1
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Bestion E, Legrand D, Baines CB, Bonte D, Coulon A, Dahirel M, Delgado M, Deshpande JN, Duncan AB, Fronhofer EA, Gounand I, Jacob S, Kaltz O, Massol F, Mathyssen E, Parmentier T, Saade C, Schtickzelle N, Zilio G, Cote J. Species interactions affect dispersal: a meta-analysis. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230127. [PMID: 38913065 DOI: 10.1098/rstb.2023.0127] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 03/06/2024] [Indexed: 06/25/2024] Open
Abstract
Context-dependent dispersal allows organisms to seek and settle in habitats improving their fitness. Despite the importance of species interactions in determining fitness, a quantitative synthesis of how they affect dispersal is lacking. We present a meta-analysis asking (i) whether the interaction experienced and/or perceived by a focal species (detrimental interaction with predators, competitors, parasites or beneficial interaction with resources, hosts, mutualists) affects its dispersal; and (ii) how the species' ecological and biological background affects the direction and strength of this interaction-dependent dispersal. After a systematic search focusing on actively dispersing species, we extracted 397 effect sizes from 118 empirical studies encompassing 221 species pairs; arthropods were best represented, followed by vertebrates, protists and others. Detrimental species interactions increased the focal species' dispersal (adjusted effect: 0.33 [0.06, 0.60]), while beneficial interactions decreased it (-0.55 [-0.92, -0.17]). The effect depended on the dispersal phase, with detrimental interactors having opposite impacts on emigration and transience. Interaction-dependent dispersal was negatively related to species' interaction strength, and depended on the global community composition, with cues of presence having stronger effects than the presence of the interactor and the ecological complexity of the community. Our work demonstrates the importance of interspecific interactions on dispersal plasticity, with consequences for metacommunity dynamics.This article is part of the theme issue 'Diversity-dependence of dispersal: interspecific interactions determine spatial dynamics'.
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Affiliation(s)
- Elvire Bestion
- Station d'Ecologie Théorique et Expérimentale, CNRS, UAR 2029, Moulis 09200, France
| | - Delphine Legrand
- Station d'Ecologie Théorique et Expérimentale, CNRS, UAR 2029, Moulis 09200, France
| | - Celina B Baines
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, Canada M5S 3B2
| | - Dries Bonte
- Terrestrial Ecology Unit (TEREC), Department of Biology, Ghent University, K.L. Ledeganckstraat 35, Ghent 9000, Belgium
| | - Aurelie Coulon
- Centre d'Ecologie et des Sciences de la Conservation (CESCO), MNHN, CNRS, Sorbonne University, Paris, Concarneau 75005, France
- Centre d'Ecologie Fonctionelle et Evolutive (CEFE), University of Montpellier, CNRS, Montpellier 34293, France
| | - Maxime Dahirel
- Terrestrial Ecology Unit (TEREC), Department of Biology, Ghent University, K.L. Ledeganckstraat 35, Ghent 9000, Belgium
| | - María Delgado
- Biodiversity Research Institute (IMIB), CSIC/UO/PA, Campus de Mieres, Edificio de Investigación, Mieres, Asturias 33600, Spain
| | - Jhelam N Deshpande
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier 34095, France
| | - Alison B Duncan
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier 34095, France
| | | | - Isabelle Gounand
- Institut d'écologie et des sciences de l'environnement (iEES Paris), Sorbonne Université, CNRS, UPEC, CNRS, IRD, INRA, Paris 75005, France
| | - Staffan Jacob
- Station d'Ecologie Théorique et Expérimentale, CNRS, UAR 2029, Moulis 09200, France
| | - Oliver Kaltz
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier 34095, France
| | - François Massol
- Institut Pasteur de Lille, University Lille, CNRS, Inserm, CHU Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, Lille 59019, France
| | | | - Thomas Parmentier
- Terrestrial Ecology Unit (TEREC), Department of Biology, Ghent University, K.L. Ledeganckstraat 35, Ghent 9000, Belgium
- Research Unit of Environmental and Evolutionary Biology, Namur Institute of Complex Systems, and Institute of Life, Earth, and the Environment, University of Namur, Rue de Bruxelles 61, Namur 5000, Belgium
| | - Camille Saade
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier 34095, France
| | | | - Giacomo Zilio
- Centre d'Ecologie Fonctionelle et Evolutive (CEFE), University of Montpellier, CNRS, Montpellier 34293, France
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier 34095, France
| | - Julien Cote
- Centre de Recherche sur la Biodiversité et l'Environnement (CRBE), UMR 5300 CNRS-IRD-TINP-UT3, Université Toulouse III - Paul Sabatier, Bât. 4R1, 118 route de Narbonne, Toulouse 31062, France
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2
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Alzate A, Hagen O. Dispersal-diversity feedbacks and their consequences for macroecological patterns. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230131. [PMID: 38913062 DOI: 10.1098/rstb.2023.0131] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 04/08/2024] [Indexed: 06/25/2024] Open
Abstract
Dispersal is a key process in ecology and evolution. While the effects of dispersal on diversity are broadly acknowledged, our understanding of the influence of diversity on dispersal remains limited. This arises from the dynamic, context-dependent, nonlinear and ubiquitous nature of dispersal. Diversity outcomes, such as competition, mutualism, parasitism and trophic interactions can feed back on dispersal, thereby influencing biodiversity patterns at several spatio-temporal scales. Here, we shed light on the dispersal-diversity causal links by discussing how dispersal-diversity ecological and evolutionary feedbacks can impact macroecological patterns. We highlight the importance of dispersal-diversity feedbacks for advancing our understanding of macro-eco-evolutionary patterns and their challenges, such as establishing a unified framework for dispersal terminology and methodologies across various disciplines and scales. This article is part of the theme issue 'Diversity-dependence of dispersal: interspecific interactions determine spatial dynamics'.
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Affiliation(s)
- Adriana Alzate
- Aquaculture and Fisheries Group, Wageningen University and Research , Wageningen, The Netherlands
- Naturalis Biodiversity Center , Leiden, The Netherlands
| | - Oskar Hagen
- German Centre For Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig , Leipzig, Germany
- Department of Ecological Modelling, Helmholtz Centre for Environmental Research GmbH - UFZ , Leipzig, Germany
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3
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Shi Y, Li W, Guo X. Exploring environment-specific regulation: Characterizing bacterioplankton community dynamics in a typical lake of Inner Mongolia, China. ENVIRONMENTAL RESEARCH 2024; 253:119154. [PMID: 38754616 DOI: 10.1016/j.envres.2024.119154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 05/12/2024] [Accepted: 05/14/2024] [Indexed: 05/18/2024]
Abstract
Lakes serve as heterogeneous ecosystems with rich microbiota. Although previous studies on bacterioplankton have advanced our understanding, there are gaps in our knowledge concerning variations in the taxonomic composition and community assembly processes of bacterioplankton across different environment conditions. This study explored the spatial dynamics, assembly processes, and co-occurrence relationships among bacterioplankton communities in 35 surface water samples collected from Hulun Lake (a grassland-type lake), Wuliangsuhai Lake (an irrigated agricultural recession type lake), and Daihai Lake (an inland lake with mixed farming and grazing) in the Inner Mongolia Plateau, China. The results indicated a significant geographical distance decay pattern, with biomarkers (Proteobacteria and Bacteroidota) exhibiting differences in the contributions of different bacteria branches to the lakes. The relative abundance of Proteobacteria (42.23%) were high in Hulun Lake and Wuliangsuhai Lake. Despite Actinobacteriota was most dominant, Firmicutes accounted for approximately 17.07% in Daihai Lake, suggested the potential detection of anthropogenic impacts on bacteria within the agro-pastoral inland lake. Lake heterogeneity caused bacterioplankton responses to phosphorus, chlorophyll a, and salinity in Hulun Lake, Wuliangsuhai Lake, and Daihai Lake. Although bacterioplankton community assembly processes in irrigated agricultural recession type lake were more affected by dispersal limitation than those in grassland-type lake and inland lake with mixed farming and grazing (approximately 52.7% in Hulun Lake), dispersal limitation and undominated processes were key modes of bacterioplankton community assembly in three lakes. This suggested stochastic processes exerted a greater impact on bacterioplankton community assembly in a typical Inner Mongolia Lake than deterministic processes. Overall, the bacterioplankton communities displayed the potential for collaboration, with lowest connectivity observed in irrigated agricultural recession type lake, which reflected the complex dynamic patterns of aquatic bacteria in typical Inner Mongolia Plateau lakes. These findings enhanced our understanding of the interspecific relationships and assembly processes among microorganisms in lakes with distinct habitats.
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Affiliation(s)
- Yujiao Shi
- Water Conservancy and Civil Engineering College, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Wenbao Li
- Water Conservancy and Civil Engineering College, Inner Mongolia Agricultural University, Hohhot, 010018, China; Inner Mongolia Key Laboratory of Protection and Utilization of Water Resources, Hohhot, 010018, China.
| | - Xin Guo
- Water Conservancy and Civil Engineering College, Inner Mongolia Agricultural University, Hohhot, 010018, China
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4
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Zhang C, Lin Y, Xue Q, Mo X, He M, Liu J. Nitrogen supply neutralizes the nanoplastic-plant interaction in a coastal wetland. ENVIRONMENTAL RESEARCH 2024; 251:118572. [PMID: 38437902 DOI: 10.1016/j.envres.2024.118572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/25/2024] [Accepted: 02/26/2024] [Indexed: 03/06/2024]
Abstract
The presence of nanoplastics posed a potential threat to coastal saline-alkaline wetlands where nitrogen (N) fertilizer is being implemented as an important ecological restoration measure. Notwithstanding, the effects of N inputs on plant community in polypropylene-nanoplastics (PP-NPs) coexistence environments are largely unknown. To address this, we investigated the effects of PP-NPs addition alone or combined N supply on community aboveground biomass, morphological traits, diversity, composition, niche differentiation, interspecific interactions, and assembly. Our results showed that the PP-NPs addition alone reduced community aboveground biomass and morphological traits. However, the addition of high concentration (0.5%) PP-NPs alone favored community α-diversity and reduced community stability, which could be weakened through combined N supply. Overall, the effect of PP-NPs addition alone on plant community composition was greater than that of combined N supply. We also demonstrated PP-NPs addition alone and combined N supply reduced the niche breadth of the plant community and affected the niche overlap of dominant species. In the assembly of plant communities, stochastic processes played a dominant role. We conclude that N fertilization can amend the terrestrial nanoplastics pollution, thus mitigating the effects of PP-NPs on the plant community.
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Affiliation(s)
- Chunping Zhang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Center for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Yingchao Lin
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, National & Local Joint Engineering Research Center on Biomass Resource Utilization, College of Environmental Science and Engineering, Nankai University, Tianjin, 300350, China
| | - Qing Xue
- School of Geographic and Environmental Science, Tianjin Key Laboratory of Water Resources and Environment, Tianjin Normal University, Tianjin, 300387, China
| | - Xunqiang Mo
- School of Geographic and Environmental Science, Tianjin Key Laboratory of Water Resources and Environment, Tianjin Normal University, Tianjin, 300387, China
| | - Mengxuan He
- School of Geographic and Environmental Science, Tianjin Key Laboratory of Water Resources and Environment, Tianjin Normal University, Tianjin, 300387, China.
| | - Jie Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Center for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China; Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, National & Local Joint Engineering Research Center on Biomass Resource Utilization, College of Environmental Science and Engineering, Nankai University, Tianjin, 300350, China.
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5
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Martinez-Villegas L, Lado P, Klompen H, Wang S, Cummings C, Pesapane R, Short SM. The microbiota of Amblyomma americanum reflects known westward expansion. PLoS One 2024; 19:e0304959. [PMID: 38857239 PMCID: PMC11164389 DOI: 10.1371/journal.pone.0304959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 05/22/2024] [Indexed: 06/12/2024] Open
Abstract
Amblyomma americanum, a known vector of multiple tick-borne pathogens, has expanded its geographic distribution across the United States in the past decades. Tick microbiomes may play a role shaping their host's life history and vectorial capacity. Bacterial communities associated with A. americanum may reflect, or enable, geographic expansion and studying the microbiota will improve understanding of tick-borne disease ecology. We examined the microbiota structure of 189 adult ticks collected in four regions encompassing their historical and current geographic distribution. Both geographic region of origin and sex were significant predictors of alpha diversity. As in other tick models, within-sample diversity was low and uneven given the presence of dominant endosymbionts. Beta diversity analyses revealed that bacterial profiles of ticks of both sexes collected in the West were significantly different from those of the Historic range. Biomarkers were identified for all regions except the historical range. In addition, Bray-Curtis dissimilarities overall increased with distance between sites. Relative quantification of ecological processes showed that, for females and males, respectively, drift and dispersal limitation were the primary drivers of community assembly. Collectively, our findings highlight how microbiota structural variance discriminates the western-expanded populations of A. americanum ticks from the Historical range. Spatial autocorrelation, and particularly the detection of non-selective ecological processes, are indicative of geographic isolation. We also found that prevalence of Ehrlichia chaffeensis, E. ewingii, and Anaplasma phagocytophilum ranged from 3.40-5.11% and did not significantly differ by region. Rickettsia rickettsii was absent from our samples. Our conclusions demonstrate the value of synergistic analysis of biogeographic and microbial ecology data in investigating range expansion in A. americanum and potentially other tick vectors as well.
