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Pearman WS, Duffy GA, Liu XP, Gemmell NJ, Morales SE, Fraser CI. Macroalgal microbiome biogeography is shaped by environmental drivers rather than geographical distance. ANNALS OF BOTANY 2024; 133:169-182. [PMID: 37804485 PMCID: PMC10921836 DOI: 10.1093/aob/mcad151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 10/06/2023] [Indexed: 10/09/2023]
Abstract
BACKGROUND AND AIMS Contrasting patterns of host and microbiome biogeography can provide insight into the drivers of microbial community assembly. Distance-decay relationships are a classic biogeographical pattern shaped by interactions between selective and non-selective processes. Joint biogeography of microbiomes and their hosts is of increasing interest owing to the potential for microbiome-facilitated adaptation. METHODS In this study, we examine the coupled biogeography of the model macroalga Durvillaea and its microbiome using a combination of genotyping by sequencing (host) and 16S rRNA amplicon sequencing (microbiome). Alongside these approaches, we use environmental data to characterize the relationship between the microbiome, the host, and the environment. KEY RESULTS We show that although the host and microbiome exhibit shared biogeographical structure, these arise from different processes, with host biogeography showing classic signs of geographical distance decay, but with the microbiome showing environmental distance decay. Examination of microbial subcommunities, defined by abundance, revealed that the abundance of microbes is linked to environmental selection. As microbes become less common, the dominant ecological processes shift away from selective processes and towards neutral processes. Contrary to expectations, we found that ecological drift does not promote structuring of the microbiome. CONCLUSIONS Our results suggest that although host macroalgae exhibit a relatively 'typical' biogeographical pattern of declining similarity with increasing geographical distance, the microbiome is more variable and is shaped primarily by environmental conditions. Our findings suggest that the Baas Becking hypothesis of 'everything is everywhere, the environment selects' might be a useful hypothesis to understand the biogeography of macroalgal microbiomes. As environmental conditions change in response to anthropogenic influences, the processes structuring the microbiome of macroalgae might shift, whereas those governing the host biogeography are less likely to change. As a result, increasingly decoupled host-microbe biogeography might be observed in response to such human influences.
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Affiliation(s)
- William S Pearman
- Department of Marine Science, University of Otago, New Zealand
- Department of Anatomy, School of Biomedical Sciences, University of Otago, New Zealand
- Department of Microbiology & Immunology, School of Biomedical Sciences, University of Otago, New Zealand
| | - Grant A Duffy
- Department of Marine Science, University of Otago, New Zealand
| | - Xiaoyue P Liu
- Department of Marine Science, University of Otago, New Zealand
| | - Neil J Gemmell
- Department of Anatomy, School of Biomedical Sciences, University of Otago, New Zealand
| | - Sergio E Morales
- Department of Microbiology & Immunology, School of Biomedical Sciences, University of Otago, New Zealand
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2
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Magura T, Mizser S, Horváth R, Tóth M, Likó I, Lövei GL. Urbanization reduces gut bacterial microbiome diversity in a specialist ground beetle, Carabus convexus. Mol Ecol 2024; 33:e17265. [PMID: 38214370 DOI: 10.1111/mec.17265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 12/19/2023] [Accepted: 01/04/2024] [Indexed: 01/13/2024]
Abstract
Urbanization is rapidly shaping and transforming natural environments, creating networks of modified land types. These urbanization-driven modifications lead to local extinctions of several species, but the surviving ones also face numerous novel selection pressures, including exposure to pollutants, habitat alteration, and shifts in food availability and diversity. Based on the assumption that the environmental pool of microorganisms is reduced in urban habitats due to habitat alteration, biodiversity loss, and pollution, we hypothesized that the diversity of bacterial microbiome in digestive tracts of arthropods would be lower in urban than rural habitats. Investigating the gut bacterial communities of a specialist ground beetle, Carabus convexus, in forested rural versus urban habitats by next generation high-throughput sequencing of the bacterial 16S rRNA gene, we identified 3839 bacterial amplicon sequence variants. The composition of gut bacterial samples did not significantly differ by habitat (rural vs. urban), sex (female vs. male), sampling date (early vs. late spring), or their interaction. The microbiome diversity (evaluated by the Rényi diversity function), however, was higher in rural than urban adults. Our findings demonstrate that urbanization significantly reduced the diversity of the gut bacterial microbiome in C. convexus.
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Affiliation(s)
- Tibor Magura
- Department of Ecology, Faculty of Science and Technology, University of Debrecen, Debrecen, Hungary
- HUN-REN-UD Anthropocene Ecology Research Group, Debrecen, Hungary
| | - Szabolcs Mizser
- Department of Ecology, Faculty of Science and Technology, University of Debrecen, Debrecen, Hungary
| | - Roland Horváth
- Department of Ecology, Faculty of Science and Technology, University of Debrecen, Debrecen, Hungary
- HUN-REN-UD Anthropocene Ecology Research Group, Debrecen, Hungary
| | - Mária Tóth
- Department of Ecology, Faculty of Science and Technology, University of Debrecen, Debrecen, Hungary
- HUN-REN-UD Anthropocene Ecology Research Group, Debrecen, Hungary
| | - István Likó
- UD-GenoMed Medical Genomic Technologies Ltd, Clinical Centre, University of Debrecen, Debrecen, Hungary
| | - Gábor L Lövei
- HUN-REN-UD Anthropocene Ecology Research Group, Debrecen, Hungary
- Department of Agroecology, Flakkebjerg Research Centre, Aarhus University, Slagelse, Denmark
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3
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Seabloom EW, Caldeira MC, Davies KF, Kinkel L, Knops JMH, Komatsu KJ, MacDougall AS, May G, Millican M, Moore JL, Perez LI, Porath-Krause AJ, Power SA, Prober SM, Risch AC, Stevens C, Borer ET. Globally consistent response of plant microbiome diversity across hosts and continents to soil nutrients and herbivores. Nat Commun 2023; 14:3516. [PMID: 37316485 DOI: 10.1038/s41467-023-39179-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 06/01/2023] [Indexed: 06/16/2023] Open
Abstract
All multicellular organisms host a diverse microbiome composed of microbial pathogens, mutualists, and commensals, and changes in microbiome diversity or composition can alter host fitness and function. Nonetheless, we lack a general understanding of the drivers of microbiome diversity, in part because it is regulated by concurrent processes spanning scales from global to local. Global-scale environmental gradients can determine variation in microbiome diversity among sites, however an individual host's microbiome also may reflect its local micro-environment. We fill this knowledge gap by experimentally manipulating two potential mediators of plant microbiome diversity (soil nutrient supply and herbivore density) at 23 grassland sites spanning global-scale gradients in soil nutrients, climate, and plant biomass. Here we show that leaf-scale microbiome diversity in unmanipulated plots depended on the total microbiome diversity at each site, which was highest at sites with high soil nutrients and plant biomass. We also found that experimentally adding soil nutrients and excluding herbivores produced concordant results across sites, increasing microbiome diversity by increasing plant biomass, which created a shaded microclimate. This demonstration of consistent responses of microbiome diversity across a wide range of host species and environmental conditions suggests the possibility of a general, predictive understanding of microbiome diversity.
