Trends in Microbial Community Composition and Function by Soil Depth

Naylor, Dan; McClure, Ryan; Jansson, Janet K.

doi:10.3390/microorganisms10030540

Cited by 84 publications

(54 citation statements)

References 231 publications

(581 reference statements)

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“…Subsoil accounts for the majority of agricultural soil, however, microbial communities in subsoils are far less studied compared to those in topsoils (Naylor et al 2022). Besides greater sampling efforts associated with subsoil collection, molecular investigations of subsoil communities are often facing challenges recovering DNA from subsoil (e.g.…”

Section: Discussionmentioning

confidence: 99%

“…Although subsoil makes up the majority of agricultural soil, microorganisms in subsoils are highly understudied as compared to those in topsoils (e.g. Naylor et al 2022), especially in temperate agroforestry systems. Furthermore, certain benefits of agroforestry systems, such as the 'safety-net'-role of the trees, occur in the subsoil rather than topsoil.…”

Section: Introductionmentioning

confidence: 99%

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Digging deeper: microbial communities in subsoil are strongly promoted by trees in temperate agroforestry systems

et al. 2022

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Aims Temperate alley-cropping agroforestry systems maintain agricultural production while offering several environmental benefits. Central benefits of agroforestry systems such as the ‘safety-net’-role of the trees for leached nutrients are mainly due to processes occurring below the soil surface: the subsoil. Microorganisms in the subsoil may play a key role in the ‘safety-net’-function as they can improve the capturing and uptake of nutrients by the trees. Systematic investigations of microbial communities in temperate agroforestry systems, however, are restricted to topsoil. Methods We quantified bacteria, fungi, and functional groups of microorganisms in the topsoil and subsoil of two alley-cropping systems using real-time PCR. Topsoil and subsoil samples were collected in the tree rows and at multiple distances from the trees within the crop rows of the agroforestry systems as well as at an adjacent monoculture cropland. Results Microbial population size decreased with soil depth likely due to limited resource availability in subsoil. Tree rows in agroforestry systems not only promote soil microbial populations in both the topsoil and subsoil but the promotion also extends gradually into the crop rows of the systems. The promotion of microorganisms through trees is stronger in subsoil than topsoil, pointing at more intense resource scarcity in the subsoil than topsoil. Conclusions We propose that tree root-derived resources and root litter, which are scarce in agricultural subsoils, triggered the strong positive response of the subsoil community to the trees. Finally, we provide initial evidence that subsoil microorganisms contribute to the ‘safety-net’-role of the trees in agroforestry systems.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Digging deeper: microbial communities in subsoil are strongly promoted by trees in temperate agroforestry systems

et al. 2022

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“…However, most soil microbiome studies either do not include soil physicochemical properties or limit measurements to pH, soil organic carbon (SOC), total nitrogen (TN), total carbon (TC), moisture, and/or temperature, which do not fully reflect the complex soil chemical matrix and its various constituent elements (e.g., N, C, K, P, Zn, Fe, Ca, Mn, Mg). Soil properties vary with soil depth [ 22 ], as shown for SOC, total N [ 23 , 24 ], and total P [ 25 ]. Moreover, soil properties, particularly pH, are dynamic and fluctuate with changes in climate [ 26 ], environment [ 27 ], and the aboveground population [ 28 ].…”

Section: Soil Physicochemical Properties Improves Our Understanding O...mentioning

confidence: 99%

Current Challenges and Pitfalls in Soil Metagenomics

2022

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Soil microbial communities are essential components of agroecological ecosystems that influence soil fertility, nutrient turnover, and plant productivity. Metagenomics data are increasingly easy to obtain, but studies of soil metagenomics face three key challenges: (1) accounting for soil physicochemical properties; (2) incorporating untreated controls; and (3) sharing data. Accounting for soil physicochemical properties is crucial for better understanding the changes in soil microbial community composition, mechanisms, and abundance. Untreated controls provide a good baseline to measure changes in soil microbial communities and separate treatment effects from random effects. Sharing data increases reproducibility and enables meta-analyses, which are important for investigating overall effects. To overcome these challenges, we suggest establishing standard guidelines for the design of experiments for studying soil metagenomics. Addressing these challenges will promote a better understanding of soil microbial community composition and function, which we can exploit to enhance soil quality, health, and fertility.

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“…Most represented by Comamonadaceae, a family that consists of many copiotrophic spore formers, rapidly responding to fresh input of labile nutrients (Fierer et al, 2007;Ho et al, 2017). This suggests that mineral-weathering Burkholderiales (Naylor et al, 2022) are readily responsive to thawing soil conditions. Similarly, the active Bacteroidetes order Sphingobacteriales dominated recently thawed permafrost.…”

Section: Dominant Prokaryotes In Thawing Permafrost Soilmentioning

confidence: 99%

Abrupt permafrost thaw triggers microbial bloom and grazer succession

Scheel

Zervas

Tveit

et al. 2022

Preprint

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Permafrost soils store a substantial part of the global soil carbon, but due to global warming, abrupt erosion and consecutive thaw make these carbon stocks vulnerable to microbial decomposition into greenhouse gases. Although in temperate systems trophic interactions promote soil carbon storage, their role in Arctic permafrost microbiomes, especially during thaw, remains largely unknown. Here, we investigated the microbial response to in situ thawing and rapid permafrost erosion. We sequenced the total RNA of a 1 m deep soil core from an active abrupt erosion site to analyse the microbial community in the active layer soil, recently thawed and intact permafrost, consisting of up to 26 500-year-old material. We found maximum RNA:DNA ratios in recently thawed permafrost, indicating upregulation of protein biosynthesis upon thaw. At the same depths, the relative abundance of several prokaryotic orders, including Sphingobacteriales, Burkholderiales, and Nitrosomonadales increased in relative abundance. Bacterial predators were mainly dominated by Myxococcales. Protozoa were overall less abundant but doubled in relative abundance between the active layer and recently thawed permafrost. Cercozoa, Amoebozoa, and Ciliophora were the most abundant protozoan predators, replacing myxobacteria at deeper thaw depths. Overall, connections between the active layer and especially upper thawed layers were visible and suggest migration, while no layer formed a distinct community. Our findings highlight the importance of predation and population dynamics as well as the rapid development of a microbial bloom in abruptly thawing permafrost.

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Trends in Microbial Community Composition and Function by Soil Depth

Cited by 84 publications

References 231 publications

Digging deeper: microbial communities in subsoil are strongly promoted by trees in temperate agroforestry systems

Digging deeper: microbial communities in subsoil are strongly promoted by trees in temperate agroforestry systems

Current Challenges and Pitfalls in Soil Metagenomics

Abrupt permafrost thaw triggers microbial bloom and grazer succession

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