Conservation tillage and moderate nitrogen application changed the composition, assembly pattern and interaction network of abundant and rare microbial community on straw surface

Zhang, Houping; Zhu, Yuanpeng; Yu, Claire; Li, Yüze; Long, M. I. E.; Li, Xiao Wei; Liao, Yuncheng; Wang, Weiyan; Wen, Xiaoxia

doi:10.1016/j.apsoil.2023.105060

Cited by 4 publications

(2 citation statements)

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“…In this study, OTUs were classified, after combining data from both sampling dates, into four categories according to their relative abundance, as proposed by Liu et al . ( 55 ), used in subsequent works ( 24 – 27 , 56 , 60 ) and described in Fig. S5: (i) always-rare taxa, with an abundance < 0.01% in all samples; (ii) conditionally rare taxa, with an abundance < 1% in all samples and <0.01% in some samples (maximum 33% of samples); (iii) moderate taxa, with an abundance < 1% and >0.01% in all samples; and (iv) dominant taxa, with an abundance ≥ 1% of all sequences in all samples or that fluctuates strongly, i.e.…”

Section: Methodsmentioning

confidence: 99%

“…Most often, this has been done with dominant microorganisms or entire communities, but in recent years, the functional importance of less prevalent taxa has been increasingly recognized ( 23 ). This led to the formal definition of two types of rare taxa, namely the always-rare taxa (i.e., with very small relative abundance in all samples) and the conditionally rare taxa (i.e., with a relative abundance that is low in some samples and very low in others) ( 24 – 26 ). Indeed, members of the rare biosphere can be metabolically active and contribute significantly to ecosystem functioning ( 23 , 27 ).…”

Section: Introductionmentioning

confidence: 99%

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Stochastic and deterministic assembly processes of microbial communities in relation to natural attenuation of black stains in Lascaux Cave

Bontemps,

Moënne-Loccoz,

Hugoni

2024

mSystems

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Community assembly processes are complex and understanding them represents a challenge in microbial ecology. Here, we used Lascaux Cave as a stable, confined environment to quantify the importance of stochastic vs deterministic processes during microbial community dynamics across the three domains of life in relation to an anthropogenic disturbance that had resulted in the side-by-side occurrence of a resistant community (unstained limestone), an impacted community (present in black stains), and a resilient community (attenuated stains). Metabarcoding data showed that the microbial communities of attenuated stains, black stains, and unstained surfaces differed, with attenuated stains being in an intermediate position. We found four scenarios to explain community response to disturbance in stable conditions for the three domains of life. Specifically, we proposed the existence of a fourth, not-documented yet scenario that concerns the always-rare microbial taxa, where stochastic processes predominate even after disturbance but are replaced by deterministic processes during post-disturbance recovery. This suggests a major role of always-rare taxa in resilience, perhaps because they might provide key functions required for ecosystem recovery. IMPORTANCE The importance of stochastic vs deterministic processes in cave microbial ecology has been a neglected topic so far, and this work provided an opportunity to do so in a context related to the dynamics of black-stain alterations in Lascaux, a UNESCO Paleolithic cave. Of particular significance was the discovery of a novel scenario for always-rare microbial taxa in relation to disturbance, in which stochastic processes are replaced later by deterministic processes during post-disturbance recovery, i.e., during attenuation of black stains.

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