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Affiliation(s)
- Eric W Seabloom
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN, 55108, USA.
| | - Maria C Caldeira
- Forest Research Centre, Associate Laboratory TERRA, School of Agriculture, University of Lisbon, Lisbon, Portugal
| | - Kendi F Davies
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80305, USA
| | - Linda Kinkel
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, 55108, USA
| | - Johannes M H Knops
- Health and Environmental Sciences Department, Xi'an Jiaotong-Liverpool University, Suzhou, China
| | | | | | - Georgiana May
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN, 55108, USA
| | - Michael Millican
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, 55108, USA
| | - Joslin L Moore
- Arthur Rylah Institute for Environmental Research, 123 Brown Street, Heidelberg, VIC, 3084, Australia
- School of Biological Sciences, Monash University, 25 Rainforest Walk, Clayton, VIC, 3800, Australia
- School of Agriculture, Food and Ecosystem Sciences, The University of Melbourne, VIC, 3010, Australia
| | - Luis I Perez
- IFEVA-Facultad de Agronomía (UBA)/CONICET, Departamento de Recursos Naturales, Catedra ´ de Ecología, Av. San Martín, 4453, Buenos Aires, C1417DSE, Argentina
| | - Anita J Porath-Krause
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN, 55108, USA
| | - Sally A Power
- Hawkesbury Institute for the Environment, Locked Bag 1797, Penrith, NSW, 2751, Australia
| | | | - Anita C Risch
- Swiss Federal Institute for Forest, Snow and Landscape Research, Birmensdorf, Switzerland
| | - Carly Stevens
- Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, UK
| | - Elizabeth T Borer
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN, 55108, USA
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4
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Lin H, Liu C, Peng Z, Tan B, Wang K, Liu Z. Distribution pattern of endophytic bacteria and fungi in tea plants. Front Microbiol 2022; 13:872034. [PMID: 36212870 PMCID: PMC9538792 DOI: 10.3389/fmicb.2022.872034] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 07/07/2022] [Indexed: 11/13/2022] Open
Abstract
Endophytes are critical for plant growth and health. Tea is an economically important crop in China. However, little is known about the distribution pattern and potential functions of endophytic communities in tea trees. In this study, two genotypes (BXZ and MF) cultivated under the same conditions were selected, and endophytic bacteria and fungi were analyzed through 16S rRNA and ITS high-throughput sequencing technologies, respectively. For endophytic bacteria, root tissues harbored the most diverse endophytes, followed by stems and old leaves, and new leaves possessed the lowest diversity. In contrast, old leave tissues harbored more diverse endophytic fungi than did root and stem tissues. Most of the dominant endophytes showed obvious cultivar and tissue preferences. Tissue type played a more important role in shaping community structure than did cultivar. Nevertheless, some endophytic bacterial groups, which mainly affiliated to Chryseobacterium, Sphingomonas, Rhizobium, Morganella, Methylobacterium and Comamonadaceae, could parasitize different tissues, and the average relative abundance of endophytic bacteria was as high as 72.57%. Some endophytic fungal populations, such as Colletotrichum, Uwebraunia, Cladosporium, and Devriesia, could also parasitize tea, and the relative abundance accounted for approximately 25.70–97.26%. The cooperative relationship between endophytic bacteria and fungi in the new leaves was stronger than that in the old leaves, which can better participate in the metabolism of tea material.
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Affiliation(s)
- Haiyan Lin
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, China
- National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, China
| | - Changwei Liu
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, China
- National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, China
| | - Zhong Peng
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, China
- National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, China
| | - Bin Tan
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, China
- National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, China
| | - Kunbo Wang
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, China
- National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, China
- Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, China
| | - Zhonghua Liu
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, China
- National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, China
- Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, China
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5
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Oliveira JMM, Henriques I, Read DS, Gweon HS, Morgado RG, Peixoto S, Correia A, Soares AMVM, Loureiro S. Gut and faecal bacterial community of the terrestrial isopod Porcellionides pruinosus: potential use for monitoring exposure scenarios. ECOTOXICOLOGY (LONDON, ENGLAND) 2021; 30:2096-2108. [PMID: 34553289 DOI: 10.1007/s10646-021-02477-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 09/01/2021] [Indexed: 06/13/2023]
Abstract
This work aimed to characterize the gut and faeces bacterial communities (BC) of Porcellionides pruinosus using high-throughput sequencing. Isopods were collected from the field and kept in laboratory conditions similar to those normally applied in ecotoxicology tests. Faeces and purged guts of isopods (n = 3 × 30) were analysed by pyrosequencing the V3-V4 region of 16 S rRNA encoding gene. Results showed that gut and faecal BCs were dominated by Proteobacteria, particularly by an OTU (Operational Taxonomic Unit) affiliated to genus Coxiella. Diversity and richness values were statistically higher for faecal BC, mainly due to the occurrence of several low-abundance phylotypes. These results may reflect faecal carriage of bacterial groups that cannot settle in the gut. BCs of P. pruinosus comprised: (1) common members of the soil microbiota, (2) bacterial symbionts, (3) bacteria related to host metabolic/ecological features, and (4) bacterial etiological agents. Comparison of BC of this isopod species with the BC from other invertebrates revealed common bacterial groups across taxa. The baseline information provided by this work will assist the design and data interpretation of future ecotoxicological or biomonitoring assays where the analysis of P. pruinosus BC should be included as an additional indicator. CAPSULE: Terrestrial isopods bacterial communities might support ecotoxicological assays and biomonitoring processes as a valuable tool.
