Deterministic processes dominate soil microbial community assembly in subalpine coniferous forests on the Loess Plateau

Zhao, Pengyu; Bao, Jiabing; Wang, Xue; Liu, Yi; Li, Cui; Chai, Bo

doi:10.7717/peerj.6746

Cited by 23 publications

(14 citation statements)

References 51 publications

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“…In general, the phylogenetic diversity of sampled lake communities allows, in contrast to solely abundance-based diversity metrics, the incorporation of historical and evolutionary components of community structure [28] helping to explain current spatial patterns. We used the net relatedness index (NRI) to infer whether co-occurring sequence types within two specific diatom genera in within-lake locations differed in observed and expected mean phylogenetic diversity [30].…”

Section: Phylogenetic Intra-lake Diversity and Its Relation To Lake Wmentioning

confidence: 99%

“…This signal is interpreted as environmental filtering, which arises from the adaptation of taxa to specific niche conditions. Environmental filtering has been reported for microbial communities [28,78,79], however patterns of clustering of closely-related sequence types might also result from differential dispersal or adaptive radiation events [78]. Adaptive radiation is simply defined as the divergence of closely related taxa into ecologically distinct lineages [80].…”

Section: Phylogenetic Intra-lake Diversity and Its Relation To Lake Wmentioning

confidence: 99%

“…In general, genetic and morphological investigations of diatoms from water or sediment samples show a good overlap between the overall taxa composition, although genetic studies show stronger differences in the relative abundance of sequence reads per sample and indicate higher diversity as well as assigning taxa to a higher taxonomic level depending on the completeness of the reference database [22,24,27]. Besides retrieving taxonomic community compositions by metabarcoding, phylogenetically informative genetic markers also provide an estimation of the phylogenetic diversity [28], which is limited in short barcodes but can be sufficient to display phylogenetic patterns within genera [29]. In general, phylogenetic diversity analyses allow the assessment of whether communities are phylogenetically clustered, which is mostly caused by environmental filtering or if they are phylogenetically over dispersed, which can be a result of biotic interactions [30,31].…”

Section: Introductionmentioning

confidence: 99%

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Lake-depth related pattern of genetic and morphological diatom diversity in boreal Lake Bolshoe Toko, Eastern Siberia

et al. 2020

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Large, old and heterogenous lake systems are valuable sources of biodiversity. The analysis of current spatial variability within such lakes increases our understanding of the origin and establishment of biodiversity. The environmental sensitivity and the high taxonomic richness of diatoms make them ideal organisms to investigate intra-lake variability. We investigated modern intra-lake diatom diversity in the large and old sub-arctic Lake Bolshoe Toko in Siberia. Our study uses diatom-specific metabarcoding, applying a short rbcL marker combined with next-generation sequencing and morphological identification to analyse the diatom diversity in modern sediment samples of 17 intra-lake sites. We analysed abundance-based compositional taxonomic diversity and generic phylogenetic diversity to investigate the relationship of diatom diversity changes with water depth. The two approaches show differences in taxonomic identification and alpha diversity, revealing a generally higher diversity with the genetic approach. With respect to beta diversity and ordination analyses, both approaches result in similar patterns. Water depth or related lake environmental conditions are significant factors influencing intra-lake diatom patterns, showing many significant negative correlations between alpha and beta diversity and water depth. Further, one near-shore and two lagoon lake sites characterized by low (0-10m) and medium (10-30m) water depth are unusual with unique taxonomic compositions. At deeper (>30m) water sites we identified strongest phylogenetic clustering in Aulacoseira, but generally much less in Staurosira, which supports that water depth is a strong environmental filter on the Aulacoseira communities. Our study demonstrates the utility of combining analyses of genetic and morphological as well as phylogenetic diversity to decipher compositional and generic phylogenetic patterns, which are relevant in understanding intra-lake heterogeneity as a source of biodiversity in the sub-arctic glacial Lake Bolshoe Toko.

