Testing the Resource Hypothesis of Species–Area Relationships: Extinction Cannot Work Alone
Abstract
:1. Introduction
2. Materials and Methods
2.1. Preparation of Microbial Seed Solution for Pao Cai
2.2. Preparation of Dry Matter
2.3. Establishment of the Microcosmic System
2.4. Sample Collection and Determination of Environmental Factors
2.5. Microbial Analyses
2.6. Data Analyses
3. Results
3.1. Overview of the Diversity and Extinction Rates of Microbes
3.2. Resources Cannot Shape Microbial SAR
3.3. Resources Do Not Alter the Structure and Complexity of Microbial Interactions Networks in the Microcosm
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
- Arrhenius, O. Species and Area. J. Ecol. 1921, 9, 95–99. [Google Scholar] [CrossRef] [Green Version]
- MacArthur, R.H.; Wilson, E.O. An Equilibrium Theory of Insular Zoogeography. Evolution 1963, 17, 373–387. [Google Scholar] [CrossRef]
- MacArthur, R.H.; Wilson, E.O. The Theory of Island Biogeography; Princeton University Press: Princeton, NJ, USA, 2001; ISBN 9781400881376. [Google Scholar]
- Lomolino, M.V. Ecology’s Most General, yet Protean Pattern: The Species-Area Relationship. J. Biogeogr. 2000, 27, 17–26. [Google Scholar] [CrossRef]
- Matias, M.G.; Gravel, D.; Guilhaumon, F.; Desjardins-Proulx, P.; Loreau, M.; Münkemüller, T.; Mouquet, N. Estimates of Species Extinctions from Species-Area Relationships Strongly Depend on Ecological Context. Ecography 2014, 37, 431–442. [Google Scholar] [CrossRef]
- Preston, F.W. Time and Space and the Variation of Species. Ecology 1960, 41, 611–627. [Google Scholar] [CrossRef]
- Preston, F.W. The Canonical Distribution of Commonness and Rarity: Part II. Ecology 1962, 43, 410–432. [Google Scholar] [CrossRef]
- Simberloff, D. Experimental Zoogeography of Islands: Effects of Island Size. Ecology 1976, 57, 629–648. [Google Scholar] [CrossRef]
- Connor, E.F.; Simberloff, D. The Assembly of Species Communities: Chance or Competition? Ecology 1979, 60, 1132–1140. [Google Scholar] [CrossRef]
- MacArthur, R.H. Patterns of Species Diversity. Biol. Rev. 1965, 40, 510–533. [Google Scholar] [CrossRef]
- Connor, E.F.; McCoy, E.D. Species-Area Relationships. In Encyclopedia of Biodiversity, 2nd ed.; Levin, S.A., Ed.; Elsevier Inc.: Amsterdam, The Netherlands, 2013; pp. 640–650. [Google Scholar]
- Root, R.B. Organization of a Plant-Arthropod Association in Simple and Diverse Habitats: The Fauna of Collards (Brassica Oleracea). Ecol. Monogr. 1973, 43, 95–124. [Google Scholar] [CrossRef]
- Grez, A.A.; González, R.H. Resource Concentration Hypothesis: Effect of Host Plant Patch Size on Density of Herbivorous Insects. Oecologia 1995, 103, 471–474. [Google Scholar] [CrossRef] [PubMed]
- Rhainds, M.; English-Loeb, G. Testing the Resource Concentration Hypothesis with Tarnished Plant Bug on Strawberry: Density of Hosts and Patch Size Influence the Interaction between Abundance of Nymphs and Incidence of Damage. Ecol. Entomol. 2003, 28, 348–358. [Google Scholar] [CrossRef]
- Chase, J.M.; Gooriah, L.; May, F.; Ryberg, W.A.; Schuler, M.S.; Craven, D.; Knight, T.M. A Framework for Disentangling Ecological Mechanisms Underlying the Island Species-Area Relationship. Front. Biogeogr. 2019, 11, e40844. [Google Scholar] [CrossRef] [Green Version]
- MacDonald, Z.G.; Deane, D.C.; He, F.; Lamb, C.T.; Sperling, F.A.H.; Acorn, J.H.; Nielsen, S.E. Distinguishing Effects of Area per Se and Isolation from the Sample-Area Effect for True Islands and Habitat Fragments. Ecography 2021, 44, 1051–1066. [Google Scholar] [CrossRef]
