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Zhao C, Li H, Gao C, Tian H, Guo Y, Liu G, Li Y, Liu D, Sun B. Moringa oleifera leaf polysaccharide regulates fecal microbiota and colonic transcriptome in calves. Int J Biol Macromol 2023; 253:127108. [PMID: 37776927 DOI: 10.1016/j.ijbiomac.2023.127108] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 09/22/2023] [Accepted: 09/25/2023] [Indexed: 10/02/2023]
Abstract
This study investigated the effects of Moringa oleifera polysaccharide on growth performance indicators, serum biochemical indicators, immune organ indicators, colonic morphology, colonic microbiomics and colonic transcriptomics in newborn calves. 21 newborn calves were randomly divided into three groups of 7 calves per treatment group: control group (no Moringa oleifera polysaccharide addition); low-dose group (Moringa oleifera polysaccharide 0.5 g/kg); and high-dose group (Moringa oleifera polysaccharide 1 g/kg). This trial used gavage to feed MOP to calves. The test lasted 8 weeks. Calves were humanely electroshocked on the last day of the trial and slaughtered afterwards. Thymus, spleen, blood and colonic contents were collected for further testing. The results of this trial showed that MOP significantly increased the body weight of newborn calves and reduced the rate of calf diarrhea, thus promoting calf growth. Fecal scores showed a linear decrease with the addition of MOP. In terms of serum biochemistry, feeding MOP significantly increased serum ALB levels in a linear fashion. In terms of serum antioxidants, feeding MOP linearly increased CAT and T-AOC levels and decreased MDA concentrations, and in terms of serum immunity, feeding MOP linearly increased IgA, IgG, and IgM levels. At the same time, MOP regulated the abundance of Firmicutes and Bacteroidetes in the intestinal tract of calves, which reduced the occurrence of diarrhea. In addition, moringa polysaccharide could regulate genes related to inflammatory signaling pathways such as MAPK signaling pathway, TGF-beta signaling pathway, PI3K-Akt signaling pathway and TNF signaling pathway in calves' intestine to reduce the occurrence of intestinal inflammation. In conclusion, MOP can be used as a novel ruminant additive for the prevention of enteritis in calves.
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Affiliation(s)
- Chao Zhao
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Hangfan Li
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Chongya Gao
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Hanchen Tian
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Yongqing Guo
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Guangbin Liu
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Yaokun Li
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Dewu Liu
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Baoli Sun
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
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Liepman RS, Swink JM, Habing GG, Boyaka PN, Caddey B, Costa M, Gomez DE, Toribio RE. Effects of Intravenous Antimicrobial Drugs on the Equine Fecal Microbiome. Animals (Basel) 2022; 12:1013. [PMID: 35454258 PMCID: PMC9030835 DOI: 10.3390/ani12081013] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 03/30/2022] [Accepted: 04/07/2022] [Indexed: 02/05/2023] Open
Abstract
Alterations in the gastrointestinal microbiota after antimicrobial therapy in horses can result in loss of colonization resistance and changes in bacterial metabolic function. It is hypothesized that these changes facilitate gastrointestinal inflammation, pathogen expansion and the development of diarrhea. The objectives of this study were to determine the effect of intravenous administration of antimicrobial drugs (ceftiofur, enrofloxacin, oxytetracycline) on equine fecal bacterial communities over time, to investigate whether those changes are detectable after 5 days of treatment and whether they persist over time (30 days). Sixteen horses were randomly assigned into 4 treatment groups: group 1 (enrofloxacin, n = 4); group 2 (ceftiofur sodium, n = 4); group 3 (oxytetracycline, n = 4); group 4 (0.9% saline solution, placebo, n = 4). Antimicrobial therapy was administered for 5 days. Fecal samples were obtained before (day 0) and at 3, 5 and 30 days of the study period. Bacterial DNA was amplified using specific primers to the hypervariable region V1−V3 of the 16S rRNA gene using a 454 FLX-Titanium pyrosequencer. Antimicrobial therapy failed to cause any changes in physical examination parameters, behavior, appetite or fecal output or consistency throughout the study in any horse. There was a significant effect of treatment on alpha diversity indices (richness) over the treatment interval for ceftiofur on days 0 vs. 3 (p < 0.05), but not for other antimicrobials (p > 0.05). Microbial composition was significantly different (p < 0.05) across treatment group and day, but not for interactions between treatment and day, regardless of taxonomic level and beta-diversity distance metric. The most significant antimicrobial effects on relative abundance were noted after intravenous administration of ceftiofur and enrofloxacin. The relative abundance of Fibrobacteres was markedly lower on day 3 compared to other days in the ceftiofur and enrofloxacin treatment groups. There was an increase in Clostridia and Lachnospiraceae from day 0 to days 3 and 5 in ceftiofur and enrofloxacin treated groups. These findings showed the negative effect of antimicrobial drugs on bacterial communities associated with gut health (Fibrobacteres and Lachnospiraceae) and indicate that changes in specific taxa could predispose horses to gastrointestinal inflammation and the development of diarrhea.
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Affiliation(s)
- Rachel S. Liepman
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210, USA; (R.S.L.); (J.M.S.)
| | - Jacob M. Swink
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210, USA; (R.S.L.); (J.M.S.)
| | - Greg G. Habing
- Department of Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210, USA;
| | - Prosper N. Boyaka
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210, USA;
| | - Benjamin Caddey
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada;
| | - Marcio Costa
- Department of Veterinary Biomedical Sciences, Faculté de Médecine Vétérinaire, University of Montreal, Saint Hyacinthe, QC J2S 2M2, Canada;
| | - Diego E. Gomez
- Department of Clinical Studies, Ontario Veterinary College, University of Guelph, Guelph, ON N1G 2W1, Canada;
| | - Ramiro E. Toribio
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210, USA; (R.S.L.); (J.M.S.)
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The acidified drinking water-induced changes in the behavior and gut microbiota of wild-type mice depend on the acidification mode. Sci Rep 2021; 11:2877. [PMID: 33536529 PMCID: PMC7858586 DOI: 10.1038/s41598-021-82570-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 01/18/2021] [Indexed: 02/06/2023] Open
Abstract
Acidification of drinking water to a pH between 2.5 and 3.0 is widely used to prevent the spread of bacterial diseases in animal colonies. Besides hydrochloric acid (HCl), sulfuric acid (H2SO4) is also used to acidify drinking water. Here we examined the effects of H2SO4-acidified drinking water (pH = 2.8) received from weaning (postnatal day 21) on the behavior and gut microflora of 129S6/SvEv mice, a mouse strain commonly used in transgenic studies. In contrast to HCl-acidified water, H2SO4-acidified water only temporarily impaired the pole-descending ability of mice (at 3 months of age), and did not change the performance in an accelerating rotarod test. As compared to 129S6/SvEv mice receiving non-acidified or HCl-acidified drinking water, the gut microbiota of 129S6/SvEv mice on H2SO4-acidified water displayed significant alterations at every taxonomic level especially at 6 months of age. Our results demonstrate that the effects of acidified drinking water on the behavior and gut microbiota of 129S6/SvEv mice depends on the acid used for acidification. To shed some light on how acidified drinking water affects the physiology of 129S6/SvEv mice, we analyzed the serum and fecal metabolomes and found remarkable, acidified water-induced alterations.
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Parker C, Zhao J, Pearce DA, Kovács AD. Comparative analysis of the gut microbiota composition in the Cln1 R151X and Cln2 R207X mouse models of Batten disease and in three wild-type mouse strains. Arch Microbiol 2020; 203:85-96. [PMID: 32749661 DOI: 10.1007/s00203-020-02007-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/27/2020] [Accepted: 07/25/2020] [Indexed: 02/07/2023]
Abstract
Accumulated evidence indicates that the gut microbiota affects brain function and may be altered in neurological diseases. In this study, we analyzed the gut microbiota in Cln1R151X and Cln2R207X mice, models of the childhood neurodegenerative disorders, infantile CLN1 and late infantile CLN2 Batten diseases. Significant alterations were found in the overall gut microbiota composition and also at the individual taxonomic ranks as compared to wild-type mice. The disease-specific alterations in the gut microbiota of Cln1R151X and Cln2R207X mice may contribute to the disease phenotypes observed in these mouse models. We also compared the gut microbiota composition of three wild-type mouse strains frequently used in transgenic studies: 129S6/SvEv, C57BL/6J and mixed 129S6/SvEv × C57BL/6J. Our results show that the gut microbiota of 129S6/SvEv and C57BL/6J mice differs remarkably, which likely contributes to the known, pronounced differences in behavior and disease susceptibility between these two wild-type mouse strains.
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Affiliation(s)
- Camille Parker
- Pediatrics and Rare Diseases Group, Sanford Research, 2301 E. 60th Street N., Sioux Falls, SD, 57014, USA
| | - Jing Zhao
- Population Health Group, Sanford Research, Sioux Falls, SD, 57104, USA.,Department of Internal Medicine, University of South Dakota, Sioux Falls, SD, 57105, USA.,Center for Biostatistics, Ohio State University, Columbus, OH, 43210, USA
| | - David A Pearce
- Pediatrics and Rare Diseases Group, Sanford Research, 2301 E. 60th Street N., Sioux Falls, SD, 57014, USA.,Department of Pediatrics, Sanford School of Medicine, University of South Dakota, Sioux Falls, SD, 57105, USA
| | - Attila D Kovács
- Pediatrics and Rare Diseases Group, Sanford Research, 2301 E. 60th Street N., Sioux Falls, SD, 57014, USA. .,Department of Pediatrics, Sanford School of Medicine, University of South Dakota, Sioux Falls, SD, 57105, USA.
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Wang JC, Moore CA, Epperson MV, Sedaghat AR. Association of the sinonasal bacterial microbiome with clinical outcomes in chronic rhinosinusitis: a systematic review. Int Forum Allergy Rhinol 2020; 10:433-443. [PMID: 32052920 PMCID: PMC9290466 DOI: 10.1002/alr.22524] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 12/15/2019] [Accepted: 12/18/2019] [Indexed: 12/16/2022]
Abstract
Background The association between sinonasal microbiome and clinical outcomes of patients with chronic rhinosinusitis (CRS) is unclear. We performed a systematic review of prior studies evaluating the CRS microbiome in relation to clinical outcomes. Methods Computerized searches of PubMed/Medline, Cochrane, and EMBASE were updated through October 2019 revealing a total of 9 studies including 244 CRS patients. A systematic review of the literature was performed, including data extraction focusing on sample region, sequencing platforms, predominant organisms, and outcomes measures. Results Nine criterion‐meeting studies included 244 CRS patients, with varied results. Eight studies used 16s–ribosomal RNA (16s‐rRNA) gene sequencing to assess the sinonasal microbiome and 1 used 16s‐rRNA PhyloChip analysis. Seven studies used Sino‐Nasal Outcome Test scores, 1 applied another CRS symptom metric, and 1 used need for additional procedures/antibiotics as the primary clinical outcome. Three studies suggest that baseline abundance of phylum Actinobacteria (specifically genus Corynebacterium) was predictive of better surgical outcome. One study found C. tuberculostearicum was positively correlated with symptom severity. Another study revealed genus Escherichia was overrepresented in CRS and had positive correlation with increased symptom scores. In addition, 1 study identified Acinetobacter johnsonii to be associated with improvement in symptom scores while supporting Pseudomonas aeruginosa as having a negative impact on quality of life. Conclusion Microbiome data are varied in their association with clinical outcomes of CRS patients. Further research is required to identify if predominance of certain microbes within the microbiome is predictive of CRS patients’ outcomes.
