Microbial Life Deep Underfoot

Lennon, Jay T.

doi:10.1128/mbio.03201-19

Cited by 12 publications

(9 citation statements)

References 5 publications

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“…This pattern is consistent with the results of the present study. A possible reason for the vertical distribution of soil microbes is the harsher environment in deeper soil layers, where the soil density is higher, oxygen concentrations are lower, and carbon and nutrients are less available [69]. For Calonectria, which includes some important pathogens of various agricultural, horticultural, and forestry crops worldwide, as well as for other genera of fungi in forests, no systematic research has been conducted to examine the species diversity and distribution characteristics in different soil layers.…”

Section: Discussionmentioning

confidence: 99%

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

Liu

Chen

2021

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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: Discussionmentioning

confidence: 99%

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

Liu

Chen

2021

JoF

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“…We found lower expression for glucose-1-phosphate adenylyltransferase (Table 4), which has been considered the rate-limiting step of bacterial glycogen biosynthesis [105] or the first step of glycogen hydrolysis [106]. Glycogen can serve as an alternative carbon source for bacterial survival in carbon-depleted anaerobic environments [106] or to prolong the lifespan of microorganisms while dormant [107]. Thus, the lower expression of glucose-1-phosphate adenylyltransferase, an oxygen-regulated gene negatively affected by O 2 availability, following rainfall provides further evidence that the increase in soil oxygenation made available more easily metabolized carbon substrates (e.g., aromatic DOC) [103] such that microbes no longer needed to synthesize and degrade glycogen, or possibly that microbial cells may have started to leave their dormant state.…”

Section: Tussock Tundra Community Responds To Rainfall-induced Soil Oxidationmentioning

confidence: 97%

Rainfall Alters Permafrost Soil Redox Conditions, but Meta-Omics Show Divergent Microbial Community Responses by Tundra Type in the Arctic

2021

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Soil anoxia is common in the annually thawed surface (‘active’) layer of permafrost soils, particularly when soils are saturated, and supports anaerobic microbial metabolism and methane (CH4) production. Rainfall contributes to soil saturation, but can also introduce oxygen, causing soil oxidation and altering anoxic conditions. We simulated a rainfall event in soil mesocosms from two dominant tundra types, tussock tundra and wet sedge tundra, to test the impacts of rainfall-induced soil oxidation on microbial communities and their metabolic capacity for anaerobic CH4 production and aerobic respiration following soil oxidation. In both types, rainfall increased total soil O2 concentration, but in tussock tundra there was a 2.5-fold greater increase in soil O2 compared to wet sedge tundra due to differences in soil drainage. Metagenomic and metatranscriptomic analyses found divergent microbial responses to rainfall between tundra types. Active microbial taxa in the tussock tundra community, including bacteria and fungi, responded to rainfall with a decline in gene expression for anaerobic metabolism and a concurrent increase in gene expression for cellular growth. In contrast, the wet sedge tundra community showed no significant changes in microbial gene expression from anaerobic metabolism, fermentation, or methanogenesis following rainfall, despite an initial increase in soil O2 concentration. These results suggest that rainfall induces soil oxidation and enhances aerobic microbial respiration in tussock tundra communities but may not accumulate or remain in wet sedge tundra soils long enough to induce a community-wide shift from anaerobic metabolism. Thus, rainfall may serve only to maintain saturated soil conditions that promote CH4 production in low-lying wet sedge tundra soils across the Arctic.

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“…In general, living conditions for soil organisms and roots are harsher in deeper soil layers, where the soil density is higher, oxygen concentrations are lower, and carbon and nutrients are less available (Lennon, 2020). Carbon and nutrients typically are more available in the upper soil, mainly due to larger quantities of leaf and fine root litter and root exudates, as well as more biotic activity (Eldridge et al, 2016;Liu et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2021

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Soil microorganisms such as bacteria and fungi 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 the soil microbiome to a depth of 2 m in Swiss drought-exposed forests of European beech and oaks on calcareous bedrock. We aimed to disentangle the effects of soil depth, tree (beech, oak), and substrate (soil, roots) on microbial abundance, diversity, and community structure. With increasing soil depth, organic carbon, nitrogen, and clay content decreased significantly. Similarly, fine root biomass, microbial biomass (DNA content, fungal abundance), and microbial alpha-diversity decreased and were consequently significantly related to these physicochemical parameters. In contrast, bacterial abundance tended to increase with soil depth, and the bacteria to fungi ratio increased significantly with greater depth. Tree species was only significantly related to the fungal Shannon index but not to the bacterial Shannon index. Microbial community analyses revealed that bacterial and fungal communities varied significantly across the soil layers, more strongly for bacteria than for fungi. Both communities were also significantly affected by tree species and substrate. In deep soil layers, poorly known bacterial taxa from Nitrospirae, Chloroflexi, Rokubacteria, Gemmatimonadetes, Firmicutes and GAL 15 were overrepresented. Furthermore, archaeal phyla such as Thaumarchaeota and Euryarchaeota were more abundant in subsoils than topsoils. Fungal taxa that were predominantly found in deep soil layers belong to the ectomycorrhizal Boletus luridus and Hydnum vesterholtii. Both taxa are reported for the first time in such deep soil layers. Saprotrophic fungal taxa predominantly recorded in deep soil layers were unknown species of Xylaria. Finally, our results show that the microbial community structure found in fine roots was well represented in the bulk soil. Overall, we recorded poorly known bacterial and archaeal phyla, as well as ectomycorrhizal fungi that were not previously known to colonize deep soil layers. Our study contributes to an integrated perspective on the vertical distribution of the soil microbiome at a fine spatial scale in drought-exposed forests.

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Microbial Life Deep Underfoot

Cited by 12 publications

References 5 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

Rainfall Alters Permafrost Soil Redox Conditions, but Meta-Omics Show Divergent Microbial Community Responses by Tundra Type in the Arctic

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

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