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Salloum PM, Jorge F, Poulin R. Different trematode parasites in the same snail host: Species-specific or shared microbiota? Mol Ecol 2023; 32:5414-5428. [PMID: 37615348 DOI: 10.1111/mec.17111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 08/07/2023] [Accepted: 08/10/2023] [Indexed: 08/25/2023]
Abstract
The concept that microbes associated with macroorganisms evolve as a unit has swept evolutionary ecology. However, this idea is controversial due to factors such as imperfect vertical transmission of microbial lineages and high microbiome variability among conspecific individuals of the same population. Here, we tested several predictions regarding the microbiota of four trematodes (Galactosomum otepotiense, Philophthalmus attenuatus, Acanthoparyphium sp. and Maritrema novaezealandense) that parasitize the same snail host population. We predicted that each parasite species would harbour a distinct microbiota, with microbial composition similarity decreasing with increasing phylogenetic distance among parasite species. We also predicted that trematode species co-infecting the same individual host would influence each other's microbiota. We detected significant differences in alpha and beta diversity, as well as differential abundance, in the microbiota of the four trematode species. We found no evidence that phylogenetically closely related trematodes had more similar microbiota. We also uncovered indicator bacterial taxa that were significantly associated with each trematode species. Trematode species sharing the same snail host showed evidence of mostly one-sided bacterial exchanges, with the microbial community of one species approaching that of the other. We hypothesize that natural selection acting on specific microbial lineages may be important to maintain differences in horizontally acquired microbes, with vertical transmission also playing a role. In particular, one trematode species had a more consistent and diverse bacteriota than the others, potentially a result of stronger stabilizing pressures. We conclude that species-specific processes shape microbial community assembly in different trematodes exploiting the same host population.
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Affiliation(s)
| | - Fátima Jorge
- Otago Micro and Nano Imaging, Electron Microscopy Unit, University of Otago, Dunedin, New Zealand
| | - Robert Poulin
- Department of Zoology, University of Otago, Dunedin, New Zealand
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Huang RZ, Wang Q, Sun JY, Yang SW, Zhao YP, Liu JF, Xiao WF. Comparison of species composition and community characteristics of Quercus forests on south and north slopes of Taibai Mountain, China. Ying Yong Sheng Tai Xue Bao 2023; 34:2055-2064. [PMID: 37681369 DOI: 10.13287/j.1001-9332.202308.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
We examined species composition, community characteristics, diversity, and community similarity of five Quercus communities composed of three Quercus species (Q. variabilis, Q. aliena var. acutiserrata, Q. wutaishanica) on the altitudinal gradient on the south and north slopes of Taibai Mountain. The results showed that there was an altitudinal transition pattern from Q. variabilis pure forest to Q. variabilis-Q. aliena var. acutiserrata mixed forest, Q. aliena var. acutiserrata pure forest, Q. aliena var. acutiserrata-Q. wutaishanica mixed forest and Q. wutaishanica pure forest on the south and north slopes of Taibai Mountain. The main companion species of Quercus community on the north slope were Pinus armandii, Castanea seguinii, and Sorbus alnifolia, and were Pinus tabuliformis, C. seguinii, Carpinus cordata, and Q. spinosa on the south slope. Species richness, woody plant density, and Quercus species dominance on the north slope of Taibai Mountain were higher than those on the south slope. α diversity of tree layer in Quercus community on the south and north slopes of Taibai Mountain increased first, then decreased and then increased with altitude. α diversity of tree layer was higher in mixed forests than pure forests. α diversity of shrub layer was higher than that of tree layer and herb layer in Quercus community on south and north slopes. β diversity fluctuated greatly along the altitudinal gradient on the south and north slopes, indicating that species composition changed greatly with altitude. Results of redundancy analysis showed that mean warmest month temperature, altitude and tree height accounted for 79.0% of the community diversity on the north slope, and that soil water content, tree height, canopy density and mean annual temperature accounted for 79.6% of the community diversity on the south slope. Overall, Quercus dominance was higher on the north slope of Taibai Mountain, and the substitution distribution pattern of Quercus species was clearer than that on the south slope. Environmental factors related to temperature and precipitation jointly affected α diversity of Quercus communities.