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Affiliation(s)
- James C Wang
- Department of Otolaryngology-Head and Neck Surgery, University of Cincinnati College of Medicine, Cincinnati, OH
| | - Charles A Moore
- Department of Otolaryngology-Head and Neck Surgery, University of Cincinnati College of Medicine, Cincinnati, OH
| | - Madison V Epperson
- Department of Otolaryngology-Head and Neck Surgery, University of Cincinnati College of Medicine, Cincinnati, OH
| | - Ahmad R Sedaghat
- Department of Otolaryngology-Head and Neck Surgery, University of Cincinnati College of Medicine, Cincinnati, OH
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Abdelatty AM, Badr OAM, Mohamed SA, Khattab MS, Dessouki SHM, Farid OAA, Elolimy AA, Sakr OG, Elhady MA, Mehesen G, Bionaz M. Long term conjugated linoleic acid supplementation modestly improved growth performance but induced testicular tissue apoptosis and reduced sperm quality in male rabbit. PLoS One 2020; 15:e0226070. [PMID: 31923252 PMCID: PMC6953797 DOI: 10.1371/journal.pone.0226070] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 11/19/2019] [Indexed: 12/20/2022] Open
Abstract
Conjugated linoleic acid (CLA) is known for its multiple benefits including improvement of growth, increasing lean mass, and anti-carcinogenic effects. However, when used in long-term supplementations CLA does not improve semen parameters in boar and bull and reduces fertility in Japanese quails. The content of unsaturated fatty acids in dietary lipids plays a significant role in spermatogenesis owning the high proportion of unsaturated fatty acids in plasma membrane of sperms. Whether CLA plays a role in testicular tissue and epididymal fat is still unknown. Therefore, in this study we hypothesize that long-term supplementation of equal proportion of CLA isomer mix (c9,t11-CLA and t10,c12- CLA) in rabbit bucks might alter male reproductive potentials. Twelve V-Line weaned male rabbits were used in 26 weeks trial, rabbits were individually raised and randomly allocated into three dietary groups. Control group (CON) received a basal diet, a group received 0.5% CLA (CLA 0.5%), and a group received 1% CLA (CLA 1%). Rabbits were euthanized at the end of the trial and several parameters were evaluated related to growth, semen quality, and testicular and epididymal tissue histopathology and transcriptome. The long-term supplementation of CLA increased feed intake by 5% and body weight by 2-3%. CLA 1% decreased sperm progressive motility. In testicular tissue L-carnitine and α-tocopherol were decreased by CLA supplementation. In epididymal fat, CLA tended to decrease concentration of polyunsaturated fatty acids, the expression of SCD5 gene was upregulated by CLA 1% and CASP3 gene was upregulated by CLA 0.5%. Transcription of PPARG was downregulated by CLA. Feeding 1% CLA also decreased testicular epithelial thickness. Long-term supplementation of CLA modestly enhanced male rabbit growth, but negatively impacted male reproduction, especially at high dose of CLA.
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Affiliation(s)
- A. M. Abdelatty
- Department of Nutrition and Clinical Nutrition, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
| | - O. A. M. Badr
- Department of Genetics and Genetic Engineering, Faculty of Agriculture, Benha University, Qalyubia, Egypt
| | - S. A. Mohamed
- Department of Genetics and Genetic Engineering, Faculty of Agriculture, Benha University, Qalyubia, Egypt
| | - M. S. Khattab
- Department of Pathology, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
| | - SH. M. Dessouki
- Department of Animal Production, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - O. A. A. Farid
- Department of Physiology, National Organization for Drug Control and Research, Giza, Egypt
| | - A. A. Elolimy
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, United States of America
- Arkansas Children’s Nutrition Center, Little Rock, AR, United States of America
- Department of Animal Production, National Research Centre, Giza, Egypt
| | - O. G. Sakr
- Department of Animal Production, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - M. A. Elhady
- Department of Toxicology and Forensic Medicine, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
| | - G. Mehesen
- Department of Animal Production, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - M. Bionaz
- Department of Animal and Rangeland Sciences, Oregon State University, Corvallis, OR, United States of America
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Changes in motor behavior, neuropathology, and gut microbiota of a Batten disease mouse model following administration of acidified drinking water. Sci Rep 2019; 9:14962. [PMID: 31628420 PMCID: PMC6802212 DOI: 10.1038/s41598-019-51488-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 10/02/2019] [Indexed: 12/14/2022] Open
Abstract
CLN3 mutations cause the fatal neurodegenerative disorder, CLN3 Batten disease. The Cln3−/− mouse model displays characteristic features of the human disease including motor deficits. When mice received acidified drinking water (pH 2.5–2.9) instead of normal tap water (pH 8.4) for several generations, the motor skills of Cln3−/− mice normalized to control levels, indicating a disease-modifying effect of acidified water. Here we investigated if acidified water administered from postnatal day 21 has therapeutic benefits in Cln3−/− mice. Indeed, acidified water temporarily attenuated the motor deficits, had beneficial effects on behavioral parameters and prevented microglial activation in the brain of Cln3−/− mice. Interestingly, in control mice, acidified drinking water caused brain region-specific glial activation and significant changes in motor performance. Since the gut microbiota can influence neurological functions, we examined it in our disease model and found that the gut microbiota of Cln3−/− mice was markedly different from control mice, and acidified water differentially changed the gut microbiota composition in these mice. These results indicate that acidified water may provide therapeutic benefit to CLN3 Batten disease patients, and that the pH of drinking water is a major environmental factor that strongly influences the results of murine behavioral and pathological studies.
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Schmidtberg H, Shukla SP, Halitschke R, Vogel H, Vilcinskas A. Symbiont-mediated chemical defense in the invasive ladybird Harmonia axyridis. Ecol Evol 2019; 9:1715-1729. [PMID: 30847067 PMCID: PMC6392489 DOI: 10.1002/ece3.4840] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 10/07/2018] [Accepted: 11/29/2018] [Indexed: 01/05/2023] Open
Abstract
The volatile alkylpyrazines methyl- and methoxypyrazines (MPs) present in the reflex bleeds of coccinellid beetles such as the harlequin ladybird beetle Harmonia axyridis are important semiochemicals that function in antipredatory defense behavior. Pyrazines have also been coadapted from a primarily defensive role into pheromones that function in intraspecific communication, attraction, and aggregation behavior. However, the biosynthesis of MPs in ladybird beetles is poorly understood. Here, we tested the hypothesis that MPs could be produced by microbial symbionts in H. axyridis, which generates four different MPs. The evaluation of tissue-specific MP production showed that MP concentrations were highest in the gut tissue and hemolymph of the beetles rather than the fat body tissue as the presumed site of MP biosynthesis. Furthermore, manipulation of gut microbiota by antibiotic-containing diets resulted in a lower MP content in adult beetles. The analysis of the bacterial community of the digestive tract revealed the presence of bacteria of the genera Serratia and Lactococcus which are reportedly able to produce MPs. In line with the known diet-dependent production of MP in H. axyridis, we determined that the presence or relative abundance of some of the potential MP producers (Enterococcus and Staphylococcus) is also diet-dependent. We hypothesize a potential role of the microbiota in MP production in H. axyridis as a possible example for outsourcing the synthesis of ecologically important semiochemicals to its gut bacteria.
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Affiliation(s)
- Henrike Schmidtberg
- Institute for Insect BiotechnologyJustus‐Liebig‐University of GiessenGiessenGermany
| | - Shantanu P. Shukla
- Entomology DepartmentMax‐Planck Institute for Chemical EcologyJenaGermany
| | - Rayko Halitschke
- Institute for Insect BiotechnologyJustus‐Liebig‐University of GiessenGiessenGermany
- Entomology DepartmentMax‐Planck Institute for Chemical EcologyJenaGermany
| | - Heiko Vogel
- Entomology DepartmentMax‐Planck Institute for Chemical EcologyJenaGermany
| | - Andreas Vilcinskas
- Institute for Insect BiotechnologyJustus‐Liebig‐University of GiessenGiessenGermany
- Department of BioresourcesFraunhofer Institute for Molecular Biology and Applied EcologyGiessenGermany
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State-of-the-Art Adult Chronic Rhinosinusitis Microbiome: Perspective for Future Studies in Pediatrics. SINUSITIS 2018. [DOI: 10.3390/sinusitis3010001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
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Hu J, Dong H, Xu Q, Ling W, Qu J, Qiang Z. Impacts of water quality on the corrosion of cast iron pipes for water distribution and proposed source water switch strategy. WATER RESEARCH 2018; 129:428-435. [PMID: 29179122 DOI: 10.1016/j.watres.2017.10.065] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2017] [Revised: 10/23/2017] [Accepted: 10/28/2017] [Indexed: 06/07/2023]
Abstract
Switch of source water may induce "red water" episodes. This study investigated the impacts of water quality on iron release, dissolved oxygen consumption (ΔDO), corrosion scale evolution and bacterial community succession in cast iron pipes used for drinking water distribution at pilot scale, and proposed a source water switch strategy accordingly. Three sets of old cast iron pipe section (named BP, SP and GP) were excavated on site and assembled in a test base, which had historically transported blended water, surface water and groundwater, respectively. Results indicate that an increasing Cl- or SO42- concentration accelerated iron release, but alkalinity and calcium hardness exhibited an opposite tendency. Disinfectant shift from free chlorine to monochloramine slightly inhibited iron release, while the impact of peroxymonosulfate depended on the source water historically transported in the test pipes. The ΔDO was highly consistent with iron release in all three pipe systems. The mass ratio of magnetite to goethite in the corrosion scales of SP was higher than those of BP and GP and kept almost unchanged over the whole operation period. Siderite and calcite formation confirmed that an increasing alkalinity and hardness inhibited iron release. Iron-reducing bacteria decreased in the BP but increased in the SP and GP; meanwhile, sulfur-oxidizing, sulfate-reducing and iron oxidizing bacteria increased in all three pipe systems. To avoid the occurrence of "red water", a source water switch strategy was proposed based on the difference between local and foreign water qualities.
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Affiliation(s)
- Jun Hu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 18 Shuang-qing Road, Beijing 100085, China
| | - Huiyu Dong
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 18 Shuang-qing Road, Beijing 100085, China
| | - Qiang Xu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 18 Shuang-qing Road, Beijing 100085, China
| | - Wencui Ling
- Beijing Municipal Research Institute of Environmental Protection, 59 Beiyingfang Middle Street, Beijing 100037, China
| | - Jiuhui Qu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 18 Shuang-qing Road, Beijing 100085, China
| | - Zhimin Qiang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 18 Shuang-qing Road, Beijing 100085, China.
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Hornick KM, Buschmann AH. Insights into the diversity and metabolic function of bacterial communities in sediments from Chilean salmon aquaculture sites. ANN MICROBIOL 2017. [DOI: 10.1007/s13213-017-1317-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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12
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Salem H, Bauer E, Kirsch R, Berasategui A, Cripps M, Weiss B, Koga R, Fukumori K, Vogel H, Fukatsu T, Kaltenpoth M. Drastic Genome Reduction in an Herbivore's Pectinolytic Symbiont. Cell 2017; 171:1520-1531.e13. [PMID: 29153832 DOI: 10.1016/j.cell.2017.10.029] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 10/10/2017] [Accepted: 10/17/2017] [Indexed: 02/07/2023]
Abstract
Pectin, an integral component of the plant cell wall, is a recalcitrant substrate against enzymatic challenges by most animals. In characterizing the source of a leaf beetle's (Cassida rubiginosa) pectin-degrading phenotype, we demonstrate its dependency on an extracellular bacterium housed in specialized organs connected to the foregut. Despite possessing the smallest genome (0.27 Mb) of any organism not subsisting within a host cell, the symbiont nonetheless retained a functional pectinolytic metabolism targeting the polysaccharide's two most abundant classes: homogalacturonan and rhamnogalacturonan I. Comparative transcriptomics revealed pectinase expression to be enriched in the symbiotic organs, consistent with enzymatic buildup in these structures following immunostaining with pectinase-targeting antibodies. Symbiont elimination results in a drastically reduced host survivorship and a diminished capacity to degrade pectin. Collectively, our findings highlight symbiosis as a strategy for an herbivore to metabolize one of nature's most complex polysaccharides and a universal component of plant tissues.