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Affiliation(s)
- Jacinta M M Oliveira
- CESAM- Centre for Environmental and Marine Studies, Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - Isabel Henriques
- University of Coimbra, CESAM & Department of Life Sciences, Faculty of Sciences and Technology, Calçada Martins de Freitas, 3000-456, Coimbra, Portugal.
| | - Daniel S Read
- Centre for Ecology & Hydrology, Maclean Building, Benson Lane, Crowmarsh Gifford, Wallingford, Oxfordshire, OX10 8BB, UK
| | - Hyun S Gweon
- Centre for Ecology & Hydrology, Maclean Building, Benson Lane, Crowmarsh Gifford, Wallingford, Oxfordshire, OX10 8BB, UK
- School of Biological Sciences, University of Reading, Whiteknights, Reading, Berkshire, RG6 6AH, UK
| | - Rui G Morgado
- CESAM- Centre for Environmental and Marine Studies, Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - Sara Peixoto
- CESAM- Centre for Environmental and Marine Studies, Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - António Correia
- CESAM- Centre for Environmental and Marine Studies, Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - Amadeu M V M Soares
- CESAM- Centre for Environmental and Marine Studies, Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - Susana Loureiro
- CESAM- Centre for Environmental and Marine Studies, Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
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6
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Porath‐Krause A, Strauss AT, Henning JA, Seabloom EW, Borer ET. Pitfalls and pointers: An accessible guide to marker gene amplicon sequencing in ecological applications. Methods Ecol Evol 2021. [DOI: 10.1111/2041-210x.13764] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Anita Porath‐Krause
- Department of Ecology, Evolution, and Behavior University of Minnesota St. Paul MN USA
| | - Alexander T. Strauss
- Department of Ecology, Evolution, and Behavior University of Minnesota St. Paul MN USA
| | - Jeremiah A. Henning
- Department of Ecology, Evolution, and Behavior University of Minnesota St. Paul MN USA
| | - Eric W. Seabloom
- Department of Ecology, Evolution, and Behavior University of Minnesota St. Paul MN USA
| | - Elizabeth T. Borer
- Department of Ecology, Evolution, and Behavior University of Minnesota St. Paul MN USA
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7
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O'Keeffe KR, Simha A, Mitchell CE. Indirect interactions among co-infecting parasites and a microbial mutualist impact disease progression. Proc Biol Sci 2021; 288:20211313. [PMID: 34375557 DOI: 10.1098/rspb.2021.1313] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Interactions among parasites and other microbes within hosts can impact disease progression, yet study of such interactions has been mostly limited to pairwise combinations of microbes. Given the diversity of microbes within hosts, indirect interactions among more than two microbial species may also impact disease. To test this hypothesis, we performed inoculation experiments that investigated interactions among two fungal parasites, Rhizoctonia solani and Colletotrichum cereale, and a systemic fungal endophyte, Epichloë coenophiala, within the grass, tall fescue (Lolium arundinaceum). Both direct and indirect interactions impacted disease progression. While the endophyte did not directly influence R. solani disease progression or C. cereale symptom development, the endophyte modified the interaction between the two parasites. The magnitude of the facilitative effect of C. cereale on the growth of R. solani tended to be greater when the endophyte was present. Moreover, this interaction modification strongly affected leaf mortality. For plants lacking the endophyte, parasite co-inoculation did not increase leaf mortality compared to single-parasite inoculations. By contrast, for endophyte-infected plants, parasite co-inoculation increased leaf mortality compared to inoculation with R. solani or C. cereale alone by 1.9 or 4.9 times, respectively. Together, these results show that disease progression can be strongly impacted by indirect interactions among microbial symbionts.
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Affiliation(s)
- Kayleigh R O'Keeffe
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Anita Simha
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Biology, Duke University, Durham, NC, USA
| | - Charles E Mitchell
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Environment, Ecology and Energy Program, University of North Carolina, Chapel Hill, NC, USA
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8
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Watson M, Bushley K, Seabloom EW, May G. Response of fungal endophyte communities within Andropogon gerardii (Big bluestem) to nutrient addition and herbivore exclusion. FUNGAL ECOL 2021. [DOI: 10.1016/j.funeco.2021.101043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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9
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Lumibao CY, Kimbrough ER, Day RH, Conner WH, Krauss KW, Van Bael SA. Divergent biotic and abiotic filtering of root endosphere and rhizosphere soil fungal communities along ecological gradients. FEMS Microbiol Ecol 2020; 96:5860278. [PMID: 32562419 DOI: 10.1093/femsec/fiaa124] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 06/19/2020] [Indexed: 12/11/2022] Open
Abstract
Plant roots assemble in two distinct microbial compartments: the rhizosphere (microbes in soil surrounding roots) and the endosphere (microbes within roots). Our knowledge of fungal community assembly in these compartments is limited, especially in wetlands. We tested the hypothesis that biotic factors would have direct effects on rhizosphere and endosphere assembly, while abiotic factors would have direct and indirect effects. Using a field study, we examined the influences of salinity, water level and biotic factors on baldcypress (Taxodium distichum) fungal communities. We found that endosphere fungi, unlike rhizosphere fungi, were correlated with host density and canopy cover, suggesting that hosts can impose selective filters on fungi colonizing their roots. Meanwhile, local abiotic conditions strongly influenced both rhizosphere and endosphere diversity in opposite patterns, e.g. highest endosphere diversity (hump-shaped) and lowest rhizosphere diversity (U-shaped) at intermediate salinity levels. These results indicate that the assembly and structure of the root endosphere and rhizosphere within a host can be shaped by different processes. Our results also highlight the importance of assessing how environmental changes affect plant and plant-associated fungal communities in wetland ecosystems where saltwater intrusion and sea level rise are major threats to both plant and fungal communities.
