Bacterial communities of the Salvia lyrata rhizosphere explained by spatial structure and sampling grain

Dickey, Jonathan; Fordyce, James A.; Lebeis, Sarah L.

doi:10.1007/s00248-020-01594-7

Cited by 9 publications

(6 citation statements)

References 65 publications

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“…Given that young roots are typically found at deeper soil layers than mature roots, there likely exists a connection between root depth, root age, exudate release and microbial recruitment patterns. Indeed, depth has repeatedly been found to be a significant variable driving rhizosphere microbiome composition [ 93 , 143 , 145 , 148 , 149 ]. However, the relationship between the rhizosphere microbiome and depth is not necessarily linearly correlated.…”

Section: Changes In Microbial Community Composition With Depthmentioning

confidence: 99%

“…Meanwhile, mid-level rhizospheres may be comparatively less diverse due to a lower C content [ 93 , 150 ]. In addition, deeper rhizospheres tend to select for a more consistent community composition between replicates [ 148 , 149 ], as they are less subject to fluctuating environmental conditions or diurnal cycles.…”

Section: Changes In Microbial Community Composition With Depthmentioning

confidence: 99%

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Trends in Microbial Community Composition and Function by Soil Depth

2022

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Microbial communities play important roles in soil health, contributing to processes such as the turnover of organic matter and nutrient cycling. As soil edaphic properties such as chemical composition and physical structure change from surface layers to deeper ones, the soil microbiome similarly exhibits substantial variability with depth, with respect to both community composition and functional profiles. However, soil microbiome studies often neglect deeper soils, instead focusing on the top layer of soil. Here, we provide a synthesis on how the soil and its resident microbiome change with depth. We touch upon soil physicochemical properties, microbial diversity, composition, and functional profiles, with a special emphasis on carbon cycling. In doing so, we seek to highlight the importance of incorporating analyses of deeper soils in soil studies.

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Section: Changes In Microbial Community Composition With Depthmentioning

confidence: 99%

Section: Changes In Microbial Community Composition With Depthmentioning

confidence: 99%

Trends in Microbial Community Composition and Function by Soil Depth

2022

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“…Third, we should consider unique limitations and prospects of microbial ecology (microbial morphology and physiology, DNAbased studies, destructive sampling, horizontal gene transfer, the effect of spatial scale relative to the system, pooling across replicates within sites for DNA sequencing) and interpret findings in this light. For example, Dickey et al (2020) shows that rhizosphere bacterial communities vary within the rhizosphere habitat and that DNA sequencing resolution affects estimates of microbial richness. When comparing macroecological rules across the tree of life, collection methods and statistics should be standardized as much as possible to avoid over-estimating microbial diversity.…”

Section: Best Practices In Microbial Macroecologymentioning

confidence: 99%

The Utility of Macroecological Rules for Microbial Biogeography

et al. 2021

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Macroecological rules have been developed for plants and animals that describe large-scale distributional patterns and attempt to explain the underlying physiological and ecological processes behind them. Similarly, microorganisms exhibit patterns in relative abundance, distribution, diversity, and traits across space and time, yet it remains unclear the extent to which microorganisms follow macroecological rules initially developed for macroorganisms. Additionally, the usefulness of these rules as a null hypothesis when surveying microorganisms has yet to be fully evaluated. With rapid advancements in sequencing technology, we have seen a recent increase in microbial studies that utilize macroecological frameworks. Here, we review and synthesize these macroecological microbial studies with two main objectives: (1) to determine to what extent macroecological rules explain the distribution of host-associated and free-living microorganisms, and (2) to understand which environmental factors and stochastic processes may explain these patterns among microbial clades (archaea, bacteria, fungi, and protists) and habitats (host-associated and free living; terrestrial and aquatic). Overall, 78% of microbial macroecology studies focused on free living, aquatic organisms. In addition, most studies examined macroecological rules at the community level with only 35% of studies surveying organismal patterns across space. At the community level microorganisms often tracked patterns of macroorganisms for island biogeography (74% confirm) but rarely followed Latitudinal Diversity Gradients (LDGs) of macroorganisms (only 32% confirm). However, when microorganisms and macroorganisms shared the same macroecological patterns, underlying environmental drivers (e.g., temperature) were the same. Because we found a lack of studies for many microbial groups and habitats, we conclude our review by outlining several outstanding questions and creating recommendations for future studies in microbial ecology.

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“…In addition, soil sampling methods (e.g., rhizosphere versus bulk soil cores) could also play a crucial role in determining soil microbial responses to precipitation alterations, soil nutrients, soil depth, and other environmental factors (Dickey et al, 2020; Naylor et al, 2022; Raczka et al, 2022; Zheng et al, 2019). In the current study, we reported the results of a 4‐year field experiment using the PLFA method.…”

Section: Discussionmentioning

confidence: 99%

Soil microbial responses to large changes in precipitation with nitrogen deposition in an arid ecosystem

et al. 2023

Ecology

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Climatic change severely affects terrestrial ecosystem functioning by modifying soil microbial communities, especially in arid ecosystems. However, how precipitation patterns affect soil microbes and the underlying mechanisms remain largely unclear, particularly under long‐term dry–wet cycling and vice versa in field settings. In this study, a field experiment was conducted to quantify soil microbial responses and resilience to precipitation changes with nitrogen addition. We established five levels of precipitation with nitrogen addition over the first 3 years and then balanced this with compensatory precipitation in the fourth year (i.e., reversed the precipitation treatments), to recover to the levels expected over 4 years in a desert steppe ecosystem. Soil microbial community biomass increased with increasing precipitation, and the reversed precipitation reversed these responses. The soil microbial response ratio was constrained by the initial reduction in precipitation, whereas the resilience and limitation/promotion index of most microbial groups tended to increase. Nitrogen addition reduced the response rates of most microbial groups, depending on the soil depth. The soil microbial response and limitation/promotion index could be distinguished by antecedent soil features. The precipitation regime can regulate the responses of soil microbial communities to climatic change via two potential mechanisms: (1) concurrent nitrogen deposition and (2) soil chemical and biological mediation. Soil microbial behaviors and their associations with soil properties should be considered when assessing the responses of terrestrial ecosystems to climatic change.

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Bacterial communities of the Salvia lyrata rhizosphere explained by spatial structure and sampling grain

Cited by 9 publications

References 65 publications

Trends in Microbial Community Composition and Function by Soil Depth

Trends in Microbial Community Composition and Function by Soil Depth

The Utility of Macroecological Rules for Microbial Biogeography

Soil microbial responses to large changes in precipitation with nitrogen deposition in an arid ecosystem

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