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Affiliation(s)
- Hassan Salem
- Insect Symbiosis Research Group, Max Planck Institute for Chemical Ecology, Jena 07745, Germany; Department of Biology, Emory University, Atlanta, GA 30320, USA.
| | - Eugen Bauer
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette 4365, Luxembourg
| | - Roy Kirsch
- Department of Entomology, Max Planck Institute for Chemical Ecology, Jena 07745, Germany
| | - Aileen Berasategui
- Insect Symbiosis Research Group, Max Planck Institute for Chemical Ecology, Jena 07745, Germany; Department of Biology, Emory University, Atlanta, GA 30320, USA; Department of Biochemistry, Max Planck Institute for Chemical Ecology, Jena 07745, Germany
| | - Michael Cripps
- AgResearch, Lincoln Research Centre, Lincoln 7608, New Zealand
| | - Benjamin Weiss
- Insect Symbiosis Research Group, Max Planck Institute for Chemical Ecology, Jena 07745, Germany; Department of Evolutionary Ecology, Johannes Gutenberg University, Mainz 55128, Germany
| | - Ryuichi Koga
- National Institute for Advanced Industrial Science and Technology, Tsukuba 305-8566, Japan
| | - Kayoko Fukumori
- National Institute for Advanced Industrial Science and Technology, Tsukuba 305-8566, Japan
| | - Heiko Vogel
- Department of Entomology, Max Planck Institute for Chemical Ecology, Jena 07745, Germany
| | - Takema Fukatsu
- National Institute for Advanced Industrial Science and Technology, Tsukuba 305-8566, Japan
| | - Martin Kaltenpoth
- Insect Symbiosis Research Group, Max Planck Institute for Chemical Ecology, Jena 07745, Germany; Department of Evolutionary Ecology, Johannes Gutenberg University, Mainz 55128, Germany
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Ontiveros-Valencia A, Zhou C, Ilhan ZE, de Saint Cyr LC, Krajmalnik-Brown R, Rittmann BE. Total electron acceptor loading and composition affect hexavalent uranium reduction and microbial community structure in a membrane biofilm reactor. WATER RESEARCH 2017; 125:341-349. [PMID: 28881210 DOI: 10.1016/j.watres.2017.08.060] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2017] [Revised: 08/26/2017] [Accepted: 08/28/2017] [Indexed: 06/07/2023]
Abstract
Molecular microbiology tools (i.e., 16S rDNA gene sequencing) were employed to elucidate changes in the microbial community structure according to the total electron acceptor loading (controlled by influent flow rate and/or medium composition) in a H2-based membrane biofilm reactor evaluated for removal of hexavalent uranium. Once nitrate, sulfate, and dissolved oxygen were replaced by U(VI) and bicarbonate and the total acceptor loading was lowered, slow-growing bacteria capable of reducing U(VI) to U(IV) dominated in the biofilm community: Replacing denitrifying bacteria Rhodocyclales and Burkholderiales were spore-producing Clostridiales and Natranaerobiales. Though potentially competing for electrons with U(VI) reducers, homo-acetogens helped attain steady U(VI) reduction, while methanogenesis inhibited U(VI) reduction. U(VI) reduction was reinstated through suppression of methanogenesis by addition of bromoethanesulfonate or by competition from SRB when sulfate was re-introduced. Predictive metagenome analysis further points out community changes in response to alterations in the electron-acceptor loading: Sporulation and homo-acetogenesis were critical factors for strengthening stable microbial U(VI) reduction. This study documents that sporulation was important to long-term U(VI) reduction, whether or not microorganisms that carry out U(VI) reduction mediated by cytochrome c3, such as SRB and ferric-iron-reducers, were inhibited.
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Affiliation(s)
- Aura Ontiveros-Valencia
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, 1001 South McAllister Ave, Tempe, AZ 85287-5701, USA; Escuela de Ingenieria y Ciencias, Tecnologico de Monterrey, Campus Monterrey, Ave. Eugenio Garza Sada 2501, Monterrey, NL 64849, Mexico; Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, 156 Fitzpatrick Hall, Notre Dame, IN 46617, USA
| | - Chen Zhou
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, 1001 South McAllister Ave, Tempe, AZ 85287-5701, USA.
| | - Zehra Esra Ilhan
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, 1001 South McAllister Ave, Tempe, AZ 85287-5701, USA
| | - Louis Cornette de Saint Cyr
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, 1001 South McAllister Ave, Tempe, AZ 85287-5701, USA; Institut Sup'Biotech de Paris, France
| | - Rosa Krajmalnik-Brown
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, 1001 South McAllister Ave, Tempe, AZ 85287-5701, USA
| | - Bruce E Rittmann
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, 1001 South McAllister Ave, Tempe, AZ 85287-5701, USA
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14
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Salt Marsh Bacterial Communities before and after the Deepwater Horizon Oil Spill. Appl Environ Microbiol 2017; 83:AEM.00784-17. [PMID: 28778895 DOI: 10.1128/aem.00784-17] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 07/11/2017] [Indexed: 11/20/2022] Open
Abstract
Coastal salt marshes along the northern Gulf of Mexico shoreline received varied types and amounts of weathered oil residues after the 2010 Deepwater Horizon oil spill. At the time, predicting how marsh bacterial communities would respond and/or recover to oiling and other environmental stressors was difficult because baseline information on community composition and dynamics was generally unavailable. Here, we evaluated marsh vegetation, physicochemistry, flooding frequency, hydrocarbon chemistry, and subtidal sediment bacterial communities from 16S rRNA gene surveys at 11 sites in southern Louisiana before the oil spill and resampled the same marshes three to four times over 38 months after the spill. Calculated hydrocarbon biomarker indices indicated that oil replaced native natural organic matter (NOM) originating from Spartina alterniflora and marine phytoplankton in the marshes between May 2010 and September 2010. At all the studied marshes, the major class- and order-level shifts among the phyla Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria occurred within these first 4 months, but another community shift occurred at the time of peak oiling in 2011. Two years later, hydrocarbon levels decreased and bacterial communities became more diverse, being dominated by Alphaproteobacteria (Rhizobiales), Chloroflexi (Dehalococcoidia), and Planctomycetes Compositional changes through time could be explained by NOM source differences, perhaps due to vegetation changes, as well as marsh flooding and salinity excursions linked to freshwater diversions. These findings indicate that persistent hydrocarbon exposure alone did not explain long-term community shifts.IMPORTANCE Significant deterioration of coastal salt marshes in Louisiana has been linked to natural and anthropogenic stressors that can adversely affect how ecosystems function. Although microorganisms carry out and regulate most biogeochemical reactions, the diversity of bacterial communities in coastal marshes is poorly known, with limited investigation of potential changes in bacterial communities in response to various environmental stressors. The Deepwater Horizon oil spill provided an unprecedented opportunity to study the long-term effects of an oil spill on microbial systems in marshes. Compared to previous studies, the significance of our research stems from (i) a broader geographic range of studied marshes, (ii) an extended time frame of data collection that includes prespill conditions, (iii) a more accurate procedure using biomarker indices to understand oiling, and (iv) an examination of other potential stressors linked to in situ environmental changes, aside from oil exposure.
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15
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Insights into Butyrate Production in a Controlled Fermentation System via Gene Predictions. mSystems 2017; 2:mSystems00051-17. [PMID: 28761933 PMCID: PMC5516221 DOI: 10.1128/msystems.00051-17] [Citation(s) in RCA: 128] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 06/25/2017] [Indexed: 02/01/2023] Open
Abstract
Butyrate is a common fatty acid produced in important fermentative systems, such as the human/animal gut and other H2 production systems. Despite its importance, there is little information on the partnerships between butyrate producers and other bacteria. The objective of this work was to uncover butyrate-producing microbial communities and possible metabolic routes in a controlled fermentation system aimed at butyrate production. The butyrogenic reactor was operated at 37°C and pH 5.5 with a hydraulic retention time of 31 h and a low hydrogen partial pressure (PH2). High-throughput sequencing and metagenome functional prediction from 16S rRNA data showed that butyrate production pathways and microbial communities were different during batch (closed) and continuous-mode operation. Lactobacillaceae, Lachnospiraceae, and Enterococcaceae were the most abundant phylotypes in the closed system without PH2 control, whereas Prevotellaceae, Ruminococcaceae, and Actinomycetaceae were the most abundant phylotypes under continuous operation at low PH2. Putative butyrate producers identified in our system were from Prevotellaceae, Clostridiaceae, Ruminococcaceae, and Lactobacillaceae. Metagenome prediction analysis suggests that nonbutyrogenic microorganisms influenced butyrate production by generating butyrate precursors such as acetate, lactate, and succinate. 16S rRNA gene analysis suggested that, in the reactor, a partnership between identified butyrogenic microorganisms and succinate (i.e., Actinomycetaceae), acetate (i.e., Ruminococcaceae and Actinomycetaceae), and lactate producers (i.e., Ruminococcaceae and Lactobacillaceae) took place under continuous-flow operation at low PH2. IMPORTANCE This study demonstrates how bioinformatics tools, such as metagenome functional prediction from 16S rRNA genes, can help understand biological systems and reveal microbial interactions in controlled systems (e.g., bioreactors). Results obtained from controlled systems are easier to interpret than those from human/animal studies because observed changes may be specifically attributed to the design conditions imposed on the system. Bioinformatics analysis allowed us to identify potential butyrogenic phylotypes and associated butyrate metabolism pathways when we systematically varied the PH2 in a carefully controlled fermentation system. Our insights may be adapted to butyrate production studies in biohydrogen systems and gut models, since butyrate is a main product and a crucial fatty acid in human/animal colon health.
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16
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Fumasoli A, Bürgmann H, Weissbrodt DG, Wells GF, Beck K, Mohn J, Morgenroth E, Udert KM. Growth of Nitrosococcus-Related Ammonia Oxidizing Bacteria Coincides with Extremely Low pH Values in Wastewater with High Ammonia Content. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:6857-6866. [PMID: 28509546 PMCID: PMC5538757 DOI: 10.1021/acs.est.7b00392] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Ammonia oxidation decreases the pH in wastewaters where alkalinity is limited relative to total ammonia. The activity of ammonia oxidizing bacteria (AOB), however, typically decreases with pH and often ceases completely in slightly acidic wastewaters. Nevertheless, nitrification at low pH has been reported in reactors treating human urine, but it has been unclear which organisms are involved. In this study, we followed the population dynamics of ammonia oxidizing organisms and reactor performance in synthetic fully hydrolyzed urine as the pH decreased over time in response to a decrease in the loading rate. Populations of the β-proteobacterial Nitrosomonas europaea lineage were abundant at the initial pH close to 6, but the growth of a possibly novel Nitrosococcus-related AOB genus decreased the pH to the new level of 2.2, challenging the perception that nitrification is inhibited entirely at low pH values, or governed exclusively by β-proteobacterial AOB or archaea. With the pH shift, nitrite oxidizing bacteria were not further detected, but nitrous acid (HNO2) was still removed through chemical decomposition to nitric oxide (NO) and nitrate. The growth of acid-tolerant γ-proteobacterial AOB should be prevented, by keeping the pH above 5.4, which is a typical pH limit for the N. europaea lineage. Otherwise, the microbial community responsible for high-rate nitrification can be lost, and strong emissions of hazardous volatile nitrogen compounds such as NO are likely.
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Affiliation(s)
- Alexandra Fumasoli
- Eawag,
Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
| | - Helmut Bürgmann
- Eawag,
Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum, Switzerland
| | - David G. Weissbrodt
- Eawag,
Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Institute
of Environmental Engineering, ETH Zürich, 8093 Zürich, Switzerland
- Center
for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, 9100 Aalborg, Denmark
- Department
of Biotechnology, Delft University of Technology, Delft, 2629 HZ, The Netherlands
| | - George F. Wells
- Eawag,
Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Department
of Civil and Environmental Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Karin Beck
- Eawag,
Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum, Switzerland
| | - Joachim Mohn
- Laboratory
for Air Pollution/Environmental Technology, Empa, Swiss Federal Laboratories for Materials Science and Technology, 8600 Dübendorf, Switzerland
| | - Eberhard Morgenroth
- Eawag,
Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Institute
of Environmental Engineering, ETH Zürich, 8093 Zürich, Switzerland
| | - Kai M. Udert
- Eawag,
Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Phone: +41 58 765 5360; fax: +41 58 765 5808; e-mail: ; address: Process Engineering, Überlandstrasse 133, 8600
Dübendorf, Switzerland
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17
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Vogel H, Shukla SP, Engl T, Weiss B, Fischer R, Steiger S, Heckel DG, Kaltenpoth M, Vilcinskas A. The digestive and defensive basis of carcass utilization by the burying beetle and its microbiota. Nat Commun 2017; 8:15186. [PMID: 28485370 PMCID: PMC5436106 DOI: 10.1038/ncomms15186] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Accepted: 03/07/2017] [Indexed: 12/22/2022] Open
Abstract
Insects that use ephemeral resources must rapidly digest nutrients and simultaneously protect them from competitors. Here we use burying beetles (Nicrophorus vespilloides), which feed their offspring on vertebrate carrion, to investigate the digestive and defensive basis of carrion utilization. We characterize gene expression and microbiota composition in the gut, anal secretions, and on carcasses used by the beetles. We find a strict functional compartmentalization of the gut involving differential expression of immune effectors (antimicrobial peptides and lysozymes), as well as digestive and detoxifying enzymes. A distinct microbial community composed of Firmicutes, Proteobacteria and a clade of ascomycetous yeasts (genus Yarrowia) is present in larval and adult guts, and is transmitted to the carcass via anal secretions, where the yeasts express extracellular digestive enzymes and produce antimicrobial compounds. Our results provide evidence of potential metabolic cooperation between the host and its microbiota for digestion, detoxification and defence that extends from the beetle's gut to its nutritional resource.