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Affiliation(s)
- Rui-Zhi Huang
- Institute of Forest Ecology, Environment and Nature Conservation, Chinese Academy of Forestry, Beijing 100091, China
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Qi Wang
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Jing-Yi Sun
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Shao-Wei Yang
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Yi-Pei Zhao
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Jian-Feng Liu
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Wen-Fa Xiao
- Institute of Forest Ecology, Environment and Nature Conservation, Chinese Academy of Forestry, Beijing 100091, China
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3
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Wu H, Dong S, Rao B. Latitudinal trends in the structure, similarity and beta diversity of plant communities invaded by Alternanthera philoxeroides in heterogeneous habitats. Front Plant Sci 2022; 13:1021337. [PMID: 36275507 PMCID: PMC9583019 DOI: 10.3389/fpls.2022.1021337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 09/22/2022] [Indexed: 06/16/2023]
Abstract
Variations in latitudinal gradients could lead to changes in the performance and ecological effects of invasive plants and thus may affect the species composition, distribution and interspecific substitution of native plant communities. However, variations in structure, similarity and beta (β) diversity within invaded communities across latitudinal gradients in heterogeneous habitats remain unclear. In this study, we conducted a two-year field survey along 21°N to 37°N in China, to examine the differential effects of the amphibious invasive plant Alternanthera philoxeroides on native plant communities in terrestrial and aquatic habitats. We compared the differences in the invasion importance value (IV), species distribution, community similarity (Jaccard index and Sorenson index) and β diversity (Bray-Curtis index and βsim index) between terrestrial and aquatic communities invaded by A. philoxeroides, as well as analyzed their latitudinal trends. We found that the IV of A. philoxeroides and β diversity in aquatic habitats were all significantly higher than that of terrestrial, while the terrestrial habitat had a higher community similarity values. The aquatic A. philoxeroides IV increased with increasing latitude, while the terrestrial IV had no significant latitudinal trend. With increasing latitude, the component proportion of cold- and drought-tolerant species in the terrestrial communities increased, and the dominant accompanying species in the aquatic communities gradually changed from hygrophytes and floating plants to emerged and submerged plants. In addition, the aquatic communities had lower community similarity values and higher β diversity in higher latitudinal regions, while terrestrial communities had the opposite parameters in these regions. Our study indicates that the bioresistance capacities of the native communities to invasive A. philoxeroides in heterogeneous habitats are different; A. philoxeroides invasion leads to higher community homogenization in terrestrial habitats than in aquatic habitats, and terrestrial communities experience more severe homogenization in higher latitudinal regions. These findings are crucial for predicting the dynamics of invasive plant communities under rapid global change.
