Network analysis and subsequent culturing reveal keystone taxa involved in microbial litter decomposition dynamics

Zheng, Haiping; Yang, Tianjie; Bao, Yanzhuo; He, Ping; Yang, Kun; Mei, Xinlan; Xu, Yangchun; Shen, Qirong; Banerjee, Samiran

doi:10.1016/j.soilbio.2021.108230

Cited by 130 publications

(70 citation statements)

References 90 publications

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“…Of note, other authors have questioned the suitability of network hubs to infer keystone taxa altogether (Banerjee et al 2019a, b;Röttjers and Faust 2019). Predicted network hubs requires experimental validation to uncover their biological importance as keystones (Banerjee et al 2019a, b;Zheng et al 2021). Experimental validation of keystones often involves comparing the effects of removal and/or addition of keystone candidate and other community members (Ze et al 2012;Röttjers and Faust 2019).…”

Section: How To Identify Network Hubs and What Is Their Relevance For Keystone Taxa Inference?mentioning

confidence: 99%

Anti-tick microbiota vaccines: how can this actually work?

et al. 2021

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The main importance of ticks resides in their ability to harbor and transmit microorganisms that cause disease to animals and humans. In addition to pathogens, ticks coexist and interact with symbionts, and commensal bacteria that together form an ecological unit, the tick holobiont. The holobiont is an additional organismal level on which natural selection operates. The components of the tick hologenome, composed of host and microbiome genomes, are complimentary. In agreement with this proposition, antibiotic treatment produces disturbance of the tick-microbiota homeostasis which in turn decreases tick fitness and affects tick-pathogen interactions. Accordingly, we hypothesized that immune targeting of key members of the bacterial community of the tick microbiome by host antibodies could cause microbial dysbiosis with consequences for tick physiology and vector competence. Anti-tick microbiota vaccines were recently introduced as a tool to target the microbiota of vector arthropods by immunizing the vertebrate hosts against live keystone bacteria or tick microbiota bacterial proteins. This tool can also be used to target tick endosymbionts. Decreased abundance of selected keystone bacteria and/or endosymbionts may reshape the structure of tick microbial communities in a predictable manner. This tool can be used to manipulate the tick microbiome against ticks and transmitted pathogens. In this opinion, we explore the possibilities of this methodology for the control of ticks and tick-borne diseases.

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Section: How To Identify Network Hubs and What Is Their Relevance For Keystone Taxa Inference?mentioning

confidence: 99%

Anti-tick microbiota vaccines: how can this actually work?

et al. 2021

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“…However, it must be noted that the key fungi within our network analysis are based on statistical analysis and therefore do not represent real-world relationships among fungal communities, which remain to be verified ( Freilich et al, 2018 ). Therefore, future studies should selectively exclude some key species in verifying the role they play in species interactions and microbial community functions ( Zheng et al, 2021 ).…”

Section: Discussionmentioning

confidence: 99%

Litter Decomposition of Imperata cylindrica in a Copper Tailing Areas With Different Restoration History: Fungal Community Dynamics and Driving Factors

et al. 2021

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Microorganisms drive litter decomposition while maintaining the chemical cycle of ecosystems. We used the dominant vegetation (Imperata cylindrica) in the mining area selected for this study for this experiment to explore fungal community characteristics, key fungal groups, and their associative driving factors during I. cylindrica litter decomposition. Maximum litter C/N values occurred 100days after the commencement of the decomposition experiment during all different recovery years in this copper tailings area. Heavy metals in litter [copper (Cu), zinc (Zn), plumbum (Pb), and cadmium (Cd)] accumulated gradually with decomposition. The dominant fungal phyla observed in the community were Ascomycota and Basidiomycota, while the classes Sordariomycetes and Eurotiomycetes significantly increased as litter decomposition progressed. Degrees of connectivity and interaction between fungal communities were highest during the early litter decomposition stage. Sordariomycetes, Dothideomycetes, and Leotiomycetes all played critical roles in maintaining fungal community relationships. The effect of physicochemical properties and enzyme activities in I. cylindrica litter was significant on the dominant fungi, while driving factors that affected fungal communities differed over different recovery stages. Total nitrogen (TN), heavy metals, pH, and enzyme activities in the little were significantly correlated with fungal community composition. Litter properties throughout the litter decomposition process mainly affected the dynamics of the fungal community structure. The main environmental factors that affected fungal community structure were copper content and pH. Dichotomopilus, Trichoderma, Knufia, Phialophora, Oxyporus, and Monocillium, which all played important roles in litter decomposition, positively correlated with heavy metals, sucrase, and catalase. Finally, results from this study will help us better clarify litter decomposition mechanisms in degraded ecosystems as well as provide a scientific basis for improving species cycling and nutrient transformation efficiency in mining ecosystems.

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“…We generated random networks compare to our networks to test our networks were not random by erdos.renyi.game function in igraph [29]. Microbial taxa that frequently co-occur with other taxa in microbial cooccurrence networks are thought to be ecologically important, so the 10 keystone genera with the highest node degrees of co-occurrence were selected [27,[30][31][32]…”

Section: Discussionmentioning

confidence: 99%

Soil inoculum identity and rate jointly steer microbiomes and plant communities in the field

Han

et al. 2021

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Inoculation with soil from distinctly different ecosystems has been reported to induce directional changes in the plant and soil communities, however, a major question is how specific these inoculations are and whether different inocula collected from a similar ecosystem will also lead to differential ecosystem development at the recipient site. We conducted a soil inoculation field experiment at a degraded grassland with two different soil inocula both from grasslands and used three inoculation depths. We then measured the development of plant and soil communities over a period of three years following soil inoculation. Our results show that soil and plant communities diverged and that these effects were stronger with increasing inoculation amount. Inoculation with upland meadow soil at the recipient site resulted in more complex biotic networks than inoculation with meadow steppe soil. Our experiment highlights that soil inoculation can promote restoration of degraded ecosystems but that the direction and speed of ecosystem development depend on the origin of the inoculum and the amount of inoculum used.

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Network analysis and subsequent culturing reveal keystone taxa involved in microbial litter decomposition dynamics

Cited by 130 publications

References 90 publications

Anti-tick microbiota vaccines: how can this actually work?

Anti-tick microbiota vaccines: how can this actually work?

Litter Decomposition of Imperata cylindrica in a Copper Tailing Areas With Different Restoration History: Fungal Community Dynamics and Driving Factors

Soil inoculum identity and rate jointly steer microbiomes and plant communities in the field

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