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Affiliation(s)
- Luis Martinez-Villegas
- Department of Entomology, The Ohio State University, Columbus, Ohio, United States of America
| | - Paula Lado
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, Ohio, United States of America
| | - Hans Klompen
- Department of Evolution, Ecology, and Organismal Biology and Museum of Biological Diversity, The Ohio State University, Columbus, Ohio, United States of America
| | - Selena Wang
- Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, Ohio, United States of America
| | - Caleb Cummings
- Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, Ohio, United States of America
| | - Risa Pesapane
- Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, Ohio, United States of America
- School of Environment and Natural Resources, College of Food, Agricultural, and Environmental Sciences, The Ohio State University, Columbus, Ohio, United States of America
| | - Sarah M. Short
- Department of Entomology, The Ohio State University, Columbus, Ohio, United States of America
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Shen Z, Yu B, Gong Y, Shao K, Gao G, Tang X. Unraveling the impact of climatic warming and wetting on eukaryotic microbial diversity and assembly mechanisms: A 10-year case study in Lake Bosten, NW China. WATER RESEARCH 2024; 256:121559. [PMID: 38579508 DOI: 10.1016/j.watres.2024.121559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 03/29/2024] [Accepted: 03/30/2024] [Indexed: 04/07/2024]
Abstract
Over the last six decades, northwest China has undergone a significant climatic shift from "warm-dry" to "warm-wet", profoundly impacting the structures and functions of lake ecosystem across the region. However, the influences of this climatic transition on the diversity patterns, co-occurrence network, and assembly processes of eukaryotic microbial communities in lake ecosystem, along with the underlying mechanisms, remain largely unexplored. To bridge this knowledge gap, our study focused on Lake Bosten, the largest inland freshwater body in China, conducting a comprehensive analysis. Firstly, we examined the dynamics of key water quality parameters in the lake based on long-term monitoring data (1992-2022). Subsequently, we collected 93 water samples spanning two distinctive periods: low water level (WL) and high total dissolved solids (TDS) (PerWLTDS; 2010-2011; attributed to "warm-dry" climate), and high WL and low TDS (PerTDSWL; 2021-2022; associated with "warm-wet" climate). Eukaryotic microorganisms were further investigated using 18S rRNA gene sequencing and various statistical methods. Our findings revealed that climatic warming and wetting significantly increased eukaryotic microbial α-diversity (all Wilcox. test: P<0.05), while simultaneously reducing β-diversity (all Wilcox. test: P<0.001) and network complexity. Through the two sampling periods, assembly mechanisms of eukaryotic microorganisms were predominantly influenced by dispersal limitation (DL) and drift (DR) within stochastic processes, alongside homogeneous selection (HoS) within deterministic processes. WL played a mediating role in eukaryotic microbial DL and HoS processes in the PerTDSWL, whereas water quality and α-diversity influenced the DL process in the PerWLTDS. Collectively, these results underscore the direct and indirect impacts of "warm-wet" conditions on the eukaryotic microorganisms within Lake Bosten. This study provides valuable insights into the evolutionary dynamics of lake ecosystems under such climatic conditions and aids in predicting the ecological ramifications of global climatic changes.
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Affiliation(s)
- Zhen Shen
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, PR China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Bobing Yu
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, PR China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Yi Gong
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, PR China
| | - Keqiang Shao
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, PR China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Guang Gao
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, PR China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Xiangming Tang
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, PR China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, PR China.
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7
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Metzler P, Ksiazek-Mikenas K, Chaudhary VB. Tracking arbuscular mycorrhizal fungi to their source: active inoculation and passive dispersal differentially affect community assembly in urban soils. THE NEW PHYTOLOGIST 2024; 242:1814-1824. [PMID: 38294152 DOI: 10.1111/nph.19526] [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: 06/30/2023] [Accepted: 12/17/2023] [Indexed: 02/01/2024]
Abstract
Communities of arbuscular mycorrhizal (AM) fungi assemble passively over time via biotic and abiotic mechanisms. In degraded soils, AM fungal communities can assemble actively when humans manage mycorrhizas for ecosystem restoration. We investigated mechanisms of urban AM fungal community assembly in a 2-yr green roof experiment. We compared AM fungal communities in inoculated and uninoculated trays to samples from two potential sources: the inoculum and air. Active inoculation stimulated more distinct and diverse AM fungal communities, an effect that intensified over time. In the treatment trays, 45% of AM fungal taxa were detected in the inoculum, 2% were detected in aerial samples, 23% were detected in both inoculum and air, and 30% were not detected in either source. Passive dispersal of AM fungi likely resulted in the successful establishment of a small number of species, but active inoculation with native AM fungal species resulted in an immediate shift to a diverse and unique fungal community. When urban soils are constructed or modified by human activity, this is an opportunity for intervention with AM fungi that will persist and add diversity to that system.
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Affiliation(s)
- Paul Metzler
- Environmental Studies Department, Dartmouth College, Hanover, NH, 03755, USA
| | | | - V Bala Chaudhary
- Environmental Studies Department, Dartmouth College, Hanover, NH, 03755, USA
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8
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Zhu G, Luan L, Zhou S, Dini-Andreote F, Bahram M, Yang Y, Geisen S, Zheng J, Wang S, Jiang Y. Body size mediates the functional potential of soil organisms by diversity and community assembly across soil aggregates. Microbiol Res 2024; 282:127669. [PMID: 38442455 DOI: 10.1016/j.micres.2024.127669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 02/20/2024] [Accepted: 02/27/2024] [Indexed: 03/07/2024]
Abstract
Body size is an important life-history trait that affects organism niche occupancy and ecological interactions. However, it is still unclear to what extent the assembly process of organisms with different body sizes affects soil biogeochemical cycling processes at the aggregate level. Here, we examined the diversity and community assembly of soil microorganisms (bacteria, fungi, and protists) and microfauna (nematodes) with varying body sizes. The microbial functional potential associated with carbon, nitrogen, phosphorus, and sulfur metabolism within three soil aggregate sizes (large macroaggregates, > 2 mm; small macroaggregates, 0.25-2 mm; and microaggregates, < 0.25 mm) were determined by metagenomics. We found that the smallest microbes (bacteria) had higher α-diversity and lower β-diversity and were mostly structured by stochastic processes, while all larger organisms (fungi, protists, and nematodes) had lower α-diversity and were relatively more influenced by deterministic processes. Structural equation modeling indicated that the microbial functional potential associated with carbon, nitrogen, phosphorus, and sulfur metabolism was mainly influenced by the bacterial and protist diversity in microaggregates. In contrast, the microbial functional potential was primarily mediated by the assembly processes of four organism groups, especially the nematode community in macroaggregates. This study reveals the important roles of soil organisms with different body sizes in the functional potential related to nutrient cycling, and provides new insights into the ecological processes structuring the diversity and community assembly of organisms of different body sizes at the soil aggregate level, with implications for soil nutrient cycling dynamics.
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Affiliation(s)
- Guofan Zhu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Lu Luan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Shungui Zhou
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Francisco Dini-Andreote
- Department of Plant Science & Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Mohammad Bahram
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Tartu 51005, Estonia
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Stefan Geisen
- Laboratory of Nematology, Wageningen University, Wageningen 6700 ES, Netherlands
| | - Jie Zheng
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Shaopeng Wang
- Institute of Ecology, Key Laboratory for Earth Surface Processes of the Ministry of Education, College of Urban and Environmental Sciences, Peking University, Beijing, China
| | - Yuji Jiang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China; Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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9
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Lancaster J, Downes BJ, Kayll ZJ. Bigger is not necessarily better: empirical tests show that dispersal proxies misrepresent actual dispersal ability. Proc Biol Sci 2024; 291:20240172. [PMID: 38772418 DOI: 10.1098/rspb.2024.0172] [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: 01/21/2024] [Accepted: 04/05/2024] [Indexed: 05/23/2024] Open
Abstract
Tests for the role of species' relative dispersal abilities in ecological and biogeographical models rely heavily on dispersal proxies, which are seldom substantiated by empirical measures of actual dispersal. This is exemplified by tests of dispersal-range size relationships and by metacommunity research that often features invertebrates, particularly freshwater insects. Using rare and unique empirical data on dispersal abilities of caddisflies, we tested whether actual dispersal abilities were associated with commonly used dispersal proxies (metrics of wing size and shape; expert opinion). Across 59 species in 12 families, wing morphology was not associated with actual dispersal. Within some families, individual wing metrics captured some dispersal differences among species, although useful metrics varied among families and predictive power was typically low. Dispersal abilities assigned by experts were either no better than random or actually poorer than random. Our results cast considerable doubt on research underpinned by dispersal proxies and scrutiny of previous research results may be warranted. Greater progress may lie in employing innovative survey and experimental design to measure actual dispersal in the field.
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Affiliation(s)
- Jill Lancaster
- School of Geography, Earth and Atmospheric Sciences, The University of Melbourne , , Victoria, 3010, Australia
| | - Barbara J Downes
- School of Geography, Earth and Atmospheric Sciences, The University of Melbourne , , Victoria, 3010, Australia
| | - Zachary J Kayll
- School of Geography, Earth and Atmospheric Sciences, The University of Melbourne , , Victoria, 3010, Australia
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Li Z, Feng C, Lei J, He X, Wang Q, Zhao Y, Qian Y, Zhan X, Shen Z. Farmland Microhabitat Mediated by a Residual Microplastic Film: Microbial Communities and Function. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:3654-3664. [PMID: 38318812 DOI: 10.1021/acs.est.3c07717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
How the plastisphere mediated by the residual microplastic film in farmlands affects microhabitat systems is unclear. Here, microbial structure, assembly, and biogeochemical cycling in the plastisphere and soil in 33 typical farmland sites were analyzed by amplicon sequencing of 16S rRNA genes and ITS and metagenome analysis. The results indicated that residual microplastic film was colonized by microbes, forming a unique niche called the plastisphere. Notable differences in the microbial community structure and function were observed between soil and plastisphere. Residual microplastic film altered the microbial symbiosis and assembly processes. Stochastic processes significantly dominated the assembly of the bacterial community in the plastisphere and soil but only in the plastisphere for the fungal community. Deterministic processes significantly dominated the assembly of fungal communities only in soil. Moreover, the plastisphere mediated by the residual microplastic film acted as a preferred vector for pathogens and microorganisms associated with plastic degradation and the nitrogen and sulfur cycle. The abundance of genes associated with denitrification and sulfate reduction activity in the plastisphere was pronouncedly higher than that of soil, which increase the potential risk of nitrogen and sulfur loss. The results will offer a scientific understanding of the harm caused by the residual microplastic film in farmlands.
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Affiliation(s)
- Zhenling Li
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, P. R. China
- The Key Laboratory of Poyang Lake Wetland and Watershed Research, Ministry of Education, School of Geography and Environment, Jiangxi Normal University, Nanchang 330022, P. R. China
| | - Chenghong Feng
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, P. R. China
- The Key Laboratory of Water and Sediment Sciences, Ministry of Education, School of Environment, Beijing Normal University, Beijing 100875, P. R. China
| | - Jinming Lei
- The Key Laboratory of Water and Sediment Sciences, Ministry of Education, School of Environment, Beijing Normal University, Beijing 100875, P. R. China
| | - Xiaokang He
- The Key Laboratory of Water and Sediment Sciences, Ministry of Education, School of Environment, Beijing Normal University, Beijing 100875, P. R. China
| | - Qixuan Wang
- The Key Laboratory of Water and Sediment Sciences, Ministry of Education, School of Environment, Beijing Normal University, Beijing 100875, P. R. China
| | - Yue Zhao
- The Key Laboratory of Water and Sediment Sciences, Ministry of Education, School of Environment, Beijing Normal University, Beijing 100875, P. R. China
| | - Yibin Qian
- National Plot Zone for Ecological Conservation (Hainan) Research Center, Hainan Research Academy of Environmental Sciences, Haikou 571127, P. R. China
| | - Xinmin Zhan
- Civil Engineering, University of Galway, Galway H91 TK33, Ireland
| | - Zhenyao Shen
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, P. R. China
- The Key Laboratory of Water and Sediment Sciences, Ministry of Education, School of Environment, Beijing Normal University, Beijing 100875, P. R. China
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11
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Deng N, Liu C, Tian Y, Song Q, Niu Y, Ma F. Assembly processes of rhizosphere and phyllosphere bacterial communities in constructed wetlands created via transformation of rice paddies. Front Microbiol 2024; 15:1337435. [PMID: 38444812 PMCID: PMC10913029 DOI: 10.3389/fmicb.2024.1337435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 01/16/2024] [Indexed: 03/07/2024] Open
Abstract
Constructed wetlands are an efficient and cost-effective method of restoring degraded wetlands, in which the microorganisms present make a significant contribution to the ecosystem. In this study, we comprehensively investigated the patterns of diversity and assembly processes of 7 types of constructed wetlands at the rhizosphere and phyllosphere levels. The results showed that the rhizosphere communities of the constructed wetlands exhibited a more balanced structure than that of paddy fields, and 5 types of constructed wetland demonstrated higher potential diversity than that of paddy fields. However, the opposite trend was observed for the phyllosphere communities. Analysis of mean nearest taxon difference indicated that both deterministic and stochastic processes affected the establishment of the rhizosphere and phyllosphere communities, and stochastic processes may have had a larger effect. An iCAMP model showed that dispersal limitation was the most important factor (67% relative contribution) in the rhizosphere community, while drift was the most important (47% relative contribution) in the phyllosphere community. Mantel tests suggested that sucrase, average height, top height, total biomass, belowground biomass, maximum water-holding capacity, and capillary porosity were significantly correlated with processes in the rhizosphere community, whereas factors such as the deterministic process, average height, top height, and SOC were significantly correlated with deterministic processes in the phyllosphere community. Our results can assist in the evaluation of artificial restorations, and can provide understanding of the ecological processes of microbial communities, as well as new insights into the manipulation of microorganisms in polluted wetland ecosystems.
