through polyphasic approaches, including sequence analyses of the 16S rRNA gene and housekeeping genes (rpoA and pheS), determination of average nucleotide identity and in silico DNA-DNA hybridization, fatty acid methyl ester analysis, and phenotypic characterization. Phylogenetic analyses based on 16S rRNA, rpoA and pheS gene sequences revealed that strain NFFJ11T belonged to the genus Companilactobacillus. The 16S rRNA gene sequence of strain NFFJ11T exhibited high similarity to Companilactobacillus formosensis S215T (99.66 %), Companilactobacillus farciminis Rv4 naT (99.53 %), Companilactobacillus crustorum LMG 23699T (99.19 %), Companilactobacillus futsaii YM 0097T (99.06 %), Companilactobacillus zhachilii HBUAS52074T (98.86 %) and Companilactobacillus heilongiiangensis S4-3T (98.66 %). However, average nucleotide identity and in silico DNA-DNA hybridization values for these type strains were in the range of 79.90-92.93 % and 23.80-49.30 %, respectively, which offer evidence that strain NFFJ11T belongs to a novel species of the genus Companilactobacillus. The cell-wall peptidoglycan type was A4α (l-Lys-d-Asp) and the G+C content of the genomic DNA was 35.7 mol%. The main fatty acids of strain NFFJ11T were C18 : 1 ω9c (43.3 %), C16 : 0 (20.1 %) and summed feature 7 (18.3 %; comprising any combination of C19 : 1 ω7c, C19 : 1 ω6c and C19 : 0 cyclo ω10c). Through polyphasic taxonomic analysis, it was observed that strain NFFJ11T represents a novel species belonging to the genus Companilactobacillus, for which the name Companilactobacillus pabuli sp. nov. is proposed. The type strain is NFFJ11T (= KACC 21771T= JCM 34088T).
Collapse
Affiliation(s)
- Ji Young Jung
- Nakdonggang National Institute of Biological Resources, 137, Donam 2-gil, Sangju-si, Gyeongsangbuk-do 37242, Republic of Korea
| | - Hye Kyeong Kang
- Nakdonggang National Institute of Biological Resources, 137, Donam 2-gil, Sangju-si, Gyeongsangbuk-do 37242, Republic of Korea
| | - Hyun Mi Jin
- Nakdonggang National Institute of Biological Resources, 137, Donam 2-gil, Sangju-si, Gyeongsangbuk-do 37242, Republic of Korea
| | - Sang-Soo Han
- Nakdonggang National Institute of Biological Resources, 137, Donam 2-gil, Sangju-si, Gyeongsangbuk-do 37242, Republic of Korea
| | - Young Chul Kwon
- Nonghyup TMR agricultural Co., Ltd., 65, Ogwang 1-gil, Gongseong-myeon, Sangju-si, Gyeongsangbuk-do 37268, Republic of Korea
| | - Jong Jun Eun
- Nonghyup TMR agricultural Co., Ltd., 65, Ogwang 1-gil, Gongseong-myeon, Sangju-si, Gyeongsangbuk-do 37268, Republic of Korea
| | - Sang Cheol Kim
- Nakdonggang National Institute of Biological Resources, 137, Donam 2-gil, Sangju-si, Gyeongsangbuk-do 37242, Republic of Korea
| | - Min Jeong Seo
- Nakdonggang National Institute of Biological Resources, 137, Donam 2-gil, Sangju-si, Gyeongsangbuk-do 37242, Republic of Korea
| | - Byung-Gon Ryu
- Nakdonggang National Institute of Biological Resources, 137, Donam 2-gil, Sangju-si, Gyeongsangbuk-do 37242, Republic of Korea
| | - Eu Jin Chung
- Nakdonggang National Institute of Biological Resources, 137, Donam 2-gil, Sangju-si, Gyeongsangbuk-do 37242, Republic of Korea
| |
Collapse
|
22
|
Geldert C, Abdo Z, Stewart JE, H S A. Dietary supplementation with phytochemicals improves diversity and abundance of honey bee gut microbiota. J Appl Microbiol 2020; 130:1705-1720. [PMID: 33058297 DOI: 10.1111/jam.14897] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 09/21/2020] [Accepted: 10/10/2020] [Indexed: 12/20/2022]
Abstract
AIM Determine the impact of beneficial phytochemicals on diversity and abundance of the gut microbiome in the honey bee (Apis mellifera). METHODS AND RESULTS Eight-day-old honey bee workers were fed 25 ppm of phytochemical (caffeine, gallic acid, p-coumaric acid or kaempferol) in 20% sucrose. Guts of bees collected at 3 and 6 days were excised and subjected to next-generation sequencing for bacterial 16S and fungal ITS regions. Although phytochemical supplementation fostered gut microbial diversity and abundance, the patterns differed between phytochemicals and there was a temporal stabilization of the bacterial community. While bacterial and fungal communities responded differently, all phytochemical treatments displayed increased abundance of the most represented bacterial genera, Snodgrassella sp. and Lactobacillus sp. CONCLUSIONS Phytochemical supplementation improves gut microbial diversity and abundance, reiterating the need for diverse habitats that provide bees with access to pollen and nectar rich in these micronutrients. Diverse gut microbiota can provide a strong line of defense for bees against biotic stressors while improving worker bee lifespan. SIGNIFICANCE AND IMPACT OF THE STUDY This is the first report on the impact of phytochemical supplementation on gut microbiota in honey bees and these findings have implications for strategic hive management through standardization of effective phytochemical and probiotic feed supplements.