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Affiliation(s)
- Heiko Vogel
- Department of Entomology, Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany
| | - Shantanu P Shukla
- Department of Entomology, Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany.,Max Planck Institute for Chemical Ecology, Research Group Insect Symbiosis, D-07745 Jena, Germany
| | - Tobias Engl
- Max Planck Institute for Chemical Ecology, Research Group Insect Symbiosis, D-07745 Jena, Germany.,Department for Evolutionary Ecology, Johannes Gutenberg University, D-55128 Mainz, Germany
| | - Benjamin Weiss
- Max Planck Institute for Chemical Ecology, Research Group Insect Symbiosis, D-07745 Jena, Germany.,Department for Evolutionary Ecology, Johannes Gutenberg University, D-55128 Mainz, Germany
| | - Rainer Fischer
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), D-52074 Aachen, Germany
| | - Sandra Steiger
- University of Ulm, Institute of Evolutionary Ecology and Conservation Genomics, D-89081 Ulm, Germany
| | - David G Heckel
- Department of Entomology, Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany
| | - Martin Kaltenpoth
- Max Planck Institute for Chemical Ecology, Research Group Insect Symbiosis, D-07745 Jena, Germany.,Department for Evolutionary Ecology, Johannes Gutenberg University, D-55128 Mainz, Germany
| | - Andreas Vilcinskas
- Institute for Insect Biotechnology, Justus Liebig University of Giessen, D-35392 Giessen, Germany
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18
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Flórez LV, Scherlach K, Gaube P, Ross C, Sitte E, Hermes C, Rodrigues A, Hertweck C, Kaltenpoth M. Antibiotic-producing symbionts dynamically transition between plant pathogenicity and insect-defensive mutualism. Nat Commun 2017; 8:15172. [PMID: 28452358 PMCID: PMC5414355 DOI: 10.1038/ncomms15172] [Citation(s) in RCA: 113] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Accepted: 03/06/2017] [Indexed: 11/17/2022] Open
Abstract
Pathogenic and mutualistic bacteria associated with eukaryotic hosts often lack distinctive genomic features, suggesting regular transitions between these lifestyles. Here we present evidence supporting a dynamic transition from plant pathogenicity to insect-defensive mutualism in symbiotic Burkholderia gladioli bacteria. In a group of herbivorous beetles, these symbionts protect the vulnerable egg stage against detrimental microbes. The production of a blend of antibiotics by B. gladioli, including toxoflavin, caryoynencin and two new antimicrobial compounds, the macrolide lagriene and the isothiocyanate sinapigladioside, likely mediate this defensive role. In addition to vertical transmission, these insect symbionts can be exchanged via the host plant and retain the ability to initiate systemic plant infection at the expense of the plant's fitness. Our findings provide a paradigm for the transition between pathogenic and mutualistic lifestyles and shed light on the evolution and chemical ecology of this defensive mutualism.
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Affiliation(s)
- Laura V. Flórez
- Insect Symbiosis Research Group, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straβe 8, 07745 Jena, Germany
- Department for Evolutionary Ecology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University, Johann-Joachim-Becher-Weg 13, 55128 Mainz, Germany
| | - Kirstin Scherlach
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Products Research and Infection Biology, HKI, Beutenbergstraβe 11a, 07745 Jena, Germany
| | - Paul Gaube
- Insect Symbiosis Research Group, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straβe 8, 07745 Jena, Germany
| | - Claudia Ross
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Products Research and Infection Biology, HKI, Beutenbergstraβe 11a, 07745 Jena, Germany
| | - Elisabeth Sitte
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Products Research and Infection Biology, HKI, Beutenbergstraβe 11a, 07745 Jena, Germany
| | - Cornelia Hermes
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Products Research and Infection Biology, HKI, Beutenbergstraβe 11a, 07745 Jena, Germany
| | - Andre Rodrigues
- Department of Biochemistry and Microbiology, UNESP-São Paulo State University, Av. 24A, n. 1515-Bela Vista, Rio Claro, São Paulo 13506-900, Brazil
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Products Research and Infection Biology, HKI, Beutenbergstraβe 11a, 07745 Jena, Germany
- Chair for Natural Product Chemistry, Friedrich Schiller University, 07743 Jena, Germany
| | - Martin Kaltenpoth
- Insect Symbiosis Research Group, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straβe 8, 07745 Jena, Germany
- Department for Evolutionary Ecology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University, Johann-Joachim-Becher-Weg 13, 55128 Mainz, Germany
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Distinct Biogeographic Patterns for Archaea, Bacteria, and Fungi along the Vegetation Gradient at the Continental Scale in Eastern China. mSystems 2017; 2:mSystems00174-16. [PMID: 28191504 PMCID: PMC5296412 DOI: 10.1128/msystems.00174-16] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2016] [Accepted: 01/05/2017] [Indexed: 11/20/2022] Open
Abstract
The natural forest ecosystem in Eastern China, from tropical forest to boreal forest, has declined due to cropland development during the last 300 years, yet little is known about the historical biogeographic patterns and driving processes for the major domains of microorganisms along this continental-scale natural vegetation gradient. We predicted the biogeographic patterns of soil archaeal, bacterial, and fungal communities across 110 natural forest sites along a transect across four vegetation zones in Eastern China. The distance decay relationships demonstrated the distinct biogeographic patterns of archaeal, bacterial, and fungal communities. While historical processes mainly influenced bacterial community variations, spatially autocorrelated environmental variables mainly influenced the fungal community. Archaea did not display a distance decay pattern along the vegetation gradient. Bacterial community diversity and structure were correlated with the ratio of acid oxalate-soluble Fe to free Fe oxides (Feo/Fed ratio). Fungal community diversity and structure were influenced by dissolved organic carbon (DOC) and free aluminum (Ald), respectively. The role of these environmental variables was confirmed by the correlations between dominant operational taxonomic units (OTUs) and edaphic variables. However, most of the dominant OTUs were not correlated with the major driving variables for the entire communities. These results demonstrate that soil archaea, bacteria, and fungi have different biogeographic patterns and driving processes along this continental-scale natural vegetation gradient, implying different community assembly mechanisms and ecological functions for archaea, bacteria, and fungi in soil ecosystems. IMPORTANCE Understanding biogeographic patterns is a precursor to improving our knowledge of the function of microbiomes and to predicting ecosystem responses to environmental change. Using natural forest soil samples from 110 locations, this study is one of the largest attempts to comprehensively understand the different patterns of soil archaeal, bacterial, and fungal biogeography at the continental scale in eastern China. These patterns in natural forest sites could ascertain reliable soil microbial biogeographic patterns by eliminating anthropogenic influences. This information provides guidelines for monitoring the belowground ecosystem's decline and restoration. Meanwhile, the deviations in the soil microbial communities from corresponding natural forest states indicate the extent of degradation of the soil ecosystem. Moreover, given the association between vegetation type and the microbial community, this information could be used to predict the long-term response of the underground ecosystem to the vegetation distribution caused by global climate change.
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20
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Adam N, Erler T, Kallenbach M, Kaltenpoth M, Kunert G, Baldwin IT, Schuman MC. Sex ratio of mirid populations shifts in response to hostplant co-infestation or altered cytokinin signaling . JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2017; 59:44-59. [PMID: 27862998 PMCID: PMC5234700 DOI: 10.1111/jipb.12507] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Accepted: 11/08/2016] [Indexed: 05/11/2023]
Abstract
Herbivore species sharing a host plant often compete. In this study, we show that host plant-mediated interaction between two insect herbivores - a generalist and a specialist - results in a sex ratio shift of the specialist's offspring. We studied demographic parameters of the specialist Tupiocoris notatus (Hemiptera: Miridae) when co-infesting the host plant Nicotiana attenuata (Solanaceae) with the generalist leafhopper Empoasca sp. (Hemiptera: Cicadellidae). We show that the usually female-biased sex ratio of T. notatus shifts toward a higher male proportion in the offspring on plants co-infested by Empoasca sp. This sex ratio change did not occur after oviposition, nor is it due differential mortality of female and male nymphs. Based on pyrosequencing and PCR of bacterial 16S rRNA amplicons, we concluded that sex ratio shifts were unlikely to be due to infection with Wolbachia or other known sex ratio-distorting endosymbionts. Finally, we used transgenic lines of N. attenuata to evaluate if the sex ratio shift could be mediated by changes in general or specialized host plant metabolites. We found that the sex ratio shift occurred on plants deficient in two cytokinin receptors (irCHK2/3). Thus, cytokinin-regulated traits can alter the offspring sex ratio of the specialist T. notatus.
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Affiliation(s)
- Nora Adam
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, 07745 Jena, Germany
- German Centre for Integrative Biodiversity Research (iDiv), Deutscher Platz 5e, 04103 Leipzig, Germany
| | - Theresa Erler
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, 07745 Jena, Germany
| | - Mario Kallenbach
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, 07745 Jena, Germany
| | - Martin Kaltenpoth
- Max Planck Research Group Insect Symbiosis, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, 07745 Jena, Germany
| | - Grit Kunert
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, 07745 Jena, Germany
| | - Ian T. Baldwin
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, 07745 Jena, Germany
| | - Meredith C. Schuman
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, 07745 Jena, Germany
- German Centre for Integrative Biodiversity Research (iDiv), Deutscher Platz 5e, 04103 Leipzig, Germany
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21
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Lee JT, Frank DN, Ramakrishnan V. Microbiome of the paranasal sinuses: Update and literature review. Am J Rhinol Allergy 2016; 30:3-16. [PMID: 26867525 DOI: 10.2500/ajra.2016.30.4255] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND Our understanding of the resident microbiome of the paranasal sinuses has changed considerably in recent years. Once presumed to be sterile, healthy sinus cavities are now known to harbor a diverse assemblage of microorganisms, and, it is hypothesized that alterations in the kinds and quantities of these microbes may play a role in the pathogenesis of chronic rhinosinusitis (CRS). OBJECTIVES To review the current literature regarding the sinus microbiome and collate research findings from relevant studies published to date. METHODS A systematic literature review was performed on all molecular studies that investigated the microbial communities of the paranasal sinuses. Methods of detection, microbiome composition, and comparative profiling between patients with and without CRS were explored. RESULTS A complex consortium of microorganisms has been demonstrated in the sinuses of both patients with and without CRS. However, the latter generally have been characterized by reduced biodiversity compared with controls, with selective enrichment of particular microbes (e.g., Staphylococcus aureus). Such disruptions in the resident microbiome may contribute to disease pathogenesis by enhancing the virulence of potential pathogens and adversely modulating immune responses. CONCLUSION The advent of culture-independent molecular approaches has led to a greater appreciation of the intricate microbial ecology of the paranasal sinuses. Microbiota composition, distribution, and abundance impact mucosal health and influence pathogen growth and function. A deeper understanding of the host-microbiome relationship and its constituents may encourage development of new treatment paradigms for CRS, which target restoration of microbiome homeostasis and cultivation of optimal microbial communities.
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Affiliation(s)
- Jivianne T Lee
- Department of Otolaryngology-Head and Neck Surgery, Orange County Sinus Institute, Southern California Permanente Medical Group, Irvine, California, USA
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22
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Weiss B, Kaltenpoth M. Bacteriome-Localized Intracellular Symbionts in Pollen-Feeding Beetles of the Genus Dasytes (Coleoptera, Dasytidae). Front Microbiol 2016; 7:1486. [PMID: 27713733 PMCID: PMC5031591 DOI: 10.3389/fmicb.2016.01486] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 09/07/2016] [Indexed: 01/28/2023] Open
Abstract
Several insect taxa are associated with intracellular symbionts that provision limiting nutrients to their hosts. Such tightly integrated symbioses are especially common in insects feeding on nutritionally challenging diets like phloem sap or vertebrate blood, but also occur in seed-eating and omnivorous taxa. Here, we characterize an intracellular symbiosis in pollen-feeding beetles of the genus Dasytes (Coleoptera, Dasytidae). High-throughput tag-encoded 16S amplicon pyrosequencing of adult D. plumbeus and D. virens revealed a single gamma-proteobacterial symbiont ('Candidatus Dasytiphilus stammeri') that amounts to 52.4-98.7% of the adult beetles' entire microbial community. Almost complete 16S rRNA sequences phylogenetically placed the symbiont into a clade comprising Buchnera and other insect endosymbionts, but sequence similarities to these closest relatives were surprisingly low (83.4-87.4%). Using histological examination, three-dimensional reconstructions, and fluorescence in situ hybridization, we localized the symbionts in three mulberry-shaped bacteriomes that are associated with the mid- to hind-gut transition in adult male and female beetles. Given the specialized pollen-feeding habits of the adults that contrasts with the larvae's carnivorous lifestyle, the symbionts may provision limiting essential amino acids or vitamins as in other intracellular symbioses, or they might produce digestive enzymes that break up the fastidious pollen walls and thereby contribute to the host's nutrition. In either case, the presence of gamma-proteobacterial symbionts in pollen-feeding beetles indicates that intracellular mutualists are more widely distributed across insects with diverse feeding habits than previously recognized.