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Affiliation(s)
- Nan Deng
- Hunan Academy of Forestry, Changsha, Hunan, China
- Hunan Cili Forest Ecosystem State Research Station, Cili, Changsha, Hunan, China
| | - Caixia Liu
- Hunan Academy of Forestry, Changsha, Hunan, China
- Hunan Cili Forest Ecosystem State Research Station, Cili, Changsha, Hunan, China
| | - Yuxin Tian
- Hunan Academy of Forestry, Changsha, Hunan, China
- Hunan Cili Forest Ecosystem State Research Station, Cili, Changsha, Hunan, China
- Dongting Lake National Positioning Observation and Research Station of Wetland Ecosystem of Hunan Province, Yueyang, China
- International Technological Cooperation Base for Ecosystem Management and Sustainable Utilization of Water Resources in Dongting Lake Basin, Changsha, China
| | - Qingan Song
- Hunan Academy of Forestry, Changsha, Hunan, China
- Hunan Cili Forest Ecosystem State Research Station, Cili, Changsha, Hunan, China
| | - Yandong Niu
- Hunan Academy of Forestry, Changsha, Hunan, China
- Hunan Cili Forest Ecosystem State Research Station, Cili, Changsha, Hunan, China
- Dongting Lake National Positioning Observation and Research Station of Wetland Ecosystem of Hunan Province, Yueyang, China
- International Technological Cooperation Base for Ecosystem Management and Sustainable Utilization of Water Resources in Dongting Lake Basin, Changsha, China
| | - Fengfeng Ma
- Hunan Academy of Forestry, Changsha, Hunan, China
- Hunan Cili Forest Ecosystem State Research Station, Cili, Changsha, Hunan, China
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12
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Ning D, Wang Y, Fan Y, Wang J, Van Nostrand JD, Wu L, Zhang P, Curtis DJ, Tian R, Lui L, Hazen TC, Alm EJ, Fields MW, Poole F, Adams MWW, Chakraborty R, Stahl DA, Adams PD, Arkin AP, He Z, Zhou J. Environmental stress mediates groundwater microbial community assembly. Nat Microbiol 2024; 9:490-501. [PMID: 38212658 DOI: 10.1038/s41564-023-01573-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 11/28/2023] [Indexed: 01/13/2024]
Abstract
Community assembly describes how different ecological processes shape microbial community composition and structure. How environmental factors impact community assembly remains elusive. Here we sampled microbial communities and >200 biogeochemical variables in groundwater at the Oak Ridge Field Research Center, a former nuclear waste disposal site, and developed a theoretical framework to conceptualize the relationships between community assembly processes and environmental stresses. We found that stochastic assembly processes were critical (>60% on average) in shaping community structure, but their relative importance decreased as stress increased. Dispersal limitation and 'drift' related to random birth and death had negative correlations with stresses, whereas the selection processes leading to dissimilar communities increased with stresses, primarily related to pH, cobalt and molybdenum. Assembly mechanisms also varied greatly among different phylogenetic groups. Our findings highlight the importance of microbial dispersal limitation and environmental heterogeneity in ecosystem restoration and management.
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Affiliation(s)
- Daliang Ning
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
- School of Biological Sciences, University of Oklahoma, Norman, OK, USA
| | - Yajiao Wang
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
- School of Biological Sciences, University of Oklahoma, Norman, OK, USA
| | - Yupeng Fan
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
- School of Biological Sciences, University of Oklahoma, Norman, OK, USA
| | - Jianjun Wang
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Joy D Van Nostrand
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Liyou Wu
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
- School of Biological Sciences, University of Oklahoma, Norman, OK, USA
| | - Ping Zhang
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Daniel J Curtis
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Renmao Tian
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
- Institute for Food Safety and Health, Illinois Institute of Technology, Bedford Park, IL, USA
| | - Lauren Lui
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Terry C Hazen
- Department of Earth and Planetary Sciences, Bredesen Center, Department of Civil and Environmental Sciences, Center for Environmental Biotechnology, and Institute for a Secure and Sustainable Environment, University of Tennessee, Knoxville, TN, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- Department of Bioengineering, University of California, Berkeley, CA, USA
| | - Eric J Alm
- Department of Biological Engineering, Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Matthew W Fields
- Center for Biofilm Engineering and Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Farris Poole
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Romy Chakraborty
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - David A Stahl
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - Paul D Adams
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Bioengineering, University of California, Berkeley, CA, USA
| | - Adam P Arkin
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Bioengineering, University of California, Berkeley, CA, USA
| | - Zhili He
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
- Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Jizhong Zhou
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA.
- School of Biological Sciences, University of Oklahoma, Norman, OK, USA.
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, USA.
- School of Computer Science, University of Oklahoma, Norman, OK, USA.
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13
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Huang Z, Pan B, Zhao X, Liu X, Liu X, Zhao G. Hydrological disturbances enhance stochastic assembly processes and decrease network stability of algae communities in a highland floodplain system. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 903:166207. [PMID: 37567295 DOI: 10.1016/j.scitotenv.2023.166207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 07/19/2023] [Accepted: 08/08/2023] [Indexed: 08/13/2023]
Abstract
Floodplains are hotspots for biodiversity research and conservation worldwide. Hydrological disturbances can profoundly influence the ecological processes and functions of floodplain systems by altering key biological groups such as algae communities. However, the impacts of flood disturbance on the assembly processes and co-occurrence patterns of algae communities in floodplain ecosystems are still unclear. To ascertain the response patterns of algae communities to flood disturbance, we characterized planktonic and benthic algae communities in 144 water and sediment samples collected from the Tibetan floodplain during non-flood and flood periods based on 23S ribosomal RNA gene sequencing. Results showed that planktonic algae exhibited higher diversity and greater compositional variations compared with benthic communities after flood disturbance. Flooding promoted algae community homogenization at horizontal (rivers vs. oxbow lakes) and vertical levels (water vs. sediment). Stochastic processes governed the assembly of distinct algae communities, and their ecological impacts were enhanced in response to flooding. In the non-flood period, dispersal limitation (81.78 %) was the primary ecological process driving algae community assembly. In the flood period, the relative contribution of ecological drift (72.91 %) to algae community assembly markedly increased, with dispersal limitation (22.61 %) being less important. Flooding reduced the interactions among algae taxa, resulting in lower network complexity and stability. Compared with the planktonic algae subnetworks, the benthic subnetworks showed greater stability in the face of flooding. Findings of this study broaden our understanding of how algae communities respond to hydrological disturbances from an ecological perspective and could be useful for the management of highland floodplain ecosystems.
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Affiliation(s)
- Zhenyu Huang
- State Key Laboratory of Eco-hydraulic in Northwest Arid Region of China, Xi'an University of Technology, Xi'an, Shaanxi 710048, PR China.
| | - Baozhu Pan
- State Key Laboratory of Eco-hydraulic in Northwest Arid Region of China, Xi'an University of Technology, Xi'an, Shaanxi 710048, PR China.
| | - Xiaohui Zhao
- State Key Laboratory of Eco-hydraulic in Northwest Arid Region of China, Xi'an University of Technology, Xi'an, Shaanxi 710048, PR China.
| | - Xing Liu
- State Key Laboratory of Eco-hydraulic in Northwest Arid Region of China, Xi'an University of Technology, Xi'an, Shaanxi 710048, PR China.
| | - Xinyuan Liu
- State Key Laboratory of Eco-hydraulic in Northwest Arid Region of China, Xi'an University of Technology, Xi'an, Shaanxi 710048, PR China.
| | - Gengnan Zhao
- State Key Laboratory of Eco-hydraulic in Northwest Arid Region of China, Xi'an University of Technology, Xi'an, Shaanxi 710048, PR China.
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14
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Schauberger C, Seki D, Cutts EM, Glud RN, Thamdrup B. Uniform selective pressures within redox zones drive gradual changes in microbial community composition in hadal sediments. Environ Microbiol 2023; 25:1594-1604. [PMID: 36999247 DOI: 10.1111/1462-2920.16377] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 03/19/2023] [Indexed: 04/01/2023]
Abstract
Microbial communities in marine sediments are highly diverse, yet the processes that give rise to this complexity are unclear. It has been proposed that benthic microbial communities must be continuously re-seeded from the water column because dispersal within the sediment is severely limited. Previous studies consistently report that the composition of the microbial community gradually changes with sediment depth. However, the relative contributions of the processes that underlie these compositional gradients have not been determined, and it is unknown whether microbial dispersal is indeed too slow to outpace burial. Here, we applied ecological statistical frameworks to 16S rRNA gene amplicon-based community composition data from Atacama Trench sediments to investigate the links between biogeochemistry, burial, and microbial community assembly processes. We confirm that dispersal limitation affects microbial communities and find that gradual changes in community composition are driven by selective pressures that change abruptly across the discrete boundaries between redox zones rather than along continuous biogeochemical gradients, while selective pressures are uniform within each zone. The gradual changes in community composition over centimetres of depth within a zone hence reflects a decades-long response to the abruptly changing selective pressures.
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Affiliation(s)
- Clemens Schauberger
- Hadal & Nordcee, Department of Biology, University of Southern Denmark, Odense, Denmark
| | - David Seki
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Elise M Cutts
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Ronnie N Glud
- Hadal & Nordcee, Department of Biology, University of Southern Denmark, Odense, Denmark
- Department of Ocean and Environmental Sciences, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo, 108-8477, Japan
| | - Bo Thamdrup
- Hadal & Nordcee, Department of Biology, University of Southern Denmark, Odense, Denmark
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15
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Wu L, Yang Y, Ning D, Gao Q, Yin H, Xiao N, Zhou BY, Chen S, He Q, Zhou J. Assessing mechanisms for microbial taxa and community dynamics using process models. MLIFE 2023; 2:239-252. [PMID: 38817815 PMCID: PMC10989933 DOI: 10.1002/mlf2.12076] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 04/27/2023] [Accepted: 05/27/2023] [Indexed: 06/01/2024]
Abstract
Disentangling the assembly mechanisms controlling community composition, structure, distribution, functions, and dynamics is a central issue in ecology. Although various approaches have been proposed to examine community assembly mechanisms, quantitative characterization is challenging, particularly in microbial ecology. Here, we present a novel approach for quantitatively delineating community assembly mechanisms by combining the consumer-resource model with a neutral model in stochastic differential equations. Using time-series data from anaerobic bioreactors that target microbial 16S rRNA genes, we tested the applicability of three ecological models: the consumer-resource model, the neutral model, and the combined model. Our results revealed that model performances varied substantially as a function of population abundance and/or process conditions. The combined model performed best for abundant taxa in the treatment bioreactors where process conditions were manipulated. In contrast, the neutral model showed the best performance for rare taxa. Our analysis further indicated that immigration rates decreased with taxa abundance and competitions between taxa were strongly correlated with phylogeny, but within a certain phylogenetic distance only. The determinism underlying taxa and community dynamics were quantitatively assessed, showing greater determinism in the treatment bioreactors that aligned with the subsequent abnormal system functioning. Given its mechanistic basis, the framework developed here is expected to be potentially applicable beyond microbial ecology.
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Affiliation(s)
- Linwei Wu
- Institute of Ecology, Key Laboratory for Earth Surface Processes of the Ministry of Education, College of Urban and Environmental SciencesPeking UniversityBeijingChina
- Institute for Environmental GenomicsUniversity of OklahomaNormanOKUSA
- Department of Microbiology and Plant BiologyUniversity of OklahomaNormanOKUSA
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of EnvironmentTsinghua UniversityBeijingChina
| | - Daliang Ning
- Institute for Environmental GenomicsUniversity of OklahomaNormanOKUSA
- Department of Microbiology and Plant BiologyUniversity of OklahomaNormanOKUSA
| | - Qun Gao
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of EnvironmentTsinghua UniversityBeijingChina
| | - Huaqun Yin
- School of Minerals Processing and BioengineeringCentral South UniversityChangshaChina
| | - Naija Xiao
- Institute for Environmental GenomicsUniversity of OklahomaNormanOKUSA
- Department of Microbiology and Plant BiologyUniversity of OklahomaNormanOKUSA
| | - Benjamin Y. Zhou
- Department of Mathematics, Lunt HallNorthwestern UniversityEvanstonIllinoisUSA
| | - Si Chen
- Department of Civil and Environmental EngineeringThe University of TennesseeKnoxvilleTennesseeUSA
- Institute for a Secure and Sustainable EnvironmentThe University of TennesseeKnoxvilleTennesseeUSA
| | - Qiang He
- Department of Civil and Environmental EngineeringThe University of TennesseeKnoxvilleTennesseeUSA
- Institute for a Secure and Sustainable EnvironmentThe University of TennesseeKnoxvilleTennesseeUSA
| | - Jizhong Zhou
- Institute for Environmental GenomicsUniversity of OklahomaNormanOKUSA
- Department of Microbiology and Plant BiologyUniversity of OklahomaNormanOKUSA
- School of Civil Engineering and Environmental SciencesUniversity of OklahomaNormanOklahomaUSA
- Earth and Environmental Sciences, Lawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
- School of Computer ScienceUniversity of OklahomaNormanOKUSA
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16
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Draghi JA. Bet-hedging via dispersal aids the evolution of plastic responses to unreliable cues. J Evol Biol 2023. [PMID: 37224140 DOI: 10.1111/jeb.14182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 01/19/2023] [Accepted: 04/23/2023] [Indexed: 05/26/2023]
Abstract
Adaptive plasticity is expected to evolve when informative cues predict environmental variation. However, plastic responses can be maladaptive even when those cues are informative, if prediction mistakes are shared across members of a generation. These fitness costs can constrain the evolution of plasticity when initial plastic mutants use of cues of only moderate reliability. Here, we model the barriers to the evolution of plasticity produced by these constraints and show that dispersal across a metapopulation can overcome them. Constraints are also lessened, though not eliminated, when plastic responses are free to evolve gradually and in concert with increased reliability. Each of these factors be viewed as a form of bet-hedging: by lessening correlations in the fates of relatives, dispersal acts as diversifying bet-hedging, while producing submaximal responses to a cue can be understood as a conservative bet-hedging strategy. While poor information may constrain the evolution of plasticity, the opportunity for bet-hedging may predict when that constraint can be overcome.