Collapse
Affiliation(s)
- C Geldert
- College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Z Abdo
- College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - J E Stewart
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, USA
| | - Arathi H S
- USDA/ARS, WRRC Invasive Species and Pollinator Health Research Unit, Davis, CA, USA
| |
Collapse
|
23
|
Diet Breadth Affects Bacterial Identity but Not Diversity in the Pollen Provisions of Closely Related Polylectic and Oligolectic Bees. INSECTS 2020; 11:insects11090645. [PMID: 32962223 PMCID: PMC7564857 DOI: 10.3390/insects11090645] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 09/02/2020] [Accepted: 09/17/2020] [Indexed: 12/18/2022]
Abstract
Simple Summary Solitary bees are important pollinators in managed and wild ecosystems. Across the bee phylogeny, bees may forage on a single species of plant, few plant species, or a broad diversity of plants. During foraging, these bees are often exposed to microbes, and in turn, may inoculate the brood cell and pollen provision of their offspring with these microbes. It is becoming evident that pollen-associated microbes are important to bee health, but it is not known how diet breadth impacts bees’ exposure to microbes. In this study, we collected pollen provisions from the bees Osmia lignaria and Osmia ribifloris at four different sites, then characterized the bacterial populations within the pollen provisions with 16S rRNA gene sequencing. We found that diet breadth did not have large effects on the bacteria found in the pollen provisions. We also note that the bacterial communities were slightly different between bee species and site, and there was minimal overlap in the unique bacterial variants between sites and bee species too. Our research supports the hypothesis of environmental transmission for solitary bee microbes, and we suggest future studies investigate the impacts of microbes on larval health. Abstract Mounting evidence suggests that microbes found in the pollen provisions of wild and solitary bees are important drivers of larval development. As these microbes are also known to be transmitted via the environment, most likely from flowers, the diet breadth of a bee may affect the diversity and identity of the microbes that occur in its pollen provisions. Here, we tested the hypothesis that, due to the importance of floral transmission of microbes, diet breadth affects pollen provision microbial community composition. We collected pollen provisions at four sites from the polylectic bee Osmia lignaria and the oligolectic bee Osmia ribifloris. We used high-throughput sequencing of the bacterial 16S rRNA gene to characterize the bacteria found in these provisions. We found minimal overlap in the specific bacterial variants in pollen provisions across the host species, even when the bees were constrained to foraging from the same flowers in cages at one site. Similarly, there was minimal overlap in the specific bacterial variants across sites, even within the same host species. Together, these findings highlight the importance of environmental transmission and host specific sorting influenced by diet breadth for microbes found in pollen provisions. Future studies addressing the functional consequences of this filtering, along with tests for differences between more species of oligoletic and polylectic bees will provide rich insights into the microbial ecology of solitary bees.
Collapse
|
24
|
Li TT, Liu DD, Fu ML, Gu CT. Proposal of Lactobacillus kosoi Chiou et al. 2018 as a later heterotypic synonym of Lactobacillus micheneri McFrederick et al. 2018, elevation of Lactobacillus plantarum subsp. argentoratensis to the species level as Lactobacillus argentoratensis sp. nov., and Lactobacillus zhaodongensis sp. nov., isolated from traditional Chinese pickle and the intestinal tract of a honey bee ( Apis mellifera). Int J Syst Evol Microbiol 2020; 70:3123-3133. [PMID: 32250238 DOI: 10.1099/ijsem.0.004141] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Lactobacillus kosoi Chiou et al. 2018 and Lactobacillus micheneri McFrederick et al. 2018 are closely related, and they share 100 % 16S rRNA gene sequence similarity, 99.6 % pheS gene sequence similarity, 100 % rpoA gene sequence similarity, 97.3 % average nucleotide identity (ANI) value and 76.6 % in silico DNA-DNA hybridization (isDDH) value, indicating that they represent the same species. Fatty acid methyl esters (FAME) analysis and phenotypic characterization also indicated that L. kosoi and L. micheneri are very similar. We propose L. kosoi Chiou et al. 2018 as a later heterotypic synonym of L. micheneri McFrederick et al. 2018. The taxonomic position of Lactobacillus plantarum subsp. argentoratensis in the L. plantarum group was re-examined using a polyphasic approach, including sequence analyses of 16S rRNA, pheS, rpoA and recA genes, average nucleotide identity analysis, in silico DNA-DNA hybridization, fatty acid methyl ester analysis and phenotypic characterization. Results of 16S rRNA gene sequence analysis indicated that L. plantarum subsp. argentoratensis was closely related to L. plantarum subsp. plantarum, L. pentosus and L. paraplantarum in the L. plantarum group, sharing 99.6-99.7 % 16S rRNA gene sequence similarities. Results of pheS, rpoA and recA gene sequence analyses indicated that L. plantarum subsp. argentoratensis was most closely related to L. plantarum subsp. plantarum, having 91.8 % pheS gene sequence similarity, 98.9 % rpoA gene sequence similarity and 93.1 % recA gene sequence similarity. L. plantarum subsp. argentoratensis DSM 16365T shared 95.6 % ANI value and 62.9 % isDDH value with L. plantarum subsp. plantarum ATCC 14917T. The low isDDH value confirmed that L. plantarum subsp. argentoratensis and L. plantarum subsp. plantarum represent two different species, rather than two different subspecies in the L. plantarum group. On the basis of the data from polyphasic characterization obtained in the present study and in previous studies, L. plantarum subsp. argentoratensis is elevated to the species level and represents a novel species of the genus Lactobacillus, for which the name Lactobacillus argentoratensis sp. nov. is proposed and the type strain is DKO 22T (=CIP 108320T=DSM 16365T=JCM 16169T). Two novel Gram-stain-positive bacterial strains, designated 1206-1T and F027-1-2, were isolated from traditional pickle in Heilongjiang Province, PR China, and from the intestinal tract of a honey bee (Apis mellifera) in Hubei Province, PR China, respectively. The two bacteria were characterized by a polyphasic approach, including 16S rRNA gene sequence analysis, pheS gene sequence analysis, rpoA gene sequence analysis, fatty acid methyl ester analysis, average nucleotide identity analysis, in silico DNA-DNA hybridization analysis and an analysis of phenotypic features. The results of 16S rRNA gene sequence analysis indicated that strains 1206-1T and F027-1-2 were distantly related to Lactobacillus sharpeae, Lactobacillus hulanensis, Lactobacillus songhuajiangensis, Lactobacillus pantheris, Lactobacillus thailandensis, Lactobacillus camelliae, Lactobacillus jixianensis, Lactobacillus nasuensis, Lactobacillus baoqingensis, Lactobacillus manihotivorans and Lactobacillus porcinae. Strain 1206-1T exhibited 94.2-96.4 % 16S rRNA gene sequence similarities, 69.5-83.3 % pheS gene sequence similarities and 73.1-90.3 % rpoA gene sequence similarities to type strains of phylogenetically related species. ANI and isDDH values between strain 1206-1T and the type strains of phylogenetically related species were 52.7-73.7 % and 21.1-30.1 %, respectively. On the basis of the data obtained in the present study, a novel species, Lactobacillus zhaodongensis sp. nov. is proposed and the type strain is 1206-1T (=CCM 8981T=CCTCC AB 2019200T=LMG 31620T).
