Rare microbial taxa as the major drivers of ecosystem multifunctionality in long-term fertilized soils

Chen, Qinglin; Ding, Jing; Zhu, Dong; Hu, Hang‐Wei; Delgado‐Baquerizo, Manuel; Ma, Yuehui; He, Ji‐Zheng; Zhu, Yong‐Guan

doi:10.1016/j.soilbio.2019.107686

Cited by 287 publications

(156 citation statements)

References 49 publications

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“…The composition and diversity of soil microbial community play central roles in ecosystem multifunctionality in drylands and long-term fertilized soils (23)(24)(25). Here, our results suggest that citrus planting significantly alters ecosystem multifunctionality, confirming that land use types have significant impacts on soil ecological functions (48).…”

Section: Citrus Planting Reduces Soil Ecosystem Multifunctionalitysupporting

confidence: 64%

“…To obtain a quantitative multifunctionality index for each site, we first normalized (logtransformation when needed) and standardized each of the 8 functions measured: (1) carbon-related functions, including soil dissolved carbon (DOC), soil labile carbon (LOC), and microbial biomass carbon (MBC); (2) nitrogenrelated functions, including nitrate N (NO3N), ammonium N (NH4N), microbial biomass N (MBN); and (3) phosphorus-related functions, including available P (Olsen P) and microbial biomass P (MBP). These single standardized ecosystem functions were used to calculate a multifunctionality index using a average approach (23)(24)(25)(26)(27). Multifunctionality can provide a direct and easy-to-interpret measure of the ability of different communities to sustain multiple functions simultaneously.…”

Section: Assessment Of Multifunctionalitymentioning

confidence: 99%

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Impacts of Intensive Land use on Soil Biodiversity and Ecosystem Functions in Central China

Zeng¹,

Meitang²,

Delgado‐Baquerizo³

et al. 2020

Preprint

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Background: The impacts of the conversion of natural to agricultural ecosystem on soil biodiversity and ecosystem functions are still disputable. Here, we compared the soil biodiversity (bacteria and fungi) and ecosystem functions of citrus orchards in different stages of succession (5–30 years) with those in adjacent natural ecosystems. Different management strategies were also considered for one of this stage (15 years). Results: The results indicate that changes from natural vegetation land to citrus orchards would lead to reduced soil bacterial diversity, as well as significant declines in multiple ecosystem functions associated with C cycle after 30 years of citrus plantation. However, the functions associated with N and P cycle were enhanced by the plantation. Citrus plantation negatively affected the C cycle by reducing the soil microbial diversity. Reduction in soil bacterial biodiversity was indirectly driven by increased soil acidification resulting from citrus plantation, while wheat straw addition could alleviate the reduction (15-year stage). Compared with natural vegetation, citrus plantation also reduced the relative abundance of multiple phylotypes, including Alphaproteobacteria, Deltaproteobacteria, Subgroup_6, Subgroup_4, Anaerolineae and Bacteroidia. The ecological clusters of soil bacteria and fungi were significantly associated with multiple ecosystem functions, suggesting that citrus planting altered multiple ecosystem functions via ecological clusters. Conclusions: Taken together, our results indicate that soil biodiversity, soil functions and C:N:P coupling are sensitive to the conversion of natural vegetation land to agricultural land, and further suggest that proper management of soil acidification can address some negative impacts of land use conversion on soil biodiversity and functions.

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Section: Citrus Planting Reduces Soil Ecosystem Multifunctionalitysupporting

confidence: 64%

Section: Assessment Of Multifunctionalitymentioning

confidence: 99%

Impacts of Intensive Land use on Soil Biodiversity and Ecosystem Functions in Central China

Zeng¹,

Meitang²,

Delgado‐Baquerizo³

et al. 2020

Preprint

Self Cite

View full text Add to dashboard Cite

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“…Even though Staphylococcus was rare in our study, Staphylococcus might increase in abundance after two weeks because Staphylococcus is an opportunist with fast community succession (Schulfer et al, 2018). Rare microbes in certain favorable conditions may occasionally become dominant (Shade et al, 2014) and more important in providing certain functional traits (Chen et al, 2020).…”

Section: Discussionmentioning

confidence: 63%

“…In fact, the differences among average sequencing library sizes in our study were very small (around 16%). Chen et al (2020) showed that rare microbes might have a more important role in driving multiple functions than do dominant microbes. For instance, rare microbes may in uence and change the composition of gut microbiota after a diet change (Benjamino et al, 2018).…”

Section: Discussionmentioning

confidence: 99%

A network approach to investigating the key microbes and stability of gut microbial communities in a mouse neuropathic pain model