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Section: Phylogenetic Intra-lake Diversity and Its Relation To Lake Wmentioning

confidence: 99%

Section: Phylogenetic Intra-lake Diversity and Its Relation To Lake Wmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Lake-depth related pattern of genetic and morphological diatom diversity in boreal Lake Bolshoe Toko, Eastern Siberia

et al. 2020

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“…In the last few years, the study of community assembly in natural ecosystems has shifted its focus from a descriptive “who is there?” approach, to elucidating the relative contribution of stochastic vs. deterministic processes on community assembly (e.g. [97] , [98] , [99] ). Both approaches are indeed pertinent to increase our understanding of the particular ecosystem under investigation.…”

Section: Experimental Systemsmentioning

confidence: 99%

Experimental and computational approaches to unravel microbial community assembly

Cárcer

2020

Computational and Structural Biotechnology Journal

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Microbial communities have a preponderant role in the life support processes of our common home planet Earth. These extremely diverse communities drive global biogeochemical cycles, and develop intimate relationships with most multicellular organisms, with a significant impact on their fitness. Our understanding of their composition and function has enjoyed a significant thrust during the last decade thanks to the rise of high-throughput sequencing technologies. Intriguingly, the diversity patterns observed in nature point to the possible existence of fundamental community assembly rules. Unfortunately, these rules are still poorly understood, despite the fact that their knowledge could spur a scientific, technological, and economic revolution, impacting, for instance, agricultural, environmental, and health-related practices. In this minireview, I recapitulate the most important wet lab techniques and computational approaches currently employed in the study of microbial community assembly, and briefly discuss various experimental designs. Most of these approaches and considerations are also relevant to the study of microbial microevolution, as it has been shown that it can occur in ecological relevant timescales. Moreover, I provide a succinct review of various recent studies, chosen based on the diversity of ecological concepts addressed, experimental designs, and choice of wet lab and computational techniques. This piece aims to serve as a primer to those new to the field, as well as a source of new ideas to the more experienced researchers.

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“…Certainly, both deterministic processes (environmental selection) and stochastic processes (ecological drift and dispersal) influence fungal community assembly ( Li et al, 2019 ). However, at a fine scale, the limitation of fungal community assembly is mainly due to deterministic processes ( Xun et al, 2019 ; Zhao et al, 2019 ). Fungi present high abundance in soil microbial community, and they can be classified into different functional groups according to the trophic mode ( Hawksworth and Lucking, 2017 ).…”

Section: Introductionmentioning

confidence: 99%

Short-Term Thinning Influences the Rhizosphere Fungal Community Assembly of Pinus massoniana by Altering the Understory Vegetation Diversity

Liu

Yin

et al. 2021

Front. Microbiol.

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Thinning can significantly promote forest productivity and ecological function. Rhizosphere fungi play an indispensable role in regulating nutrient cycling between plants and the environment, and their community composition can positively respond to anthropogenic disturbance. However, the initial effects of thinning on rhizosphere fungal community assembly have seldom been reported. In this research, we studied the alterations in the rhizosphere fungal communities of 29-year-old Pinus massoniana in East Sichuan 2 years after three different thinning intensity treatments. In addition, the responses of fungal community and functional group composition to alterations in understory vegetation and soil physiochemical properties were analyzed. Three thinning intensities were set, which were 0 (CK), 25% (LIT), and 50% (HIT), respectively. The results suggested that the richness index and Shannon index of understory vegetation increased significantly with increasing thinning intensity. The alpha diversity indices of rhizosphere fungal community and soil physiochemical properties did not show significant differences among the three treatments. The relative abundances of 17 fungal indicator species varied regularly with increasing thinning intensity, and most of them belong to Hypocreales and Eurotiales, indicating that these two orders were potential indicators for different thinning treatments. Rhizosphere fungal community assembly was determined by deterministic process, and it was driven by the diversity of understory vegetation in the initial stage of thinning. The Simpson index and Pielou index of herbs were useful measures of the main environmental factors driving the differentiation of fungal functional group composition. Based on network analysis, thinning resulted in distinct co-occurrence patterns of rhizosphere fungal functional groups. This research elucidates the initial role of thinning in rhizosphere fungal community assembly of P. massoniana and has practical significance for the functional restoration and protection of local forest ecosystem.

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Deterministic processes dominate soil microbial community assembly in subalpine coniferous forests on the Loess Plateau

Cited by 23 publications

References 51 publications

Lake-depth related pattern of genetic and morphological diatom diversity in boreal Lake Bolshoe Toko, Eastern Siberia

Lake-depth related pattern of genetic and morphological diatom diversity in boreal Lake Bolshoe Toko, Eastern Siberia

Experimental and computational approaches to unravel microbial community assembly

Short-Term Thinning Influences the Rhizosphere Fungal Community Assembly of Pinus massoniana by Altering the Understory Vegetation Diversity

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