Collapse
Affiliation(s)
- Ting Ting Li
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, PR China
| | - Dan Dan Liu
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, PR China
| | - Mei Ling Fu
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, PR China
| | - Chun Tao Gu
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, PR China
| |
Collapse
|
25
|
Zheng J, Wittouck S, Salvetti E, Franz CMAP, Harris HMB, Mattarelli P, O'Toole PW, Pot B, Vandamme P, Walter J, Watanabe K, Wuyts S, Felis GE, Gänzle MG, Lebeer S. A taxonomic note on the genus Lactobacillus: Description of 23 novel genera, emended description of the genus Lactobacillus Beijerinck 1901, and union of Lactobacillaceae and Leuconostocaceae. Int J Syst Evol Microbiol 2020; 70:2782-2858. [PMID: 32293557 DOI: 10.1099/ijsem.0.004107] [Citation(s) in RCA: 1543] [Impact Index Per Article: 385.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The genus Lactobacillus comprises 261 species (at March 2020) that are extremely diverse at phenotypic, ecological and genotypic levels. This study evaluated the taxonomy of Lactobacillaceae and Leuconostocaceae on the basis of whole genome sequences. Parameters that were evaluated included core genome phylogeny, (conserved) pairwise average amino acid identity, clade-specific signature genes, physiological criteria and the ecology of the organisms. Based on this polyphasic approach, we propose reclassification of the genus Lactobacillus into 25 genera including the emended genus Lactobacillus, which includes host-adapted organisms that have been referred to as the Lactobacillus delbrueckii group, Paralactobacillus and 23 novel genera for which the names Holzapfelia, Amylolactobacillus, Bombilactobacillus, Companilactobacillus, Lapidilactobacillus, Agrilactobacillus, Schleiferilactobacillus, Loigolactobacilus, Lacticaseibacillus, Latilactobacillus, Dellaglioa, Liquorilactobacillus, Ligilactobacillus, Lactiplantibacillus, Furfurilactobacillus, Paucilactobacillus, Limosilactobacillus, Fructilactobacillus, Acetilactobacillus, Apilactobacillus, Levilactobacillus, Secundilactobacillus and Lentilactobacillus are proposed. We also propose to emend the description of the family Lactobacillaceae to include all genera that were previously included in families Lactobacillaceae and Leuconostocaceae. The generic term 'lactobacilli' will remain useful to designate all organisms that were classified as Lactobacillaceae until 2020. This reclassification reflects the phylogenetic position of the micro-organisms, and groups lactobacilli into robust clades with shared ecological and metabolic properties, as exemplified for the emended genus Lactobacillus encompassing species adapted to vertebrates (such as Lactobacillus delbrueckii, Lactobacillus iners, Lactobacillus crispatus, Lactobacillus jensensii, Lactobacillus johnsonii and Lactobacillus acidophilus) or invertebrates (such as Lactobacillus apis and Lactobacillus bombicola).
Collapse
Affiliation(s)
- Jinshui Zheng
- Huazhong Agricultural University, State Key Laboratory of Agricultural Microbiology, Hubei Key Laboratory of Agricultural Bioinformatics, Wuhan, Hubei, PR China
| | - Stijn Wittouck
- Research Group Environmental Ecology and Applied Microbiology, Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | - Elisa Salvetti
- Dept. of Biotechnology, University of Verona, Verona, Italy
| | - Charles M A P Franz
- Max Rubner-Institut, Department of Microbiology and Biotechnology, Kiel, Germany
| | - Hugh M B Harris
- School of Microbiology & APC Microbiome Ireland, University College Cork, Co. Cork, Ireland
| | - Paola Mattarelli
- University of Bologna, Dept. of Agricultural and Food Sciences, Bologna, Italy
| | - Paul W O'Toole
- School of Microbiology & APC Microbiome Ireland, University College Cork, Co. Cork, Ireland
| | - Bruno Pot
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Vrije Universiteit Brussel, Brussels, Belgium
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Jens Walter
- Department of Biological Sciences, University of Alberta, Edmonton, Canada.,Department of Agricultural, Food & Nutritional Science, University of Alberta, Edmonton, Canada
| | - Koichi Watanabe
- Food Industry Research and Development Institute, Bioresource Collection and Research Center, Hsinchu, Taiwan, ROC.,National Taiwan University, Dept. of Animal Science and Technology, Taipei, Taiwan, ROC
| | - Sander Wuyts
- Research Group Environmental Ecology and Applied Microbiology, Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | | | - Michael G Gänzle
- Hubei University of Technology, College of Bioengineering and Food Science, Wuhan, Hubei, PR China.,Department of Agricultural, Food & Nutritional Science, University of Alberta, Edmonton, Canada
| | - Sarah Lebeer
- Research Group Environmental Ecology and Applied Microbiology, Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| |
Collapse
|
26
|
Comparative genomics of Lactobacillus species as bee symbionts and description of Lactobacillus bombintestini sp. nov., isolated from the gut of Bombus ignitus. J Microbiol 2020; 58:445-455. [PMID: 32222941 DOI: 10.1007/s12275-020-9596-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 02/20/2020] [Accepted: 02/21/2020] [Indexed: 12/18/2022]
Abstract
The Lactobacillus genus is widely used for fermentation of plant materials and dairy products. These species are typically found in highly specialized environments, with the bee gut serving as one of the niche locations in which Lactobacillus is detected. Lactobacillus species isolated from the bee gut and bee-related habitats were phylogenetically classified into three distinct groups, Lactobacillus kunkeei, Firm-4, and Firm-5. The L. kunkeei group was clearly differentiated from other members of the Lactobacillus buchneri group isolated from non-bee habitats. In comparison with non-bee members of the L. buchneri group, three bee-symbiotic Lactobacillus groups had a small-sized genome with low G + C content and showed a sharp reduction in the number of genes involved in energy production, carbohydrate transport and metabolism, and amino acid transport and metabolism. In addition, all three groups lacked the mutY gene, which encodes A/G-specific adenine glycosylase. The phylogenetic dendrogram based on the presence or absence of 1,199 functional genes indicated that these bee-symbiotic groups experienced convergent evolution. The occurrence of convergent evolution is thought to stem from the three bee-symbiotic groups sharing a similar habitat, i.e., the bee gut. The causative factor underlying genomic reduction was postulated to be mutY, which was absent in all three groups. Here, a novel strain, BHWM-4T, isolated from the gut of Bombus ignites was studied using polyphasic taxonomy and classified as a new member of the L. kunkeei group. The strain was Gram-positive, facultative anaerobic, and rod-shaped. The 16S ribosomal RNA gene sequence and genome analysis revealed that strain BHWM-4T was clustered into the L. kunkeei group, forming a compact cluster with L. kunkeei and Lactobacillus apinorum. Biochemical, chemotaxonomic, and genotypic data of strain BHWM-4T supports the proposal of a novel species, Lactobacillus bombintestini sp. nov., whose type strain is BHWM-4T (= KACC 19317 = NBRC 113067T).