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Affiliation(s)
- Hao Wu
- College of Life Sciences, Xinyang Normal University, Xinyang, China
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Sijin Dong
- College of Life Sciences, Xinyang Normal University, Xinyang, China
| | - Benqiang Rao
- College of Life Sciences, Xinyang Normal University, Xinyang, China
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Tikhonov G, Opedal ØH, Abrego N, Lehikoinen A, de Jonge MMJ, Oksanen J, Ovaskainen O. Joint species distribution modelling with the r-package Hmsc. Methods Ecol Evol 2020; 11:442-447. [PMID: 32194928 PMCID: PMC7074067 DOI: 10.1111/2041-210x.13345] [Citation(s) in RCA: 110] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 12/16/2019] [Indexed: 11/28/2022]
Abstract
Joint Species Distribution Modelling (JSDM) is becoming an increasingly popular statistical method for analysing data in community ecology. Hierarchical Modelling of Species Communities (HMSC) is a general and flexible framework for fitting JSDMs. HMSC allows the integration of community ecology data with data on environmental covariates, species traits, phylogenetic relationships and the spatio-temporal context of the study, providing predictive insights into community assembly processes from non-manipulative observational data of species communities.The full range of functionality of HMSC has remained restricted to Matlab users only. To make HMSC accessible to the wider community of ecologists, we introduce Hmsc 3.0, a user-friendly r implementation.We illustrate the use of the package by applying Hmsc 3.0 to a range of case studies on real and simulated data. The real data consist of bird counts in a spatio-temporally structured dataset, environmental covariates, species traits and phylogenetic relationships. Vignettes on simulated data involve single-species models, models of small communities, models of large species communities and models for large spatial data. We demonstrate the estimation of species responses to environmental covariates and how these depend on species traits, as well as the estimation of residual species associations. We demonstrate how to construct and fit models with different types of random effects, how to examine MCMC convergence, how to examine the explanatory and predictive powers of the models, how to assess parameter estimates and how to make predictions. We further demonstrate how Hmsc 3.0 can be applied to normally distributed data, count data and presence-absence data.The package, along with the extended vignettes, makes JSDM fitting and post-processing easily accessible to ecologists familiar with r.
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Affiliation(s)
- Gleb Tikhonov
- Department of Computer ScienceAalto UniversityEspooFinland
- Organismal and Evolutionary Biology Research ProgrammeUniversity of HelsinkiHelsinkiFinland
| | - Øystein H. Opedal
- Organismal and Evolutionary Biology Research ProgrammeUniversity of HelsinkiHelsinkiFinland
- Centre for Biodiversity DynamicsDepartment of BiologyNorwegian University of Science and TechnologyTrondheimNorway
| | - Nerea Abrego
- Department of Agricultural SciencesUniversity of HelsinkiHelsinkiFinland
| | - Aleksi Lehikoinen
- The Helsinki Lab of OrnithologyFinnish Museum of Natural HistoryUniversity of HelsinkiHelsinkiFinland
| | - Melinda M. J. de Jonge
- Department of Environmental ScienceInstitute for Water and Wetland ResearchRadboud UniversityNijmegenThe Netherlands
| | - Jari Oksanen
- Botany UnitFinnish Museum of Natural HistoryUniversity of HelsinkiHelsinkiFinland
| | - Otso Ovaskainen
- Organismal and Evolutionary Biology Research ProgrammeUniversity of HelsinkiHelsinkiFinland
- Centre for Biodiversity DynamicsDepartment of BiologyNorwegian University of Science and TechnologyTrondheimNorway
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Su X, Jing G, McDonald D, Wang H, Wang Z, Gonzalez A, Sun Z, Huang S, Navas J, Knight R, Xu J. Reply to Sun et al., "Identifying Composition Novelty in Microbiome Studies: Improvement of Prediction Accuracy". mBio 2019; 10:e01234-19. [PMID: 31387904 DOI: 10.1128/mBio.01234-19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Wolfe JD, Alexander JD, Stephens JL, Ralph CJ. A novel approach to understanding bird communities using informed diversity estimates at local and regional scales in northern California and southern Oregon. Ecol Evol 2019; 9:4431-4442. [PMID: 31031917 PMCID: PMC6476868 DOI: 10.1002/ece3.5008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 12/11/2018] [Accepted: 12/27/2018] [Indexed: 11/20/2022] Open
Abstract
Assessment and preservation of biodiversity has been a central theme of conservation biology since the discipline's inception. However, when diversity estimates are based purely on measures of presence-absence, or even abundance, they do not directly assess in what way focal habitats support the life history needs of individual species making up biological communities. Here, we move beyond naïve measures of occurrence and introduce the concept of "informed diversity" indices which scale estimates of avian species richness and community assemblage by two critical phases of their life cycle: breeding and molt. We tested the validity of the "informed diversity" concept using bird capture data from multiple locations in northern California and southern Oregon to examine patterns of species richness among breeding, molting, and naïve (based solely on occurrence) bird communities at the landscape and local scales using linear regression, community similarity indices, and a Detrended Correspondence Analysis (DCA). At the landscape scale, we found a striking pattern of increased species richness for breeding, molting, and naïve bird communities further inland and at higher elevations throughout the study area. At the local scale, we found that some sites with species-rich naïve communities were in fact species-poor when informed by breeding status, indicating that naïve richness may mask more biologically meaningful patterns of diversity. We suggest that land managers use informed diversity estimates instead of naïve measures of diversity to identify ecologically valuable wildlife habitat.
