Deep Soil Layers of Drought-Exposed Forests Harbor Poorly Known Bacterial and Fungal Communities

Frey, Beat; Walthert, Lorenz; Perez-Mon, Carla; Stierli, Beat; Köchli, Roger; Dharmarajah, Alexander; Brunner, Ivano

doi:10.3389/fmicb.2021.674160

Cited by 56 publications

(49 citation statements)

References 108 publications

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“…These studies have characterized the diversity of Calonectria species well. Results of a number of other studies indicated that microbial diversity and richness are typically affected by the soil depth [62][63][64][65][66][67], and shallower layers usually have a higher level of microbial diversity [62,63,[66][67][68]. This pattern is consistent with the results of the present study.…”

Section: Discussionsupporting

confidence: 92%

Species Diversity and Distribution Characteristics of Calonectria in Five Soil Layers in a Eucalyptus Plantation

Liu

Chen

2021

JoF

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The genus Calonectria includes pathogens of various agricultural, horticultural, and forestry crops. Species of Calonectria are commonly collected from soils, fruits, leaves, stems, and roots. Some species of Calonectria isolated from soils are considered as important plant pathogens. Understanding the species diversity and distribution characteristics of Calonectria species in different soil layers will help us to clarify their long-term potential harm to plants and their patterns of dissemination. To our knowledge, no systematic research has been conducted concerning the species diversity and distribution characteristics of Calonectria in different soil layers. In this study, 1000 soil samples were collected from five soil layers (0–20, 20–40, 40–60, 60–80, and 80–100 cm) at 100 sampling points in one 15-year-old Eucalyptus urophylla hybrid plantation in southern China. A total of 1037 isolates of Calonectria present in all five soil layers were obtained from 93 of 100 sampling points. The 1037 isolates were identified based on DNA sequence comparisons of the translation elongation factor 1-alpha (tef1), β-tubulin (tub2), calmodulin (cmdA), and histone H3 (his3) gene regions, as well as the combination of morphological characteristics. These isolates were identified as C. hongkongensis (665 isolates; 64.1%), C. aconidialis (250 isolates; 24.1%), C. kyotensis (58 isolates; 5.6%), C. ilicicola (47 isolates; 4.5%), C. chinensis (2 isolates; 0.2%), and C. orientalis (15 isolates; 1.5%). With the exception of C. orientalis, which resides in the C. brassicae species complex, the other five species belonged to the C. kyotensis species complex. The results showed that the number of sampling points that yielded Calonectria and the number (and percentage) of Calonectria isolates obtained decreased with increasing depth of the soil. More than 84% of the isolates were obtained from the 0–20 and 20–40 cm soil layers. The deeper soil layers had comparatively lower numbers but still harbored a considerable number of Calonectria. The diversity of five species in the C. kyotensis species complex decreased with increasing soil depth. The genotypes of isolates in each Calonectria species were determined by tef1 and tub2 gene sequences. For each species in the C. kyotensis species complex, in most cases, the number of genotypes decreased with increasing soil depth. The 0–20 cm soil layer contained all of the genotypes of each species. To our knowledge, this study presents the first report of C. orientalis isolated in China. This species was isolated from the 40–60 and 60–80 cm soil layers at only one sampling point, and only one genotype was present. This study has enhanced our understanding of the species diversity and distribution characteristics of Calonectria in different soil layers.

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Section: Discussionsupporting

confidence: 92%

Species Diversity and Distribution Characteristics of Calonectria in Five Soil Layers in a Eucalyptus Plantation

Liu

Chen

2021

JoF

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“…The sites are covered mainly by European beech (Fagus sylvatica L.) or by oak species (Quercus spp. ), with oak sites having warmer and drier soils than European beech sites (see also Frey et al, 2021). All of the forest stands have a near natural tree species composition originating from natural regeneration and have been unmanaged for several decades (Frey et al, 2021).…”

Section: Forest Sitesmentioning

confidence: 99%

“…), with oak sites having warmer and drier soils than European beech sites (see also Frey et al, 2021). All of the forest stands have a near natural tree species composition originating from natural regeneration and have been unmanaged for several decades (Frey et al, 2021). The forest sites are part of the research platforms WSL Forest Soil Database.…”

Section: Forest Sitesmentioning

confidence: 99%

“…Deep soil layers harbor poorly known bacterial and fungal communities ( Brewer et al, 2019 ; Robin et al, 2019 ; Liu et al, 2020 ; Frey et al, 2021 ). It is assumed that living conditions in deeper soils for soil organisms and plant roots are harsher in deeper soils, as a result of higher soil density, lower oxygen concentrations, and lower carbon (C) and nutrient availability ( Lennon, 2020 ).…”