Collapse
|
27
|
Vuong HQ, McFrederick QS. Comparative Genomics of Wild Bee and Flower Isolated Lactobacillus Reveals Potential Adaptation to the Bee Host. Genome Biol Evol 2020; 11:2151-2161. [PMID: 31243442 PMCID: PMC6685495 DOI: 10.1093/gbe/evz136] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/24/2019] [Indexed: 01/18/2023] Open
Abstract
Symbiosis with bacteria is common across insects, resulting in adaptive host phenotypes. The recently described bacterial symbionts Lactobacillus micheneri, Lactobacillus timberlakei, and Lactobacillus quenuiae are found in wild bee pollen provisions, bee guts, and flowers but have small genomes in comparison to other lactobacilli. We sequenced, assembled, and analyzed 27 new L. micheneri clade genomes to identify their possible ecological functions in flower and bee hosts. We determined possible key functions for the L. micheneri clade by identifying genes under positive selection, balancing selection, genes gained or lost, and population structure. A host adherence factor shows signatures of positive selection, whereas other orthologous copies are variable within the L. micheneri clade. The host adherence factors serve as strong evidence that these lactobacilli are adapted to animal hosts as their targets are found in the digestive tract of insects. Next, the L. micheneri clade is adapted toward a nutrient-rich environment, corroborating observations of where L. micheneri is most abundant. Additionally, genes involved in osmotolerance, pH tolerance, temperature resistance, detoxification, and oxidative stress response show signatures of selection that allow these bacteria to thrive in pollen and nectar masses in bee nests and in the bee gut. Altogether, these findings not only suggest that the L. micheneri clade is primarily adapted to the wild bee gut but also exhibit genomic features that would be beneficial to survival in flowers.
Collapse
Affiliation(s)
- Hoang Q Vuong
- Department of Entomology, University California Riverside.,Department of Plant Pathology and Microbiology, University California Riverside
| | | |
Collapse
|
28
|
Meng J, Jin D, Yang J, Lai XH, Pu J, Zhu W, Huang Y, Liang H, Lu S. Lactobacillus xujianguonis sp. nov., isolated from faeces of Marmota himalayana. Int J Syst Evol Microbiol 2020; 70:11-15. [PMID: 31560297 DOI: 10.1099/ijsem.0.003598] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two novel strains (HT111-2T and HT170-2) of the genus Lactobacillus were isolated from Marmota himalayana faecal samples collected on the Qinghai-Tibet Plateau, PR China. The isolates were Gram-stain-positive, rod-shaped, non-spore-forming bacteria with irregular circular colonies. Phylogenetic analysis and comparison of the 16S rRNA gene sequences demonstrated that the two strains form a subcluster and are closest to Lactobacillus hamsteri JCM 6256T (97.3 %) and Lactobacillus amylolyticus DSM 11664T (97.2 %). Phylogenetic analysis of two housekeeping genes (rpoA and pheS) found that strains HT111-2T and HT170-2 had the same closest relatives as the 16S rRNA gene sequence analysis did. The G+C content of strains HT111-2T and HT170-2 were 38.8 mol%. The values of in silico DNA-DNA hybridization with known Lactobacillus species were lower than the threshold (70%). Average nucleotide identity values of strain HT111-2T with L. hamsteri JCM 6256T and L. amylolyticus DSM 11664T were 77.84 % and 76.85 %, respectively. The major fatty acids of strains HT111-2T and HT170-2 were C16 : 0, C18 : 1ω9c and C18 : 0. Results of phenotypic, chemotaxonomic and phylogenetic analyses suggest strains HT111-2T and HT170-2 represent a novel species of the genus Lactobacillus, for which the name Lactobacillus xujianguonis sp. nov. is proposed with HT111-2T (=CGMCC 1.13855T=KCTC 15803T) as the type strain.
Collapse
Affiliation(s)
- Jiajia Meng
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China.,Guangxi Key Laboratory of AIDS Prevention and Treatment & Guangxi Collaborative Innovation Center for Biomedicine, School of Public Health, Guangxi Medical University, Nanning 530021, Guangxi, PR China
| | - Dong Jin
- Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Shanghai 201508, PR China.,State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
| | - Jing Yang
- Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Shanghai 201508, PR China.,State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
| | - Xin-He Lai
- School of Biology and Food Sciences, Shangqiu Normal University, Shangqiu, Henan 476000, PR China
| | - Ji Pu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
| | - Wentao Zhu
- Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Shanghai 201508, PR China
| | - Ying Huang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
| | - Hao Liang
- Guangxi Key Laboratory of AIDS Prevention and Treatment & Guangxi Collaborative Innovation Center for Biomedicine, School of Public Health, Guangxi Medical University, Nanning 530021, Guangxi, PR China
| | - Shan Lu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China.,Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Shanghai 201508, PR China
| |
Collapse
|
29
|
Yu AO, Leveau JHJ, Marco ML. Abundance, diversity and plant-specific adaptations of plant-associated lactic acid bacteria. ENVIRONMENTAL MICROBIOLOGY REPORTS 2020; 12:16-29. [PMID: 31573142 DOI: 10.1111/1758-2229.12794] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 09/11/2019] [Accepted: 09/12/2019] [Indexed: 06/10/2023]
Abstract
Lactic acid bacteria (LAB) are essential for many fruit, vegetable and grain food and beverage fermentations. However, the numbers, diversity and plant-specific adaptions of LAB found on plant tissues prior to the start of those fermentations are not well understood. When measured, these bacteria have been recovered from the aerial surfaces of plants in a range from <10 CFU g-1 to over 108.5 CFU g-1 of plant tissue and in lower quantities from the soil and rhizosphere. Plant-associated LAB include well-known generalist taxa such as Lactobacillus plantarum and Leuconostoc mesenteroides, which are essential for numerous food and beverage fermentations. Other plant-associated LAB encompass specialist taxa such as Lactobacillus florum and Fructobacillus, many of which were discovered relatively recently and their significance on plants and in foods is not yet recognized. LAB recovered from plants possess the capacity to consume plant sugars, detoxify phenolic compounds and tolerate the numerous biotic and abiotic stresses common to plant surfaces. Although most generalist and some specialist LAB grow rapidly in food and beverages fermentations and can cause spoilage of fresh and fermented fruits and vegetables, the importance of living plants as habitats for these bacteria and LAB contributions to plant microbiomes remain to be shown.