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Affiliation(s)
- Jeremy A Draghi
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA
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17
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Li X, Zhang S, Huang R, Feng L, Xu S, Liu B. Diversity and distribution variation of urban spontaneous vegetation with distinct frequencies along river corridors in a fast-growing city. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 333:117446. [PMID: 36758408 DOI: 10.1016/j.jenvman.2023.117446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 12/28/2022] [Accepted: 02/01/2023] [Indexed: 06/18/2023]
Abstract
River corridors are vital to urban ecology, regulating climate and providing habitats for animals. Spontaneous plants naturally colonize various spaces therein, where they play important roles. Previous studies have explored many factors driving spontaneous plant diversity at the city scale and in specific habitats. However, we lack a holistic understanding of the diversity and distribution of variation of spontaneous vegetation that directly reflects the effects of urbanization. We conducted a field study of 1250 sample plots along river corridors in Chengdu, a fast-growing city in China, and the spontaneous plants in fifteen microhabitat types were surveyed. Diversity and distribution patterns were examined for species with distinct dispersal abilities. There was a far greater richness of occasional species compared to dominant and common species, but occasional species were markedly less abundant. Vacant lots and natural riverbanks harbored the most species, but revetment walls and lawns also supported a considerable number of species, especially in the city center. Species diversity among different urban areas was strongly related to microhabitat conditions. The proportions of dominant, common, and occasional species varied among communities. In communities on vacant lots of less urbanized areas, the richness of dominant species was greater, whereas in green spaces created by planted vegetation, occasional species were more diverse. Green space microenvironments are hospitable to some rare species. Urbanization and microhabitats have co-effects and thus ultimately determine diversity and distribution patterns. Such patterns, if linked to ecological and ornamental value, can provide a new perspective and nature-based solutions to urban rewilding and landscape design.
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Affiliation(s)
- Xiaopeng Li
- School of Architecture, Southwest Jiaotong University, Chengdu, 611756, Sichuan, China.
| | - Sining Zhang
- School of Architecture, Southwest Jiaotong University, Chengdu, 611756, Sichuan, China.
| | - Rui Huang
- School of Architecture, Southwest Jiaotong University, Chengdu, 611756, Sichuan, China.
| | - Li Feng
- Chengdu Park City Construction and Development Research Institute, Chengdu, 610031, Sichuan, China.
| | - Sihui Xu
- School of Architecture, Southwest Jiaotong University, Chengdu, 611756, Sichuan, China.
| | - Baichuan Liu
- School of Architecture, Southwest Jiaotong University, Chengdu, 611756, Sichuan, China.
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18
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San-Jose LM, Bestion E, Pellerin F, Richard M, Di Gesu L, Salmona J, Winandy L, Legrand D, Bonneaud C, Guillaume O, Calvez O, Elmer KR, Yurchenko AA, Recknagel H, Clobert J, Cote J. Investigating the genetic basis of vertebrate dispersal combining RNA-seq, RAD-seq and quantitative genetics. Mol Ecol 2023. [PMID: 36872057 DOI: 10.1111/mec.16916] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 01/17/2023] [Accepted: 02/06/2023] [Indexed: 03/07/2023]
Abstract
Although animal dispersal is known to play key roles in ecological and evolutionary processes such as colonization, population extinction and local adaptation, little is known about its genetic basis, particularly in vertebrates. Untapping the genetic basis of dispersal should deepen our understanding of how dispersal behaviour evolves, the molecular mechanisms that regulate it and link it to other phenotypic aspects in order to form the so-called dispersal syndromes. Here, we comprehensively combined quantitative genetics, genome-wide sequencing and transcriptome sequencing to investigate the genetic basis of natal dispersal in a known ecological and evolutionary model of vertebrate dispersal: the common lizard, Zootoca vivipara. Our study supports the heritability of dispersal in semi-natural populations, with less variation attributable to maternal and natal environment effects. In addition, we found an association between natal dispersal and both variation in the carbonic anhydrase (CA10) gene, and in the expression of several genes (TGFB2, SLC6A4, NOS1) involved in central nervous system functioning. These findings suggest that neurotransmitters (serotonin and nitric oxide) are involved in the regulation of dispersal and shaping dispersal syndromes. Several genes from the circadian clock (CRY2, KCTD21) were also differentially expressed between disperser and resident lizards, supporting that the circadian rhythm, known to be involved in long-distance migration in other taxa, might affect dispersal as well. Since neuronal and circadian pathways are relatively well conserved across vertebrates, our results are likely to be generalisable, and we therefore encourage future studies to further investigate the role of these pathways in shaping dispersal in vertebrates.
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Affiliation(s)
- Luis M San-Jose
- Laboratoire Évolution and Diversité Biologique, UMR 5174, CNRS, Université Toulouse III Paul Sabatier, IRD, Toulouse, France
| | - Elvire Bestion
- Station d'Ecologie Théorique et Expérimentale, UAR 2029, CNRS, Moulis, France
| | - Félix Pellerin
- Laboratoire Évolution and Diversité Biologique, UMR 5174, CNRS, Université Toulouse III Paul Sabatier, IRD, Toulouse, France
| | - Murielle Richard
- Station d'Ecologie Théorique et Expérimentale, UAR 2029, CNRS, Moulis, France
| | - Lucie Di Gesu
- Laboratoire Évolution and Diversité Biologique, UMR 5174, CNRS, Université Toulouse III Paul Sabatier, IRD, Toulouse, France
| | - Jordi Salmona
- Laboratoire Évolution and Diversité Biologique, UMR 5174, CNRS, Université Toulouse III Paul Sabatier, IRD, Toulouse, France
| | - Laurane Winandy
- Laboratoire Évolution and Diversité Biologique, UMR 5174, CNRS, Université Toulouse III Paul Sabatier, IRD, Toulouse, France
| | - Delphine Legrand
- Station d'Ecologie Théorique et Expérimentale, UAR 2029, CNRS, Moulis, France
| | - Camille Bonneaud
- Centre for Ecology and Conservation, Biosciences, University of Exeter, Penryn, Cornwall, UK
| | - Olivier Guillaume
- Station d'Ecologie Théorique et Expérimentale, UAR 2029, CNRS, Moulis, France
| | - Olivier Calvez
- Station d'Ecologie Théorique et Expérimentale, UAR 2029, CNRS, Moulis, France
| | - Kathryn R Elmer
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Andrey A Yurchenko
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Hans Recknagel
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Jean Clobert
- Station d'Ecologie Théorique et Expérimentale, UAR 2029, CNRS, Moulis, France
| | - Julien Cote
- Laboratoire Évolution and Diversité Biologique, UMR 5174, CNRS, Université Toulouse III Paul Sabatier, IRD, Toulouse, France
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19
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Deterministic Assembly Processes Strengthen the Effects of β-Diversity on Community Biomass of Marine Bacterioplankton. mSystems 2023; 8:e0097022. [PMID: 36511690 PMCID: PMC9948717 DOI: 10.1128/msystems.00970-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The presence of more species in the community of a sampling site (α diversity) typically increases ecosystem functions via nonrandom processes like resource partitioning. When considering multiple communities, we hypothesize that higher compositional difference (β diversity) increases overall functions of these communities. Further, we hypothesize that the β diversity effect is more positive when β diversity is increased by nonrandom assembly processes. To test these hypotheses, we collected bacterioplankton along a transect of 6 sampling sites in the southern East China Sea in 14 cruises. For any pairs of the 6 sites within a cruise, we calculated the Bray-Curtis index to represent β diversity and summed bacterial biomass as a proxy to indicate the overall function of the two communities. We then calculated deviation of observed mean pairwise phylogenetic similarities among species in two communities from random to represent the influences of nonrandom processes. The bacterial β diversity was found to positively affect the summed bacterial biomass; however, the effect varied among cruises. Cross-cruise comparison indicated that the β diversity effect increased with the nonrandom processes selecting for phylogenetically dissimilar species. This study extends biodiversity-ecosystem functioning research to the scale of multiple sites and enriches the framework by considering community assembly processes. IMPORTANCE The implications of our analyses are twofold. First, we emphasize the importance of studying β diversity. We expanded the current biodiversity-ecosystem functioning framework from single to multiple sampling sites and investigated the influences of species compositional differences among sites on the overall functioning of these sites. Since natural ecological communities never exist alone, our analyses allow us to more holistically perceive the role of biodiversity in natural ecosystems. Second, we took community assembly processes into account to attain a more mechanistic understanding of the impacts of biodiversity on ecosystem functioning.
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Abril-Colón I, Alonso JC, Palacín C, Ucero A, Álvarez-Martínez JM. Factors modulating home range and resource use: a case study with Canarian houbara bustards. MOVEMENT ECOLOGY 2022; 10:49. [PMID: 36376936 PMCID: PMC9664789 DOI: 10.1186/s40462-022-00346-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 10/30/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND The home range of an animal is determined by its ecological requirements, and these may vary depending on many intrinsic and extrinsic factors, which are ultimately driven by food resources. Investigating the effects of these factors, and specifically how individuals use food resources within their home ranges is essential to understand the ecology and dynamics of animal populations, and to establish conservation measures in the case of endangered species. Here, we investigate these questions in the Canarian houbara bustard, an endangered subspecies of African houbara endemic to the Canary Islands. METHODS We analysed GPS locations of 43 houbaras in 2018-2021, using solar GSM/GPRS loggers provided with accelerometers. We assessed (1) the variation in their home range and core area with kernel density estimators in relation to several intrinsic and extrinsic factors and (2) their foraging habitat selection. RESULTS Home ranges were smallest during the breeding season (November-April), when rains triggered a rapid growth of herbaceous vegetation. Displaying males and nesting females had smaller home ranges than individuals not involved in reproduction. Both sexes used almost exclusively non-cultivated land, selecting low density Launaea arborescens shrublands, pastures and green fallows as foraging habitats. Heavier males used smaller home ranges because they spent more time displaying at a fixed display site, while heavier females moved over larger areas during the mating period, probably visiting more candidate mates. During the non-breeding season (May-October), both sexes showed larger home ranges, shifting to high density shrubland, but also partly to cultivated land. They selected sweet potato fields, green fallows, alfalfas, orchards and irrigated fields, which offered highly valuable food resources during the driest months of the year. CONCLUSIONS Our study shows how Canarian houbara, originally a desert-dwelling species that uses mostly shrublands and pastures, has developed the necessary adaptations to benefit from resources provided by current low intensity farming practices in the study area. Maintaining appropriate habitat conditions in the eastern Canary islands should constitute a key conservation measure to prevent the extinction of this endangered houbara subspecies.
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Affiliation(s)
- Inmaculada Abril-Colón
- Departamento de Ecología Evolutiva, Museo Nacional de Ciencias Naturales (CSIC), Madrid, Spain.
| | - Juan Carlos Alonso
- Departamento de Ecología Evolutiva, Museo Nacional de Ciencias Naturales (CSIC), Madrid, Spain
| | - Carlos Palacín
- Departamento de Ecología Evolutiva, Museo Nacional de Ciencias Naturales (CSIC), Madrid, Spain
| | - Alberto Ucero
- Departamento de Ecología Evolutiva, Museo Nacional de Ciencias Naturales (CSIC), Madrid, Spain
| | - José Manuel Álvarez-Martínez
- IHCantabria - Instituto de Hidráulica Ambiental de La Universidad de Cantabria, PCTCAN, C/Isabel Torres, 15, 39011, Santander, Spain
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21
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Cardenas CR, Mularo AJ, Chavez AS, Adams RMM. Limited genetic differentiation of
Mycetomoellerius mikromelanos
in Parque National Soberanía, Panama: Implications for queen dispersal. Biotropica 2022. [DOI: 10.1111/btp.13171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Cody Raul Cardenas
- Department of Evolution Ecology and Organismal Biology & Museum of Biological Diversity The Ohio State University Columbus Ohio USA
- Muséum d'Histoire Naturelle de la Ville de Genève Geneva Switzerland
- Université de Genève Faculté des Sciences Life Sciences PhD School Ecology and Evolution Geneva Switzerland
| | - Andrew J. Mularo
- Department of Evolution Ecology and Organismal Biology & Museum of Biological Diversity The Ohio State University Columbus Ohio USA
- Department of Biological Sciences Purdue University West Lafayette Indiana USA
| | - Andreas S. Chavez
- Department of Evolution Ecology and Organismal Biology & Museum of Biological Diversity The Ohio State University Columbus Ohio USA
- Translational Data Analytics Institute The Ohio State University Columbus Ohio USA
| | - Rachelle M. M. Adams
- Department of Evolution Ecology and Organismal Biology & Museum of Biological Diversity The Ohio State University Columbus Ohio USA
- Department of Entomology National Museum of Natural History Smithsonian Institution Washington District of Colombia USA
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22
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Falgueras-Cano J, Falgueras-Cano JA, Moya A. Aggregated Distribution as an Explanation for the Paradox of Plankton and Collective Animal Behavior. BIOLOGY 2022; 11:biology11101477. [PMID: 36290382 PMCID: PMC9598300 DOI: 10.3390/biology11101477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 09/09/2022] [Accepted: 09/29/2022] [Indexed: 11/07/2022]
Abstract
Simple Summary ECA is similar to a cellular automaton that mimics the evolutionary dynamics of species in metapopulations, simulating the underlying mechanisms of natural selection. In this work, we carry out an in-silico study of the effects of different dispersal strategies on the evolutionary balance of interactions between digital organisms. In ECA we see how a specific type of distribution can significantly influence the dynamics, persistence, distribution, and abundance of populations of different species within a particular habitat. In the first place, we show that an aggregate distribution is more inefficient than a uniform distribution. Still, we verify that this aggregate distribution is essential in predator–prey type interactions so that the species involved do not become extinct. We also show that the aggregate distribution does not comply with the competitive exclusion principle and, for this reason, it results in a general and straightforward explanation for the paradox of plankton and the grouping of animals. Many animals and especially some planktonic species group together in specific spaces, although some travel adrift, leaving other areas or patches free where competitors or their prey can prosper, preventing them from becoming extinct. Abstract This work analyzes the evolutionary consequences of different aggregation levels of species distribution with an Evolutionary Cellular Automaton (ECA). We have found that in habitats with the same carrying capacity, aggregated distributions preserve smaller populations than do uniform distributions, i.e., they are less efficient. Nonetheless, we have also found that aggregated distributions, among other factors, can help the evolutionary stability of some biological interactions, such as predator–prey interactions, despite their granting less individual fitness. Besides, the competitive exclusion principle does not usually stand in populations with aggregated distribution. We have applied ECA to study the effects of aggregated distribution in two notorious cases: in the so-called paradox of the plankton and in gregarious animals. In doing so, we intend to ratify long-established ecological knowledge explaining these phenomena from a new perspective. In the first case, due to aggregate distribution, large aggregations of digital organisms mimicking very abundant planktonic species, leave large patches or oceanic areas free for other less competitive organisms, which mimic rare species, to prosper. In this case, we can see how effects, such as ecological drift and the small portion, act simultaneously. In the second case of aggregation, the aggregate distribution of gregarious animals could be explained under specialized predator–prey interactions and interdemic competition. Thus, digital organisms that imitate predators reduce the competitive capacity of their prey, destabilizing their competitiveness against other species. The specialized predator also goes extinct if the prey goes extinct by natural selection. Predators that have an aggregate distribution compensate the prey and thus avoid exclusion. This way there are more predator-free patches in which the prey can prosper. However, by granting greater colonization capacity to its prey, the predator loses competitiveness. Therefore, it is a multilevel selection event in which group adaptation grows to the detriment of the predator as an individual.