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Affiliation(s)
- Candice Y Lumibao
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA, 70118, USA
| | - Elizabeth R Kimbrough
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA, 70118, USA
| | - Richard H Day
- U.S. Geological Survey, Wetland and Aquatic Research Center, 700 Cajundome Blvd., Lafayette, LA, 70506, USA
| | - William H Conner
- Baruch Institute of Coastal Ecology and Forest Science, Clemson University, P.O. Box 596, Georgetown, SC, 29442, USA
| | - Ken W Krauss
- U.S. Geological Survey, Wetland and Aquatic Research Center, 700 Cajundome Blvd., Lafayette, LA, 70506, USA
| | - Sunshine A Van Bael
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA, 70118, USA
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10
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McDermid KJ, Kittle RP, Veillet A, Plouviez S, Muehlstein L, Balazs GH. Identification of Gastrointestinal Microbiota in Hawaiian Green Turtles ( Chelonia mydas). Evol Bioinform Online 2020; 16:1176934320914603. [PMID: 32313421 PMCID: PMC7160772 DOI: 10.1177/1176934320914603] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Accepted: 02/28/2020] [Indexed: 11/25/2022] Open
Abstract
Green turtles (Chelonia mydas) have a hindgut fermentation
digestive tract, which uses cellulolytic microbes to break down plant matter in
the cecum and proximal colon. Previous studies on bacterial communities of green
turtles have not identified in situ hindgut microbiota, and
never before in Hawaiian green turtles, which comprise an isolated
metapopulation. Fresh samples using sterile swabs were taken from five locations
along the gastrointestinal tracts of eight green turtles that had required
euthanization. Bacteria were cultured, aerobically and anaerobically, on
nutrient agar and four differential and selective media. Samples at three
sections along the gastrointestinal tracts of two green turtles were analyzed
using 16S metagenomics on an Ion Torrent Personal Genome Machine. More than half
of the 4 532 104 sequences belonged to the phylum Firmicutes, followed by
Bacteroidetes and Proteobacteria, which are characteristic of herbivore gut
microbiota. Some microbiota variation existed between turtles and among
gastrointestinal sections. The 16S sequence analysis provided a better
representation of the total gastrointestinal bacterial community, much of which
cannot be cultured using traditional microbial techniques. These metagenomic
analyses serve as a foundation for a better understanding of the microbiome of
green turtles in the Hawaiian Islands and elsewhere.
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Affiliation(s)
- Karla J McDermid
- Department of Marine Science, University of Hawai'i at Hilo, Hilo, HI, USA
| | - Ronald P Kittle
- Tropical Conservation Biology and Environmental Science Graduate Program, University of Hawai'i at Hilo, Hilo, HI, USA.,Department of Biology, University of Louisiana at Lafayette, Lafayette, LA, USA
| | - Anne Veillet
- Core Genetics Lab, University of Hawai'i at Hilo, Hilo, HI, USA.,Department of Biological Sciences, University of Idaho, Moscow, ID, USA
| | - Sophie Plouviez
- Department of Biology, University of Louisiana at Lafayette, Lafayette, LA, USA
| | - Lisa Muehlstein
- Department of Marine Science, University of Hawai'i at Hilo, Hilo, HI, USA
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11
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Seabloom EW, Condon B, Kinkel L, Komatsu KJ, Lumibao CY, May G, McCulley RL, Borer ET. Effects of nutrient supply, herbivory, and host community on fungal endophyte diversity. Ecology 2019; 100:e02758. [PMID: 31306499 DOI: 10.1002/ecy.2758] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 03/21/2019] [Accepted: 04/17/2019] [Indexed: 12/13/2022]
Abstract
The microbes contained within free-living organisms can alter host growth, reproduction, and interactions with the environment. In turn, processes occurring at larger scales determine the local biotic and abiotic environment of each host that may affect the diversity and composition of the microbiome community. Here, we examine variation in the diversity and composition of the foliar fungal microbiome in the grass host, Andropogon gerardii, across four mesic prairies in the central United States. Composition of fungal endophyte communities differed among sites and among individuals within a site, but was not consistently affected by experimental manipulation of nutrient supply to hosts (A. gerardii) or herbivore reduction via fencing. In contrast, mean fungal diversity was similar among sites but was limited by total plant biomass at the plot scale. Our work demonstrates that distributed experiments motivated by ecological theory are a powerful tool to unravel the multiscale processes governing microbial community composition and diversity.
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Affiliation(s)
- Eric W Seabloom
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, Minnesota, 55108, USA
| | - Bradford Condon
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, Minnesota, 55108, USA
| | - Linda Kinkel
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, 55108, USA
| | - Kimberly J Komatsu
- Smithsonian Environmental Research Center, 647 Contees Wharf Road, Edgewater, Maryland, 21037, USA
| | - Candice Y Lumibao
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, Minnesota, 55108, USA
| | - Georgiana May
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, Minnesota, 55108, USA
| | - Rebecca L McCulley
- Department of Plant & Soil Sciences, University of Kentucky, Lexington, Kentucky, 40536-0312, USA
| | - Elizabeth T Borer
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, Minnesota, 55108, USA
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12
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McLeish MJ, Fraile A, García-Arenal F. Ecological Complexity in Plant Virus Host Range Evolution. Adv Virus Res 2018; 101:293-339. [PMID: 29908592 DOI: 10.1016/bs.aivir.2018.02.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The host range of a plant virus is the number of species in which it can reproduce. Most studies of plant virus host range evolution have focused on the genetics of host-pathogen interactions. However, the distribution and abundance of plant viruses and their hosts do not always overlap, and these spatial and temporal discontinuities in plant virus-host interactions can result in various ecological processes that shape host range evolution. Recent work shows that the distributions of pathogenic and resistant genotypes, vectors, and other resources supporting transmission vary widely in the environment, producing both expected and unanticipated patterns. The distributions of all of these factors are influenced further by competitive effects, natural enemies, anthropogenic disturbance, the abiotic environment, and herbivory to mention some. We suggest the need for further development of approaches that (i) explicitly consider resource use and the abiotic and biotic factors that affect the strategies by which viruses exploit resources; and (ii) are sensitive across scales. Host range and habitat specificity will largely determine which phyla are most likely to be new hosts, but predicting which host and when it is likely to be infected is enormously challenging because it is unclear how environmental heterogeneity affects the interactions of viruses and hosts.
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Affiliation(s)
- Michael J McLeish
- Centro de Biotecnología y Genómica de Plantas UPM-INIA, and E.T.S.I. Agrícola, Alimentaria y de Biosistemas, Campus de Montegancedo, Universidad Politécnica de Madrid, Madrid, Spain
| | - Aurora Fraile
- Centro de Biotecnología y Genómica de Plantas UPM-INIA, and E.T.S.I. Agrícola, Alimentaria y de Biosistemas, Campus de Montegancedo, Universidad Politécnica de Madrid, Madrid, Spain
| | - Fernando García-Arenal
- Centro de Biotecnología y Genómica de Plantas UPM-INIA, and E.T.S.I. Agrícola, Alimentaria y de Biosistemas, Campus de Montegancedo, Universidad Politécnica de Madrid, Madrid, Spain.
