The importance of conditionally rare taxa for the assembly and interaction of fungal communities in mangrove sediments

Zuo, Yaqiang; Zeng, Runying; Tian, Chunmiao; Wang, Jianxin; Qu, Wu

doi:10.1007/s00253-022-11949-4

Cited by 8 publications

(4 citation statements)

References 73 publications

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“…In all the networks, the proportion of positive correlation was higher than the negative correlation, which reveals that positive effects (i.e., reciprocity and/or homology, where two species exchange metabolites in favor of both) were more important than negative effects (i.e., predator–prey relationships, host–parasite relationships, and/or competition between microbes; Chen and Wen, 2021 ). This is similar to the result of global ocean plankton interactions conducted by the Tara Oceans Project ( Lima-Mendez et al, 2015 ) and fungal investigation in mangroves ( Zhang et al, 2021 ; Zuo et al, 2022 ), indicating that fungi tend to benefit each other in these marine environments.…”

Section: Discussionsupporting

confidence: 82%

“…The environmental DNA metabarcoding technology typically includes the 18S rRNA ( Zuo et al, 2022 ), ITS ( Yu et al, 2022 ), and 16S rRNA ( Huang Y. et al, 2022 ) amplicons by using special primers. This technology has been widely used in studies on the assembly mechanisms of bio-communities with the development of high-throughput sequencing.…”

Section: Introductionmentioning

confidence: 99%

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Structure and assembly process of fungal communities in the Yangtze River Estuary

Qu,

Zuo,

Zhang

et al. 2024

Front. Microbiol.

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Marine fungi are essential for the ecological function of estuarine ecosystems. However, limited studies have reported on the structure and assembly pattern of the fungal communities in estuaries. The purpose of this study is to reveal the structure and the ecological process of the fungal community in the Yangtze River Estuary (YRE) by using the amplicon sequencing method. Phyla of Ascomycota, Basidiomycota, and Chytridiomycota were dominant in the seawater and sediment samples from YRE. The null model analysis, community-neutral community model (NCM), and phylogenetic normalized stochasticity ratio (pNST) showed that the stochastic process dominated the assembly of fungal communities in YRE. Drift and homogeneous dispersal were the predominant stochastic processes for the fungal community assembly in seawater and sediment samples, respectively. The co-occurrence network analysis showed that fungal communities were more complex and closely connected in the sediment than in the seawater samples. Phyla Ascomycota, Basidiomycota, and Mucoromycota were the potential keystone taxa in the network. These findings demonstrated the importance of stochastic processes for the fungal community assembly, thereby widening our knowledge of the community structure and dynamics of fungi for future study and utilization in the YRE ecosystem.

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Section: Discussionsupporting

confidence: 82%

Section: Introductionmentioning

confidence: 99%

Structure and assembly process of fungal communities in the Yangtze River Estuary

Qu,

Zuo,

Zhang

et al. 2024

Front. Microbiol.

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“…Studies relating the potential ecological risk index (RI), the most commonly used method for assessing PTE contamination in soils, to microbial structure showed that Planctomycetes were enriched with increasing RI 55 . Rare taxa, including Planctomycetes , play important roles in metal(loid) metabolism and functional diversity 56 and can respond rapidly to maintain community stability when faced with PTE stress 57 . Planctomycetes can secrete extracellular polymeric substances that may have helped colonize halloysite nanotubes in the enriched soil.…”

Section: Resultsmentioning

confidence: 99%

Effect of freeze–thaw manipulation on phytostabilization of industrially contaminated soil with halloysite nanotubes

