scholarly journals Vulnerability and resistance in the spatial heterogeneity of soil microbial communities under resource additions

2020 ◽  
Vol 117 (13) ◽  
pp. 7263-7270 ◽  
Author(s):  
Kelly Gravuer ◽  
Anu Eskelinen ◽  
Joy B. Winbourne ◽  
Susan P. Harrison
Keyword(s):  
Spatial Variability ◽  
Spatial Heterogeneity ◽  
Soil Microbial Communities ◽  
Archaeal Community ◽  
Ecosystem Functions ◽  
Water Addition ◽  
Microbial Composition ◽  
Soil Microbial ◽  
The Face ◽  
And Function

Spatial heterogeneity in composition and function enables ecosystems to supply diverse services. For soil microbes and the ecosystem functions they catalyze, whether such heterogeneity can be maintained in the face of altered resource inputs is uncertain. In a 50-ha northern California grassland with a mosaic of plant communities generated by different soil types, we tested how spatial variability in microbial composition and function changed in response to nutrient and water addition. Fungal composition lost some of its spatial variability in response to nutrient addition, driven by decreases in mutualistic fungi and increases in antagonistic fungi that were strongest on the least fertile soils, where mutualists were initially most frequent and antagonists initially least frequent. Bacterial and archaeal community composition showed little change in their spatial variability with resource addition. Microbial functions related to nitrogen cycling showed increased spatial variability under nutrient, and sometimes water, additions, driven in part by accelerated nitrification on the initially more-fertile soils. Under anthropogenic changes such as eutrophication and altered rainfall, these findings illustrate the potential for significant changes in ecosystem-level spatial heterogeneity of microbial functions and communities.

scholarly journals Effects of Spatial Variability and Relic DNA Removal on the Detection of Temporal Dynamics in Soil Microbial Communities

mBio ◽  
2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Paul Carini ◽  
Manuel Delgado-Baquerizo ◽  
Eve-Lyn S. Hinckley ◽  
Hannah Holland‐Moritz ◽  
Tess E. Brewer ◽  
...  
Keyword(s):  
Microbial Community ◽  
Spatial Variability ◽  
Spatial Heterogeneity ◽  
Microbial Communities ◽  
Temporal Variability ◽  
Temporal Dynamics ◽  
Microbial Community Composition ◽  
Soil Microbial Communities ◽  
Environmental Preferences ◽  
Soil Microbial

ABSTRACT Few studies have comprehensively investigated the temporal variability in soil microbial communities despite widespread recognition that the belowground environment is dynamic. In part, this stems from the challenges associated with the high degree of spatial heterogeneity in soil microbial communities and because the presence of relic DNA (DNA from dead cells or secreted extracellular DNA) may dampen temporal signals. Here, we disentangle the relationships among spatial, temporal, and relic DNA effects on prokaryotic and fungal communities in soils collected from contrasting hillslopes in Colorado, USA. We intensively sampled plots on each hillslope over 6 months to discriminate between temporal variability, intraplot spatial heterogeneity, and relic DNA effects on the soil prokaryotic and fungal communities. We show that the intraplot spatial variability in microbial community composition was strong and independent of relic DNA effects and that these spatial patterns persisted throughout the study. When controlling for intraplot spatial variability, we identified significant temporal variability in both plots over the 6-month study. These microbial communities were more dissimilar over time after relic DNA was removed, suggesting that relic DNA hinders the detection of important temporal dynamics in belowground microbial communities. We identified microbial taxa that exhibited shared temporal responses and show that these responses were often predictable from temporal changes in soil conditions. Our findings highlight approaches that can be used to better characterize temporal shifts in soil microbial communities, information that is critical for predicting the environmental preferences of individual soil microbial taxa and identifying linkages between soil microbial community composition and belowground processes. IMPORTANCE Nearly all microbial communities are dynamic in time. Understanding how temporal dynamics in microbial community structure affect soil biogeochemistry and fertility are key to being able to predict the responses of the soil microbiome to environmental perturbations. Here, we explain the effects of soil spatial structure and relic DNA on the determination of microbial community fluctuations over time. We found that intensive spatial sampling was required to identify temporal effects in microbial communities because of the high degree of spatial heterogeneity in soil and that DNA from nonliving sources masks important temporal patterns. We identified groups of microbes with shared temporal responses and show that these patterns were predictable from changes in soil characteristics. These results provide insight into the environmental preferences and temporal relationships between individual microbial taxa and highlight the importance of considering relic DNA when trying to detect temporal dynamics in belowground communities.