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Affiliation(s)
- Benjamin Weiss
- Insect Symbiosis Research Group, Max Planck Institute for Chemical EcologyJena, Germany
- Department for Evolutionary Ecology, Institute for Zoology, Johannes Gutenberg University of MainzMainz, Germany
| | - Martin Kaltenpoth
- Insect Symbiosis Research Group, Max Planck Institute for Chemical EcologyJena, Germany
- Department for Evolutionary Ecology, Institute for Zoology, Johannes Gutenberg University of MainzMainz, Germany
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23
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Dohet L, Grégoire JC, Berasategui A, Kaltenpoth M, Biedermann PHW. Bacterial and fungal symbionts of parasiticDendroctonusbark beetles. FEMS Microbiol Ecol 2016; 92:fiw129. [DOI: 10.1093/femsec/fiw129] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/06/2016] [Indexed: 11/14/2022] Open
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Ontiveros-Valencia A, Penton CR, Krajmalnik-Brown R, Rittmann BE. Hydrogen-fed biofilm reactors reducing selenate and sulfate: Community structure and capture of elemental selenium within the biofilm. Biotechnol Bioeng 2016; 113:1736-44. [DOI: 10.1002/bit.25945] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 01/16/2016] [Accepted: 01/20/2016] [Indexed: 11/07/2022]
Affiliation(s)
- Aura Ontiveros-Valencia
- Swette Center for Environmental Biotechnology; Biodesign Institute, Arizona State University; 1001 South McAllister Ave. Tempe Arizona 85287-5701
| | | | - Rosa Krajmalnik-Brown
- Swette Center for Environmental Biotechnology; Biodesign Institute, Arizona State University; 1001 South McAllister Ave. Tempe Arizona 85287-5701
- School of Sustainable Engineering and the Built Environment; Arizona State University; Tempe Arizona
| | - Bruce E. Rittmann
- Swette Center for Environmental Biotechnology; Biodesign Institute, Arizona State University; 1001 South McAllister Ave. Tempe Arizona 85287-5701
- School of Sustainable Engineering and the Built Environment; Arizona State University; Tempe Arizona
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Suhr M, Banjara N, Hallen‐Adams H. Sequence‐based methods for detecting and evaluating the human gut mycobiome. Lett Appl Microbiol 2016; 62:209-15. [DOI: 10.1111/lam.12539] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 11/25/2015] [Accepted: 12/06/2015] [Indexed: 12/22/2022]
Affiliation(s)
- M.J. Suhr
- Department of Food Science and Technology University of Nebraska‐Lincoln Lincoln NE USA
| | - N. Banjara
- Department of Food Science and Technology University of Nebraska‐Lincoln Lincoln NE USA
| | - H.E. Hallen‐Adams
- Department of Food Science and Technology University of Nebraska‐Lincoln Lincoln NE USA
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Geographic patterns of co-occurrence network topological features for soil microbiota at continental scale in eastern China. ISME JOURNAL 2016; 10:1891-901. [PMID: 26771927 PMCID: PMC5029158 DOI: 10.1038/ismej.2015.261] [Citation(s) in RCA: 518] [Impact Index Per Article: 64.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 12/01/2015] [Accepted: 12/08/2015] [Indexed: 01/01/2023]
Abstract
Soil microbiota play a critical role in soil biogeochemical processes and have a profound effect on soil functions. Recent studies have revealed microbial co-occurrence patterns in soil microbial communities, yet the geographic pattern of topological features in soil microbial co-occurrence networks at the continental scale are largely unknown. Here, we investigated the shifts of topological features in co-occurrence networks inferred from soil microbiota along a continental scale in eastern China. Integrating archaeal, bacterial and fungal community datasets, we inferred a meta-community co-occurrence network and analyzed node-level and network-level topological shifts associated with five climatic regions. Both node-level and network-level topological features revealed geographic patterns wherein microorganisms in the northern regions had closer relationships but had a lower interaction influence than those in the southern regions. We further identified topological differences associated with taxonomic groups and demonstrated that co-occurrence patterns were random for archaea and non-random for bacteria and fungi. Given that microbial interactions may contribute to soil functions more than species diversity, this geographic shift of topological features provides new insight into studying microbial biogeographic patterns, their organization and impacts on soil-associated function.
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Zhang L, Zhang C, Hu C, Liu H, Bai Y, Qu J. Sulfur-based mixotrophic denitrification corresponding to different electron donors and microbial profiling in anoxic fluidized-bed membrane bioreactors. WATER RESEARCH 2015; 85:422-431. [PMID: 26364226 DOI: 10.1016/j.watres.2015.08.055] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 07/26/2015] [Accepted: 08/30/2015] [Indexed: 06/05/2023]
Abstract
Sulfur-based mixotrophic denitrifying anoxic fluidized bed membrane bioreactors (AnFB-MBR) were developed for the treatment of nitrate-contaminated groundwater with minimized sulfate production. The nitrate removal rates obtained in the methanol- and ethanol-fed mixotrophic denitrifying AnFB-MBRs reached 1.44-3.84 g NO3 -N/L reactor d at a hydraulic retention time of 0.5 h, which were significantly superior to those reported in packed bed reactors. Compared to methanol, ethanol was found to be a more effective external carbon source for sulfur-based mixotrophic denitrification due to lower sulfate and total organic carbon concentrations in the effluent. Using pyrosequencing, the phylotypes of primary microbial groups in the reactor, including sulfur-oxidizing autotrophic denitrifiers, methanol- or ethanol-supported heterotrophic denitrifiers, were investigated in response to changes in electron donors. Principal component and heatmap analyses indicated that selection of electron donating substrates largely determined the microbial community structure. The abundance of Thiobacillus decreased from 45.1% in the sulfur-oxidizing autotrophic denitrifying reactor to 12.0% and 14.2% in sulfur-based methanol- and ethanol-fed mixotrophic denitrifying bioreactors, respectively. Heterotrophic Methyloversatilis and Thauera bacteria became more dominant in the mixotrophic denitrifying bioreactors, which were possibly responsible for the observed methanol- and ethanol-associated denitrification.
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Affiliation(s)
- Lili Zhang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Research Center of the Ministry of Education for High Gravity Engineering and Technology, Beijing University of Chemical Technology, Beijing 100029, China; State Key Laboratory of Organic-Inorganic Composites, Beijing University of Chemical Technology, Beijing 100029, China
| | - Chao Zhang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Chengzhi Hu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
| | - Huijuan Liu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yaohui Bai
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Jiuhui Qu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
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Sudakaran S, Retz F, Kikuchi Y, Kost C, Kaltenpoth M. Evolutionary transition in symbiotic syndromes enabled diversification of phytophagous insects on an imbalanced diet. ISME JOURNAL 2015; 9:2587-604. [PMID: 26023876 DOI: 10.1038/ismej.2015.75] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Revised: 03/25/2015] [Accepted: 04/03/2015] [Indexed: 11/09/2022]
Abstract
Evolutionary adaptations for the exploitation of nutritionally challenging or toxic host plants represent a major force driving the diversification of phytophagous insects. Although symbiotic bacteria are known to have essential nutritional roles for insects, examples of radiations into novel ecological niches following the acquisition of specific symbionts remain scarce. Here we characterized the microbiota across bugs of the family Pyrrhocoridae and investigated whether the acquisition of vitamin-supplementing symbionts enabled the hosts to diversify into the nutritionally imbalanced and chemically well-defended seeds of Malvales plants as a food source. Our results indicate that vitamin-provisioning Actinobacteria (Coriobacterium and Gordonibacter), as well as Firmicutes (Clostridium) and Proteobacteria (Klebsiella) are widespread across Pyrrhocoridae, but absent from the sister family Largidae and other outgroup taxa. Despite the consistent association with a specific microbiota, the Pyrrhocoridae phylogeny is neither congruent with a dendrogram based on the hosts' microbial community profiles nor phylogenies of individual symbiont strains, indicating frequent horizontal exchange of symbiotic partners. Phylogenetic dating analyses based on the fossil record reveal an origin of the Pyrrhocoridae core microbiota in the late Cretaceous (81.2-86.5 million years ago), following the transition from crypt-associated beta-proteobacterial symbionts to an anaerobic community localized in the M3 region of the midgut. The change in symbiotic syndromes (that is, symbiont identity and localization) and the acquisition of the pyrrhocorid core microbiota followed the evolution of their preferred host plants (Malvales), suggesting that the symbionts facilitated their hosts' adaptation to this imbalanced nutritional resource and enabled the subsequent diversification in a competition-poor ecological niche.
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Affiliation(s)
- Sailendharan Sudakaran
- Insect Symbiosis Research Group, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Franziska Retz
- Insect Symbiosis Research Group, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Yoshitomo Kikuchi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST) Hokkaido, Sapporo, Japan
| | - Christian Kost
- Experimental Ecology and Evolution Research Group, Max Planck Institute for Chemical Ecology, Jena, Germany.,Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| | - Martin Kaltenpoth
- Insect Symbiosis Research Group, Max Planck Institute for Chemical Ecology, Jena, Germany
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A review of neosporosis and pathologic findings of Neospora caninum infection in wildlife. INTERNATIONAL JOURNAL FOR PARASITOLOGY-PARASITES AND WILDLIFE 2015; 4:216-38. [PMID: 25973393 PMCID: PMC4427759 DOI: 10.1016/j.ijppaw.2015.04.002] [Citation(s) in RCA: 124] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 04/16/2015] [Accepted: 04/17/2015] [Indexed: 11/24/2022]
Abstract
Neospora caninum is an apicomplexan parasite that is the etiologic agent of neosporosis, a devastating infectious disease regarded as a major cause of reproductive loss in cattle and neuromuscular disease in dogs worldwide. This protozoan pathogen is maintained in the environment by a heteroxenous life cycle that involves a definitive canid host and a wide range of intermediate hosts. In recent years, a number of wildlife species have been investigated for their possible involvement in the N. caninum life cycle and many have been implicated as intermediate hosts. However, in many instances these studies have utilized serological and molecular techniques to detect infection in clinically normal animals, and investigation of possible associated morbidity, mortality, and pathology has been neglected. As such, the occurrence and importance of Neospora-associated disease in wildlife species are unknown. In order to improve our understanding of the significance of N. caninum infection in nondomestic species, the present review provides an up-to-date summary of clinical neosporosis and N. caninum-associated pathologic lesions in naturally and experimentally infected wildlife species. We provide a list of all free-ranging and captive wildlife species identified with N. caninum infection to date using currently available diagnostic tools. The advantages and disadvantages of diagnostic methods in wildlife are addressed in order to recommend optimal diagnosis of confirming N. caninum infection and neosporosis in nondomestic species. Although current data would suggest that N. caninum infection does not adversely impact wildlife populations, there is a need for greater international uniformity in the diagnosis of N. caninum infection and neosporosis in nondomestic species in order to assess the true consequences of parasite infection.
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Profiling microbial communities in manganese remediation systems treating coal mine drainage. Appl Environ Microbiol 2015; 81:2189-98. [PMID: 25595765 DOI: 10.1128/aem.03643-14] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Water discharging from abandoned coal mines can contain extremely high manganese levels. Removing this metal is an ongoing challenge. Passive Mn(II) removal beds (MRBs) contain microorganisms that oxidize soluble Mn(II) to insoluble Mn(III/IV) minerals, but system performance is unpredictable. Using amplicon pyrosequencing, we profiled the bacterial, fungal, algal, and archaeal communities in four MRBs, performing at different levels, in Pennsylvania to determine whether they differed among MRBs and from surrounding soil and to establish the relative abundance of known Mn(II) oxidizers. Archaea were not detected; PCRs with archaeal primers returned only nontarget bacterial sequences. Fungal taxonomic profiles differed starkly between sites that remove the majority of influent Mn and those that do not, with the former being dominated by Ascomycota (mostly Dothideomycetes) and the latter by Basidiomycota (almost entirely Agaricomycetes). Taxonomic profiles for the other groups did not differ significantly between MRBs, but operational taxonomic unit-based analyses showed significant clustering by MRB with all three groups (P < 0.05). Soil samples clustered separately from MRBs in all groups except fungi, whose soil samples clustered loosely with their respective MRB. Known Mn(II) oxidizers accounted for a minor proportion of bacterial sequences (up to 0.20%) but a greater proportion of fungal sequences (up to 14.78%). MRB communities are more diverse than previously thought, and more organisms may be capable of Mn(II) oxidation than are currently known.
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Leonhardt SD, Kaltenpoth M. Microbial communities of three sympatric Australian stingless bee species. PLoS One 2014; 9:e105718. [PMID: 25148082 PMCID: PMC4141829 DOI: 10.1371/journal.pone.0105718] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 07/25/2014] [Indexed: 01/29/2023] Open
Abstract
Bacterial symbionts of insects have received increasing attention due to their prominent role in nutrient acquisition and defense. In social bees, symbiotic bacteria can maintain colony homeostasis and fitness, and the loss or alteration of the bacterial community may be associated with the ongoing bee decline observed worldwide. However, analyses of microbiota associated with bees have been largely confined to the social honeybees (Apis mellifera) and bumblebees (Bombus spec.), revealing – among other taxa – host-specific lactic acid bacteria (LAB, genus Lactobacillus) that are not found in solitary bees. Here, we characterized the microbiota of three Australian stingless bee species (Apidae: Meliponini) of two phylogenetically distant genera (Tetragonula and Austroplebeia). Besides common plant bacteria, we find LAB in all three species, showing that LAB are shared by honeybees, bumblebees and stingless bees across geographical regions. However, while LAB of the honeybee-associated Firm4–5 clusters were present in Tetragonula, they were lacking in Austroplebeia. Instead, we found a novel clade of likely host-specific LAB in all three Australian stingless bee species which forms a sister clade to a large cluster of Halictidae-associated lactobacilli. Our findings indicate both a phylogenetic and geographical signal of host-specific LAB in stingless bees and highlight stingless bees as an interesting group to investigate the evolutionary history of the bee-LAB association.