- Hambäck, P.A.; Englund, G. Patch Area, Population Density and the Scaling of Migration Rates: The Resource Concentration Hypothesis Revisited. Ecol. Lett. 2005, 8, 1057–1065. [Google Scholar] [CrossRef]
- Nathan, R. The Challenges of Studying Dispersal. Trends Ecol. Evol. 2001, 16, 481–483. [Google Scholar] [CrossRef]
- Stork, N.E. Re-Assessing Current Extinction Rates. Biodivers. Conserv. 2010, 19, 357–371. [Google Scholar] [CrossRef]
- He, F.; Hubbell, S.P. Species-Area Relationships Always Overestimate Extinction Rates from Habitat Loss. Nature 2011, 473, 368–371. [Google Scholar] [CrossRef]
- Axelsen, J.B.; Roll, U.; Stone, L.; Solow, A. Species-Area Relationships Always Overestimate Extinction Rates from Habitat Loss: Comment. Ecology 2013, 94, 761–763. [Google Scholar] [CrossRef] [Green Version]
- Vellend, M. Empirical Evidence: Ecological Drift and Dispersal. In The Theory of Ecological Communities; Princeton University Press: Princeton, NJ, USA, 2016; pp. 138–157. [Google Scholar]
- Pagel, M. Evolutionary Trees Can’t Reveal Speciation and Extinction Rates. Nature 2020, 580, 461–462. [Google Scholar] [CrossRef]
- Deng, W.; Yuan, C.-L.; Li, N.; Liu, S.-R.; Yang, X.-Y.; Xiao, W. Island Formation History Determines Microbial Species-Area Relationships. Microb. Ecol. 2021. [Google Scholar] [CrossRef] [PubMed]
- Wang, W.; Zhai, S.; Xia, Y.; Wang, H.; Ruan, D.; Zhou, T.; Zhu, Y.; Zhang, H.; Zhang, M.; Ye, H.; et al. Ochratoxin A Induces Liver Inflammation: Involvement of Intestinal Microbiota. Microbiome 2019, 7, 151. [Google Scholar] [CrossRef] [PubMed]
- Manter, D.K.; Vivanco, J.M. Use of the ITS Primers, ITS1F and ITS4, to Characterize Fungal Abundance and Diversity in Mixed-Template Samples by QPCR and Length Heterogeneity Analysis. J. Microbiol. Methods 2007, 71, 7–14. [Google Scholar] [CrossRef] [PubMed]
- Carvalho, J.C.; Cardoso, P.; Borges, P.A.V.; Schmera, D.; Podani, J. Measuring Fractions of Beta Diversity and Their Relationships to Nestedness: A Theoretical and Empirical Comparison of Novel Approaches. Oikos 2013, 122, 825–834. [Google Scholar] [CrossRef] [Green Version]
- Callahan, B.J.; McMurdie, P.J.; Rosen, M.J.; Han, A.W.; Johnson, A.J.A.; Holmes, S.P. DADA2: High-Resolution Sample Inference from Illumina Amplicon Data. Nat. Methods 2016, 13, 581–583. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Bokulich, N.A.; Kaehler, B.D.; Rideout, J.R.; Dillon, M.; Bolyen, E.; Knight, R.; Huttley, G.A.; Gregory Caporaso, J. Optimizing Taxonomic Classification of Marker-Gene Amplicon Sequences with QIIME 2′s Q2-Feature-Classifier Plugin. Microbiome 2018, 6, 90. [Google Scholar] [CrossRef]
- Liu, C.; Cui, Y.; Li, X.; Yao, M. Microeco: An R Package for Data Mining in Microbial Community Ecology. FEMS Microbiol. Ecol. 2021, 97, fiaa255. [Google Scholar] [CrossRef]
- Dixon, P. VEGAN, a Package of R Functions for Community Ecology. J. Veg. Sci. 2003, 14, 927–930. [Google Scholar] [CrossRef]
- Gómez-Rubio, V. ggplot2—Elegant Graphics for Data Analysis. J. Stat. Softw. 2017, 77, 1–3. [Google Scholar] [CrossRef] [Green Version]
- Wen, T.; Xie, P.; Yang, S.; Niu, G.; Liu, X.; Ding, Z.; Xue, C.; Liu, Y.-X.; Shen, Q.; Yuan, J. ggClusterNet: An R Package for Microbiome Network Analysis and Modularity-Based Multiple Network Layouts. iMeta 2022, 1, e32. [Google Scholar] [CrossRef]