Collapse
Affiliation(s)
- Annabelle O Yu
- Department of Food Science & Technology, University of California Davis, Davis, CA, USA
| | - Johan H J Leveau
- Department of Plant Pathology, University of California Davis, Davis, CA, USA
| | - Maria L Marco
- Department of Food Science & Technology, University of California Davis, Davis, CA, USA
| |
Collapse
|
30
|
Palmer-Young EC, Ngor L, Nevarez RB, Rothman JA, Raffel TR, McFrederick QS. Temperature dependence of parasitic infection and gut bacterial communities in bumble bees. Environ Microbiol 2019; 21:4706-4723. [PMID: 31573120 PMCID: PMC7316186 DOI: 10.1111/1462-2920.14805] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 09/13/2019] [Indexed: 11/30/2022]
Abstract
High temperatures (e.g., fever) and gut microbiota can both influence host resistance to infection. However, effects of temperature-driven changes in gut microbiota on resistance to parasites remain unexplored. We examined the temperature dependence of infection and gut bacterial communities in bumble bees infected with the trypanosomatid parasite Crithidia bombi. Infection intensity decreased by over 80% between 21 and 37°C. Temperatures of peak infection were lower than predicted based on parasite growth in vitro, consistent with mismatches in thermal performance curves of hosts, parasites and gut symbionts. Gut bacterial community size and composition exhibited slight but significant, non-linear, and taxon-specific responses to temperature. Abundance of total gut bacteria and of Orbaceae, both negatively correlated with infection in previous studies, were positively correlated with infection here. Prevalence of the bee pathogen-containing family Enterobacteriaceae declined with temperature, suggesting that high temperature may confer protection against diverse gut pathogens. Our results indicate that resistance to infection reflects not only the temperature dependence of host and parasite performance, but also temperature-dependent activity of gut bacteria. The thermal ecology of gut parasite-symbiont interactions may be broadly relevant to infectious disease, both in ectothermic organisms that inhabit changing climates, and in endotherms that exhibit fever-based immunity.
Collapse
Affiliation(s)
- Evan C Palmer-Young
- Department of Entomology, University of California Riverside, Riverside, CA, USA
| | - Lyna Ngor
- Department of Entomology, University of California Riverside, Riverside, CA, USA
| | | | - Jason A. Rothman
- Department of Entomology, University of California Riverside, Riverside, CA, USA
| | - Thomas R Raffel
- Department of Biology, Oakland University, Rochester, MI, USA
| | - Quinn S McFrederick
- Department of Entomology, University of California Riverside, Riverside, CA, USA
| |
Collapse
|
31
|
Rothman JA, Leger L, Kirkwood JS, McFrederick QS. Cadmium and Selenate Exposure Affects the Honey Bee Microbiome and Metabolome, and Bee-Associated Bacteria Show Potential for Bioaccumulation. Appl Environ Microbiol 2019; 85:e01411-19. [PMID: 31471302 PMCID: PMC6803295 DOI: 10.1128/aem.01411-19] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Accepted: 08/26/2019] [Indexed: 01/12/2023] Open
Abstract
Honey bees are important insect pollinators used heavily in agriculture and can be found in diverse environments. Bees may encounter toxicants such as cadmium and selenate by foraging on plants growing in contaminated areas, which can result in negative health effects. Honey bees are known to have a simple and consistent microbiome that conveys many benefits to the host, and toxicant exposure may impact this symbiotic microbial community. We used 16S rRNA gene sequencing to assay the effects that sublethal cadmium and selenate treatments had over 7 days and found that both treatments significantly but subtly altered the composition of the bee microbiome. Next, we exposed bees to cadmium and selenate and then used untargeted liquid chromatography-mass spectrometry (LC-MS) metabolomics to show that chemical exposure changed the bees' metabolite profiles and that compounds which may be involved in detoxification, proteolysis, and lipolysis were more abundant in treatments. Finally, we exposed several strains of bee-associated bacteria in liquid culture and found that each strain removed cadmium from its medium but that only Lactobacillus Firm-5 microbes assimilated selenate, indicating the possibility that these microbes may reduce the metal and metalloid burden on their host. Overall, our report shows that metal and metalloid exposure can affect the honey bee microbiome and metabolome and that strains of bee-associated bacteria can bioaccumulate these toxicants.IMPORTANCE Bees are important insect pollinators that may encounter environmental pollution when foraging upon plants grown in contaminated areas. Despite the pervasiveness of pollution, little is known about the effects of these toxicants on honey bee metabolism and their symbiotic microbiomes. Here, we investigated the impact of selenate and cadmium exposure on the gut microbiome and metabolome of honey bees. We found that exposure to these chemicals subtly altered the overall composition of the bees' microbiome and metabolome and that exposure to toxicants may negatively impact both host and microbe. As the microbiome of animals can reduce mortality upon metal or metalloid challenge, we grew bee-associated bacteria in media spiked with selenate or cadmium. We show that some bacteria can remove these toxicants from their media in vitro and suggest that bacteria may reduce metal burden in their hosts.