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13
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David AS, Seabloom EW, May G. Disentangling environmental and host sources of fungal endophyte communities in an experimental beachgrass study. Mol Ecol 2017; 26:6157-6169. [DOI: 10.1111/mec.14354] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 08/15/2017] [Accepted: 09/05/2017] [Indexed: 11/29/2022]
Affiliation(s)
- Aaron S. David
- Department of Ecology, Evolution, and Behavior University of Minnesota Saint Paul MN USA
| | - Eric W. Seabloom
- Department of Ecology, Evolution, and Behavior University of Minnesota Saint Paul MN USA
| | - Georgiana May
- Department of Ecology, Evolution, and Behavior University of Minnesota Saint Paul MN USA
- Department of Plant Biology University of Minnesota Saint Paul MN USA
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14
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Tiede J, Scherber C, Mutschler J, McMahon KD, Gratton C. Gut microbiomes of mobile predators vary with landscape context and species identity. Ecol Evol 2017; 7:8545-8557. [PMID: 29075470 PMCID: PMC5648672 DOI: 10.1002/ece3.3390] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 07/19/2017] [Accepted: 07/26/2017] [Indexed: 01/01/2023] Open
Abstract
Landscape context affects predator–prey interactions and predator diet composition, yet little is known about landscape effects on insect gut microbiomes, a determinant of physiology and condition. Here, we combine laboratory and field experiments to examine the effects of landscape context on the gut bacterial community and body condition of predatory insects. Under laboratory conditions, we found that prey diversity increased bacterial richness in insect guts. In the field, we studied the performance and gut microbiota of six predatory insect species along a landscape complexity gradient in two local habitat types (soybean fields vs. prairie). Insects from soy fields had richer gut bacteria and lower fat content than those from prairies, suggesting better feeding conditions in prairies. Species origin mediated landscape context effects, suggesting differences in foraging of exotic and native predators on a landscape scale. Overall, our study highlights complex interactions among gut microbiota, predator identity, and landscape context.
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Affiliation(s)
- Julia Tiede
- Institute of Landscape Ecology University of Muenster Muenster Germany.,Department of Crop Sciences University of Goettingen Goettingen Germany.,Department of Entomology University of Wisconsin-Madison Madison WI USA
| | - Christoph Scherber
- Institute of Landscape Ecology University of Muenster Muenster Germany.,Department of Crop Sciences University of Goettingen Goettingen Germany
| | - James Mutschler
- Departments of Civil and Environmental Engineering and Bacteriology University of Wisconsin-Madison Madison WI USA
| | - Katherine D McMahon
- Departments of Civil and Environmental Engineering and Bacteriology University of Wisconsin-Madison Madison WI USA
| | - Claudio Gratton
- Department of Entomology University of Wisconsin-Madison Madison WI USA
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15
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Delgado ML, Singh P, Funk JA, Moore JA, Cannell EM, Kanesfsky J, Manning SD, Scribner KT. Intestinal Microbial Community Dynamics of White-Tailed Deer (Odocoileus virginianus) in an Agroecosystem. MICROBIAL ECOLOGY 2017; 74:496-506. [PMID: 28293696 DOI: 10.1007/s00248-017-0961-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 02/28/2017] [Indexed: 06/06/2023]
Abstract
The intestinal microbiota has important functions that contribute to host health. The compositional dynamics of microbial communities are affected by many factors, including diet and presence of pathogens. In contrast to humans and domestic mammals, the composition and seasonal dynamics of intestinal microbiota of wildlife species remain comparatively understudied. White-tailed deer (Odocoileus virginianus) is an ecologically and economically important wildlife species that inhabits agricultural ecosystems and is known to be a reservoir of enteric pathogens. Nevertheless, there is a lack of knowledge of white-tailed deer intestinal microbiota diversity and taxonomic composition. This study's first objective was to characterize and compare the intestinal microbiota of 66 fecal samples from white-tailed deer collected during two sampling periods (March and June) using 16S rDNA pyrosequencing. Associations between community diversity and composition and factors including season, sex, host genetic relatedness, and spatial location were quantified. Results revealed that white-tailed deer intestinal microbiota was predominantly comprised of phyla Firmicutes and Proteobacteria, whose relative frequencies varied significantly between sampling periods. The second objective was to examine the associations between the presence of Escherichia coli and Salmonella, and microbiota composition and diversity. Results indicated that relative abundance of some microbial taxa varied when a pathogen was present. This study provides insights into microbial compositional dynamics of a wildlife species inhabiting coupled natural and agricultural landscapes. Data focus attention on the high prevalence of Proteobacteria particularly during the summer and highlight the need for future research regarding the role of white-tailed deer as a natural pathogen reservoir in agroecosystems.
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Affiliation(s)
- M Lisette Delgado
- Department of Fisheries and Wildlife, Michigan State University, 480 Wilson Rd, East Lansing, MI, 48824, USA.