Section: Introductionmentioning

confidence: 99%

“…In a first survey of the deep soil horizons in Swiss beech and oak forests, we observed the occurrence of poorly known bacterial taxa belonging to Nitrospirae, Chloroflexi, Rokubacteria, Gemmatimonadetes, and Firmicutes ( Frey et al, 2021 ). Furthermore, archaeal phyla such as Thaumarchaeota and Euryarchaeota were more abundant in the deep soil than in the topsoil.…”

Section: Introductionmentioning

confidence: 99%

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Shotgun Metagenomics of Deep Forest Soil Layers Show Evidence of Altered Microbial Genetic Potential for Biogeochemical Cycling

Frey

Varliero

et al. 2022

Front. Microbiol.

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Soil microorganisms such as Bacteria and Archaea play important roles in the biogeochemical cycling of soil nutrients, because they act as decomposers or are mutualistic or antagonistic symbionts, thereby influencing plant growth and health. In the present study, we investigated the vertical distribution of soil metagenomes to a depth of 1.5 m in Swiss forests of European beech and oak species on calcareous bedrock. We explored the functional genetic potential of soil microorganisms with the aim to disentangle the effects of tree genus and soil depth on the genetic repertoire, and to gain insight into the microbial C and N cycling. The relative abundance of reads assigned to taxa at the domain level indicated a 5–10 times greater abundance of Archaea in the deep soil, while Bacteria showed no change with soil depth. In the deep soil there was an overrepresentation of genes for carbohydrate-active enzymes, which are involved in the catalyzation of the transfer of oligosaccharides, as well as in the binding of carbohydrates such as chitin or cellulose. In addition, N-cycling genes (NCyc) involved in the degradation and synthesis of N compounds, in nitrification and denitrification, and in nitrate reduction were overrepresented in the deep soil. Consequently, our results indicate that N-transformation in the deep soil is affected by soil depth and that N is used not only for assimilation but also for energy conservation, thus indicating conditions of low oxygen in the deep soil. Using shotgun metagenomics, our study provides initial findings on soil microorganisms and their functional genetic potential, and how this may change depending on soil properties, which shift with increasing soil depth. Thus, our data provide novel, deeper insight into the “dark matter” of the soil.

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Vertical distribution of bacterial community diversity in the Greater Khingan Mountain permafrost region

Cui

et al. 2022

Ecology and Evolution

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Soil microorganisms are crucial contributors to the function of permafrost ecosystems, as well as the regulation of biogeochemical cycles. However, little is known about the distribution patterns and drivers of high‐latitude permafrost microbial communities subject to climate change and human activities. In this study, the vertical distribution patterns of soil bacterial communities in the Greater Khingan Mountain permafrost region were systematically analyzed via Illumina Miseq high‐throughput sequencing. Bacterial diversity in the active layer was significantly higher than in the permafrost layer. Principal coordinate analysis (PCoA) indicated that the bacterial community structure in the active layer and the permafrost layer was completely separated. Permutational multivariate analysis of variance (PERMANOVA) detected statistically significant differentiation across the different depths. The relative abundance of the dominant phyla Chloroflexi (17.92%–52.79%) and Actinobacteria (6.34%–34.52%) was significantly higher in the permafrost layer than in the active layer, whereas that of Acidobacteria (4.98%–38.82%) exhibited the opposite trend, and the abundance of Proteobacteria (2.49%–22.51%) generally decreased with depth. More importantly, the abundance of bacteria linked to human infectious diseases was significantly higher in the permafrost layer according to Tax4Fun prediction analysis. Redundancy analysis (RDA) showed that ammonium nitrogen (NH4+‐N), total organic carbon (TOC), and total phosphorus (TP) were major factors affecting the bacterial community composition. Collectively, our findings provide insights into the soil bacterial vertical distribution patterns and major environmental drivers in high‐latitude permafrost regions, which is key to grasping the response of cold region ecosystem processes to global climate changes.

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Deep Soil Layers of Drought-Exposed Forests Harbor Poorly Known Bacterial and Fungal Communities

Cited by 56 publications

References 108 publications

Species Diversity and Distribution Characteristics of Calonectria in Five Soil Layers in a Eucalyptus Plantation

Species Diversity and Distribution Characteristics of Calonectria in Five Soil Layers in a Eucalyptus Plantation

Shotgun Metagenomics of Deep Forest Soil Layers Show Evidence of Altered Microbial Genetic Potential for Biogeochemical Cycling

Vertical distribution of bacterial community diversity in the Greater Khingan Mountain permafrost region

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