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Affiliation(s)
- Jared D. Wolfe
- School of Forest Resources and Environmental SciencesMichigan Technological UniversityHoughtonMichigan
- Klamath Bird ObservatoryAshlandOregon
- U.S.D.A. Forest ServicePacific Southwest Research StationArcataCalifornia
| | - John D. Alexander
- U.S.D.A. Forest ServicePacific Southwest Research StationArcataCalifornia
| | - Jaime L. Stephens
- U.S.D.A. Forest ServicePacific Southwest Research StationArcataCalifornia
| | - C. John Ralph
- Klamath Bird ObservatoryAshlandOregon
- U.S.D.A. Forest ServicePacific Southwest Research StationArcataCalifornia
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7
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Su X, Jing G, McDonald D, Wang H, Wang Z, Gonzalez A, Sun Z, Huang S, Navas J, Knight R, Xu J. Identifying and Predicting Novelty in Microbiome Studies. mBio 2018; 9:e02099-18. [PMID: 30425147 DOI: 10.1128/mBio.02099-18] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
With the expansion of microbiome sequencing globally, a key challenge is to relate new microbiome samples to the existing space of microbiome samples. Here, we present Microbiome Search Engine (MSE), which enables the rapid search of query microbiome samples against a large, well-curated reference microbiome database organized by taxonomic similarity at the whole-microbiome level. Tracking the microbiome novelty score (MNS) over 8 years of microbiome depositions based on searching in more than 100,000 global 16S rRNA gene amplicon samples, we detected that the structural novelty of human microbiomes is approaching saturation and likely bounded, whereas that in environmental habitats remains 5 times higher. Via the microbiome focus index (MFI), which is derived from the MNS and microbiome attention score (MAS), we objectively track and compare the structural-novelty and attracted-attention scores of individual microbiome samples and projects, and we predict future trends in the field. For example, marine and indoor environments and mother-baby interactions are likely to receive disproportionate additional attention based on recent trends. Therefore, MNS, MAS, and MFI are proposed "alt-metrics" for evaluating a microbiome project or prospective developments in the microbiome field, both of which are done in the context of existing microbiome big data.IMPORTANCE We introduce two concepts to quantify the novelty of a microbiome. The first, the microbiome novelty score (MNS), allows identification of microbiomes that are especially different from what is already sequenced. The second, the microbiome attention score (MAS), allows identification of microbiomes that have many close neighbors, implying that considerable scientific attention is devoted to their study. By computing a microbiome focus index based on the MNS and MAS, we objectively track and compare the novelty and attention scores of individual microbiome samples and projects over time and predict future trends in the field; i.e., we work toward yielding fundamentally new microbiomes rather than filling in the details. Therefore, MNS, MAS, and MFI can serve as "alt-metrics" for evaluating a microbiome project or prospective developments in the microbiome field, both of which are done in the context of existing microbiome big data.