Collapse
Affiliation(s)
- Jason A Rothman
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, California, USA
- Department of Entomology, University of California, Riverside, Riverside, California, USA
| | - Laura Leger
- Department of Entomology, University of California, Riverside, Riverside, California, USA
| | - Jay S Kirkwood
- Metabolomics Core Facility, Institute for Integrative Genome Biology, University of California, Riverside, Riverside, California, USA
| | - Quinn S McFrederick
- Department of Entomology, University of California, Riverside, Riverside, California, USA
| |
Collapse
|
32
|
Abstract
The Lactobacillus genus complex is a group of bacteria that constitutes an important source of strains with medical and food applications. The number of bacterial whole-genome sequences available for this taxon has been increasing rapidly in recent years. Despite this wealth of information, the species within this group are still largely defined by older techniques. Here, we constructed a completely new species-level taxonomy for the Lactobacillus genus complex based on ∼2,500 whole-genome sequences. As a result of this effort, we found that many genomes are not classified to their correct species, and we were able to correct these. In addition, we found that some published species are abnormally large, while others are too small. Finally, we discovered at least eight completely novel species that have not been published before. Our work will help the field to evolve toward a more meaningful and complete taxonomy, based on whole-genome sequences. There are more than 200 published species within the Lactobacillus genus complex (LGC), the majority of which have sequenced type strain genomes available. Although genome-based species delimitation cutoffs are accepted as the gold standard by the community, these are seldom actually checked for new or already published species. In addition, the availability of genome data is revealing inconsistencies in the species-level classification of many strains. We constructed a de novo species taxonomy for the LGC based on 2,459 publicly available genomes, using a 94% core nucleotide identity cutoff. We reconciled these de novo species with published species and subspecies names by (i) identifying genomes of type strains and (ii) comparing 16S rRNA genes of the genomes with 16S rRNA genes of type strains. We found that genomes within the LGC could be divided into 239 de novo species that were discontinuous and exclusive. Comparison of these de novo species to published species led to the identification of nine sets of published species that can be merged and one species that can be split. Further, we found at least eight de novo species that constitute new, unpublished species. Finally, we reclassified 74 genomes on the species level and identified for the first time the species of 98 genomes. Overall, the current state of LGC species taxonomy is largely consistent with genome-based species delimitation cutoffs. There are, however, exceptions that should be resolved to evolve toward a taxonomy where species share a consistent diversity in terms of sequence divergence. IMPORTANCE The Lactobacillus genus complex is a group of bacteria that constitutes an important source of strains with medical and food applications. The number of bacterial whole-genome sequences available for this taxon has been increasing rapidly in recent years. Despite this wealth of information, the species within this group are still largely defined by older techniques. Here, we constructed a completely new species-level taxonomy for the Lactobacillus genus complex based on ∼2,500 whole-genome sequences. As a result of this effort, we found that many genomes are not classified to their correct species, and we were able to correct these. In addition, we found that some published species are abnormally large, while others are too small. Finally, we discovered at least eight completely novel species that have not been published before. Our work will help the field to evolve toward a more meaningful and complete taxonomy, based on whole-genome sequences.
Collapse
|
33
|
Voulgari‐Kokota A, Ankenbrand MJ, Grimmer G, Steffan‐Dewenter I, Keller A. Linking pollen foraging of megachilid bees to their nest bacterial microbiota. Ecol Evol 2019; 9:10788-10800. [PMID: 31624582 PMCID: PMC6787775 DOI: 10.1002/ece3.5599] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 07/25/2019] [Accepted: 07/28/2019] [Indexed: 12/17/2022] Open
Abstract
Solitary bees build their nests by modifying the interior of natural cavities, and they provision them with food by importing collected pollen. As a result, the microbiota of the solitary bee nests may be highly dependent on introduced materials. In order to investigate how the collected pollen is associated with the nest microbiota, we used metabarcoding of the ITS2 rDNA and the 16S rDNA to simultaneously characterize the pollen composition and the bacterial communities of 100 solitary bee nest chambers belonging to seven megachilid species. We found a weak correlation between bacterial and pollen alpha diversity and significant associations between the composition of pollen and that of the nest microbiota, contributing to the understanding of the link between foraging and bacteria acquisition for solitary bees. Since solitary bees cannot establish bacterial transmission routes through eusociality, this link could be essential for obtaining bacterial symbionts for this group of valuable pollinators. OPEN RESEARCH BADGES This article has earned an Open Data Badge for making publicly available the digitally-shareable data necessary to reproduce the reported results. The data is available at https://www.ebi.ac.uk/ena/data/view/PRJEB27223, https://www.ebi.ac.uk/ena/data/view/PRJEB31610, and https://doi.org/10.5061/dryad.qk36k8q.
Collapse
Affiliation(s)
- Anna Voulgari‐Kokota
- Department of BioinformaticsBiocenterUniversity of WuerzburgWuerzburgGermany
- Center for Computational and Theoretical BiologyUniversity of WuerzburgWuerzburgGermany
| | - Markus J. Ankenbrand
- Department of BioinformaticsBiocenterUniversity of WuerzburgWuerzburgGermany
- Center for Computational and Theoretical BiologyUniversity of WuerzburgWuerzburgGermany
| | - Gudrun Grimmer
- Department of Animal Ecology and Tropical BiologyBiocenterUniversity of WuerzburgWuerzburgGermany
| | - Ingolf Steffan‐Dewenter
- Department of Animal Ecology and Tropical BiologyBiocenterUniversity of WuerzburgWuerzburgGermany
| | - Alexander Keller
- Department of BioinformaticsBiocenterUniversity of WuerzburgWuerzburgGermany
- Center for Computational and Theoretical BiologyUniversity of WuerzburgWuerzburgGermany
| |
Collapse
|
34
|
Voulgari-Kokota A, McFrederick QS, Steffan-Dewenter I, Keller A. Drivers, Diversity, and Functions of the Solitary-Bee Microbiota. Trends Microbiol 2019; 27:1034-1044. [PMID: 31451346 DOI: 10.1016/j.tim.2019.07.011] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 07/12/2019] [Accepted: 07/29/2019] [Indexed: 12/31/2022]
Abstract
Accumulating reports of global bee declines have drawn much attention to the bee microbiota and its importance. Most research has focused on social bees, while solitary species have received scant attention despite their enormous biodiversity, ecological importance, and agroeconomic value. We review insights from several recent studies on diversity, function, and drivers of the solitary-bee microbiota, and compare these factors with those relevant to the social-bee microbiota. Despite basic similarities, the social-bee model, with host-specific core microbiota and social transmission, is not representative of the vast majority of bee species. The solitary-bee microbiota exhibits greater variability and biodiversity, with a strong impact of environmental acquisition routes. Our synthesis identifies outstanding questions that will build understanding of these interactions, responses to environmental threats, and consequences for health.