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Affiliation(s)
- Sara D. Leonhardt
- Department of Animal Ecology and Tropical Biology, University of Würzburg, Würzburg, Germany
- * E-mail: (MK); (SL)
| | - Martin Kaltenpoth
- Insect Symbiosis Research Group, Max Planck Institute for Chemical Ecology, Jena, Germany
- * E-mail: (MK); (SL)
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Coats VC, Rumpho ME. The rhizosphere microbiota of plant invaders: an overview of recent advances in the microbiomics of invasive plants. Front Microbiol 2014; 5:368. [PMID: 25101069 PMCID: PMC4107844 DOI: 10.3389/fmicb.2014.00368] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Accepted: 07/01/2014] [Indexed: 11/23/2022] Open
Abstract
Plants in terrestrial systems have evolved in direct association with microbes functioning as both agonists and antagonists of plant fitness and adaptability. As such, investigations that segregate plants and microbes provide only a limited scope of the biotic interactions that dictate plant community structure and composition in natural systems. Invasive plants provide an excellent working model to compare and contrast the effects of microbial communities associated with natural plant populations on plant fitness, adaptation, and fecundity. The last decade of DNA sequencing technology advancements opened the door to microbial community analysis, which has led to an increased awareness of the importance of an organism’s microbiome and the disease states associated with microbiome shifts. Employing microbiome analysis to study the symbiotic networks associated with invasive plants will help us to understand what microorganisms contribute to plant fitness in natural systems, how different soil microbial communities impact plant fitness and adaptability, specificity of host–microbe interactions in natural plant populations, and the selective pressures that dictate the structure of above-ground and below-ground biotic communities. This review discusses recent advances in invasive plant biology that have resulted from microbiome analyses as well as the microbial factors that direct plant fitness and adaptability in natural systems.
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Affiliation(s)
- Vanessa C Coats
- Department of Molecular and Biomedical Sciences, University of Maine Orono, ME, USA
| | - Mary E Rumpho
- Department of Molecular and Cell Biology, University of Connecticut Storrs, CT, USA
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33
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Ontiveros-Valencia A, Tang Y, Zhao HP, Friese D, Overstreet R, Smith J, Evans P, Rittmann BE, Krajmalnik-Brown R. Pyrosequencing analysis yields comprehensive assessment of microbial communities in pilot-scale two-stage membrane biofilm reactors. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2014; 48:7511-7518. [PMID: 24917125 DOI: 10.1021/es5012466] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
We studied the microbial community structure of pilot two-stage membrane biofilm reactors (MBfRs) designed to reduce nitrate (NO3(-)) and perchlorate (ClO4(-)) in contaminated groundwater. The groundwater also contained oxygen (O2) and sulfate (SO4(2-)), which became important electron sinks that affected the NO3(-) and ClO4(-) removal rates. Using pyrosequencing, we elucidated how important phylotypes of each "primary" microbial group, i.e., denitrifying bacteria (DB), perchlorate-reducing bacteria (PRB), and sulfate-reducing bacteria (SRB), responded to changes in electron-acceptor loading. UniFrac, principal coordinate analysis (PCoA), and diversity analyses documented that the microbial community of biofilms sampled when the MBfRs had a high acceptor loading were phylogenetically distant from and less diverse than the microbial community of biofilm samples with lower acceptor loadings. Diminished acceptor loading led to SO4(2-) reduction in the lag MBfR, which allowed Desulfovibrionales (an SRB) and Thiothrichales (sulfur-oxidizers) to thrive through S cycling. As a result of this cooperative relationship, they competed effectively with DB/PRB phylotypes such as Xanthomonadales and Rhodobacterales. Thus, pyrosequencing illustrated that while DB, PRB, and SRB responded predictably to changes in acceptor loading, a decrease in total acceptor loading led to important shifts within the "primary" groups, the onset of other members (e.g., Thiothrichales), and overall greater diversity.
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Affiliation(s)
- Aura Ontiveros-Valencia
- Biodesign Institute, Swette Center for Environmental Biotechnology, Arizona State University , 1001 South McAllister Avenue, Tempe, Arizona 85287-5701, United States
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Das S, Dash HR, Mangwani N, Chakraborty J, Kumari S. Understanding molecular identification and polyphasic taxonomic approaches for genetic relatedness and phylogenetic relationships of microorganisms. J Microbiol Methods 2014; 103:80-100. [PMID: 24886836 DOI: 10.1016/j.mimet.2014.05.013] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Revised: 05/22/2014] [Accepted: 05/22/2014] [Indexed: 12/29/2022]
Abstract
The major proportion of earth's biological diversity is inhabited by microorganisms and they play a useful role in diversified environments. However, taxonomy of microorganisms is progressing at a snail's pace, thus less than 1% of the microbial population has been identified so far. The major problem associated with this is due to a lack of uniform, reliable, advanced, and common to all practices for microbial identification and systematic studies. However, recent advances have developed many useful techniques taking into account the house-keeping genes as well as targeting other gene catalogues (16S rRNA, rpoA, rpoB, gyrA, gyrB etc. in case of bacteria and 26S, 28S, β-tubulin gene in case of fungi). Some uncultivable approaches using much advanced techniques like flow cytometry and gel based techniques have also been used to decipher microbial diversity. However, all these techniques have their corresponding pros and cons. In this regard, a polyphasic taxonomic approach is advantageous because it exploits simultaneously both conventional as well as molecular identification techniques. In this review, certain aspects of the merits and limitations of different methods for molecular identification and systematics of microorganisms have been discussed. The major advantages of the polyphasic approach have also been described taking into account certain groups of bacteria as case studies to arrive at a consensus approach to microbial identification.
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Affiliation(s)
- Surajit Das
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela 769 008, Odisha, India.
| | - Hirak R Dash
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela 769 008, Odisha, India
| | - Neelam Mangwani
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela 769 008, Odisha, India
| | - Jaya Chakraborty
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela 769 008, Odisha, India
| | - Supriya Kumari
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela 769 008, Odisha, India
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Ontiveros-Valencia A, Tang Y, Krajmalnik-Brown R, Rittmann BE. Managing the interactions between sulfate- and perchlorate-reducing bacteria when using hydrogen-fed biofilms to treat a groundwater with a high perchlorate concentration. WATER RESEARCH 2014; 55:215-224. [PMID: 24607522 DOI: 10.1016/j.watres.2014.02.020] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Revised: 01/11/2014] [Accepted: 02/07/2014] [Indexed: 06/03/2023]
Abstract
A groundwater containing an unusually high concentration (∼4000 μg/L) of perchlorate (ClO4(-)) and significant (∼60 mg/L) sulfate (SO4(2-)) was treated with hydrogen (H2)-fed biofilms. The objective was to manage the interactions between sulfate-reducing bacteria (SRB) and perchlorate-reducing bacteria (PRB) by controlling the H2-delivery capacity to achieve ClO4(-) reduction to below the detection limit (4 μg/L). Complete ClO4(-) reduction with minimized SO4(2-) reduction was achieved by using two membrane biofilm reactors (MBfRs) in series. The lead MBfR removed >96% ClO4(-), and the lag MBfR further reduced ClO4(-) to below the detection limit. SO4(2-) reduction ranged from 10 to 60%, and lower SO4(2-) reduction corresponded to lower H2 availability (i.e., lower H2 pressure or membranes with lower H2-delivery capacity). Minimizing SO4(2-) reduction improved ClO4(-) removal by increasing the fraction of PRB in the biofilm. High SO4(2-) flux correlated with enrichment of Desulfovibrionales, autotrophic SRB that can compete strongly with denitrifying bacteria (DB) and PRB. Increased SO4(2-) reduction also led to enrichment of: 1) Ignavibacteriales and Thiobacteriales, sulfide-oxidizing bacteria that allow sulfur cycling in the biofilm; 2) Bacteroidales, heterotrophic microorganisms likely using organic sources of carbon (e.g., acetate); and 3) Spirochaetales, which potentially utilize soluble microbial products (SMPs) from autotrophic SRB to produce acetate.
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Affiliation(s)
- Aura Ontiveros-Valencia
- Biodesign Institute, Swette Center for Environmental Biotechnology, Arizona State University, 1001 South McAllister Ave. Tempe, AZ 85287-5701, USA; School of Sustainability, Arizona State University, USA
| | - Youneng Tang
- Biodesign Institute, Swette Center for Environmental Biotechnology, Arizona State University, 1001 South McAllister Ave. Tempe, AZ 85287-5701, USA
| | - Rosa Krajmalnik-Brown
- Biodesign Institute, Swette Center for Environmental Biotechnology, Arizona State University, 1001 South McAllister Ave. Tempe, AZ 85287-5701, USA; School of Sustainable Engineering and the Built Environment, Arizona State University, USA.
| | - Bruce E Rittmann
- Biodesign Institute, Swette Center for Environmental Biotechnology, Arizona State University, 1001 South McAllister Ave. Tempe, AZ 85287-5701, USA; School of Sustainable Engineering and the Built Environment, Arizona State University, USA.
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Severe amoebic placentitis in a horse caused by an Acanthamoeba hatchetti isolate identified using next-generation sequencing. J Clin Microbiol 2014; 52:3101-4. [PMID: 24829227 DOI: 10.1128/jcm.01071-14] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A case of amoebic placentitis in a mare from eastern Australia was diagnosed postpartum by histopathological examination of the placenta. The identity of the etiological agent was confirmed as Acanthamoeba hatchetti by use of diversity profiling based on a next-generation sequencing approach.
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Krupke A, Lavik G, Halm H, Fuchs BM, Amann RI, Kuypers MMM. Distribution of a consortium between unicellular algae and the N2 fixing cyanobacterium UCYN-A in the North Atlantic Ocean. Environ Microbiol 2014; 16:3153-67. [PMID: 24612325 DOI: 10.1111/1462-2920.12431] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Revised: 02/05/2014] [Accepted: 02/13/2014] [Indexed: 11/29/2022]
Abstract
The globally abundant, uncultured unicellular cyanobacterium UCYN-A was recently discovered living in association with a eukaryotic cell closely related to a prymnesiophyte. Here, we established a double CAtalysed Reporter Deposition-Fluorescence In Situ Hybridization (CARD-FISH) approach to identify both partners and provided quantitative information on their distribution and abundance across distinct water masses along a transect in the North Atlantic Ocean. The N2 fixation activity coincided with the detection of UCYN-A cells and was only observed in oligotrophic (< 0.067 NO3(-) μM and < 0.04 PO4(3-) μM) and warm (> 18°C) surface waters. Parallel 16S ribosomal RNA gene analyses among unicellular diazotrophs indicated that only UCYN-A cells were present. UCYN-A cells were associated with an algal partner or non-associated using the double CARD-FISH approach. We demonstrated that UCYN-A cells living in association with Haptophyta were the dominant form (87.0 ± 6.1%), whereas non-associated UCYN-A cells represented only a minor fraction (5.2 ± 3.9%). Interestingly, UCYN-A cells were also detected living in association with unknown single-celled eukaryotes in small amounts (7.8 ± 5.2%), presumably Alveolata. The proposed ecological niche of UCYN-A as an oligotrophic, mesophilic and obligate symbiotic nitrogen-fixing microorganism is evident for the North Atlantic Ocean.