Brandon-Mong

Shaw

Chen

et al. 2020

Preprint

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Background Neuropathic pain is an abnormally increased sensitivity to pain, especially from mechanical or thermal stimuli. To date, the current pharmacological treatments for neuropathic pain are still unsatisfactory. The gut microbiota reportedly plays important roles in inducing neuropathic pain, so probiotics have also been used to treat it. However, the underlying questions around the interactions in and stability of the gut microbiota in a spared nerve injury-induced neuropathic pain model and the key microbes (i.e., the microbes that play critical roles) involved have not been answered. Results Here we show that spared nerve injury-induced neuropathic pain alters gut microbial diversity in mice. We successfully constructed reliable microbial interaction networks using the Metagenomic Microbial Interaction Simulator (MetaMIS) and analyzed these networks based on 177,147 simulations. Interestingly, at a higher resolution, our results showed that spared nerve injury-induced neuropathic pain altered both the stability of the microbial community and the key microbes in a gut micro-ecosystem. Oscillospira, which was classified as a low-abundance and core microbe, was identified as the key microbe in the Sham group, whereas Staphylococcus, classified as a rare and non-core microbe, was identified as the key microbe in the spared nerve injury-induced neuropathic pain group. Conclusions In summary, our results provide novel experimental evidence that spared nerve injury-induced neuropathic pain reshapes gut microbial diversity, and alters the stability and key microbes in the gut.

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“…This can lead to a skewed abundance distribution in a local microbial community, with relatively few dominant and a large number of rare species (alternatively known as a "rare biosphere") [17,19,20]. Previous studies have reported that rare and abundant species often show different distribution patterns and functional traits [21][22][23]. Therefore, disentangling the biogeography and community assembly of rare and abundant microbial taxa is essential for understanding microbedriven ecosystem processes and functions.…”

Section: Introductionmentioning

confidence: 99%

Stronger Environmental Adaption of Abundant than Rare Microbes in Wetland Soils from the Qinghai-Tibet Plateau

Wan

Gadd

Yang

et al. 2020

Preprint

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Background: Disentangling the biogeographic patterns of rare and abundant microbial sub-communities is essential in order to understand the generation and maintenance of microbial diversity with respect to the functions they provide. However, little is known about ecological assembly processes and environmental adaptation of rare and abundant microbial sub-communities across large spatial-scale wetlands. Using Illumina sequencing, we investigated the taxonomic and phylogenetic β-diversity of rare and abundant bacterial and fungal sub-communities in Qinghai-Tibet Plateau wetland soils. Additionally, we determined environmental breadths and phylogenetic signals of ecological preferences of rare and abundant microbial sub-communities, and investigated community assembly processes of microbial taxa. Results: We found that both taxonomic and phylogenetic similarities of rare and abundant microbial sub-communities attenuated with geographical distance. Based on threshold indicator taxa analysis and Blomberg’s K statistic, abundant microbial taxa exhibited broader environmental thresholds and stronger phylogenetic signals for ecological traits than rare microbial taxa. The strong correlations between community compositional dissimilarity and phylogenetic distance of rare microbial sub-communities also revealed that rare taxa may be more sensitive to environmental changes. In addition, the rare microbial sub-communities exhibited closer phylogenetic clustering compared with abundant microbial sub-communities. The null model analysis revealed that dispersal limitation belonging to stochastic process dominated ecological assembly of abundant bacterial sub-community, and rare and abundant fungal sub-communities; variable selection belonging to deterministic process governed community assembly of rare bacterial taxa. Neutral model analysis and variation partitioning analysis further confirmed that abundant microbial sub-communities were less environmentally constrained. Soil ammonia nitrogen was the crucial factor in mediating the balance between stochasticity and determinism of both rare and abundant microbial sub-communities, as reflected by distinct differences in stochastic process with higher ammonia nitrogen content.Conclusions: Abundant microbial sub-communities may have better environmental adaptation potential and are less dispersed by environmental changes compared with rare microbial sub-communities. Our findings extend knowledge of the adaptation of rare and abundant microbial taxa to ongoing environmental change and could facilitate prediction of biodiversity loss caused by global climate change and increasing human activity in wetlands of the Qinghai-Tibet Plateau.

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Rare microbial taxa as the major drivers of ecosystem multifunctionality in long-term fertilized soils

Cited by 287 publications

References 49 publications

Impacts of Intensive Land use on Soil Biodiversity and Ecosystem Functions in Central China

Impacts of Intensive Land use on Soil Biodiversity and Ecosystem Functions in Central China

A network approach to investigating the key microbes and stability of gut microbial communities in a mouse neuropathic pain model

Stronger Environmental Adaption of Abundant than Rare Microbes in Wetland Soils from the Qinghai-Tibet Plateau

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