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Affiliation(s)
- Javier Falgueras-Cano
- Institute for Integrative Systems Biology (I2SysBio), University of Valencia and CSIC, 46980 Valencia, Spain
| | | | - Andrés Moya
- Institute for Integrative Systems Biology (I2SysBio), University of Valencia and CSIC, 46980 Valencia, Spain
- Genomics and Health Area, Foundation for the Promotion of Sanitary and Biomedical Research (FISABIO), 46020 Valencia, Spain
- Biomedical Research Center Network of Epidemiology and Public Health (CIBEResp), 28029 Madrid, Spain
- Correspondence:
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23
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Jacquet C, Carraro L, Altermatt F. Meta‐ecosystem dynamics drive the spatial distribution of functional groups in river networks. OIKOS 2022. [DOI: 10.1111/oik.09372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Claire Jacquet
- Dept of Aquatic Ecology, Swiss Federal Inst. of Aquatic Science and Technology Eawag Dübendorf Switzerland
- Dept of Evolutionary Biology and Environmental Studies, Univ. of Zurich Zürich Switzerland
| | - Luca Carraro
- Dept of Aquatic Ecology, Swiss Federal Inst. of Aquatic Science and Technology Eawag Dübendorf Switzerland
- Dept of Evolutionary Biology and Environmental Studies, Univ. of Zurich Zürich Switzerland
| | - Florian Altermatt
- Dept of Aquatic Ecology, Swiss Federal Inst. of Aquatic Science and Technology Eawag Dübendorf Switzerland
- Dept of Evolutionary Biology and Environmental Studies, Univ. of Zurich Zürich Switzerland
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24
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Niche filtering, competition and species turnover in a metacommunity of freshwater molluscs. OIKOS 2022. [DOI: 10.1111/oik.09157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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25
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Chen H(D, Ma Z(S. Niche-Neutral Continuum Seems to Explain the Global Niche Differentiation and Local Drift of the Human Digestive Tract Microbiome. Front Microbiol 2022; 13:912240. [PMID: 36033847 PMCID: PMC9400020 DOI: 10.3389/fmicb.2022.912240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 06/09/2022] [Indexed: 12/03/2022] Open
Abstract
The human digestive tract (DT) is differentiated into diverse niches and harbors the greatest microbiome diversity of our bodies. Segata et al. (2012) found that the microbiome of diverse habitats along the DT may be classified as four categories or niches with different microbial compositions and metabolic potentials. Nonetheless, few studies have offered theoretical interpretations of the observed patterns, not to mention quantitative mechanistic parameters. Such parameters should capture the essence of the fundamental processes that shape the microbiome distribution, beyond simple ecological metrics such as diversity or composition descriptors, which only capture the manifestations of the mechanisms. Here, we aim to get educated guesses for such parameters by adopting an integrated approach with multisite neutral (MSN) and niche-neutral hybrid (NNH) modeling, via reanalyzing Segata’s 16s-rRNA samples covering 10 DT-sites from over 200 healthy individuals. We evaluate the relative importance of the four essential processes (drift, dispersal, speciation, and selection) in shaping the microbiome distribution and dynamics along DT, which are assumed to form a niche-neutral continuum. Furthermore, the continuum seems to be hierarchical: the selection or niche differentiations seem to play a predominant role (> 90% based on NNH) at the global (the DT metacommunity) level, but the neutral drifts seem to be prevalent (> 90% based on MSN/NNH) at the local sites except for the gut site. An additional finding is that the DT appears to have a fifth niche for the DT microbiome, namely, Keratinized gingival (KG), while in Segata’s original study, only four niches were identified. Specifically, in Segata’s study, KG was classified into the same niche type including buccal mucosa (BM), hard palate (HP), and KG. However, it should be emphasized that the proposal of the fifth niche of KG requires additional verification in the future studies.
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Affiliation(s)
- Hongju (Daisy) Chen
- Computational Biology and Medical Ecology Lab, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- College of Mathematics, Honghe University, Yunnan, China
| | - Zhanshan (Sam) Ma
- Computational Biology and Medical Ecology Lab, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
- *Correspondence: Zhanshan (Sam) Ma,
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26
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Hanusch M, He X, Ruiz-Hernández V, Junker RR. Succession comprises a sequence of threshold-induced community assembly processes towards multidiversity. Commun Biol 2022; 5:424. [PMID: 35523944 PMCID: PMC9076875 DOI: 10.1038/s42003-022-03372-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 04/14/2022] [Indexed: 01/26/2023] Open
Abstract
Research on successions and community assembly both address the same processes such as dispersal, species sorting, and biotic interactions but lack unifying concepts. Recent theoretical advances integrated both research lines proposing a sequence of stochastic and deterministic processes along successional gradients. Shifts in ecosystem states along successional gradients are predicted to occur abruptly once abiotic and biotic factors dominate over dispersal as main driver. Considering the multidiversity composed of five organismal groups including plants, animals, and microbes, our results imply that stochastic, likely dispersal-dominated, processes are replaced by rather deterministic processes such as environmental filtering and biotic interactions after around 60 years of succession in a glacier forefield. The niche-based character of later successional processes is further supported by a decline in multi-beta-diversity. Our results may update concepts of community assembly by considering multiple taxa, help to bridge the gap between research on successions and community assembly, and provide insights into the emergence of multidiverse and complex ecosystems.
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Affiliation(s)
- Maximilian Hanusch
- Department of Environment and Biodiversity, Paris Lodron University Salzburg, 5020, Salzburg, Austria
| | - Xie He
- Department of Environment and Biodiversity, Paris Lodron University Salzburg, 5020, Salzburg, Austria
| | - Victoria Ruiz-Hernández
- Department of Environment and Biodiversity, Paris Lodron University Salzburg, 5020, Salzburg, Austria
| | - Robert R Junker
- Department of Environment and Biodiversity, Paris Lodron University Salzburg, 5020, Salzburg, Austria.
- Evolutionary Ecology of Plants, Department of Biology, Philipps-University Marburg, 35043, Marburg, Germany.
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27
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Chen J, Liu H, Bai Y, Qi J, Qi W, Liu H, Peng J, Qu J. Mixing regime shapes the community assembly process, microbial interaction and proliferation of cyanobacterial species Planktothrix in a stratified lake. J Environ Sci (China) 2022; 115:103-113. [PMID: 34969441 DOI: 10.1016/j.jes.2021.07.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 07/04/2021] [Accepted: 07/05/2021] [Indexed: 06/14/2023]
Abstract
Lake mixing influences aquatic chemical properties and microbial community composition, and thus, we hypothesized that it would alter microbial community assembly and interaction. To clarify this issue, we explored the community assembly processes and cooccurrence networks in four seasons at two depths (epilimnion and hypolimnion) in a mesotrophic and stratified lake (Chenghai Lake), which formed stratification in the summer and turnover in the winter. During the stratification period, the epilimnion and hypolimnion went through contrary assembly processes but converged to similar assembly patterns in the mixing period. In a highly homogeneous selection environment, species with low niche breadth were filtered, resulting in decreased species richness. Water mixing in the winter homogenized the environment, resulting in a simpler microbial cooccurrence network. Interestingly, we observed a high abundance of the cyanobacterial genus Planktothrix in the winter, probably due to nutrient redistribution and Planktothrix adaptivity to the winter environment in which mixing played important roles. Our study provides deeper fundamental insights into how environmental factors influence microbial community structure through community assembly processes.
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Affiliation(s)
- Junwen Chen
- Center for Water and Ecology, State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Huacong Liu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yaohui Bai
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Jing Qi
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Weixiao Qi
- Center for Water and Ecology, State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Huijuan Liu
- Center for Water and Ecology, State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Jianfeng Peng
- Center for Water and Ecology, State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Jiuhui Qu
- Center for Water and Ecology, State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China; Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
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28
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Consistency of mobile and sedentary movement extremes exhibited by an invasive fish, Silver Carp Hypophthalmichthys molitrix. Biol Invasions 2022. [DOI: 10.1007/s10530-022-02795-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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29
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McIntosh AR, Greig HS, Howard S. Regulation of open populations of a stream insect through larval density-dependence. J Anim Ecol 2022; 91:1582-1595. [PMID: 35362147 PMCID: PMC9541859 DOI: 10.1111/1365-2656.13696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 03/15/2022] [Indexed: 12/01/2022]
Abstract
In organisms with complex life cycles, the various stages occupy different habitats creating demographically open populations. The dynamics of these populations will depend on the occurrence and timing of stochastic influences relative to demographic density dependence, but understanding of these fundamentals, especially in the face of climate warming, has been hampered by the difficulty of empirical studies. Using a logically feasible organism, we conducted a replicated density‐perturbation experiment to manipulate late‐instar larvae of nine populations of a stream caddisfly, Zelandopsyche ingens, and measured the resulting abundance over 2 years covering the complete life cycle of one cohort to evaluate influences on dynamics. Negative density feedback occurred in the larval stage, and was sufficiently strong to counteract variation in abundance due to manipulation of larval density, adult caddis dispersal in the terrestrial environment as well as downstream drift of newly hatched and older larvae in the current. This supports theory indicating regulation of open populations must involve density dependence in local populations sufficient to offset variability associated with dispersal, especially during recruitment, and pinpoints the occurrence to late in the larval life cycle and driven by food resource abundance. There were large variations in adult, egg mass and early instar abundance that were not related to abundance in the previous stage, or the manipulation, pointing to large stochastic influences. Thus, the results also highlight the complementary nature of stochastic and deterministic influences on open populations. Such density dependence will enhance population persistence in situations where variable dispersal and transitioning between life stages frequently creates mismatches between abundance and the local availability of resources, such as might become more common with climate warming.
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Affiliation(s)
- Angus R McIntosh
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
| | - Hamish S Greig
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand.,Present address: School of Biology and Ecology, University of Maine, ME, USA
| | - Simon Howard
- Manaaki Whenua Landcare Research, Lincoln, New Zealand
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30
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Cheek RG, Forester BR, Salerno PE, Trumbo DR, Chen N, Sillett TS, Morrison SA, Ghalambor CK, Funk WC. Habitat-linked genetic variation supports microgeographic adaptive divergence in an island-endemic bird species. Mol Ecol 2022; 31:2830-2846. [PMID: 35315161 PMCID: PMC9325526 DOI: 10.1111/mec.16438] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 03/03/2022] [Accepted: 03/14/2022] [Indexed: 11/27/2022]
Abstract
We investigated the potential mechanisms driving habitat-linked genetic divergence within a bird species endemic to a single 250 km2 island. The island scrub-jay (Aphelocoma insularis) exhibits microgeographic divergence in bill morphology across pine-oak ecotones on Santa Cruz Island, California (USA) similar to adaptive differences described in mainland congeners over much larger geographic scales. To test whether individuals exhibit genetic differentiation related to habitat type and divergence in bill length, we genotyped over 3,000 single nucleotide polymorphisms (SNPs) in 123 adult island scrub-jay males from across Santa Cruz Island using restriction site-associated DNA sequencing (RADseq). Neutral landscape genomic analyses revealed that genome-wide genetic differentiation was primarily related to geographic distance and differences in habitat composition. We also found 168 putatively adaptive loci associated with habitat type using multivariate redundancy analysis (RDA) while controlling for spatial effects. Finally, two genome-wide association analyses revealed a polygenic basis to variation in bill length with multiple loci detected in or near genes known to affect bill morphology in other birds. Our findings support the hypothesis that divergent selection at microgeographic scales can cause adaptive divergence in the presence of ongoing gene flow.
