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Long-term stability of soil bacterial and fungal community structures revealed in their abundant and rare fractions.

ABSTRACT: Despite the importance of soil microorganisms for ecosystem services, long-term surveys of their communities are largely missing. Using metabarcoding, we assessed temporal dynamics of soil bacterial and fungal communities in three land-use types, i.e., arable land, permanent grassland, and forest, over five years. Soil microbial communities remained relatively stable and differences over time were smaller than those among sites. Temporal variability was highest in arable soils. Indications for consistent shifts in community structure over five years were only detected at one site for bacteria and at two sites for fungi, which provided further support for long-term stability of soil microbial communities. A sliding window analysis was applied to assess the effect of OTU abundance on community structures. Partial communities with decreasing OTU abundances revealed a gradually decreasing structural similarity with entire communities. This contrasted with the steep decline of OTU abundances, as subsets of rare OTUs (<0.01%) revealed correlations of up to 0.97 and 0.81 with the entire bacterial and fungal communities. Finally, 23.4% of bacterial and 19.8% of fungal OTUs were identified as scarce, i.e., neither belonging to site-cores nor correlating to environmental factors, while 67.3% of bacterial and 64.9% of fungal OTUs were identified as rare but not scarce. Our results demonstrate high stability of soil microbial communities in their abundant and rare fractions over five years. This provides a step towards defining site-specific normal operating ranges of soil microbial communities, which is a prerequisite for detecting community shifts that may occur due to changing environmental conditions or anthropogenic activities.

SUBMITTER: Gschwend F

PROVIDER: S-EPMC8456938 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Microbial communities commonly consist of a large number of rare taxa (RT) and few abundant taxa (AT), and it is important to identify the differences of the community assembly processes between RT and AT in response to environmental changes. However, the community assembly processes governing AT and RT in coastal wetland soils along an inundation gradient remain elusive. Here, an in situ mesocosm, with continuous inundation gradients and native mangrove Kandelia obovata or exotic cordgrass Spartina alterniflora, was established to determine the patterns and driving factors of community turnover and assembly processes of AT and RT. We found that RT exhibited a remarkably lower turnover rate than AT, and the niche breadth of RT was significantly narrower than that of AT. In comparison with AT, RT presented stronger phylogenetic signals for ecological preferences across environmental gradients. Null model analyses revealed that RT were more phylogenetically clustered and primarily governed by homogeneous selection, while AT were more overdispersed and dominated by dispersal limitation. Soil water content was the most decisive factor for community turnover and assembly processes of both AT and RT. Structural equation modeling analysis showed that RT were strongly associated with K. obovata biomass rather than S. alterniflora biomass, suggesting a strong relationship between RT and the growth of mangrove K. obovata Overall, our study revealed distinct assembly processes of soil AT and RT communities in coastal wetlands, which is crucial for mechanistic understanding of the establishment and maintenance of soil microbial diversity in coastal wetlands under conditions of global environmental changes.IMPORTANCE Coastal wetlands are one of the important ecosystems that play a crucial role in the regulation of climate change. Rare taxa (RT) exist in one habitat along with abundant taxa (AT). In this study, we found that RT exhibited narrower niche breadth and stronger phylogenetic signals than AT. Null model analyses showed that RT were more phylogenetically clustered and primarily governed by homogeneous selection, while AT were more overdispersed and dominated by dispersal limitation. Revealing the differences in the community assembly processes between AT and RT in coastal wetlands is critical to understand the establishment and maintenance of soil microbial diversity in coastal wetlands with regard to environmental changes.

Project description:Global climate change has emerged as a critical environmental problem. Different types of climate extremes drive soil microbial communities to alternative states, leading to a series of consequences for soil microbial ecosystems and related functions. An effective method is urgently needed for buffering microbial communities to tackle environmental disturbances. Here, we conducted a series of mesocosm experiments in which the organic (NOF) and chemical fertilizer (NCF) long-term-amended soil microbiotas were subjected to environmental disturbances that included drought, flooding, freeze-thaw cycles, and heat. We subsequently tracked the temporal dynamics of rare and abundant bacterial taxa in NOF and NCF treatment soils to assess the efficiencies of organic amendments in recovery of soil microbiome. Our results revealed that freeze-thaw cycles and drought treatments showed weaker effects on bacterial communities than flooding and heat. The turnover between rare and abundant taxa occurred in postdisturbance succession of flooding and heat treatments, indicating that new equilibria were tightly related to the rare taxa in both NCF and NOF treatment soils. The Bayesian fits of modeling for the microbiome recovery process revealed that the stability of abundant taxa in NOF was higher than that in NCF soil. In particular, the NOF treatment soil reduced the divergence from the initial bacterial community after weak perturbations occurred. Together, we demonstrated that long-term organic input is an effective strategy to enhance the thresholds for transition to alternative states via enhancing the stability of abundant bacterial species. These findings provide a basis for the sustainable development of agricultural ecosystems in response to changing climates. IMPORTANCE Different climate extremes are expected to be a major threat to crop production, and the soil microbiome has been known to play a crucial role in agricultural ecosystems. In recent years, we have known that organic amendments are an effective method for optimizing the composition and functioning of the soil microbial community and maintaining the health of the soil ecosystem. However, the effects of organic fertilization on buffering bacterial communities against environmental disturbances and the underlying mechanisms are still unclear. We conducted a series of mesocosm experiments and showed that organic fertilizers had additional capacities in promoting the soil microbiome to withstand climate change effects. Our study provides both mechanistic insights as well as a direct guide for the sustainable development of agricultural ecosystems in response to climate change.

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Long-term stability of soil bacterial and fungal community structures revealed in their abundant and rare fractions.

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