Radziemska,

Gusiatin,

Cydzik-Kwiatkowska

et al. 2023

Sci Rep

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The latest trends in improving the performance properties of soils contaminated with potentially toxic elements (PTEs) relate to the possibility of using raw additives, including halloysite nanotubes (HNTs) due to eco-friendliness, and inexpensiveness. Lolium perenne L. was cultivated for 52 days in a greenhouse and then moved to a freezing–thawing chamber for 64 days. HNT addition into PTE-contaminated soil cultivated with grass under freezing–thawing conditions (FTC) was tested to demonstrate PTE immobilization during phytostabilization. The relative yields increased by 47% in HNT-enriched soil in a greenhouse, while under FTC decreased by 17% compared to the adequate greenhouse series. The higher PTE accumulation in roots in HNT presence was evident both in greenhouse and chamber conditions. (Cr/Cd and Cu)-relative contents were reduced in soil HNT-enriched-not-FTC-exposed, while (Cr and Cu) in HNT-enriched-FTC-exposed. PTE-immobilization was discernible by (Cd/Cr/Pb and Zn)-redistribution into the reducible fraction and (Cu/Ni and Zn) into the residual fraction in soil HNT-enriched-not-FTC-exposed. FTC and HNT facilitated transformation to the residual fraction mainly for Pb. Based on PTE-distribution patterns and redistribution indexes, HNT’s role in increasing PTE stability in soils not-FTC-exposed is more pronounced than in FTC-exposed compared to the adequate series. Sphingomonas, Acidobacterium, and Mycobacterium appeared in all soils. HNTs mitigated FTC’s negative effect on microbial diversity and increased Planctomycetia abundance.

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“…These results indicate that rare taxa play vital roles in metal(loid) metabolisms and functional diversity ( Rocca et al, 2020 ). Rare taxa can also rapidly respond to maintain community stability when faced with HMs stress ( Zuo et al, 2022 ). Planctomycetes can detoxify HMs by secreting extracellular polymeric substances ( Zhang et al, 2021 ).…”

Section: Discussionmentioning

confidence: 99%

Structural and functional characteristics of soil microbial communities in response to different ecological risk levels of heavy metals

Chen

Zhang

et al. 2022

Front. Microbiol.

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ObjectiveThe potential ecological risk index (RI) is the most commonly used method to assess heavy metals (HMs) contamination in soils. However, studies have focused on the response of soil microorganisms to different concentrations, whereas little is known about the responses of the microbial community structures and functions to HMs at different RI levels.MethodsHere, we conducted soil microcosms with low (L), medium (M) and high (H) RI levels, depending on the Pb and Cd concentrations, were conducted. The original soil was used as the control (CK). High-throughput sequencing, qPCR, and Biolog plate approaches were applied to investigate the microbial community structures, abundance, diversity, metabolic capacity, functional genes, and community assembly processes.ResultThe abundance and alpha diversity indices for the bacteria at different RI levels were significantly lower than those of the CK. Meanwhile, the abundance and ACE index for the fungi increased significantly with RI levels. Acidobacteria, Basidiomycota and Planctomycetes were enriched as the RI level increased. Keystone taxa and co-occurrence pattern analysis showed that rare taxa play a vital role in the stability and function of the microbial community at different RI levels. Network analysis indicates that not only did the complexity and vulnerability of microbial community decrease as risk levels increased, but that the lowest number of keystone taxa was found at the H level. However, the microbial community showed enhanced intraspecific cooperation to adapt to the HMs stress. The Biolog plate data suggested that the average well color development (AWCD) reduced significantly with RI levels in bacteria, whereas the fungal AWCD was dramatically reduced only at the H level. The functional diversity indices and gene abundance for the microorganisms at the H level were significantly lower than those the CK. In addition, microbial community assembly tended to be more stochastic with an increase in RI levels.ConclusionOur results provide new insight into the ecological impacts of HMs on the soil microbiome at different risk levels, and will aid in future risk assessments for Pb and Cd contamination.

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The importance of conditionally rare taxa for the assembly and interaction of fungal communities in mangrove sediments

Cited by 8 publications

References 73 publications

Structure and assembly process of fungal communities in the Yangtze River Estuary

Structure and assembly process of fungal communities in the Yangtze River Estuary

Effect of freeze–thaw manipulation on phytostabilization of industrially contaminated soil with halloysite nanotubes

Structural and functional characteristics of soil microbial communities in response to different ecological risk levels of heavy metals

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