Soil sample sizes for DNA extraction substantially affect the examination of microbial diversity and co-occurrence patterns but not abundance

Li, Ting; Zhang, Song; Hu, Jinming; Hou, Haiyan; Li, Kexin; Qing, Fan; Wang, Fang; Li, Linfeng; Cui, Xiaoyong; Liu, Dong; Che, Rongxiao

doi:10.1016/j.soilbio.2022.108902

Cited by 14 publications

(5 citation statements)

References 67 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…All the tested microbial abundances, including prokaryotes, fungi, and protists, showed increasing trends across ecosystems with moisture gradients (Fig. 2), which were consistent with the prior research across ecosystems such as desert, meadow, forest, and cropland [97]. The observed pattern was likely attributable to a combination of soil moisture with C and nutrient availability [98].…”

Section: Linear Responses Of Microbial Characteristics Along Moisture...supporting

confidence: 87%

Linear responses of soil microbiomes, metagenomic and metabolomic functioning across ecosystems along water gradients in the Altai region, northwestern China

Fu,

Qiu,

Zhao

et al. 2023

Preprint

View full text Add to dashboard Cite

Background To investigate microbial communities and their contributions to carbon and nutrient cycling along water gradients can enhance our comprehension of climate change impacts on ecosystem services. Results We conducted an assessment of microbial communities, metagenomic functions, and metabolomic profiles within four ecosystems, i.e., desert grassland (DG), shrub-steppe (SS), forest (FO) and marsh (MA) in the Altai region of Xinjiang, China. Soil total carbon (TC), total nitrogen, NH4+, and NO3- increased linearly, but pH decreased with soil water gradients. Microbial abundances and richness also increased with soil moisture except the abundances of fungi and protists being lowest in MA. Within prokaryotes, the relative abundances of Proteobacteria and Acidobacteria increased, whereas those of Actinobacteria and Thaumarchaeota decreased along water gradients. In fungi and protists, Basidiomycota and Mortierellomycota, Evosea and Endomyxa became dominant in FO and MA, respectively, but the relative abundance of Cercozoa decreased along soil moisture gradients. The β-diversity of microbiomes, metagenomic and metabolomic functioning were linearly distributed along soil moisture gradients, significantly associated with soil factors of TC, NH4+, and pH. For soil metagenomic functions, the metabolic genes related to Carbohydrate (CO2 fixation, Di- and oligosaccharides, Fermentation, and One-carbon metabolism), Iron (Iron acquisition in Vibrio and Campylobacter iron metabolism) decreased with soil moisture, while genes related to the metabolisms of Nitrogen (Ammonia assimilation, Denitrification, Nitrogen fixation, and Nitrosative stress) and Potassium (Potassium homeostasis) increased linearly along water gradients. Additionally, MA harbored the most abundant metabolomics dominated by lipids and lipid-like molecules (Erucic acid, Hypogeic acid, and Kojibiose, etc.), and organic oxygen compounds (Maltotetraose, Quinone, Sucrose, and Trehalose, etc.), except certain metabolites showing decline trends along water gradients, such as N'-Hydroxymethylnorcotinine and 5-Hydroxyenterolactone. Conclusions Our study suggests that future ecosystem succession facilitated by changes in rainfall patterns will significantly alter soil microbial taxa, functional potential and metabolite fractions.

show abstract

Section: Linear Responses Of Microbial Characteristics Along Moisture...supporting

confidence: 87%

Linear responses of soil microbiomes, metagenomic and metabolomic functioning across ecosystems along water gradients in the Altai region, northwestern China

Fu,

Qiu,

Zhao

et al. 2023

Preprint

View full text Add to dashboard Cite

show abstract

“…The moisture content was measured by drying the soils at 105°C for 24 h (Che, Deng, Wang, Rui, et al., 2018). Soil pH was examined using a pH meter with a soil‐to‐water ratio of 1:2.5 (Fu et al., 2023; Li et al., 2023). The soil total carbon and nitrogen contents were measured with an automatic elemental analyser (Che, Wang, Li, et al., 2019).…”

Section: Methodsmentioning

confidence: 99%

“…The soil total carbon and nitrogen contents were measured with an automatic elemental analyser (Che, Wang, Li, et al., 2019). After extraction with 0.5 M K 2 SO 4 , the soil

