Evaluating community–environment relationships along fine to broad taxonomic resolutions reveals evolutionary forces underlying community assembly

Lu, Hsiao Pei; Yeh, Yi Chun; Sastri, Akash R.; Shiah, Fuh Kwo; Gong, Gwo-Ching; Hsieh, Chih‐hao

doi:10.1038/ismej.2016.78

Cited by 34 publications

(34 citation statements)

References 78 publications

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“…One main peak within 1800-3000 m elevation ranges was more obvious at class than species level of bacteria. This is because broader taxonomic classification may balance the distribution uncertainty associated with finer taxonomic resolution and strengthen the phylogenetic conservatism [80]. Detrended correspondence analysis (DCA) plots of the composition of plants, bacteria, and ecosystem functions.…”

Section: Resultsmentioning

confidence: 99%

Mountain biodiversity and ecosystem functions: interplay between geology and contemporary environments

Wang

Sun

et al. 2020

The ISME Journal

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Although biodiversity and ecosystem functions are strongly shaped by contemporary environments, such as climate and local biotic and abiotic attributes, relatively little is known about how they depend on long-term geological processes. Here, along a 3000-m elevational gradient with tectonic faults on the Tibetan Plateau (that is, Galongla Mountain in Medog County, China), we study the joint effects of geological and contemporary environments on biological communities, such as the diversity and community composition of plants and soil bacteria, and ecosystem functions. We find that these biological communities and ecosystem functions generally show consistent elevational breakpoints at 2000-2800 m, which coincide with Indus-Yalu suture zone fault and are similar to the elevational breakpoints of soil bacteria on another mountain range 1000 km away. Mean annual temperature, soil pH and moisture are the primary contemporary determinants of biodiversity and ecosystem functions, which support previous findings. However, compared with the models excluding geological processes, inclusion of geological effects, such as parent rock and weathering, increases 67.9 and 35.9% of the explained variations in plant and bacterial communities, respectively. Such inclusion increases 27.6% of the explained variations in ecosystem functions. The geological processes thus provide additional links to ecosystem properties, which are prominent but show divergent effects on biodiversity and ecosystem functions: parent rock and weathering exert considerable direct effects on biodiversity, whereas indirectly influence ecosystem functions via interactions with biodiversity and contemporary environments. Thus, the integration of geological processes with environmental gradients could enhance our understanding of biodiversity and, ultimately, ecosystem functioning across different climatic zones.

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Section: Resultsmentioning

confidence: 99%

Mountain biodiversity and ecosystem functions: interplay between geology and contemporary environments

Wang

Sun

et al. 2020

The ISME Journal

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“…We evaluated the ability of the morphological and metabarcoding approaches to assess the relationship between physical-chemical characteristics and macroinvertebrate community composition. Community-environment relationships can be quantified by explained variance from a redundancy analysis (Lu et al, 2016). Both models were significant, but the metabarcoding data set explained a relatively higher percentage of variation between the environmental variables and community composition.…”

Section: Discussionmentioning

confidence: 99%

Comparison of DNA metabarcoding and morphological identification for stream macroinvertebrate biodiversity assessment and monitoring