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Affiliation(s)
- Andreas Krupke
- Helmholtz-Zentrum Potsdam Deutsches GeoForschungsZentrum GFZ Mikrobielles GeoEngineering, D-14473, Potsdam, Germany
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Partner choice and fidelity stabilize coevolution in a Cretaceous-age defensive symbiosis. Proc Natl Acad Sci U S A 2014; 111:6359-64. [PMID: 24733936 DOI: 10.1073/pnas.1400457111] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Many insects rely on symbiotic microbes for survival, growth, or reproduction. Over evolutionary timescales, the association with intracellular symbionts is stabilized by partner fidelity through strictly vertical symbiont transmission, resulting in congruent host and symbiont phylogenies. However, little is known about how symbioses with extracellular symbionts, representing the majority of insect-associated microorganisms, evolve and remain stable despite opportunities for horizontal exchange and de novo acquisition of symbionts from the environment. Here we demonstrate that host control over symbiont transmission (partner choice) reinforces partner fidelity between solitary wasps and antibiotic-producing bacteria and thereby stabilizes this Cretaceous-age defensive mutualism. Phylogenetic analyses show that three genera of beewolf wasps (Philanthus, Trachypus, and Philanthinus) cultivate a distinct clade of Streptomyces bacteria for protection against pathogenic fungi. The symbionts were acquired from a soil-dwelling ancestor at least 68 million years ago, and vertical transmission via the brood cell and the cocoon surface resulted in host-symbiont codiversification. However, the external mode of transmission also provides opportunities for horizontal transfer, and beewolf species have indeed exchanged symbiont strains, possibly through predation or nest reuse. Experimental infection with nonnative bacteria reveals that--despite successful colonization of the antennal gland reservoirs--transmission to the cocoon is selectively blocked. Thus, partner choice can play an important role even in predominantly vertically transmitted symbioses by stabilizing the cooperative association over evolutionary timescales.
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Weissbrodt DG, Shani N, Holliger C. Linking bacterial population dynamics and nutrient removal in the granular sludge biofilm ecosystem engineered for wastewater treatment. FEMS Microbiol Ecol 2014; 88:579-95. [DOI: 10.1111/1574-6941.12326] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Revised: 03/07/2014] [Accepted: 03/08/2014] [Indexed: 02/03/2023] Open
Affiliation(s)
- David G. Weissbrodt
- Laboratory for Environmental Biotechnology; School of Architecture, Civil and Environmental Engineering; Institute of Environmental Engineering; Ecole Polytechnique Fédérale de Lausanne; Lausanne Switzerland
| | - Noam Shani
- Laboratory for Environmental Biotechnology; School of Architecture, Civil and Environmental Engineering; Institute of Environmental Engineering; Ecole Polytechnique Fédérale de Lausanne; Lausanne Switzerland
| | - Christof Holliger
- Laboratory for Environmental Biotechnology; School of Architecture, Civil and Environmental Engineering; Institute of Environmental Engineering; Ecole Polytechnique Fédérale de Lausanne; Lausanne Switzerland
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González-Teuber M, Kaltenpoth M, Boland W. Mutualistic ants as an indirect defence against leaf pathogens. THE NEW PHYTOLOGIST 2014; 202:640-650. [PMID: 24392817 DOI: 10.1111/nph.12664] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Accepted: 11/28/2013] [Indexed: 05/08/2023]
Abstract
Mutualistic ants are commonly considered as an efficient indirect defence against herbivores. Nevertheless, their indirect protective role against plant pathogens has been scarcely investigated. We compared the protective role against pathogens of two different ant partners, a mutualistic and a parasitic ant, on the host plant Acacia hindsii (Fabaceae). The epiphytic bacterial community on leaves was evaluated in the presence and absence of both ant partners by cultivation and by 454 pyrosequencing of the 16S rRNA gene. Pathogen-inflicted leaf damage, epiphytic bacterial abundance (colony-forming units) and number of operational taxonomic units (OTUs) were significantly higher in plants inhabited by parasitic ants than in plants inhabited by mutualistic ants. Unifrac unweighted and weighted principal component analyses showed that the bacterial community composition on leaves changed significantly when mutualistic ants were removed from plants or when plants were inhabited by parasitic ants. Direct mechanisms provided by ant-associated bacteria would contribute to the protective role against pathogens. The results suggest that the indirect defence of mutualistic ants also covers the protection from bacterial plant pathogens. Our findings highlight the importance of considering bacterial partners in ant-plant defensive mutualisms, which can contribute significantly to ant-mediated protection from plant pathogens.
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Affiliation(s)
- Marcia González-Teuber
- Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, Beutenberg Campus, Hans-Knoell-Strasse 8, D-07745, Jena, Germany
- Departamento de Biología, Universidad de La Serena, Casilla 554, La Serena, Chile
| | - Martin Kaltenpoth
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, Beutenberg Campus, Hans-Knoell-Strasse 8, D-07745, Jena, Germany
| | - Wilhelm Boland
- Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, Beutenberg Campus, Hans-Knoell-Strasse 8, D-07745, Jena, Germany
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Pagaling E, Yang K, Yan T. Pyrosequencing reveals correlations between extremely acidophilic bacterial communities with hydrogen sulphide concentrations, pH and inert polymer coatings at concrete sewer crown surfaces. J Appl Microbiol 2014; 117:50-64. [DOI: 10.1111/jam.12491] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Revised: 02/14/2014] [Accepted: 02/27/2014] [Indexed: 01/31/2023]
Affiliation(s)
- E. Pagaling
- Department of Civil and Environmental Engineering; University of Hawai'i at Mānoa; Honolulu HI USA
| | - K. Yang
- Department of Civil and Environmental Engineering; University of Hawai'i at Mānoa; Honolulu HI USA
| | - T. Yan
- Department of Civil and Environmental Engineering; University of Hawai'i at Mānoa; Honolulu HI USA
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42
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Lai CY, Yang X, Tang Y, Rittmann BE, Zhao HP. Nitrate shaped the selenate-reducing microbial community in a hydrogen-based biofilm reactor. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2014; 48:3395-3402. [PMID: 24579788 DOI: 10.1021/es4053939] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
To study the effect of nitrate (NO3(-)) on selenate (SeO4(2-)) reduction, we tested a H2-based biofilm with a range of influent NO3(-) loadings. When SeO4(2-) was the only electron acceptor (stage 1), 40% of the influent SeO4(2-) was reduced to insoluble elemental selenium (Se(0)). SeO4(2-) reduction was dramatically inhibited when NO3(-) was added at a surface loading larger than 1.14 g of N m(-2) day(-1), when H2 delivery became limiting and only 80% of the input NO3(-) was reduced (stage 2). In stage 3, when NO3(-) was again removed from the influent, SeO4(2-) reduction was re-established and increased to 60% conversion to Se(0). SeO4(2-) reduction remained stable at 60% in stages 4 and 5, when the NO3(-) surface loading was re-introduced at ≤ 0.53 g of N m(-2) day(-1), allowing for complete NO3(-) reduction. The selenate-reducing microbial community was significantly reshaped by the high NO3(-) surface loading in stage 2, and it remained stable through stages 3-5. In particular, the abundance of α-Proteobacteria decreased from 30% in stage 1 to less than 10% of total bacteria in stage 2. β-Proteobacteria, which represented about 55% of total bacteria in the biofilm in stage 1, increased to more than 90% of phylotypes in stage 2. Hydrogenophaga, an autotrophic denitrifier, was positively correlated with NO3(-) flux. Thus, introducing a NO3(-) loading high enough to cause H2 limitation and suppress SeO4(2-) reduction had a long-lasting effect on the microbial community structure, which was confirmed by principal coordinate analysis, although SeO4(2-) reduction remained intact.
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Affiliation(s)
- Chun-Yu Lai
- Ministry of Education, Key Laboratory of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Science, Zhejiang University , Hangzhou 310029, People's Republic of China
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43
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Cleland EJ, Bassiouni A, Bassioni A, Boase S, Dowd S, Vreugde S, Wormald PJ. The fungal microbiome in chronic rhinosinusitis: richness, diversity, postoperative changes and patient outcomes. Int Forum Allergy Rhinol 2014; 4:259-65. [PMID: 24500871 DOI: 10.1002/alr.21297] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Revised: 11/25/2013] [Accepted: 12/19/2013] [Indexed: 11/11/2022]
Abstract
BACKGROUND Our understanding of fungi in chronic rhinosinusitis (CRS) has been limited by previously employed detection techniques. This study examines the fungal component of the microbiome in CRS patients and controls using a highly sensitive culture-independent molecular technique. The aims of this study include the characterization of fungal richness, prevalence, abundance, temporal changes, and their relationship with patient outcomes. METHODS Swabs were collected from the sinuses of 23 CRS patients and 11 controls. Collection occurred intraoperatively, and at 6 and 12 weeks postoperatively. DNA was extracted from the swabs and fungal outcomes were determined through 18S ribosomal DNA (rDNA) fungal tag-encoded FLX amplicon pyrosequencing. RESULTS Fungi were ubiquitous to all patients. A total of 207 fungal genera were detected, with a mean sample richness of 8.18 and 12.14 in the control and CRS groups, respectively. Malassezia was detected in all patients at surgery and was also the most abundant. Postoperatively, fungal richness decreased (p < 0.05) and was associated with declines in the prevalence of Fusarium and Neocosmospora (p < 0.05). Neocosmospora was also less abundant postoperatively (p < 0.05). No correlations were found with quality of life. CONCLUSION This is the first study to use a highly sensitive pyrosequencing technique to reveal the true diversity of fungi in the sinuses of CRS patients and postoperative changes in richness. The presence of Malassezia, a genus not previously described in the sinuses, is of great interest, and its potential as a disease modifier should see further investigation given its association with atopic disease.
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Affiliation(s)
- Edward John Cleland
- Department of Surgery-Otorhinolaryngology, Head and Neck Surgery, University of Adelaide, Adelaide, South Australia, Australia
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44
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Romick-Rosendale LE, Legomarcino A, Patel NB, Morrow AL, Kennedy MA. Prolonged antibiotic use induces intestinal injury in mice that is repaired after removing antibiotic pressure: implications for empiric antibiotic therapy. Metabolomics 2014; 10:8-20. [PMID: 26273236 PMCID: PMC4532301 DOI: 10.1007/s11306-013-0546-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Metabolic profiling of urine and fecal extracts, histological investigation of intestinal ilea, and fecal metagenomics analyses were used to investigate effects of prolonged antibiotic use in mice. The study provides insight into the effects of extended empiric antibiotic therapy in humans. Mice were administered a broad-spectrum antibiotic for four consecutive days followed by oral gavage with Clostridium butyricum, an opportunistic gram-positive pathogenic bacteria commonly isolated in fecal and blood cultures of necrotizing enterocolitis patients. Metagenomics data indicated loss of bacterial diversity after 4 days on antibiotics that was restored after removing antibiotic pressure. Histological analyses indicated damage to ileal villi after antibiotic treatment that underwent repair after lifting antibiotic pressure. Metabolic profiling confirmed intestinal injury in antibiotic-treated mice indicated by increased urinary trans-4-hydroxy-l-proline, a breakdown product of collagen present in connective tissue of ileal villi that may serve as a biomarker for antibiotic-induced injury in at risk populations.
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Affiliation(s)
| | - Anne Legomarcino
- Perinatal Institute, Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, 3333 Burnet Avenue, MLC 7009, Cincinnati, OH 45218, USA
| | - Neil B. Patel
- Department of Chemistry & Biochemistry, Miami University, 701 East High Street, Oxford, OH 45056, USA
| | - Ardythe L. Morrow
- Perinatal Institute, Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, 3333 Burnet Avenue, MLC 7009, Cincinnati, OH 45218, USA
- Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Michael A. Kennedy
- Department of Chemistry & Biochemistry, Miami University, 701 East High Street, Oxford, OH 45056, USA
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45
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Weissbrodt DG, Schneiter GS, Fürbringer JM, Holliger C. Identification of trigger factors selecting for polyphosphate- and glycogen-accumulating organisms in aerobic granular sludge sequencing batch reactors. WATER RESEARCH 2013; 47:7006-18. [PMID: 24200006 DOI: 10.1016/j.watres.2013.08.043] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Revised: 08/12/2013] [Accepted: 08/27/2013] [Indexed: 05/06/2023]
Abstract
Nutrient removal performances of sequencing batch reactors using granular sludge for intensified biological wastewater treatment rely on optimal underlying microbial selection. Trigger factors of bacterial selection and nutrient removal were investigated in these novel biofilm systems with specific emphasis on polyphosphate- (PAO) and glycogen-accumulating organisms (GAO) mainly affiliated with Accumulibacter and Competibacter, respectively. In a first dynamic reactor operated with stepwise changes in concentration and ratio of acetate and propionate (Ac/Pr) under anaerobic feeding and aerobic starvation conditions and without wasting sludge periodically, propionate favorably selected for Accumulibacter (35% relative abundance) and stable production of granular biomass. A Plackett-Burman multifactorial experimental design was then used to screen in eight runs of 50 days at stable sludge retention time of 15 days for the main effects of COD concentration, Ac/Pr ratio, COD/P ratio, pH, temperature, and redox conditions during starvation. At 95% confidence level, pH was mainly triggering direct Accumulibacter selection and nutrient removal. The overall PAO/GAO competition in granular sludge was statistically equally impacted by pH, temperature, and redox factors. High Accumulibacter abundances (30-47%), PAO/GAO ratios (2.8-8.4), and phosphorus removal (80-100%) were selected by slightly alkaline (pH > 7.3) and lower mesophilic (<20 °C) conditions, and under full aeration during fixed 2-h starvation. Nitrogen removal by nitrification and denitrification (84-97%) was positively correlated to pH and temperature. In addition to alkalinity, non-limited organic conditions, 3-carbon propionate substrate, sludge age control, and phase length adaptation under alternating aerobic-anoxic conditions during starvation can lead to efficient nutrient-removing granular sludge biofilm systems.