| | - Pallavi Singh
- Department of Microbiology and Molecular Genetics, Michigan State University, 194 Food Safety & Toxicology Building, East Lansing, MI, 48824, USA
| | - Julie A Funk
- College of Veterinary Medicine, Michigan State University, 736 Wilson Rd, East Lansing, MI, 48824, USA
| | - Jennifer A Moore
- Department of Biology, Grand Valley State University, 1 Campus Drive, Allendale, MI, 49401, USA
| | - Emily M Cannell
- Department of Fisheries and Wildlife, Michigan State University, 480 Wilson Rd, East Lansing, MI, 48824, USA
| | - Jeannette Kanesfsky
- Department of Fisheries and Wildlife, Michigan State University, 480 Wilson Rd, East Lansing, MI, 48824, USA
| | - Shannon D Manning
- Department of Microbiology and Molecular Genetics, Michigan State University, 194 Food Safety & Toxicology Building, East Lansing, MI, 48824, USA
| | - Kim T Scribner
- Department of Fisheries and Wildlife, Michigan State University, 480 Wilson Rd, East Lansing, MI, 48824, USA
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16
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Romano M. Gut Microbiota as a Trigger of Accelerated Directional Adaptive Evolution: Acquisition of Herbivory in the Context of Extracellular Vesicles, MicroRNAs and Inter-Kingdom Crosstalk. Front Microbiol 2017; 8:721. [PMID: 28473829 PMCID: PMC5397478 DOI: 10.3389/fmicb.2017.00721] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Accepted: 04/06/2017] [Indexed: 11/17/2022] Open
Abstract
According to a traditional view, the specific diet in vertebrates is one of the key factors structuring the composition of the gut microbiota. In this interpretation, the microbiota assumes a subordinate position, where the larger host shapes, through evolution and its fitness, the taxonomical composition of the hosted microbiota. The present contribution shows how the evolution of herbivory, framed within the new concept of holobiont, the possibility of inter-kingdom crosstalk and its epigenetic effects, could pave the way to a completely reversed interpretation: instead of being passively shaped, the microbiota can mold and shape the general host body structure to increase its fitness. Central elements to consider in this context are the inter-kingdom crosstalk, the possibility of transporting RNAs through nanovesicles in feces from parents to offspring, and the activation of epigenetic processes passed on vertically from generation to generation. The new hypothesis is that the gut microbiota could play a great role in the macroevolutionary dynamics of herbivorous vertebrates, causing directly through host-microbiota dialog of epigenetic nature (i.e., methylation, histone acetylation, etc.), major changes in the organisms phenotype. The vertical exchange of the same microbial communities from parents to offspring, the interaction of these microbes with fairly uniform genotypes, and the socially restricted groups where these processes take place, could all explain the reasons why herbivory has appeared several time (and independently) during the evolution of vertebrates. The new interpretation could also represent a key factor in understanding the convergent evolution of analogous body structures in very distant lineages.
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Affiliation(s)
- Marco Romano
- Museum für Naturkunde, Leibniz-Institut für Evolutions- und BiodiversitätsforschungBerlin, Germany.,Dipartimento di Scienze della Terra, Sapienza Universita di RomaRome, Italy
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17
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Payne JT, Millar JJ, Jackson CR, Ochs CA. Patterns of variation in diversity of the Mississippi river microbiome over 1,300 kilometers. PLoS One 2017; 12:e0174890. [PMID: 28350888 PMCID: PMC5370145 DOI: 10.1371/journal.pone.0174890] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Accepted: 03/16/2017] [Indexed: 12/31/2022] Open
Abstract
We examined the downriver patterns of variation in taxonomic diversity of the Mississippi River bacterioplankton microbiome along 1,300 river kilometers, or approximately one third the total length of the river. The study section included portions of the Upper, Middle, and Lower Mississippi River, confluences with five tributaries draining distinct sub-basins, river cities, and extended stretches without major inputs to the Mississippi. The composition and proportional abundance of dominant bacterial phyla was distinct for free-living and particle-associated cells, and constant along the entire reach, except for a substantial but transient disturbance near the city of Memphis, Tennessee. At a finer scale of taxonomic resolution (operational taxonomic units, OTUs), however, there were notable patterns in downriver variation in bacterial community alpha diversity (richness within a site) and beta diversity (variation in composition among sites). There was a strong and steady increase downriver in alpha diversity of OTUs on suspended particles, suggesting an increase in particle niche heterogeneity, and/or particle colonization. Relatively large shifts in beta diversity of free-living and particle-associated communities occurred following major tributary confluences and transiently at Memphis, while in long stretches between these points diversity typically varied more gradually. We conclude that the Mississippi River possesses a bacterioplankton microbiome distinct in diversity from other large river microbiomes in the Mississippi River Basin, that at major river confluences or urban point sources its OTU diversity may shift abruptly and substantially, presumably by immigration of distinct external microbiomes, but that where environmental conditions are more stable along the downriver gradient, microbiome diversity tends to vary gradually, presumably by a process of successional change in community composition.
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Affiliation(s)
- Jason T. Payne
- Department of Biology, University of Mississippi, University, Mississippi, United States of America
| | - Justin J. Millar
- Department of Biology, University of Mississippi, University, Mississippi, United States of America
| | - Colin R. Jackson
- Department of Biology, University of Mississippi, University, Mississippi, United States of America
| | - Clifford A. Ochs
- Department of Biology, University of Mississippi, University, Mississippi, United States of America
- * E-mail:
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18
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David AS, Quiram GL, Sirota JI, Seabloom EW. Quantifying the associations between fungal endophytes and biocontrol-induced herbivory of invasive purple loosestrife (Lythrum salicariaL.). Mycologia 2017; 108:625-37. [DOI: 10.3852/15-207] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 04/04/2016] [Indexed: 12/27/2022]
Affiliation(s)
- Aaron S. David
- University of Minnesota, Department of Ecology, Evolution and Behavior, 1479 Gortner Avenue, Saint Paul, Minnesota 55108
| | - Gina L. Quiram
- University of Minnesota, College of Continuing Education, 1994 Buford Ave, Saint Paul, Minnesota 55108
| | - Jennie I. Sirota
- University of Minnesota, Natural Resources, Science and Management Program, 1530 Cleveland Avenue, Saint Paul, Minnesota 55108
| | - Eric W. Seabloom
- University of Minnesota, Department of Ecology, Evolution and Behavior, 1479 Gortner Avenue, Saint Paul, Minnesota 55108
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19
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Lokmer A, Goedknegt MA, Thieltges DW, Fiorentino D, Kuenzel S, Baines JF, Wegner KM. Spatial and Temporal Dynamics of Pacific Oyster Hemolymph Microbiota across Multiple Scales. Front Microbiol 2016; 7:1367. [PMID: 27630625 PMCID: PMC5006416 DOI: 10.3389/fmicb.2016.01367] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 08/18/2016] [Indexed: 01/09/2023] Open
Abstract
Unveiling the factors and processes that shape the dynamics of host associated microbial communities (microbiota) under natural conditions is an important part of understanding and predicting an organism's response to a changing environment. The microbiota is shaped by host (i.e., genetic) factors as well as by the biotic and abiotic environment. Studying natural variation of microbial community composition in multiple host genetic backgrounds across spatial as well as temporal scales represents a means to untangle this complex interplay. Here, we combined a spatially-stratified with a longitudinal sampling scheme within differentiated host genetic backgrounds by reciprocally transplanting Pacific oysters between two sites in the Wadden Sea (Sylt and Texel). To further differentiate contingent site from host genetic effects, we repeatedly sampled the same individuals over a summer season to examine structure, diversity and dynamics of individual hemolymph microbiota following experimental removal of resident microbiota by antibiotic treatment. While a large proportion of microbiome variation could be attributed to immediate environmental conditions, we observed persistent effects of antibiotic treatment and translocation suggesting that hemolymph microbial community dynamics is subject to within-microbiome interactions and host population specific factors. In addition, the analysis of spatial variation revealed that the within-site microenvironmental heterogeneity resulted in high small-scale variability, as opposed to large-scale (between-site) stability. Similarly, considerable within-individual temporal variability was in contrast with the overall temporal stability at the site level. Overall, our longitudinal, spatially-stratified sampling design revealed that variation in hemolymph microbiota is strongly influenced by site and immediate environmental conditions, whereas internal microbiome dynamics and oyster-related factors add to their long-term stability. The combination of small and large scale resolution of spatial and temporal observations therefore represents a crucial but underused tool to study host-associated microbiome dynamics.