{NH}_{4}^{+}

‐N and

{NO}_{3}^{-}

‐N concentrations were determined through the indophenol blue and vanadium chloride spectrophotometric methods, respectively (Li et al., 2023). The aP content in the alkaline and acidic soils was measured using the methods of Olsen (1954) and Bray and Kurtz (1945) respectively.…”

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Soil microbial subcommunity assembly mechanisms are highly variable and intimately linked to their ecological and functional traits

Fan,

Liu,

Wang

et al. 2024

Molecular Ecology

Self Cite

View full text Add to dashboard Cite

Revealing the mechanisms underlying soil microbial community assembly is a fundamental objective in molecular ecology. However, despite increasing body of research on overall microbial community assembly mechanisms, our understanding of subcommunity assembly mechanisms for different prokaryotic and fungal taxa remains limited. Here, soils were collected from more than 100 sites across southwestern China. Based on amplicon high‐throughput sequencing and iCAMP analysis, we determined the subcommunity assembly mechanisms for various microbial taxa. The results showed that dispersal limitation and homogenous selection were the primary drivers of soil microbial community assembly in this region. However, the subcommunity assembly mechanisms of different soil microbial taxa were highly variable. For instance, the contribution of homogenous selection to Crenarchaeota subcommunity assembly was 70%, but it was only around 10% for the subcommunity assembly of Actinomycetes, Gemmatimonadetes and Planctomycetes. The assembly of subcommunities including microbial taxa with higher occurrence frequencies, average relative abundance and network degrees, as well as wider niches tended to be more influenced by homogenizing dispersal and drift, but less affected by heterogeneous selection and dispersal limitation. The subcommunity assembly mechanisms also varied substantially among different functional guilds. Notably, the subcommunity assembly of diazotrophs, nitrifiers, saprotrophs and some pathogens were predominantly controlled by homogenous selection, while that of denitrifiers and fungal pathogens were mainly affected by stochastic processes such as drift. These findings provide novel insights into understanding soil microbial diversity maintenance mechanisms, and the analysis pipeline holds significant value for future research.

show abstract

“…Soil DNA was extracted from 0.40 g of fresh soil using the DNeasy PowerSoil kit (Qiagen, Hilden, Germany) [30]. The quanti cation of prokaryotic 16S rRNA gene and fungal ITS copy numbers was performed using a LightCyCler96 real-time PCR System (Roche, Germany).…”

Section: Dna Extraction and Real-time Pcrmentioning

confidence: 99%

Coalescence of soil microbial communities: consequences, mechanisms, and influential factors

Chen,

Wang,

Chen

et al. 2024

Preprint

Self Cite

View full text Add to dashboard Cite

Background: Community coalescence is a major manner of microbial dispersal and a fundamental process of microbial community assembly, yet little is known about its ecological effects, mechanisms, and influential factors. Here, a series of microcosmic experiments including soil mixing, sterilization, as well as microbial extraction and inoculation, were performed to address the knowledge gaps. Results: We found that most physicochemical and microbial properties of the coalesced soils exhibited intermediate characteristics compared to the original soils. Weighted species additive effect emerged as the primary driver for soil microbial community coalescence, with contributions reaching 58.44% (prokaryotes) and 51.57% (fungi). In contrast, the contributions from environmental selection were only less than 20%. Upon the removal of soil particle barrier effects, the contributions of abiotic and biotic environmental selection to soil microbial community coalescence increased to 34.60% and 23.76%, respectively. However, their interactions substantially offset the main effects of abiotic and biotic environmental selection. Original soil differences, mixing ratios, and priority effects were critical factors affecting the consequences of soil microbial community coalescence. Nevertheless, the mechanisms underlying microbial community coalescence were similar under different mixing ratios. Conclusions: Our findings underscore the predictability of soil microbial community coalescence, providing critical insights into comprehending microbial community assembly mechanisms.

show abstract

Soil sample sizes for DNA extraction substantially affect the examination of microbial diversity and co-occurrence patterns but not abundance

Cited by 14 publications

References 67 publications

Linear responses of soil microbiomes, metagenomic and metabolomic functioning across ecosystems along water gradients in the Altai region, northwestern China

Linear responses of soil microbiomes, metagenomic and metabolomic functioning across ecosystems along water gradients in the Altai region, northwestern China

Soil microbial subcommunity assembly mechanisms are highly variable and intimately linked to their ecological and functional traits

Coalescence of soil microbial communities: consequences, mechanisms, and influential factors

Contact Info

Product

Resources

About