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8
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Shen D, Langenheder S, Jürgens K. Dispersal Modifies the Diversity and Composition of Active Bacterial Communities in Response to a Salinity Disturbance. Front Microbiol 2018; 9:2188. [PMID: 30294307 PMCID: PMC6159742 DOI: 10.3389/fmicb.2018.02188] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Accepted: 08/27/2018] [Indexed: 11/21/2022] Open
Abstract
Dispersal can influence the response of bacterial communities to environmental changes and disturbances. However, the extent to which dispersal contributes to the community response in dependence of the character and strength of the disturbance remains unclear. Here, we conducted a transplant experiment using dialysis bags in which bacterioplankton originating from brackish and marine regions of the Saint Lawrence Estuary were reciprocally incubated in the two environments for 5 days. Dispersal treatments were set-up by subjecting half of the microcosms in each environment to an exchange of cells between the marine and brackish assemblages at a daily exchange rate of 6% (v/v), and the other half of microcosms were kept as the non-dispersal treatments. Bacterial 16S rRNA sequencing was then used to examine the diversity and composition of the active communities. Alpha diversity of the marine communities that were exposed to the brackish environment was elevated greatly by dispersal, but declined in the absence of dispersal. This indicates that dispersal compensated the loss of diversity in the marine communities after a disturbance by introducing bacterial taxa that were able to thrive and coexist with the remaining community members under brackish conditions. On the contrary, alpha diversity of the brackish communities was not affected by dispersal in either environment. Furthermore, dispersal led to an increase in similarity between marine and brackish communities in both of the environments, with a greater similarity when the communities were incubated in the brackish environment. These results suggest that the higher initial diversity in the brackish than in the marine starting community made the resident community less susceptible to dispersing bacteria. Altogether, this study shows that dispersal modifies the diversity and composition of the active communities in response to a salinity disturbance, and enables the local adjustment of specific bacteria under brackish environmental conditions.
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Affiliation(s)
- Dandan Shen
- Section of Biological Oceanography, Leibniz Institute for Baltic Sea Research, Warnemünde, Germany
| | - Silke Langenheder
- Department of Ecology and Genetic/Limnology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Klaus Jürgens
- Section of Biological Oceanography, Leibniz Institute for Baltic Sea Research, Warnemünde, Germany
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Ovaskainen O, Tikhonov G, Norberg A, Guillaume Blanchet F, Duan L, Dunson D, Roslin T, Abrego N. How to make more out of community data? A conceptual framework and its implementation as models and software. Ecol Lett 2017; 20:561-576. [PMID: 28317296 DOI: 10.1111/ele.12757] [Citation(s) in RCA: 322] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 01/31/2017] [Accepted: 02/09/2017] [Indexed: 12/23/2022]
Abstract
Community ecology aims to understand what factors determine the assembly and dynamics of species assemblages at different spatiotemporal scales. To facilitate the integration between conceptual and statistical approaches in community ecology, we propose Hierarchical Modelling of Species Communities (HMSC) as a general, flexible framework for modern analysis of community data. While non-manipulative data allow for only correlative and not causal inference, this framework facilitates the formulation of data-driven hypotheses regarding the processes that structure communities. We model environmental filtering by variation and covariation in the responses of individual species to the characteristics of their environment, with potential contingencies on species traits and phylogenetic relationships. We capture biotic assembly rules by species-to-species association matrices, which may be estimated at multiple spatial or temporal scales. We operationalise the HMSC framework as a hierarchical Bayesian joint species distribution model, and implement it as R- and Matlab-packages which enable computationally efficient analyses of large data sets. Armed with this tool, community ecologists can make sense of many types of data, including spatially explicit data and time-series data. We illustrate the use of this framework through a series of diverse ecological examples.