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Affiliation(s)
- Ana Lokmer
- Coastal Ecology, Wadden Sea Station Sylt, Alfred Wegener Institute - Helmholtz Centre for Polar and Marine Research List auf Sylt, Germany
| | - M Anouk Goedknegt
- Department of Coastal Systems, Royal Netherlands Institute for Sea Research, Utrecht University Texel, Netherlands
| | - David W Thieltges
- Department of Coastal Systems, Royal Netherlands Institute for Sea Research, Utrecht University Texel, Netherlands
| | - Dario Fiorentino
- Coastal Ecology, Wadden Sea Station Sylt, Alfred Wegener Institute - Helmholtz Centre for Polar and Marine Research List auf Sylt, Germany
| | - Sven Kuenzel
- Max Planck Institute for Evolutionary Biology Plön, Germany
| | - John F Baines
- Max Planck Institute for Evolutionary BiologyPlön, Germany; Institute for Experimental Medicine, Christian-Albrechts-Universität zu KielKiel, Germany
| | - K Mathias Wegner
- Coastal Ecology, Wadden Sea Station Sylt, Alfred Wegener Institute - Helmholtz Centre for Polar and Marine Research List auf Sylt, Germany
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20
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Borer ET, Laine AL, Seabloom EW. A Multiscale Approach to Plant Disease Using the Metacommunity Concept. ANNUAL REVIEW OF PHYTOPATHOLOGY 2016; 54:397-418. [PMID: 27296140 DOI: 10.1146/annurev-phyto-080615-095959] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Plant disease arises from the interaction of processes occurring at multiple spatial and temporal scales. With new tools such as next-generation sequencing, we are learning about the diversity of microbes circulating within and among plant populations and often coinhabiting host individuals. The proliferation of pathogenic microbes depends on single-species dynamics and multispecies interactions occurring within and among host cells, the spatial organization and genetic landscape of hosts, the frequency and mode of transmission among hosts and host populations, and the abiotic environmental context. Here, we examine empirical evidence from these multiple scales to assess the utility of metacommunity theory, a theoretical framework developed for free-living organisms to further our understanding of and assist in predicting plant-pathogen infection and spread. We suggest that deeper understanding of disease dynamics can arise through the application of this conceptual framework at scales ranging from individual cells to landscapes. In addition, we use this multiscale theoretical perspective to synthesize existing knowledge, generate novel hypotheses, and point toward promising future opportunities for the study of plant pathogens in natural populations.
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Affiliation(s)
- Elizabeth T Borer
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, Minnesota 55108; ,
| | - Anna-Liisa Laine
- Centre of Excellence in Metapopulation Biology, Department of Biosciences, University of Helsinki, FI-00014, Finland;
| | - Eric W Seabloom
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, Minnesota 55108; ,
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21
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David AS, Seabloom EW, May G. Plant Host Species and Geographic Distance Affect the Structure of Aboveground Fungal Symbiont Communities, and Environmental Filtering Affects Belowground Communities in a Coastal Dune Ecosystem. MICROBIAL ECOLOGY 2016; 71:912-926. [PMID: 26626912 DOI: 10.1007/s00248-015-0712-6] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 11/16/2015] [Indexed: 06/05/2023]
Abstract
Microbial symbionts inhabit tissues of all plants and animals. Their community composition depends largely on two ecological processes: (1) filtering by abiotic conditions and host species determining the environments that symbionts are able to colonize and (2) dispersal-limitation determining the pool of symbionts available to colonize a given host and community spatial structure. In plants, the above- and belowground tissues represent such distinct habitats for symbionts that we expect different effects of filtering and spatial structuring on their symbiont communities. In this study, we characterized above- and belowground communities of fungal endophytes--fungi living asymptomatically within plants--to understand the contributions of filtering and spatial structure to endophyte community composition. We used a culture-based approach to characterize endophytes growing in leaves and roots of three species of coastal beachgrasses in dunes of the USA Pacific Northwest. For leaves, endophyte isolation frequency and OTU richness depended primarily on plant host species. In comparison, for roots, both isolation frequency and OTU richness increased from the nutrient-poor front of the dune to the higher-nutrient backdune. Endophyte community composition in leaves exhibited a distance-decay relationship across the region. In a laboratory assay, faster growth rates and lower spore production were more often associated with leaf- than root-inhabiting endophytes. Overall, our results reveal a greater importance of biotic filtering by host species and dispersal-limitation over regional geographic distances for aboveground leaf endophyte communities and stronger effects of abiotic environmental filtering and locally patchy distributions for belowground root endophyte communities.