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Affiliation(s)
- David G Weissbrodt
- Ecole Polytechnique Fédérale de Lausanne, School of Architecture, Civil and Environmental Engineering, Institute of Environmental Engineering, Laboratory for Environmental Biotechnology, Lausanne, Switzerland.
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46
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Amir I, Konikoff FM, Oppenheim M, Gophna U, Half EE. Gastric microbiota is altered in oesophagitis and Barrett's oesophagus and further modified by proton pump inhibitors. Environ Microbiol 2013; 16:2905-14. [PMID: 24112768 DOI: 10.1111/1462-2920.12285] [Citation(s) in RCA: 132] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Revised: 09/07/2013] [Accepted: 09/10/2013] [Indexed: 12/17/2022]
Abstract
Gastro-oesophageal reflux can cause inflammation, metaplasia, dysplasia and cancer of the oesophagus. Despite the increased use of proton pump inhibitors (PPIs) to treat reflux, the incidence of oesophageal adenocarcinoma has increased rapidly in Europe and in the United States in the last 25 years. The reasons for this increase remain unclear. In this study, we aimed to determine whether the microbiota of the gastric refluxate and oesophageal biopsies differs between patients with heartburn and normal-appearing oesophageal mucosa versus patients with abnormal oesophageal mucosa [oesophagitis or Barrett's oesophagus (BE)] and to elucidate the effect of PPIs on the bacterial communities using 16S rRNA gene pyrosequencing. Significant differences in the composition of gastric fluid bacteria were found between patients with heartburn and normal oesophageal tissue versus patients with oesophagitis or BE, but in the oesophagus-associated microbiota differences were relatively modest. Notably, increased levels of Enterobacteriaceae were observed in the gastric fluid of oesophagitis and BE patients. In addition, treatment with PPIs had dramatic effects on microbial communities both in the gastric fluids and the oesophageal tissue. In conclusion, gastric fluid microbiota is modified in patients with oesophagitis and BE compared with heartburn patients with normal biopsies. Furthermore, PPI treatment markedly alters gastric and oesophageal microbial populations. Determining whether the changes in bacterial composition caused by PPIs are beneficial or harmful will require further investigation.
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Affiliation(s)
- Itay Amir
- Department of Molecular Microbiology & Biotechnology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, 69978, Israel
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47
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Slapeta J, Linares MC. Combined amplicon pyrosequencing assays reveal presence of the apicomplexan "type-N" (cf. Gemmocystis cylindrus) and Chromera velia on the Great Barrier Reef, Australia. PLoS One 2013; 8:e76095. [PMID: 24098768 PMCID: PMC3786883 DOI: 10.1371/journal.pone.0076095] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 08/21/2013] [Indexed: 11/18/2022] Open
Abstract
Background The coral is predominantly composed of the metabolically dependent coral host and the photosynthetic dinoflagellate Symbiodinium sp. The system as a whole interacts with symbiotic eukaryotes, bacteria and viruses. Gemmocystiscylindrus (cf. “type-N” symbiont) belonging to the obligatory parasitic phylum Apicomplexa (Alveolata) is ubiquitous in the Caribbean coral, but its presence in the Great Barrier Reef coral has yet to be documented. Approaches allowing identification of the healthy community from the pathogenic or saprobic organisms are needed for sustainable coral reef monitoring. Methods & Principal Findings We investigated the diversity of eukaryotes associated with a common reef-building corals from the southern Great Barrier Reef. We used three tag encoded 454 amplicon pyrosequencing assays targeting eukaryote small-subunit rRNA gene to demonstrate the presence of the apicomplexan type-N and a photosynthetic sister species to Apicomplexa - Chromeravelia. Amplicon pyrosequencing revealed presence of the small-subunit rRNA genes of known eukaryotic pathogens (Cryptosporidium and Cryptococcus). We therefore conducted bacterial tag encoded amplicon pyrosequencing assay for small-subunit rRNA gene to support effluent exposure of the coral. Bacteria of faecal origin (Enterobacteriales) formed 41% of total sequences in contrast to 0-2% of the coral-associated bacterial communities with and without C. velia, respectively. Significance This is the first time apicomplexan type-N has been detected in the Great Barrier Reef. Eukaryote tag encoded amplicon pyrosequencing assays demonstrate presence of apicomplexan type-N and C. Velia in total coral DNA. The data highlight the need for combined approaches for eukaryotic diversity studies coupled with bacterial community assessment to achieve a more realistic goals of defining the holobiont community and assessing coral disease. With increasing evidence of Apicomplexa in coral reef environments, it is important not only to understand the evolution of these organisms but also identify their potential as pathogens.
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Affiliation(s)
- Jan Slapeta
- Faculty of Veterinary Science, University of Sydney, Sydney, New South Wales, Australia
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48
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Kaltenpoth M, Steiger S. Unearthing carrion beetles' microbiome: characterization of bacterial and fungal hindgut communities across the Silphidae. Mol Ecol 2013; 23:1251-1267. [PMID: 24102980 DOI: 10.1111/mec.12469] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2013] [Revised: 07/16/2013] [Accepted: 07/18/2013] [Indexed: 12/26/2022]
Abstract
Carrion beetles (Coleoptera, Silphidae) are well known for their behaviour of exploiting vertebrate carcasses for nutrition. While species in the subfamily Silphinae feed on large carcasses and on larvae of competing scavengers, the Nicrophorinae are unique in monopolizing, burying and defending small carrion, and providing extensive biparental care. As a first step towards investigating whether microbial symbionts may aid in carcass utilization or defence, we characterized the microbial hindgut communities of six Nicrophorinae (Nicrophorus spp.) and two Silphinae species (Oiceoptoma noveboracense and Necrophila americana) by deep ribosomal RNA amplicon sequencing. Across all species, bacteria in the family Xanthomonadaceae, related to Ignatzschineriao larvae, were consistently common, and several other taxa were present in lower abundance (Enterobacteriales, Burkholderiales, Bacilli, Clostridiales and Bacteroidales). Additionally, the Nicrophorinae showed high numbers of unusual Clostridiales, while the Silphinae were characterized by Flavobacteriales and Rhizobiales (Bartonella sp.). In addition to the complex community of bacterial symbionts, each species of carrion beetle harboured a diversity of ascomycetous yeasts closely related to Yarrowia lipolytica. Despite the high degree of consistency in microbial communities across the Silphidae--specifically within the Nicrophorinae--both the fungal symbiont phylogeny and distance-based bacterial community clustering showed higher congruence with sampling locality than host phylogeny. Thus, despite the possibility for vertical transmission via anal secretions, the distinct hindgut microbiota of the Silphidae appears to be shaped by frequent horizontal exchange or environmental uptake of symbionts. The microbial community profiles, together with information on host ecology and the metabolic potential of related microorganisms, allow us to propose hypotheses on putative roles of the symbionts in carcass degradation, detoxification and defence.
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Affiliation(s)
- Martin Kaltenpoth
- Insect Symbiosis Research Group, Max Planck Institute for Chemical Ecology, Hans-Knoell-Str. 8, 07745 Jena, Germany
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49
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Sison-Mangus MP, Jiang S, Tran KN, Kudela RM. Host-specific adaptation governs the interaction of the marine diatom, Pseudo-nitzschia and their microbiota. ISME JOURNAL 2013; 8:63-76. [PMID: 23985747 DOI: 10.1038/ismej.2013.138] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Revised: 07/02/2013] [Accepted: 07/14/2013] [Indexed: 01/04/2023]
Abstract
The association of phytoplankton with bacteria is ubiquitous in nature and the bacteria that associate with different phytoplankton species are very diverse. The influence of these bacteria in the physiology and ecology of the host and the evolutionary forces that shape the relationship are still not understood. In this study, we used the Pseudo-nitzschia-microbiota association to determine (1) if algal species with distinct domoic acid (DA) production are selection factors that structures the bacterial community, (2) if host-specificity and co-adaptation govern the association, (3) the functional roles of isolated member of microbiota on diatom-hosts fitness and (4) the influence of microbiota in changing the phenotype of the diatom hosts with regards to toxin production. Analysis of the pyrosequencing-derived 16S rDNA data suggests that the three tested species of Pseudo-nitzschia, which vary in toxin production, have phylogenetically distinct bacterial communities, and toxic Pseudo-nitzschia have lower microbial diversity than non-toxic Pseudo-nitzschia. Transplant experiments showed that isolated members of the microbiota are mutualistic to their native hosts but some are commensal or parasitic to foreign hosts, hinting at co-evolution between partners. Moreover, Pseudo-nitzschia host can gain protection from algalytic bacteria by maintaining association with its microbiota. Pseudo-nitzschia also exhibit different phenotypic expression with regards to DA production, and this depends on the bacterial species with which the host associates. Hence, the influences of the microbiota on diatom host physiology should be considered when studying the biology and ecology of marine diatoms.
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Affiliation(s)
- Marilou P Sison-Mangus
- 1] Department of Civil and Environmental Engineering, 716E Engineering Tower, Civil and Environmental Engineering, University of California, Irvine, Irvine, CA, USA [2] Department of Ocean Sciences and Institute for Marine Sciences, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA, USA
| | - Sunny Jiang
- Department of Civil and Environmental Engineering, 716E Engineering Tower, Civil and Environmental Engineering, University of California, Irvine, Irvine, CA, USA
| | - Kevin N Tran
- Department of Civil and Environmental Engineering, 716E Engineering Tower, Civil and Environmental Engineering, University of California, Irvine, Irvine, CA, USA
| | - Raphael M Kudela
- Department of Ocean Sciences and Institute for Marine Sciences, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA, USA
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50
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Sheik AR, Brussaard CPD, Lavik G, Lam P, Musat N, Krupke A, Littmann S, Strous M, Kuypers MMM. Responses of the coastal bacterial community to viral infection of the algae Phaeocystis globosa. ISME JOURNAL 2013; 8:212-25. [PMID: 23949664 DOI: 10.1038/ismej.2013.135] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Revised: 06/03/2013] [Accepted: 07/14/2013] [Indexed: 11/10/2022]
Abstract
The release of organic material upon algal cell lyses has a key role in structuring bacterial communities and affects the cycling of biolimiting elements in the marine environment. Here we show that already before cell lysis the leakage or excretion of organic matter by infected yet intact algal cells shaped North Sea bacterial community composition and enhanced bacterial substrate assimilation. Infected algal cultures of Phaeocystis globosa grown in coastal North Sea water contained gamma- and alphaproteobacterial phylotypes that were distinct from those in the non-infected control cultures 5 h after infection. The gammaproteobacterial population at this time mainly consisted of Alteromonas sp. cells that were attached to the infected but still intact host cells. Nano-scale secondary-ion mass spectrometry (nanoSIMS) showed ∼20% transfer of organic matter derived from the infected (13)C- and (15)N-labelled P. globosa cells to Alteromonas sp. cells. Subsequent, viral lysis of P. globosa resulted in the formation of aggregates that were densely colonised by bacteria. Aggregate dissolution was observed after 2 days, which we attribute to bacteriophage-induced lysis of the attached bacteria. Isotope mass spectrometry analysis showed that 40% of the particulate (13)C-organic carbon from the infected P. globosa culture was remineralized to dissolved inorganic carbon after 7 days. These findings reveal a novel role of viruses in the leakage or excretion of algal biomass upon infection, which provides an additional ecological niche for specific bacterial populations and potentially redirects carbon availability.
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Affiliation(s)
- Abdul R Sheik
- Max Planck Institute for Marine Microbiology, Celciusstraße 1, Bremen, Germany
| | - Corina P D Brussaard
- 1] Department of Biological Oceanography, NIOZ - Royal Netherlands Institute for Sea Research, Texel, The Netherlands [2] Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Gaute Lavik
- Max Planck Institute for Marine Microbiology, Celciusstraße 1, Bremen, Germany
| | - Phyllis Lam
- Max Planck Institute for Marine Microbiology, Celciusstraße 1, Bremen, Germany
| | - Niculina Musat
- Max Planck Institute for Marine Microbiology, Celciusstraße 1, Bremen, Germany
| | - Andreas Krupke
- Max Planck Institute for Marine Microbiology, Celciusstraße 1, Bremen, Germany
| | - Sten Littmann
- Max Planck Institute for Marine Microbiology, Celciusstraße 1, Bremen, Germany
| | - Marc Strous
- Max Planck Institute for Marine Microbiology, Celciusstraße 1, Bremen, Germany
| | - Marcel M M Kuypers
- Max Planck Institute for Marine Microbiology, Celciusstraße 1, Bremen, Germany
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