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Affiliation(s)
- Otso Ovaskainen
- Department of Biosciences, University of Helsinki, P.O. Box 65, Helsinki, FI-00014, Finland.,Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, N-7491, Trondheim, Norway
| | - Gleb Tikhonov
- Department of Biosciences, University of Helsinki, P.O. Box 65, Helsinki, FI-00014, Finland
| | - Anna Norberg
- Department of Biosciences, University of Helsinki, P.O. Box 65, Helsinki, FI-00014, Finland
| | - F Guillaume Blanchet
- Department of Mathematics and Statistics, McMaster University, 1280 Main Street West Hamilton, Ontario, L8S 4K1, Canada.,Département de biologie, Faculté des sciences, Université de Sherbrooke, 2500 Boulevard Université Sherbrooke, Québec, J1K 2R1, Canada
| | - Leo Duan
- Department of Statistical Science, Duke University, P.O. Box 90251, Durham, USA
| | - David Dunson
- Department of Statistical Science, Duke University, P.O. Box 90251, Durham, USA
| | - Tomas Roslin
- Department of Ecology, Swedish University of Agricultural Sciences, Box 7044, Uppsala, 75651, Sweden
| | - Nerea Abrego
- Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, N-7491, Trondheim, Norway.,Department of Agricultural Sciences, University of Helsinki, P.O. Box 27, Helsinki, FI-00014, Finland
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10
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Navarrete AA, Venturini AM, Meyer KM, Klein AM, Tiedje JM, Bohannan BJM, Nüsslein K, Tsai SM, Rodrigues JLM. Differential Response of Acidobacteria Subgroups to Forest-to-Pasture Conversion and Their Biogeographic Patterns in the Western Brazilian Amazon. Front Microbiol 2015; 6:1443. [PMID: 26733981 PMCID: PMC4686610 DOI: 10.3389/fmicb.2015.01443] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 12/03/2015] [Indexed: 11/13/2022] Open
Abstract
Members of the phylum Acidobacteria are among the most abundant soil bacteria on Earth, but little is known about their response to environmental changes. We asked how the relative abundance and biogeographic patterning of this phylum and its subgroups responded to forest-to-pasture conversion in soils of the western Brazilian Amazon. Pyrosequencing of 16S rRNA genes was employed to assess the abundance and composition of the Acidobacteria community across 54 soil samples taken using a spatially nested sampling scheme at the landscape level. Numerically, Acidobacteria represented 20% of the total bacterial community in forest soils and 11% in pasture soils. Overall, 15 different Acidobacteria subgroups of the current 26 subgroups were detected, with Acidobacteria subgroups 1, 3, 5, and 6 accounting together for 87% of the total Acidobacteria community in forest soils and 75% in pasture soils. Concomitant with changes in soil chemistry after forest-to-pasture conversion—particularly an increase in properties linked to soil acidity and nutrient availability—we observed an increase in the relative abundances of Acidobacteria subgroups 4, 10, 17, and 18, and a decrease in the relative abundances of other Acidobacteria subgroups in pasture relative to forest soils. The composition of the total Acidobacteria community as well as the most abundant Acidobacteria subgroups (1, 3, 5, and 6) was significantly more similar in composition across space in pasture soils than in forest soils. These results suggest that preponderant responses of Acidobacteria subgroups, especially subgroups 1, 3, 4, 5, and 6, to forest-to-pasture conversion effects in soils could be used to define management-indicators of agricultural practices in the Amazon Basin. These acidobacterial responses are at least in part through alterations on acidity- and nutrient-related properties of the Amazon soils.