Collapse
Affiliation(s)
- Anna Voulgari-Kokota
- Department of Bioinformatics, University of Würzburg, Biocenter, Am Hubland, 97074 Würzburg, Germany; Center for Computational and Theoretical Biology, University of Würzburg, Hubland Nord, Emil-Fischer Straße, 97074 Würzburg, Germany
| | - Quinn S McFrederick
- Department of Entomology, University of California, 900 University Ave, Riverside, CA 92521, USA
| | - Ingolf Steffan-Dewenter
- Department of Animal Ecology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Alexander Keller
- Department of Bioinformatics, University of Würzburg, Biocenter, Am Hubland, 97074 Würzburg, Germany; Center for Computational and Theoretical Biology, University of Würzburg, Hubland Nord, Emil-Fischer Straße, 97074 Würzburg, Germany.
| |
Collapse
|
35
|
Rothman JA, Andrikopoulos C, Cox-Foster D, McFrederick QS. Floral and Foliar Source Affect the Bee Nest Microbial Community. MICROBIAL ECOLOGY 2019; 78:506-516. [PMID: 30552443 DOI: 10.1007/s00248-018-1300-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 11/22/2018] [Indexed: 06/09/2023]
Abstract
Managed pollinators such as the alfalfa leafcutting bee, Megachile rotundata, are essential to the production of a wide variety of agricultural crops. These pollinators encounter a diverse array of microbes when foraging for food and nest-building materials on various plants. To test the hypothesis that food and nest-building source affects the composition of the bee-nest microbiome, we exposed M. rotundata adults to treatments that varied both floral and foliar source in a 2 × 2 factorial design. We used 16S rRNA gene and internal transcribed spacer (ITS) sequencing to capture the bacterial and fungal diversity of the bee nests. We found that nest microbial communities were significantly different between treatments, indicating that bee nests become inoculated with environmentally derived microbes. We did not find evidence of interactions between the fungi and bacteria within our samples. Furthermore, both the bacterial and fungal communities were quite diverse and contained numerous exact sequence variants (ESVs) of known plant and bee pathogens that differed based on treatment. Our research indicates that bees deposit plant-associated microbes into their nests, including multiple plant pathogens such as smut fungi and bacteria that cause blight and wilt. The presence of plant pathogens in larval pollen provisions highlights the potential for bee nests to act as disease reservoirs across seasons. We therefore suggest that future research should investigate the ability of bees to transmit pathogens from nest to host plant.
Collapse
Affiliation(s)
- Jason A Rothman
- Graduate Program in Microbiology, University of California, 900 University Ave., Riverside, CA, 92521, USA
- Department of Entomology, University of California, 900 University Ave., Riverside, CA, 92521, USA
| | - Corey Andrikopoulos
- Department of Biology, Utah State University, UMC5310, Logan, UT, 84322, USA
- USDA-ARS Pollinating Insect-Biology, Management, and Systematics Research, Logan, UT, 84322, USA
| | - Diana Cox-Foster
- Department of Biology, Utah State University, UMC5310, Logan, UT, 84322, USA.
- USDA-ARS Pollinating Insect-Biology, Management, and Systematics Research, Logan, UT, 84322, USA.
| | - Quinn S McFrederick
- Graduate Program in Microbiology, University of California, 900 University Ave., Riverside, CA, 92521, USA.
- Department of Entomology, University of California, 900 University Ave., Riverside, CA, 92521, USA.
| |
Collapse
|
36
|
Tohno M, Tanizawa Y, Kojima Y, Sakamoto M, Nakamura Y, Ohkuma M, Kobayashi H. Lactobacillus salitolerans sp. nov., a novel lactic acid bacterium isolated from spent mushroom substrates. Int J Syst Evol Microbiol 2019; 69:964-969. [DOI: 10.1099/ijsem.0.003224] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A taxonomic study of a Gram-stain-positive, rod-shaped, non-motile, non-spore-forming, catalase-negative bacterium, strain YK43T, isolated from spent mushroom substrates stored in Nagano, Japan was performed. Growth was detected at 15–45 °C, pH 5.0–8.5, and 0–10 % (w/v) NaCl. The genomic DNA G+C content of strain YK43T was 43.6 mol%. The predominant fatty acids were C16 : 0, C18 : 1 ω9c and summed feature 8. Based on 16S rRNA gene sequence analysis, the type strains of
Lactobacillus acidipiscis
(sequence similarity, 97.6 %) and
Lactobacillus pobuzihii
(97.4 %) were most closely related to YK43T. The average nucleotide identities were 74.1 % between strain YK43T and
L. acidipiscis
DSM 15836T and 74.0 % between YK43T and
L. pobuzihii
E100301T. Based on a multilocus sequence analysis, comparative genomic analysis and a range of phenotypic and chemotaxonomic characteristics, strain YK43T represents a novel species of the genus
Lactobacillus
, for which the name
Lactobacillus
salitolerans sp. nov. is proposed. The type strain is YK43T (=JCM 31331T = DSM 103433T).
Collapse
Affiliation(s)
- Masanori Tohno
- Central Region Agricultural Research Center, National Agriculture and Food Research Organization, Nasushiobara, Tochigi 329-2793, Japan
| | - Yasuhiro Tanizawa
- Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Yoichiro Kojima
- Central Region Agricultural Research Center, National Agriculture and Food Research Organization, Nasushiobara, Tochigi 329-2793, Japan
| | - Mitsuo Sakamoto
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
- PRIME, Japan Agency for Medical Research and Development (AMED), Tsukuba, Ibaraki 305-0074, Japan
| | - Yasukazu Nakamura
- Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Hisami Kobayashi
- Central Region Agricultural Research Center, National Agriculture and Food Research Organization, Nasushiobara, Tochigi 329-2793, Japan
| |
Collapse
|
37
|
Russell AL, Ashman TL. Associative learning of flowers by generalist bumble bees can be mediated by microbes on the petals. Behav Ecol 2019. [DOI: 10.1093/beheco/arz011] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Abstract
Communication is often vital to the maintenance of mutualisms. In plant-pollinator mutualisms, plants signal pollinators via floral displays, composed of olfactory, visual, and other plant-derived cues. While plants are understood to be associated with microbes, only recently has the role of microbial (yeast and bacteria) inhabitants of flowers as intermediaries of plant-pollinator communication been recognized. Animals frequently use microbial cues to find resources, yet no study has examined whether microbes directly mediate learned and innate pollinator responses. Here, we asked whether microbes on the flower surface, independent of their modification of floral rewards, can mediate these key components of pollinator preference. In the field, we characterized flower and bumble bee microbial abundance, and in laboratory assays we tested whether bumble bees (Bombus impatiens) discriminated flowers on the basis of an experimental floral microbial community on the petals and whether microbe-derived chemicals were effective cues. Learning of microbial community cues was associative and reward context-dependent and mediated by microbial chemicals. Deconstructing the experimental microbial community showed bees innately avoided flowers with bacteria, but were undeterred by yeast. Microbial cues thus potentially facilitate dynamic communication between plants and pollinators such as bumble bees, especially as pollinator visitation can change flower microbiota. We suggest that the study of communication in mutualism generally would benefit by considering not only the multicellular eukaryote partners, but their microbial associates.