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Affiliation(s)
- Rebecca G Cheek
- Department of Biology, Colorado State University, Fort Collins, Colorado, 80523, USA.,Graduate Degree Program in Ecology, Colorado State University, Fort Collins, Colorado, 80523, USA
| | - Brenna R Forester
- Department of Biology, Colorado State University, Fort Collins, Colorado, 80523, USA
| | - Patricia E Salerno
- Department of Biology, Colorado State University, Fort Collins, Colorado, 80523, USA.,Centro de Investigación de la Biodiversidad y Cambio Climático (BioCamb), Facultad de Ciencias de Medio Ambiente, Universidad Tecnológica Indoamérica, Quito, Ecuador
| | - Daryl R Trumbo
- Department of Biology, Colorado State University, Fort Collins, Colorado, 80523, USA
| | - Nancy Chen
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - T Scott Sillett
- Migratory Bird Center, Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, 20013, USA
| | | | - Cameron K Ghalambor
- Department of Biology, Colorado State University, Fort Collins, Colorado, 80523, USA.,Graduate Degree Program in Ecology, Colorado State University, Fort Collins, Colorado, 80523, USA.,Department of Biology, Centre for Biodiversity Dynamics (CBD), Norwegian University of Science and Technology (NTNU), N-7491, Trondheim, Norway
| | - W Chris Funk
- Department of Biology, Colorado State University, Fort Collins, Colorado, 80523, USA.,Graduate Degree Program in Ecology, Colorado State University, Fort Collins, Colorado, 80523, USA
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31
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Environmental Factors Drive Periphytic Algal Community Assembly in the Largest Long-Distance Water Diversion Channel. WATER 2022. [DOI: 10.3390/w14060914] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
Periphytic algae exist widely in different waters. However, little is known about periphytic algae in long-distance water diversion channels across watersheds. We investigated the periphytic algae and the environmental factors at twenty sampling sites in the middle route of the South-to-North Water Diversion Project (MRP). The dominant species were Desmodesmus intermedius (Hegewald), Calothrix thermalis (Bornet & Flahault), Calothrix parietina (Bornet & Flahault) and Leptolyngbya benthonica (Anagnostidis) (dominance > 0.02) as measured in a whole year. Habitat heterogeneity in the MRP led to lower spatial heterogeneity and higher temporal heterogeneity of the periphytic algal community. Stochastic processes are the major process in periphytic community assembly. In deterministic processes, homogeneous selection had the major role in structuring the periphytic community, whereas the role of heterogeneous selection was less significant. In stochastic processes, dispersal limitations had the major role in structuring the periphytic community, whereas the role of homogenizing dispersal and drift were less significant. The variation in total nitrogen and total phosphorus promoted more stochastic processes (−1.96 < βNTI < 1.96). The variations in water temperature and water velocity promoted more heterogeneous selection (βNTI > 1.96). In integrating all of this empirical evidence, we explore the role of environmental factors in the action of ecological processes shaping thecommunity assembly of the periphytic algal community.
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32
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Šantl-Temkiv T, Amato P, Casamayor EO, Lee PKH, Pointing SB. OUP accepted manuscript. FEMS Microbiol Rev 2022; 46:6524182. [PMID: 35137064 PMCID: PMC9249623 DOI: 10.1093/femsre/fuac009] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 01/31/2022] [Accepted: 02/06/2022] [Indexed: 11/30/2022] Open
Abstract
The atmosphere connects habitats across multiple spatial scales via airborne dispersal of microbial cells, propagules and biomolecules. Atmospheric microorganisms have been implicated in a variety of biochemical and biophysical transformations. Here, we review ecological aspects of airborne microorganisms with respect to their dispersal, activity and contribution to climatic processes. Latest studies utilizing metagenomic approaches demonstrate that airborne microbial communities exhibit pronounced biogeography, driven by a combination of biotic and abiotic factors. We quantify distributions and fluxes of microbial cells between surface habitats and the atmosphere and place special emphasis on long-range pathogen dispersal. Recent advances have established that these processes may be relevant for macroecological outcomes in terrestrial and marine habitats. We evaluate the potential biological transformation of atmospheric volatile organic compounds and other substrates by airborne microorganisms and discuss clouds as hotspots of microbial metabolic activity in the atmosphere. Furthermore, we emphasize the role of microorganisms as ice nucleating particles and their relevance for the water cycle via formation of clouds and precipitation. Finally, potential impacts of anthropogenic forcing on the natural atmospheric microbiota via emission of particulate matter, greenhouse gases and microorganisms are discussed.
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Affiliation(s)
- Tina Šantl-Temkiv
- Department of Biology, Aarhus University, DK-8000 Aarhus, Denmark
- Stellar Astrophysics Centre, Department of Physics and Astronomy, Aarhus University, DK-8000 Aarhus, Denmark
| | - Pierre Amato
- Institut de Chimie de Clermont-Ferrand, SIGMA Clermont, CNRS, Université Clermont Auvergne, 63178, Clermont-Ferrand, France
| | - Emilio O Casamayor
- Centre for Advanced Studies of Blanes, Spanish Council for Research (CSIC), 17300, Blanes, Spain
| | - Patrick K H Lee
- School of Energy and Environment, City University of Hong Kong, Hong Kong, China
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong, China
| | - Stephen B Pointing
- Corresponding author: Yale-NUS College, National University of Singapore, 16 College Avenue West, Singapore 138527. Tel: +65 6601 1000; E-mail:
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33
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Larroque J, Wittische J, James PMA. Quantifying and predicting population connectivity of an outbreaking forest insect pest. LANDSCAPE ECOLOGY 2021; 37:763-778. [PMID: 35273428 PMCID: PMC8897358 DOI: 10.1007/s10980-021-01382-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 12/06/2021] [Indexed: 06/14/2023]
Abstract
CONTEXT Dispersal has a key role in the population dynamics of outbreaking species such as the spruce budworm (Choristoneura fumiferana) as it can synchronize the demography of distant populations and favor the transition from endemic to epidemic states. However, we know very little about how landscape structure influences dispersal in such systems while such knowledge is essential for better forecasting of spatially synchronous population dynamics and to guide management strategies. OBJECTIVES We aimed to characterize the spatial environmental determinants of spruce budworm dispersal to determine how these features affect outbreak spread in Quebec (Canada). We then apply our findings to predict expected future landscape connectivity and explore its potential consequences on future outbreaks. METHODS We used a machine-learning landscape genetics approach on 447 larvae covering most of the outbreak area and genotyped at 3562 SNP loci to identify the main variables affecting connectivity. RESULTS We found that the connectivity between outbreak populations was driven by the combination of precipitation and host cover. Our forecasting suggests that between the current and next outbreaks, connectivity may increase between Ontario and Quebec, and might decrease in the eastern part, which could have the effect of limiting outbreak spread from Ontario and Quebec to the eastern provinces. CONCLUSIONS Although we did not identify any discrete barriers, low connectivity areas might constrain dispersal in the current and future outbreaks and should in turn, be intensively monitored. However, continued sampling as the outbreak progresses is needed to confirm the temporal stability of the observed patterns. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s10980-021-01382-9.
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Affiliation(s)
- Jeremy Larroque
- Department of Wildlife Sciences, University of Göttingen, Buesgenweg 3, 37077 Göttingen, Germany
| | - Julian Wittische
- Department of Biological Sciences, Pavillon Marie-Victorin, Université de Montréal, 90 Vincent-d'Indy Avenue, Montreal, QC H2V 2S9 Canada
| | - Patrick M A James
- Institute of Forestry and Conservation, John H. Daniels Faculty of Architecture, Landscape, and Design, University of Toronto, 33 Willcocks Street, Toronto, ON M5S 3E8 Canada
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Peterson K, Ruffley M, Parent CE. Phylogenetic diversity and community assembly in a naturally fragmented system. Ecol Evol 2021; 11:18066-18080. [PMID: 35003658 PMCID: PMC8717291 DOI: 10.1002/ece3.8404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 11/02/2021] [Accepted: 11/04/2021] [Indexed: 11/06/2022] Open
Abstract
We sought to assess effects of fragmentation and quantify the contribution of ecological processes to community assembly by measuring species richness, phylogenetic, and phenotypic diversity of species found in local and regional plant communities. Specifically, our fragmented system is Craters of the Moon National Monument and Preserve, Idaho, USA. CRMO is characterized by vegetated islands, kipukas, that are isolated in a matrix of lava. We used floristic surveys of vascular plants in 19 kipukas to create a local species list to compare traditional dispersion metrics, mean pairwise distance, and mean nearest taxon distance (MPD and MNTD), to a regional species list with phenotypic and phylogenetic data. We combined phylogenetic and functional trait data in a novel machine-learning model selection approach, Community Assembly Model Inference (CAMI), to infer probability associated with different models of community assembly given the data. Finally, we used linear regression to explore whether the geography of kipukas explained estimated support for community assembly models. Using traditional metrics of MPD and MNTD neutral processes received the most support when comparing kipuka species to regional species. Individually no kipukas showed significant support for overdispersion. Rather, five kipukas showed significant support for phylogenetic clustering using MPD and two kipukas using MNTD. Using CAMI, we inferred neutral and filtering models structured the kipuka plant community for our trait of interest. Finally, we found as species richness in kipukas increases, model support for competition decreases and lower elevation kipukas show more support for habitat filtering models. While traditional phylogenetic community approaches suggest neutral assembly dynamics, recently developed approaches utilizing machine learning and model choice revealed joint influences of assembly processes to form the kipuka plant communities. Understanding ecological processes at play in naturally fragmented systems will aid in guiding our understanding of how fragmentation impacts future changes in landscapes.
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Affiliation(s)
- Katie Peterson
- Department of Biological SciencesUniversity of IdahoMoscowIdahoUSA
| | - Megan Ruffley
- Department of Biological SciencesUniversity of IdahoMoscowIdahoUSA
- Department of Plant BiologyCarnegie Institution for ScienceStanfordCaliforniaUSA
| | - Christine E. Parent
- Department of Biological SciencesUniversity of IdahoMoscowIdahoUSA
- Institute for Interdisiplinary Data SciencesUniversity of IdahoMoscowIdahoUSA
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35
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Trense D, Hoffmann AA, Fischer K. Large- and small-scale geographic structures affecting genetic patterns across populations of an Alpine butterfly. Ecol Evol 2021; 11:14697-14714. [PMID: 34765135 PMCID: PMC8571576 DOI: 10.1002/ece3.8157] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 09/04/2021] [Accepted: 09/08/2021] [Indexed: 11/09/2022] Open
Abstract
Understanding factors influencing patterns of genetic diversity and the population genetic structure of species is of particular importance in the current era of global climate change and habitat loss. These factors include the evolutionary history of a species as well as heterogeneity in the environment it occupies, which in turn can change across time. Most studies investigating spatio-temporal genetic patterns have focused on patterns across wide geographic areas rather than local variation, but the latter can nevertheless be important particularly in topographically complex areas. Here, we consider these issues in the Sooty Copper butterfly (Lycaena tityrus) from the European Alps, using genome-wide SNPs identified through RADseq. We found strong genetic differentiation within the Alps with four genetic clusters, indicating western, central, and eastern refuges, and a strong reduction of genetic diversity from west to east. This reduction in diversity may suggest that the southwestern refuge was the largest one in comparison to other refuges. Also, the high genetic diversity in the west may result from (a) admixture of different western refuges, (b) more recent demographic changes, or (c) introgression of lowland L. tityrus populations. At small spatial scales, populations were structured by several landscape features and especially by high mountain ridges and large river valleys. We detected 36 outlier loci likely under altitudinal selection, including several loci related to membranes and cellular processes. We suggest that efforts to preserve alpine L. tityrus should focus on the genetically diverse populations in the western Alps, and that the dolomite populations should be treated as genetically distinct management units, since they appear to be currently more threatened than others. This study demonstrates the usefulness of SNP-based approaches for understanding patterns of genetic diversity, gene flow, and selection in a region that is expected to be particularly vulnerable to climate change.
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Affiliation(s)
- Daronja Trense
- Institute for Integrated Natural Sciences, ZoologyUniversity Koblenz‐LandauKoblenzGermany
| | - Ary A. Hoffmann
- Pest & Environmental Adaptation Research GroupSchool of BiosciencesBio21 InstituteParkvilleVic.Australia
| | - Klaus Fischer
- Institute for Integrated Natural Sciences, ZoologyUniversity Koblenz‐LandauKoblenzGermany
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36
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DeMalach N, Ke PJ, Fukami T. The effects of ecological selection on species diversity and trait distribution: predictions and an empirical test. Ecology 2021; 103:e03567. [PMID: 34674221 DOI: 10.1002/ecy.3567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 07/12/2021] [Accepted: 08/03/2021] [Indexed: 11/09/2022]
Abstract
Ecological selection is a major driver of community assembly. Selection is classified as stabilizing when species with intermediate trait values gain the highest reproductive success, whereas selection is considered directional when fitness is highest for species with extreme trait values. Previous studies have investigated the effects of different selection types on trait distribution, but the effects of selection on species diversity have remained unclear. Here, we propose a framework for inferring the type and strength of selection by studying species diversity and trait distribution together against null expectations. We use a simulation model to confirm our prediction that directional selection should lead to lower species diversity than stabilizing selection despite a similar effect on trait community-weighted variance. We apply the framework to a mesocosm system of annual plants to test whether differences in species diversity between two habitats that vary in productivity are related to differences in selection on seed mass. We show that, in both habitats, species diversity was lower than the null expectation, but that species diversity was lower in the more productive habitat. We attribute this difference to strong directional selection for large-seeded species in the productive habitat as indicated by trait community-weighted-mean being higher and community-weighted variance being lower than the null expectations. In the less productive habitat, we found that community-weighted variance was higher than expected by chance, suggesting that seed mass could be a driver of niche partitioning under such conditions. Altogether, our results suggest that viewing species diversity and trait distribution as interrelated patterns driven by the same process, ecological selection, is helpful in understanding community assembly.