- Ao, X.; Yan, J.; Chen, C.; Zhao, J.; Liu, S.; Zhao, K.; Chen, S.; He, L. Isolation and Identification of the Spoilage Microorganisms in Sichuan Homemade Paocai and Their Impact on Quality and Safety. Food Sci. Nutr. 2019, 7, 2939–2947. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Yang, L.; Yang, H.L.; Tu, Z.C.; Wang, X.L. High-Throughput Sequencing of Microbial Community Diversity and Dynamics during Douchi Fermentation. PLoS ONE 2016, 11, e0168166. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Chen, Z.; Kang, J.; Zhang, Y.; Yi, X.; Pang, X.; Li-Byarlay, H.; Gao, X. Differences in the Bacterial Profiles and Physicochemical between Natural and Inoculated Fermentation of Vegetables from Shanxi Province. Ann. Microbiol. 2020, 70, 66. [Google Scholar] [CrossRef]
- Jiang, L.; Xian, S.; Liu, X.; Shen, G.; Zhang, Z.; Hou, X.; Chen, A. Metagenomic Study on Chinese Homemade Paocai: The Effects of Raw Materials and Fermentation Periods on the Microbial Ecology and Volatile Components. Foods 2022, 11, 62. [Google Scholar] [CrossRef]
- An, F.; Sun, H.; Wu, J.; Zhao, C.; Li, T.; Huang, H.; Fang, Q.; Mu, E.; Wu, R. Investigating the Core Microbiota and Its Influencing Factors in Traditional Chinese Pickles. Food Res. Int. 2021, 147, 110543. [Google Scholar] [CrossRef]
- Zhiyi, F.; Weiqin, D.; Xiongbo, L.; Heng, L.; Gong, C.; Qisheng, Z. Effect of Air Exposed Storage on Quality Deterioration and Microbial Succession of Traditional Sichuan Paocai. LWT 2022, 154, 112510. [Google Scholar] [CrossRef]
- Sommers, P.; Porazinska, D.L.; Darcy, J.L.; Gendron, E.M.S.; Vimercati, L.; Solon, A.J.; Schmidt, S.K. Microbial Species–Area Relationships in Antarctic Cryoconite Holes Depend on Productivity. Microorganisms 2020, 8, 1747. [Google Scholar] [CrossRef]
- Long, Z.T.; Mohler, C.L.; Carson, W.P. Extending the Resource Concentration Hypothesis to Plant Communities: Effects of Litter and Herbivores. Ecology 2003, 84, 652–665. [Google Scholar] [CrossRef] [Green Version]
- Macarthur, R.H. Patterns of Communities in the Tropics. Biol. J. Linn. Soc. 1969, 1, 19–30. [Google Scholar] [CrossRef]
- Shen, G.; Yu, M.; Hu, X.S.; Mi, X.; Ren, H.; Sun, I.F.; Ma, K. Species-Area Relationships Explained by the Joint Effects of Dispersal Limitation and Habitat Heterogeneity. Ecology 2009, 90, 3033–3041. [Google Scholar] [CrossRef]
Positive | Negative | |||||
---|---|---|---|---|---|---|
Day | R Square | Slope | p | R Square | Slope | p |
1 | 0.0318 | 0.0258 | 0.7022 | 0.0484 | 0.0756 | 0.6355 |
3 | 0.2959 | 0.1521 | 0.2068 | 0.0514 | −0.1391 | 0.6251 |
6 | 0.1200 | 0.1618 | 0.4466 | 0.0117 | 0.0780 | 0.8171 |
9 | 0.2010 | 0.1754 | 0.3130 | <0.0001 | 0.0043 | 0.9907 |
12 | 0.2008 | −0.1952 | 0.3133 | 0.0714 | −0.1691 | 0.5624 |
15 | 0.0181 | 0.0660 | 0.7734 | 0.0760 | 0.1428 | 0.5496 |
18 | <0.0001 | 0.0002 | 0.9992 | 0.1901 | 0.1485 | 0.3282 |
21 | 0.0218 | 0.0746 | 0.7523 | 0.0148 | −0.0734 | 0.7947 |
24 | 0.1406 | 0.2738 | 0.4072 | 0.3824 | 0.3676 | 0.1388 |
27 | 0.0734 | 0.1107 | 0.5568 | 0.4594 | 0.3844 | 0.0943 |
30 | 0.1059 | 0.2606 | 0.4764 | 0.0071 | 0.0742 | 0.8928 |
Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations. |
© 2022 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
Share and Cite
Deng, W.; Liu, L.-L.; Yu, G.-B.; Li, N.; Yang, X.-Y.; Xiao, W. Testing the Resource Hypothesis of Species–Area Relationships: Extinction Cannot Work Alone. Microorganisms 2022, 10, 1993. https://doi.org/10.3390/microorganisms10101993
Deng W, Liu L-L, Yu G-B, Li N, Yang X-Y, Xiao W. Testing the Resource Hypothesis of Species–Area Relationships: Extinction Cannot Work Alone. Microorganisms. 2022; 10(10):1993. https://doi.org/10.3390/microorganisms10101993
Chicago/Turabian StyleDeng, Wei, Li-Lei Liu, Guo-Bin Yu, Na Li, Xiao-Yan Yang, and Wen Xiao. 2022. "Testing the Resource Hypothesis of Species–Area Relationships: Extinction Cannot Work Alone" Microorganisms 10, no. 10: 1993. https://doi.org/10.3390/microorganisms10101993