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Affiliation(s)
- Acacio A Navarrete
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo Piracicaba, Brazil
| | - Andressa M Venturini
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo Piracicaba, Brazil
| | - Kyle M Meyer
- Department of Biology, Institute of Ecology and Evolution, University of Oregon Eugene, OR, USA
| | - Ann M Klein
- Department of Biology, Institute of Ecology and Evolution, University of Oregon Eugene, OR, USA
| | - James M Tiedje
- Department of Plant, Soil and Microbial Sciences, Center for Microbial Ecology, Michigan State University East Lansing, MI, USA
| | - Brendan J M Bohannan
- Department of Biology, Institute of Ecology and Evolution, University of Oregon Eugene, OR, USA
| | - Klaus Nüsslein
- Department of Microbiology, University of Massachusetts Amherst, MA, USA
| | - Siu M Tsai
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo Piracicaba, Brazil
| | - Jorge L M Rodrigues
- Department of Land, Air and Water Resources, University of California, Davis Davis, CA, USA
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11
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Bulgarella M, Heimpel GE. Host range and community structure of avian nest parasites in the genus Philornis (Diptera: Muscidae) on the island of Trinidad. Ecol Evol 2015; 5:3695-703. [PMID: 26380698 PMCID: PMC4567873 DOI: 10.1002/ece3.1621] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 06/28/2015] [Accepted: 07/08/2015] [Indexed: 11/08/2022] Open
Abstract
Parasite host range can be influenced by physiological, behavioral, and ecological factors. Combining data sets on host-parasite associations with phylogenetic information of the hosts and the parasites involved can generate evolutionary hypotheses about the selective forces shaping host range. Here, we analyzed associations between the nest-parasitic flies in the genus Philornis and their host birds on Trinidad. Four of ten Philornis species were only reared from one species of bird. Of the parasite species with more than one host bird species, P. falsificus was the least specific and P. deceptivus the most specific attacking only Passeriformes. Philornis flies in Trinidad thus include both specialists and generalists, with varying degrees of specificity within the generalists. We used three quantities to more formally compare the host range of Philornis flies: the number of bird species attacked by each species of Philornis, a phylogenetically informed host specificity index (Poulin and Mouillot's S TD), and a branch length-based S TD. We then assessed the phylogenetic signal of these measures of host range for 29 bird species. None of these measures showed significant phylogenetic signal, suggesting that clades of Philornis did not differ significantly in their ability to exploit hosts. We also calculated two quantities of parasite species load for the birds - the parasite species richness, and a variant of the S TD index based on nodes rather than on taxonomic levels - and assessed the signal of these measures on the bird phylogeny. We did not find significant phylogenetic signal for the parasite species load or the node-based S TD index. Finally, we calculated the parasite associations for all bird pairs using the Jaccard index and regressed these similarity values against the number of nodes in the phylogeny separating bird pairs. This analysis showed that Philornis on Trinidad tend to feed on closely related bird species more often than expected by chance.
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Affiliation(s)
- Mariana Bulgarella
- Department of Entomology, University of Minnesota St. Paul, Minnesota, 55108
| | - George E Heimpel
- Department of Entomology, University of Minnesota St. Paul, Minnesota, 55108
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12
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Kalyuzhny M, Kadmon R, Shnerb NM. A neutral theory with environmental stochasticity explains static and dynamic properties of ecological communities. Ecol Lett 2015; 18:572-80. [PMID: 25903067 DOI: 10.1111/ele.12439] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Revised: 11/21/2014] [Accepted: 03/04/2015] [Indexed: 11/30/2022]
Abstract
Understanding the forces shaping ecological communities is crucial to basic science and conservation. Neutral theory has made considerable progress in explaining static properties of communities, like species abundance distributions (SADs), with a simple and generic model, but was criticised for making unrealistic predictions of fundamental dynamic patterns and for being sensitive to interspecific differences in fitness. Here, we show that a generalised neutral theory incorporating environmental stochasticity may resolve these limitations. We apply the theory to real data (the tropical forest of Barro Colorado Island) and demonstrate that it much better explains the properties of short-term population fluctuations and the decay of compositional similarity with time, while retaining the ability to explain SADs. Furthermore, the predictions are considerably more robust to interspecific fitness differences. Our results suggest that this integration of niches and stochasticity may serve as a minimalistic framework explaining fundamental static and dynamic characteristics of ecological communities.