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Affiliation(s)
- Niv DeMalach
- Department of Biology, Stanford University, Stanford, California, USA.,Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Po-Ju Ke
- Department of Biology, Stanford University, Stanford, California, USA.,Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA.,Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan
| | - Tadashi Fukami
- Department of Biology, Stanford University, Stanford, California, USA
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37
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Mazzei R, Rubenstein DR. Larval ecology, dispersal, and the evolution of sociality in the sea. Ethology 2021. [DOI: 10.1111/eth.13195] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Renata Mazzei
- Department of Ecology, Evolution and Environmental Biology Columbia University New York NY USA
| | - Dustin R. Rubenstein
- Department of Ecology, Evolution and Environmental Biology Columbia University New York NY USA
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38
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High-Level Diversity of Basal Fungal Lineages and the Control of Fungal Community Assembly by Stochastic Processes in Mangrove Sediments. Appl Environ Microbiol 2021; 87:e0092821. [PMID: 34190611 DOI: 10.1128/aem.00928-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Fungi are key components of microbial communities in mangrove wetlands, with important roles in the transformation of nutrients and energy. However, existing studies typically focus on cultivable fungi and seldom on the structure and driving factors of entire fungal communities. The compositions, community assembly, and interaction patterns of mangrove fungal communities on a large scale remain elusive. Here, biogeography, assembly, and co-occurrence patterns of fungal communities in mangroves across eastern to southern China were systematically analyzed by targeting the entire internal transcribed spacer (ITS) region with high-throughput Pacific Biosciences single-molecule real-time sequencing. The analysis revealed a high level of fungal diversity, including a number of basal fungal lineages not previously reported in mangroves, such as Rozellomycota and Chytridiomycota. Beta nearest-taxon index analyses suggested a determinant role of dispersal limitation on fungal community in overall and most individual mangroves, with support from the strong distance-decay patterns of community similarity. Further, nonmetric multidimensional scaling analyses revealed similar biogeographies of dominant and rare fungal communities. A minor role of environmental selection on the fungal community was noted, with geographical location and sediment depth as crucial factors driving the distribution of both, the dominant and rare taxa. Finally, network analysis revealed high modularized co-occurrence patterns of fungal community in mangrove sediments, and the keystone taxa might play important roles in microbial interactions and ecological functions. The investigation expands our understanding of biogeography, assembly patterns, driving factors, and co-occurrence relationships of mangrove fungi and will spur the further functional exploration and protection of fungal resources in mangroves. IMPORTANCE As key components of microbial community in mangroves, fungi have important ecological functions. However, the fungal community in mangroves on a large scale is generally elusive, and mangroves are declining rapidly due to climate change and anthropogenic activities. This work provides an overview of fungal community structure and biogeography in mangrove wetlands along a >9,000-km coastline across eastern to southern China. Our study observed a high number of basal fungal lineages, such as Rozellomycota and Chytridiomycota, in mangrove sediments. In addition, our results highlight a crucial role of dispersal limitation and a minor role of environmental selections on fungal communities in mangrove sediments. These novel findings add important knowledge about the structure, assembly processes, and driving factors of fungal communities in mangrove sediments.
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39
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Zheng Y, Maitra P, Gan HY, Chen L, Li S, Tu T, Chen L, Mi X, Gao C, Zhang D, Guo LD. Soil fungal diversity and community assembly: affected by island size or type? FEMS Microbiol Ecol 2021; 97:6247622. [PMID: 33890666 DOI: 10.1093/femsec/fiab062] [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] [Received: 02/28/2021] [Accepted: 04/21/2021] [Indexed: 11/14/2022] Open
Abstract
Fungi have a huge biodiversity and play important roles in soil biogeochemical cycling in island ecosystems. Although island biogeography has been widely studied for macroorganisms, fungal community assembly in true islands and its relationship with island area are less documented. We examined soil fungal communities in 18 oceanic islands of two types (eight non-coral islands and 10 coral islands) using the Illumina MiSeq sequencing technique. Our results showed that fungal α-diversity (species richness) was substantially different among the oceanic islands, with a higher value in non-coral islands than in coral islands. Fungal α-diversity was significantly affected by soil potassium and magnesium (Mg) and plant communities in non-coral islands, whereas only soil Mg significantly affected it in coral islands. Soil fungal community composition was significantly different in the non-coral and coral islands and was influenced by soil property, plant community and spatial distance. The ecological stochasticity model showed that the fungal community assembly was mainly governed by deterministic processes regardless of island type. Fungal β-diversity, but not α-diversity, increased significantly with increasing island area. These findings have implications for the better prediction of soil fungal community dynamics in island systems and biodiversity conservation in fragmented habitats.
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Affiliation(s)
- Yong Zheng
- State Key Laboratory for Subtropical Mountain Ecology of the Ministry of Science and Technology and Fujian Province, School of Geographical Sciences, Fujian Normal University, Fuzhou 350007, China.,State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Pulak Maitra
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hui-Yun Gan
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liang Chen
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shengchun Li
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Tieyao Tu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Lei Chen
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Xiangcheng Mi
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Cheng Gao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dianxiang Zhang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Liang-Dong Guo
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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40
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Abstract
Seagrasses are marine flowering plants that provide critical ecosystem services in coastal environments worldwide. Marine fungi are often overlooked in microbiome and seagrass studies, despite terrestrial fungi having critical functional roles as decomposers, pathogens, or endophytes in global ecosystems. Here, we characterize the distribution of fungi associated with the seagrass Zostera marina, using leaves, roots, and rhizosphere sediment from 16 locations across its full biogeographic range. Using high-throughput sequencing of the ribosomal internal transcribed spacer (ITS) region and 18S rRNA gene, we first measured fungal community composition and diversity. We then tested hypotheses of neutral community assembly theory and the degree to which deviations suggested that amplicon sequence variants (ASVs) were plant selected or dispersal limited. Finally, we identified a core mycobiome and investigated the global distribution of differentially abundant ASVs. We found that the fungal community is significantly different between sites and that the leaf mycobiome follows a weak but significant pattern of distance decay in the Pacific Ocean. Generally, there was evidence for both deterministic and stochastic factors contributing to community assembly of the mycobiome, with most taxa assembling through stochastic processes. The Z. marina core leaf and root mycobiomes were dominated by unclassified Sordariomycetes spp., unclassified Chytridiomycota lineages (including Lobulomycetaceae spp.), unclassified Capnodiales spp., and Saccharomyces sp. It is clear from the many unclassified fungal ASVs and fungal functional guilds that knowledge of marine fungi is still rudimentary. Further studies characterizing seagrass-associated fungi are needed to understand the roles of these microorganisms generally and when associated with seagrasses. IMPORTANCE Fungi have important functional roles when associated with land plants, yet very little is known about the roles of fungi associated with marine plants, like seagrasses. In this study, we report the results of a global effort to characterize the fungi associated with the seagrass Zostera marina across its full biogeographic range. Although we defined a putative global core fungal community, it is apparent from the many fungal sequences and predicted functional guilds that had no matches to existing databases that general knowledge of seagrass-associated fungi and marine fungi is lacking. This work serves as an important foundational step toward future work investigating the functional ramifications of fungi in the marine ecosystem.
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41
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Huanca Nuñez N, Chazdon RL, Russo SE. Seed-rain-successional feedbacks in wet tropical forests. Ecology 2021; 102:e03362. [PMID: 33834498 DOI: 10.1002/ecy.3362] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 09/09/2020] [Accepted: 02/05/2021] [Indexed: 11/06/2022]
Abstract
Tropical forest regeneration after abandonment of former agricultural land depends critically on the input of tree seeds, yet seed dispersal is increasingly disrupted in contemporary human-modified landscapes. Here, we introduce the concept of seed-rain-successional feedbacks as a deterministic process in which seed rain is shaped by successional dynamics internal to a forest site and that acts to reinforce priority effects. We used a combination of time series and chronosequence approaches to investigate how the quantity and taxonomic and functional composition of seed rain change during succession and to evaluate the strength of seed-rain-successional feedbacks, relative to other deterministic and stochastic mechanisms, in secondary wet forests of Costa Rica. We found that both successional niches and seed-rain-successional feedbacks shaped successional trajectories in the seed rain. Determinism due to successional niche assembly was supported by the increasing convergence of community structure to that of a mature forest, in terms of both functional and taxonomic composition. With successional age, the proportions of large-seeded, shade-tolerant species in the seed rain increased, whereas the proportion of animal-dispersed species did not change significantly. Seed-rain-successional feedbacks increased in strength with successional age, as the proportion of immigrant seeds (species not locally represented in the site) decreased with successional age, and the composition of the seed rain became more similar to that of the adult trees at the forest site. The deterministic assembly generated by seed-rain-successional feedback likely contributed to the increasing divergence of secondary forest sites from each other during succession. To the extent that human modification of tropical forest landscapes reduces connectivity via factors such as forest cover loss, our results suggest that seed-rain-successional feedbacks are likely to increasingly shape regeneration trajectories in and amplify floristic heterogeneity among tropical secondary forests.
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Affiliation(s)
- Nohemi Huanca Nuñez
- School of Biological Sciences, University of Nebraska, Lincoln, Nebraska, 68588-0118, USA
| | - Robin L Chazdon
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut, 06269-3043, USA
| | - Sabrina E Russo
- School of Biological Sciences, University of Nebraska, Lincoln, Nebraska, 68588-0118, USA.,Center for Plant Science Innovation, University of Nebraska, Lincoln, Nebraska, 68588-0660, USA
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42
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Papa Y, Le Bail PY, Covain R. Genetic landscape clustering of a large DNA barcoding data set reveals shared patterns of genetic divergence among freshwater fishes of the Maroni Basin. Mol Ecol Resour 2021; 21:2109-2124. [PMID: 33892518 DOI: 10.1111/1755-0998.13402] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 03/27/2021] [Accepted: 04/13/2021] [Indexed: 11/27/2022]
Abstract
The Maroni is one of the most speciose basins of the Guianas and hosts a megadiverse freshwater fish community. Although taxonomic references based on morphological identification exist for both the Surinamese and Guianese parts of the basin, there are still taxonomic uncertainties concerning the status of several species. We used COI sequences of 1284 fish in conjunction with morphological and biogeographical evidence to assist with species delineation and discovery in order to validate and standardize the current taxonomy. This resulted in a final DNA barcode data set of 199 fish species (125 genera, 36 families and eight orders; 68.86% of strictly freshwater fishes from the basin), among which 25 are new putative candidate species flagged as requiring taxonomic update. DNA barcoding delineation through Barcode Index Numbers (BINs) revealed further cryptic diversity (230 BINs in total). To explore global genetic patterns across the basin, genetic divergence landscapes were computed for 128 species, showing a global trend of high genetic divergence between the Surinamese southwest (Tapanahony and Paloemeu), the Guianese southeast (Marouini, Litany, Tampok, etc.), and the river outlet in the north. This could be explained by lower levels of connectivity between these three main areas and/or the exchange of individuals between these areas and the neighbouring basins. A new method of ordination of genetic landscapes successfully assigned species into cluster groups based on their respective pattern of genetic divergence across the Maroni Basin: genetically homogeneous species were effectively discriminated from species showing high spatial genetic fragmentation and possible lower capacity for dispersal.
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Affiliation(s)
- Yvan Papa
- Herpetology and Ichthyology, Museum of Natural History of Geneva, Geneva, Switzerland.,School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | | | - Raphaël Covain
- Herpetology and Ichthyology, Museum of Natural History of Geneva, Geneva, Switzerland
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43
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Pascoal F, Costa R, Magalhães C. The microbial rare biosphere: current concepts, methods and ecological principles. FEMS Microbiol Ecol 2021; 97:5974270. [PMID: 33175111 DOI: 10.1093/femsec/fiaa227] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 11/06/2020] [Indexed: 01/04/2023] Open
Abstract
Our ability to describe the highly diverse pool of low abundance populations present in natural microbial communities is increasing at an unprecedented pace. Yet we currently lack an integrative view of the key taxa, functions and metabolic activity which make-up this communal pool, usually referred to as the 'rare biosphere', across the domains of life. In this context, this review examines the microbial rare biosphere in its broader sense, providing an historical perspective on representative studies which enabled to bridge the concept from macroecology to microbial ecology. It then addresses our current knowledge of the prokaryotic rare biosphere, and covers emerging insights into the ecology, taxonomy and evolution of low abundance microeukaryotic, viral and host-associated communities. We also review recent methodological advances and provide a synthetic overview on how the rare biosphere fits into different conceptual models used to explain microbial community assembly mechanisms, composition and function.