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Affiliation(s)
- Aaron S David
- Department of Ecology, Evolution, and Behavior, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN, 55108, USA.
| | - Eric W Seabloom
- Department of Ecology, Evolution, and Behavior, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN, 55108, USA
| | - Georgiana May
- Department of Ecology, Evolution, and Behavior, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN, 55108, USA
- Department of Plant Biology, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN, 55108, USA
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22
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Comparison of fitness traits and their plasticity on multiple plants for Sitobion avenae infected and cured of a secondary endosymbiont. Sci Rep 2016; 6:23177. [PMID: 26979151 PMCID: PMC4793262 DOI: 10.1038/srep23177] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 03/01/2016] [Indexed: 12/13/2022] Open
Abstract
Regiella insecticola has been found to enhance the performance of host aphids on certain plants, but its functional role in adaptation of host aphids to plants is still controversial. Here we evaluate the impacts of R. insecticola infections on vital life-history traits of Sitobion avenae (Fabricius), and their underlying genetic variation and phenotypic plasticity on three plants. It was shown that effects of R. insecticola on S. avenae’s fitness (i.e., developmental time and fecundity) were neutral on oat or wheat, but negative on rye. Infections of R. insecticola modified genetic variation that underlies S. avenae’s life-history traits. This was demonstrated by comparing life-history trait heritabilities between aphid lines with and without R. insecticola. Moreover, there were enhanced negative genetic correlations between developmental time and fecundity for R. insecticola infected lines, and structural differences in G-matrices of life-history traits for the two types of aphid lines. In R. insecticola-infected aphid lines, there were increases in plasticities for developmental times of first and second instar nymphs and for fecundity, showing novel functional roles of bacterial symbionts in plant-insect interactions. The identified effects of R. insecticola infections could have significant implications for the ecology and evolution of its host populations in natural conditions.
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23
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Abstract
Groundbreaking research on the universality and diversity of microorganisms is now challenging the life sciences to upgrade fundamental theories that once seemed untouchable. To fully appreciate the change that the field is now undergoing, one has to place the epochs and foundational principles of Darwin, Mendel, and the modern synthesis in light of the current advances that are enabling a new vision for the central importance of microbiology. Animals and plants are no longer heralded as autonomous entities but rather as biomolecular networks composed of the host plus its associated microbes, i.e., "holobionts." As such, their collective genomes forge a "hologenome," and models of animal and plant biology that do not account for these intergenomic associations are incomplete. Here, we integrate these concepts into historical and contemporary visions of biology and summarize a predictive and refutable framework for their evaluation. Specifically, we present ten principles that clarify and append what these concepts are and are not, explain how they both support and extend existing theory in the life sciences, and discuss their potential ramifications for the multifaceted approaches of zoology and botany. We anticipate that the conceptual and evidence-based foundation provided in this essay will serve as a roadmap for hypothesis-driven, experimentally validated research on holobionts and their hologenomes, thereby catalyzing the continued fusion of biology's subdisciplines. At a time when symbiotic microbes are recognized as fundamental to all aspects of animal and plant biology, the holobiont and hologenome concepts afford a holistic view of biological complexity that is consistent with the generally reductionist approaches of biology.
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Affiliation(s)
- Seth R. Bordenstein
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Kevin R. Theis
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
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24
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Seabloom EW, Borer ET, Gross K, Kendig AE, Lacroix C, Mitchell CE, Mordecai EA, Power AG. The community ecology of pathogens: coinfection, coexistence and community composition. Ecol Lett 2015; 18:401-15. [PMID: 25728488 DOI: 10.1111/ele.12418] [Citation(s) in RCA: 117] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 09/20/2014] [Accepted: 01/14/2015] [Indexed: 12/11/2022]
Abstract
Disease and community ecology share conceptual and theoretical lineages, and there has been a resurgence of interest in strengthening links between these fields. Building on recent syntheses focused on the effects of host community composition on single pathogen systems, we examine pathogen (microparasite) communities using a stochastic metacommunity model as a starting point to bridge community and disease ecology perspectives. Such models incorporate the effects of core community processes, such as ecological drift, selection and dispersal, but have not been extended to incorporate host-pathogen interactions, such as immunosuppression or synergistic mortality, that are central to disease ecology. We use a two-pathogen susceptible-infected (SI) model to fill these gaps in the metacommunity approach; however, SI models can be intractable for examining species-diverse, spatially structured systems. By placing disease into a framework developed for community ecology, our synthesis highlights areas ripe for progress, including a theoretical framework that incorporates host dynamics, spatial structuring and evolutionary processes, as well as the data needed to test the predictions of such a model. Our synthesis points the way for this framework and demonstrates that a deeper understanding of pathogen community dynamics will emerge from approaches working at the interface of disease and community ecology.
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Affiliation(s)
- Eric W Seabloom
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN, USA
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25
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Kowalski KP, Bacon C, Bickford W, Braun H, Clay K, Leduc-Lapierre M, Lillard E, McCormick MK, Nelson E, Torres M, White J, Wilcox DA. Advancing the science of microbial symbiosis to support invasive species management: a case study on Phragmites in the Great Lakes. Front Microbiol 2015; 6:95. [PMID: 25745417 PMCID: PMC4333861 DOI: 10.3389/fmicb.2015.00095] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 01/26/2015] [Indexed: 01/03/2023] Open
Abstract
A growing body of literature supports microbial symbiosis as a foundational principle for the competitive success of invasive plant species. Further exploration of the relationships between invasive species and their associated microbiomes, as well as the interactions with the microbiomes of native species, can lead to key new insights into invasive success and potentially new and effective control approaches. In this manuscript, we review microbial relationships with plants, outline steps necessary to develop invasive species control strategies that are based on those relationships, and use the invasive plant species Phragmites australis (common reed) as an example of how development of microbial-based control strategies can be enhanced using a collective impact approach. The proposed science agenda, developed by the Collaborative for Microbial Symbiosis and Phragmites Management, contains a foundation of sequential steps and mutually-reinforcing tasks to guide the development of microbial-based control strategies for Phragmites and other invasive species. Just as the science of plant-microbial symbiosis can be transferred for use in other invasive species, so too can the model of collective impact be applied to other avenues of research and management.
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Affiliation(s)
- Kurt P. Kowalski
- U.S. Geological Survey, Great Lakes Science CenterAnn Arbor, MI, USA
| | - Charles Bacon
- U.S. Department of Agriculture, Agricultural Research ServiceAthens, GA, USA
| | - Wesley Bickford
- U.S. Geological Survey, Great Lakes Science CenterAnn Arbor, MI, USA
| | | | - Keith Clay
- Department of Biology, Indiana UniversityBloomington, IN, USA
| | | | | | | | - Eric Nelson
- Department of Plant Pathology and Plant-Microbe Biology, Cornell UniversityIthaca, NY, USA
| | - Monica Torres
- Department of Plant Biology and Pathology, Rutgers UniversityNew Brunswick, NJ, USA
| | - James White
- Department of Plant Biology and Pathology, Rutgers UniversityNew Brunswick, NJ, USA
| | - Douglas A. Wilcox
- Department of Environmental Science and Biology, The College at Brockport, State University of New YorkBrockport, NY, USA
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