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Affiliation(s)
- Michael Kalyuzhny
- Department of Ecology, Evolution, and Behavior, Institute of Life Sciences, Hebrew University of Jerusalem, Givat-Ram, Jerusalem, 91904, Israel
| | - Ronen Kadmon
- Department of Ecology, Evolution, and Behavior, Institute of Life Sciences, Hebrew University of Jerusalem, Givat-Ram, Jerusalem, 91904, Israel
| | - Nadav M Shnerb
- Department of Physics, Bar-Ilan University, Ramat Gan, 52900, Israel
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Peng Z, Zhou S. Community assembly rules affect the diversity of expanding communities. Ecol Evol 2014; 4:4041-52. [PMID: 25505532 PMCID: PMC4242558 DOI: 10.1002/ece3.1251] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Revised: 08/22/2014] [Accepted: 09/01/2014] [Indexed: 11/17/2022] Open
Abstract
Despite centuries of interest in species range limits, few studies have taken a whole community into consideration. Actually, multiple species may simultaneously respond to environmental changes, for example, global warming, leading a series of dynamical communities toward the advancing front. We investigated multiple species range expansions through the analysis of a two-species dispersion model and simulations of multiple species assemblages regulated by neutral and fecundity-survival trade-offs (FSTs), respectively, and found that species assemblages regulated by different mechanisms would initiate different expanding patterns in geographic ranges in response to environmental changes. The neutral model generally predicts a higher biodiversity near the core of an expanding range, and a lower community similarity compared with a FST model. Without considering the evolution of life history traits, an assortment of the reproduction ability happens at the advancing front under FSTs at the expense of a higher death rate or lower competitive ability. These results emphasize the importance of community assembly rules to the biodiversity maintenance of range expanding communities.
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Affiliation(s)
- Zechen Peng
- State Key Laboratory of Grassland Agro-ecosystems, School of Life Sciences, Lanzhou UniversityLanzhou, 730000, China
| | - Shurong Zhou
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University2005 Songhu Road, Shanghai, 200438, China
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Sæther BE, Engen S, Grøtan V. Species diversity and community similarity in fluctuating environments: parametric approaches using species abundance distributions. J Anim Ecol 2013; 82:721-38. [PMID: 23578202 DOI: 10.1111/1365-2656.12068] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Accepted: 02/07/2013] [Indexed: 11/30/2022]
Abstract
Here we review recent advances in characterizing pattern of variation in community structure in space and time based on parametric approaches utilizing the full distribution of abundances of species rather than some summary indices. Assessment of biodiversity based on the structure of rank-abundance plots or simple species diversity indices, which describe properties of the sample of individuals, may reveal limited information about the underlying species abundance distribution of the community because the number of individuals counted are dependent on the sampling intensity. For instance, assuming Poisson sampling and an underlying lognormal species abundance distribution implies that observed abundances (counts) are a sample from a Poisson lognormal distribution. A convenient property of this distribution is that the estimate of σ(2) can be used as an inverse measure of species diversity in a community as well as the number of unobserved species can be estimated approximately without bias for unknown sampling intensities. If two communities can be described by a bivariate lognormal species abundance model, then the correlation between the log abundances of species in the two communities is an index of similarity that can be estimated without knowledge of sampling intensities using the bivariate Poisson lognormal distribution. This method is even applicable as an approximation when the abundance distribution deviates from the lognormal. An analysis of the interrelationship between the parameters of the lognormal species abundance distribution in communities of species from a wide variety of taxa shows that the canonical hypothesis of Preston in general, for a given number of species, gives far too large variances in the distribution of log abundances. A general feature in community dynamics is that a large component of the variance in the species abundance distribution is caused by heterogeneity among species in the population dynamics as well as environmental noise. This pattern is in contrast to the assumptions of the neutral theory of community dynamics. The choice of species abundance distribution should be a consequence of specific assumptions about the dynamics of the species. We suggest that such specific assumptions for the choice of species abundance model will facilitate more robust comparisons of changes in community structure in time and space.
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Affiliation(s)
- Bernt-Erik Sæther
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, Realfagbygget NO 7491, Trondheim, Norway
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