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Affiliation(s)
- Francisco Pascoal
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Terminal de Cruzeiros do Porto de Leixoes, Avenida General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal
| | - Rodrigo Costa
- Department of Bioengineering, Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico, University of Lisbon, Av. Rovisco Pais 1049-001, Lisbon, Portugal.,Centre of Marine Sciences (CCMAR), University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal.,U.S. Department of Energy Joint Genome Institute, 1 Cyclotron Road, CA 94720, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, CA 94720 Berkeley, USA
| | - Catarina Magalhães
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Terminal de Cruzeiros do Porto de Leixoes, Avenida General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal.,Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal.,School of Science, University of Waikato, Gate 1, Knighton Road 3240, Hamilton, New Zealand.,Ocean Frontier Institute, Dalhousie University, Steele Ocean Sciences Building, Dalhousie University 1355 Oxford St., B3H4R2 Halifax, NS, Canada
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44
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Hudon SF, Zaiats A, Roser A, Roopsind A, Barber C, Robb BC, Pendleton BA, Camp MJ, Clark PE, Davidson MM, Frankel‐Bricker J, Fremgen‐Tarantino M, Forbey JS, Hayden EJ, Richards LA, Rodriguez OK, Caughlin TT. Unifying community detection across scales from genomes to landscapes. OIKOS 2021. [DOI: 10.1111/oik.08393] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
| | | | - Anna Roser
- Boise State Univ. Boise ID USA
- Center for Natural Climate Solutions, Conservation International Arlington VA USA
| | | | | | | | | | | | - Patrick E. Clark
- Northwest Watershed Research Center, USDA Agricultural Research Service Boise ID USA
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45
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Liao J, Bergholz P, Wiedmann M. Adjacent Terrestrial Landscapes Impact the Biogeographical Pattern of Soil Escherichia coli Strains in Produce Fields by Modifying the Importance of Environmental Selection and Dispersal. Appl Environ Microbiol 2021; 87:e02516-20. [PMID: 33452036 PMCID: PMC8105029 DOI: 10.1128/aem.02516-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 01/04/2021] [Indexed: 11/20/2022] Open
Abstract
High-quality habitats for wildlife (e.g., forest) provide essential ecosystem services while increasing species diversity and habitat connectivity. Unfortunately, the presence of such habitats adjacent to produce fields may increase risk for contamination of fruits and vegetables by enteric bacteria, including Escherichia coliE. coli survives in extrahost environments (e.g., soil) and could be dispersed across landscapes by wildlife. Understanding how terrestrial landscapes impact the distribution of soil E. coli strains is of importance in assessing the contamination risk of agricultural products. Here, using multilocus sequence typing, we characterized 938 E. coli soil isolates collected from two watersheds with different landscape patterns in New York State, USA, and compared the distribution of E. coli and the influence that environmental selection and dispersal have on the distribution between these two watersheds. Results showed that for the watershed with widespread produce fields, sparse forests, and limited interaction between the two land use types, E. coli composition was significantly different between produce field sites and forest sites; this distribution appears to be shaped by relatively strong environmental selection, likely from soil phosphorus, and slight dispersal limitation. For the watershed with more forested areas and stronger interaction between produce field sites and forest sites, E. coli composition between these two land use types was relatively homogeneous; this distribution appeared to be a consequence of wildlife-driven dispersal, inferred by competing models. Collectively, our results suggest that terrestrial landscape attributes could impact the biogeographic pattern of enteric bacteria by adjusting the importance of environmental selection and dispersal.IMPORTANCE Understanding the ecology of enteric bacteria in extrahost environments is important for the development and implementation of strategies to minimize preharvest contamination of produce with enteric pathogens. Our findings suggest that watershed landscape is an important factor influencing the importance of ecological drivers and dispersal patterns of E. coli Agricultural areas in such watersheds may have a higher risk of produce contamination due to fewer environmental constraints and higher potential of dispersal of enteric bacteria between locations. Thus, there is a perceived trade-off between priorities of environmental conservation and public health in on-farm food safety, with limited ecological data supporting or refuting the role of wildlife in dispersing pathogens under normal operating conditions. By combining field sampling and spatial modeling, we explored ecological principles underlying the biogeographic pattern of enteric bacteria at the regional level, which can benefit agricultural, environmental, and public health scientists who aim to reduce the risk of food contamination by enteric bacteria while minimizing negative impacts on wildlife habitats.
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Affiliation(s)
- Jingqiu Liao
- Department of Food Science, Cornell University, Ithaca, New York, USA
- Graduate Field of Microbiology, Cornell University, Ithaca, New York, USA
| | - Peter Bergholz
- Department of Microbiological Sciences, North Dakota State University, Fargo, North Dakota, USA
| | - Martin Wiedmann
- Department of Food Science, Cornell University, Ithaca, New York, USA
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46
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Ma Z(S. Niche-neutral theoretic approach to mechanisms underlying the biodiversity and biogeography of human microbiomes. Evol Appl 2021; 14:322-334. [PMID: 33664779 PMCID: PMC7896709 DOI: 10.1111/eva.13116] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 08/05/2020] [Accepted: 08/13/2020] [Indexed: 12/13/2022] Open
Abstract
The human microbiome consists of five major regional biomes distributed in or on our five body sites including skin, oral, lung, gut, and reproductive tract. Its biogeography (the spatial and temporal distribution of its biodiversity) has far-reaching implications to our health and diseases. Nevertheless, we currently have very limited understanding on the mechanisms shaping the biogeography, since it is often rather difficult to determine the relative importance of drift, dispersal, speciation, and selection, the four processes (mechanisms) determining the patterns of microbial biogeography and community dynamics according to a recent synthesis in community ecology and biogeography. To disentangle these mechanisms, I utilize multisite neutral (MSN) model and niche-neutral hybrid (NNH) model to analyze large number of truly multisite microbiome samples covering all five major human microbiome habitats, including 699 metacommunities and 5,420 local communities. Approximately 89% of metacommunities and 92% local communities exhibit patterns indistinguishable from neutral, and 20% indistinguishable from niche-neutral hybrid model, indicating the relative significance of stochastic neutral forces versus deterministic niche selection in shaping the biogeography of human microbiome. These findings cast supporting evidence to van der Gast's revision to classic Bass-Becking doctrine of microbial biogeography: "Some things are everywhere and some things are not. Sometimes the environment selects and sometimes it doesn't," offering the first educated guess for "some" and "sometimes" in the revised doctrine. Furthermore, the logistic/Cox regression models describing the relationships among community neutrality, niche differentiation, and key community/species characteristics (including community diversity, community/species dominance, speciation, and migration rates) were constructed to quantitatively describe the niche-neutral continuum and the influences of community/species properties on the continuum.
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Affiliation(s)
- Zhanshan (Sam) Ma
- Computational Biology and Medical Ecology LabState Key Laboratory of Genetic Resources and EvolutionKunming Institute of ZoologyChinese Academy of SciencesKunmingChina
- Center for Excellence in Animal Evolution and GeneticsChinese Academy of SciencesKunmingChina
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Abstract
Perhaps more than any other ecological discipline, invasion biology has married the practices of basic science and the application of that science. The conceptual frameworks of population regulation, metapopulations, supply-side ecology, and community assembly have all to some degree informed the regulation, management, and prevention of biological invasions. Invasion biology needs to continue to adopt emerging frameworks and paradigms to progress as both a basic and applied science. This need is urgent as the biological invasion problem continues to worsen. The development of metacommunity theory in the last two decades represents a paradigm-shifting approach to community ecology that emphasizes the multi-scale nature of community assembly and biodiversity regulation. Work on metacommunities has demonstrated that even relatively simple processes at local scales are often heavily influenced by regional-scale processes driven primarily by the dispersal of organisms. Often the influence of dispersal interacts with, or even swamps, the influence of local-scale drivers like environmental conditions and species interactions. An emphasis on dispersal and a focus on multi-scale processes enable metacommunity theory to contribute strongly to the advancement of invasion biology. Propagule pressure of invaders has been identified as one of the most important drivers facilitating invasion, so the metacommunity concept, designed to address how dispersal-driven dynamics affect community structure, can directly address many of the central questions of invasion biology. Here we revisit many of the important concepts and paradigms of biological invasions—propagule pressure, biotic resistance, enemy release, functional traits, neonative species, human-assisted transport,—and view those concepts through the lens of metacommunity theory. In doing so, we accomplish several goals. First, we show that work on metacommunities has generated multiple predictions, models, and the tools that can be directly applied to invasion scenarios. Among these predictions is that invasibility of a community should decrease with both local controls on community assembly, and the dispersal rates of native species. Second, we demonstrate that framing biological invasions in metacommunity terms actually unifies several seemingly disparate concepts central to invasion biology. Finally, we recommend several courses of action for the control and management of invasive species that emerge from applying the concepts of metacommunity theory.
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48
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Stothart MR, Greuel RJ, Gavriliuc S, Henry A, Wilson AJ, McLoughlin PD, Poissant J. Bacterial dispersal and drift drive microbiome diversity patterns within a population of feral hindgut fermenters. Mol Ecol 2020; 30:555-571. [PMID: 33231332 DOI: 10.1111/mec.15747] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 11/16/2020] [Accepted: 11/17/2020] [Indexed: 12/15/2022]
Abstract
Studies of microbiome variation in wildlife often emphasize host physiology and diet as proximate selective pressures acting on host-associated microbiota. In contrast, microbial dispersal and ecological drift are more rarely considered. Using amplicon sequencing, we characterized the bacterial microbiome of adult female (n = 86) Sable Island horses (Nova Scotia, Canada) as part of a detailed individual-based study of this feral population. Using data on sampling date, horse location, age, parental status, and local habitat variables, we contrasted the ability of spatiotemporal, life history, and environmental factors to explain microbiome diversity among Sable Island horses. We extended inferences made from these analyses with both phylogeny-informed and phylogeny-independent null modelling approaches to identify deviations from stochastic expectations. Phylogeny-informed diversity measures were correlated with spatial and local habitat variables, but null modelling results suggested that heterogeneity in ecological drift, rather than differential selective pressures acting on the microbiome, was responsible for these correlations. Conversely, phylogeny-independent diversity measures were best explained by host spatial and social structure, suggesting that taxonomic composition of the microbiome was shaped most strongly by bacterial dispersal. Parental status was important but correlated with measures of β-dispersion rather than β-diversity (mares without foals had lower alpha diversity and more variable microbiomes than mares with foals). Our results suggest that between host microbiome variation within the Sable Island horse population is driven more strongly by bacterial dispersal and ecological drift than by differential selective pressures. These results emphasize the need to consider alternative ecological processes in the study of microbiomes.
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Affiliation(s)
- Mason R Stothart
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Ruth J Greuel
- Department of Biology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Stefan Gavriliuc
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Astrid Henry
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Alastair J Wilson
- Centre for Ecology and Conservation, University of Exeter, Penryn, UK
| | | | - Jocelyn Poissant
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
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49
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Organism body size structures the soil microbial and nematode community assembly at a continental and global scale. Nat Commun 2020; 11:6406. [PMID: 33335105 PMCID: PMC7747634 DOI: 10.1038/s41467-020-20271-4] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 11/18/2020] [Indexed: 11/22/2022] Open
Abstract
Body size is a key life-history trait that influences community assembly by affecting how ecological processes operate at the organism level. However, the extent to which the relative influences of ecological processes mediate the assembly of differentially sized soil organisms is still unknown. Here, we investigate the community assembly of differentially sized soil microorganisms and microfauna using a continental-scale sampling effort combined with a global-scale meta-analysis. Our results reveal a general relationship between organism body size and the stochastic-deterministic balance operating on community assembly. The smallest microorganisms (bacteria) are relatively more influenced by dispersal-based stochastic processes, while larger ones (fungi, protists and nematodes) are more structured by selection-based deterministic processes. This study elucidates a significant and consistent relationship between an organism life-history trait and how distinct ecological processes operate in mediating their respective community assemblages, thus providing a better understanding of the mechanisms supporting soil biodiversity. It is unclear whether body size affects community assembly mechanisms of soil biota. Here, the authors analyse soil microbial and nematode communities sampled along a 4000-km transect in China and global soil microbiome data to show that bacterial assembly is governed by high dispersal, whereas larger taxa are more influenced by deterministic processes.
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50
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Huber P, Metz S, Unrein F, Mayora G, Sarmento H, Devercelli M. Environmental heterogeneity determines the ecological processes that govern bacterial metacommunity assembly in a floodplain river system. THE ISME JOURNAL 2020; 14:2951-2966. [PMID: 32719401 PMCID: PMC7784992 DOI: 10.1038/s41396-020-0723-2] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 06/26/2020] [Accepted: 07/16/2020] [Indexed: 01/09/2023]
Abstract
How diversity is structured has been a central goal of microbial ecology. In freshwater ecosystems, selection has been found to be the main driver shaping bacterial communities. However, its relative importance compared with other processes (dispersal, drift, diversification) may depend on spatial heterogeneity and the dispersal rates within a metacommunity. Still, a decrease in the role of selection is expected with increasing dispersal homogenization. Here, we investigate the main ecological processes modulating bacterial assembly in contrasting scenarios of environmental heterogeneity. We carried out a spatiotemporal survey in the floodplain system of the Paraná River. The bacterioplankton metacommunity was studied using both statistical inferences based on phylogenetic and taxa turnover as well as co-occurrence networks. We found that selection was the main process determining community assembly even at both extremes of environmental heterogeneity and homogeneity, challenging the general view that the strength of selection is weakened due to dispersal homogenization. The ecological processes acting on the community also determined the connectedness of bacterial networks associations. Heterogeneous selection promoted more interconnected networks increasing β-diversity. Finally, spatiotemporal heterogeneity was an important factor determining the number and identity of the most highly connected taxa in the system. Integrating all these empirical evidences, we propose a new conceptual model that elucidates how the environmental heterogeneity determines the action of the ecological processes shaping the bacterial metacommunity.
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Affiliation(s)
- Paula Huber
- Instituto Nacional de Limnología (INALI), Consejo Nacional de Investigaciones Científicas y Técnicas - Universidad Nacional del Litoral, (CONICET-UNL), Ciudad Universitaria, Paraje El Pozo, C. P. 3000, Santa Fe, Argentina.
| | - Sebastian Metz
- Instituto Tecnológico de Chascomús (INTECH), UNSAM-CONICET, Intendente Marino Km 8.2, CP 7130, Chascomús, Buenos Aires, Argentina
| | - Fernando Unrein
- Instituto Tecnológico de Chascomús (INTECH), UNSAM-CONICET, Intendente Marino Km 8.2, CP 7130, Chascomús, Buenos Aires, Argentina
| | - Gisela Mayora
- Instituto Nacional de Limnología (INALI), Consejo Nacional de Investigaciones Científicas y Técnicas - Universidad Nacional del Litoral, (CONICET-UNL), Ciudad Universitaria, Paraje El Pozo, C. P. 3000, Santa Fe, Argentina
| | - Hugo Sarmento
- Departamento de Hydrobiologia, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz, São Carlos, São Paulo, 13565-905, Brazil
| | - Melina Devercelli
- Instituto Nacional de Limnología (INALI), Consejo Nacional de Investigaciones Científicas y Técnicas - Universidad Nacional del Litoral, (CONICET-UNL), Ciudad Universitaria, Paraje El Pozo, C. P. 3000, Santa Fe, Argentina
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