Collapse
Affiliation(s)
- Avery L Russell
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Tia-Lynn Ashman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| |
Collapse
|
38
|
McFrederick QS, Rehan SM. Wild Bee Pollen Usage and Microbial Communities Co-vary Across Landscapes. MICROBIAL ECOLOGY 2019; 77:513-522. [PMID: 30069710 DOI: 10.1007/s00248-018-1232-y] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Accepted: 07/12/2018] [Indexed: 05/11/2023]
Abstract
Bees forage for pollen and nectar at flowers but simultaneously acquire pathogenic, commensal, and likely beneficial microbes from these same flowers. Characterizing pollen usage of wild bees is therefore crucial to their conservation yet remains a challenging task. To understand pollen usage across landscapes and how this affects microbial communities found in the pollen provisions collected from flowers, we studied the generalist small carpenter bee Ceratina australensis. We collected C. australensis nests from three different climatic zones across eastern and southern Australia. To characterize the plant, fungal, and bacterial composition of these pollen provisions, we used a metabarcoding and next-generation sequencing approach. We found that the species richness of plant types, fungi, and bacteria was highest in a subtropical zone compared to a temperate or a grassland zone. The composition of these communities also differentiated by zone, particularly in pollen composition and fungal communities. Moreover, pollen composition strongly correlated with fungal community composition, suggesting that variation in pollen usage across landscapes results in variation in microbial communities. While how these pollen usage and microbial community patterns affect bee health merits additional work, these data further our understanding of how flowering plant community composition affects not only the pollen usage of a generalist bee but also its associated microbial communities.
Collapse
Affiliation(s)
- Quinn S McFrederick
- Department of Entomology, University of California, Riverside, 900 University Avenue, Riverside, CA, 92521, USA.
| | - Sandra M Rehan
- Department of Biological Sciences, University of New Hampshire, 38 Academic Way, Durham, NH, 03824, USA
| |
Collapse
|
39
|
van Schooten B, Godoy-Vitorino F, McMillan WO, Papa R. Conserved microbiota among young Heliconius butterfly species. PeerJ 2018; 6:e5502. [PMID: 30310733 PMCID: PMC6173163 DOI: 10.7717/peerj.5502] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Accepted: 08/01/2018] [Indexed: 12/03/2022] Open
Abstract
Background Insects are the most diverse group of animals which have established intricate evolutionary interactions with bacteria. However, the importance of these interactions is still poorly understood. Few studies have focused on a closely related group of insect species, to test the similarities and differences between their microbiota. Heliconius butterflies are a charismatic recent insect radiation that evolved the unique ability to use pollen as a protein source, which affected life history traits and resulted in an elevated speciation rates. We hypothesize that different Heliconius butterflies sharing a similar trophic pollen niche, harbor a similar gut flora within species, population and sexes. Methods To test our hypothesis, we characterized the microbiota of 38 adult male and female butterflies representing six species of Heliconius butterflies and 2 populations of the same species. We sequenced the V4 region of the 16S rRNA gene with the Roche 454 system and analyzed the data with standard tools for microbiome analysis. Results Overall, we found a low microbial diversity with only 10 OTUs dominating across all individuals, mostly Proteobacteria and Firmicutes, which accounted for 99.5% of the bacterial reads. When rare reads were considered, we identified a total of 406 OTUs across our samples. We identified reads within Phyla Chlamydiae, found in 5 butterflies of four species. Interestingly, only three OTUs were shared among all 38 individuals (Bacillus, Enterococcus and Enterobacteriaceae). Altogether, the high individual variation overshadowed species and sex differences. Thus, bacterial communities were not structured randomly with 13% of beta-diversity explained by species, and 40 rare OTUs being significantly different across species. Finally, 13 OTUs, including the intercellular symbiont Spiroplasma, varied significantly in relative abundance between males and females. Discussion The Heliconius microbial communities in these 38 individuals show a low diversity with few differences in the rare microbes between females, males, species or populations. Indeed, Heliconius butterflies, similarly to other insects, are dominated by few OTUs, mainly from Proteobacteria and Firmicutes. The overall low microbial diversity observed contrasts with the high intra-species variation in microbiome composition. This could indicate that much of the microbiome maybe acquired from their surroundings. The significant differences between species and sexes were restricted to rare taxa, which could be important for microbial community stability under changing conditions as seen in other host-microbiome systems. The presence of symbionts like Spiroplasma or Chlamydiae, identified in this study for the first time in Heliconius, could play a vital role in their behavior and evolution by vertical transmission. Altogether, our study represents a step forward into the description of the microbial diversity in a charismatic group of closely related butterflies.
Collapse
Affiliation(s)
- Bas van Schooten
- Department of Biology, University of Puerto Rico, Rio Piedras Campus, San Juan, Puerto Rico
| | - Filipa Godoy-Vitorino
- Department of Microbiology and Medical Zoology, School of Medicine, University of Puerto Rico, Medical Sciences Campus, San Juan, Puerto Rico
| | | | - Riccardo Papa
- Department of Biology, University of Puerto Rico, Rio Piedras Campus, San Juan, Puerto Rico.,Smithsonian Tropical Research Institute, Panamá, Panama.,University of Puerto Rico, Molecular Sciences and Research Center, San Juan, Puerto Rico
| |
Collapse
|