Serrana

Miyake

Gamboa

et al. 2018

Preprint

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10Conventional morphology-based identification is commonly used for routine assessment of freshwater 11 ecosystems. However, cost and time efficient techniques such as high-throughput sequencing (HTS) based 12 approaches may resolve the constraints encountered in conducting morphology-based surveys. Here, we 13 characterized stream macroinvertebrate species diversity and community composition via metabarcoding and 14 morphological analysis from environmental samples collected from the Shigenobu River Basin in Ehime 15 Prefecture, Japan. We compared diversity metrics and assessed both approaches' ability to evaluate the 16 relationship between macroinvertebrate community and environmental variables. In total, we morphologically 17 identified 45 taxa (3 families, six subfamilies, 31 genera, and five species) from 8,276 collected individuals 18 from ten study sites. We detected 44 species by metabarcoding, with 35 species collapsed into 11 groups 19 matching the morphologically identified taxa. A significant positive correlation between logged depth (number 20 of HTS reads) and abundance of morphological taxa was observed, which implied that quantitative data can 21 be used for subsequent analyses. Relatively higher estimates of alpha diversity were calculated from the 22 metabarcoding data in comparison to morphology-based data. However, beta diversity estimates between 23 metabarcoding and morphology data based on both incidence and abundance-based matrices were 24 correlated proving that community differences between sampling sites were preserved in the molecular data. 25 Also, both models were significant, but metabarcoding data (93%) explained a relatively higher percentage of 26 variation in the relationship between community composition and the environmental variables than 27 morphological data (91%). Overall, we present both the feasibility and limitations of HTS-driven estimations 28 of taxonomic richness, community composition, and diversity metrics, and that metabarcoding was proven 29 comparable and more sensitive against morphology-based analysis for stream macroinvertebrate biodiversity 30 assessment and environmental monitoring. 31 32 community composition 33 42 al., 2016). 43 Conventional morphological analysis is most commonly used in routine monitoring programs evaluating 44 environmental quality changes. However, this is not only time consuming but has serious issues with accuracy, 45 and consistency in the level of taxonomic identification that highly depends on taxonomic expertise (Hajibabaei 46 et al., 2011). Specifically, small organisms such as the larval stages of stream macroinvertebrates frequently 47 used for river biomonitoring are often difficult or impossible to identify at finer taxonomic resolution (e.g., 48 species level) (Sweeny et al., 2011). A promising alternative approach is DNA metabarcoding -a combination 49 of amplicon-based high-throughput sequencing (HTS) analysis and DNA taxonomy (Hebert et al., 2003). High-50 throughput amplicon sequencing can process large number ...

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“…In the case of aquatic bacteria, there are many distinct biogeographical patterns within phyla in freshwater lakes (e.g., Newton, Jones, Eiler, McMahon, & Bertilsson, ), and spatial or temporal separation of phyla and other higher taxonomic ranks across freshwater lakes and many other environments. The idea that such biogeographical patterns may reflect ecological coherence at higher taxonomic resolution levels is also partly supported (Abarenkov et al, ; Lennon, Aanderud, Lehmkuhl, & Schoolmaster, ; Lindström & Langenheder, ; Lu et al, ; Philippot et al, ).…”

Section: Introductionmentioning

confidence: 95%

Elevational patterns and hierarchical determinants of biodiversity across microbial taxonomic scales

et al. 2019

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Microbial biogeography is gaining increasing attention due to recent molecular methodological advance. However, the diversity patterns and their environmental determinants across taxonomic scales are still poorly studied. By sampling along an extensive elevational gradient in subarctic ponds of Finland and Norway, we examined the diversity patterns of aquatic bacteria and fungi from whole community to individual taxa across taxonomic coverage and taxonomic resolutions. We further quantified cross‐phylum congruence in multiple biodiversity metrics and evaluated the relative importance of climate, catchment and local pond variables as the hierarchical drivers of biodiversity across taxonomic scales. Bacterial community showed significantly decreasing elevational patterns in species richness and evenness, and U‐shaped patterns in local contribution to beta diversity (LCBD). Conversely, no significant species richness and evenness patterns were found for fungal community. Elevational patterns in species richness and LCBD, but not in evenness, were congruent across bacterial phyla. When narrowing down the taxonomic scope towards higher resolutions, bacterial diversity showed weaker and more complex elevational patterns. Taxonomic downscaling also indicated a notable change in the relative importance of biodiversity determinants with stronger local environmental filtering, but decreased importance of climatic variables. This suggested that niche conservatism of temperature preference was phylogenetically deeper than that of water chemistry variables. Our results provide novel perspectives for microbial biogeography and highlight the importance of taxonomic scale dependency and hierarchical drivers when modelling biodiversity and species distribution responses to future climatic scenarios.

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Evaluating community–environment relationships along fine to broad taxonomic resolutions reveals evolutionary forces underlying community assembly

Cited by 34 publications

References 78 publications

Mountain biodiversity and ecosystem functions: interplay between geology and contemporary environments

Mountain biodiversity and ecosystem functions: interplay between geology and contemporary environments

Comparison of DNA metabarcoding and morphological identification for stream macroinvertebrate biodiversity assessment and monitoring

Elevational patterns and hierarchical determinants of biodiversity across microbial taxonomic scales

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