Unraveling the effects of spatial variability and relic DNA on the temporal dynamics of soil microbial communities

2018 ◽  
Author(s):  
Paul Carini ◽  
Manuel Delgado-Baquerizo ◽  
Eve-Lyn S. Hinckley ◽  
Hannah Holland-Moritz ◽  
Tess E Brewer ◽  
...  
Keyword(s):  
Microbial Community ◽  
Spatial Variability ◽  
Spatial Heterogeneity ◽  
Microbial Communities ◽  
Temporal Variability ◽  
Temporal Dynamics ◽  
Microbial Community Composition ◽  
Soil Microbial Communities ◽  
Soil Microbial ◽  
Over Time

AbstractFew studies have comprehensively investigated the temporal variability in soil microbial communities despite widespread recognition that the belowground environment is dynamic. In part, this stems from the challenges associated with the high degree of spatial heterogeneity in soil microbial communities and because the presence of relic DNA (DNA from non-living cells) may dampen temporal signals. Here we disentangle the relationships among spatial, temporal, and relic DNA effects on bacterial, archaeal, and fungal communities in soils collected from contrasting hillslopes in Colorado, USA. We intensively sampled plots on each hillslope over six months to discriminate between temporal variability, intra-plot spatial heterogeneity, and relic DNA effects on the soil prokaryotic and fungal communities. We show that the intra-plot spatial variability in microbial community composition was strong and independent of relic DNA effects with these spatial patterns persisting throughout the study. When controlling for intra-plot spatial variability, we identified significant temporal variability in both plots over the six-month study. These microbial communities were more dissimilar over time after relic DNA was removed, suggesting that relic DNA hinders the detection of important temporal dynamics in belowground microbial communities. We identified microbial taxa that exhibited shared temporal responses and show these responses were often predictable from temporal changes in soil conditions. Our findings highlight approaches that can be used to better characterize temporal shifts in soil microbial communities, information that is critical for predicting the environmental preferences of individual soil microbial taxa and identifying linkages between soil microbial community composition and belowground processes.ImportanceNearly all microbial communities are dynamic in time. Understanding how temporal dynamics in microbial community structure affect soil biogeochemistry and fertility are key to being able to predict the responses of the soil microbiome to environmental perturbations. Here we explain the effects of soil spatial structure and relic DNA on the determination of microbial community fluctuations over time. We found that intensive spatial sampling is required to identify temporal effects in microbial communities because of the high degree of spatial heterogeneity in soil and that DNA from non-living microbial cells masks important temporal patterns. We identified groups of microbes that display correlated behavior over time and show that these patterns are predictable from soil characteristics. These results provide insight into the environmental preferences and temporal relationships between individual microbial taxa and highlight the importance of considering relic DNA when trying to detect temporal dynamics in belowground communities.

scholarly journals Spatial heterogeneity of physicochemical properties explains differences in microbial composition in arid soils from Cuatro Cienegas, Mexico

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2459 ◽  
Author(s):  
Silvia Pajares ◽  
Ana E. Escalante ◽  
Ana M. Noguez ◽  
Felipe García-Oliva ◽  
Celeste Martínez-Piedragil ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Spatial Heterogeneity ◽  
Abiotic Factors ◽  
Soil Microbial Communities ◽  
Arid Ecosystems ◽  
Arid Soils ◽  
Chemical Parameters ◽  
Microbial Composition ◽  
Soil Microbial Diversity ◽  
Soil Microbial

Arid ecosystems are characterized by high spatial heterogeneity, and the variation among vegetation patches is a clear example. Soil biotic and abiotic factors associated with these patches have also been well documented as highly heterogeneous in space. Given the low vegetation cover and little precipitation in arid ecosystems, soil microorganisms are the main drivers of nutrient cycling. Nonetheless, little is known about the spatial distribution of microorganisms and the relationship that their diversity holds with nutrients and other physicochemical gradients in arid soils. In this study, we evaluated the spatial variability of soil microbial diversity and chemical parameters (nutrients and ion content) at local scale (meters) occurring in a gypsum-based desert soil, to gain knowledge on what soil abiotic factors control the distribution of microbes in arid ecosystems. We analyzed 32 soil samples within a 64 m2plot and: (a) characterized microbial diversity using T-RFLPs of the bacterial 16S rRNA gene, (b) determined soil chemical parameters, and (c) identified relationships between microbial diversity and chemical properties. Overall, we found a strong correlation between microbial composition heterogeneity and spatial variation of cations (Ca2, K+) and anions (HCO${}_{3}^{-}$, Cl−, SO${}_{4}^{2-}$) content in this small plot. Our results could be attributable to spatial differences of soil saline content, favoring the patchy emergence of salt and soil microbial communities.

scholarly journals Soil microbial diversity–biomass relationships are driven by soil carbon content across global biomes

2021 ◽  
Author(s):  
Felipe Bastida ◽  
David J. Eldridge ◽  
Carlos García ◽  
G. Kenny Png ◽  
Richard D. Bardgett ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Soil Carbon ◽  
Soil Microbial Communities ◽  
Ecosystem Functions ◽  
Arid Environments ◽  
Soil Microbial Diversity ◽  
Soil Biodiversity ◽  
Soil C ◽  
Soil Microbial ◽  
Biomass Ratio

AbstractThe relationship between biodiversity and biomass has been a long standing debate in ecology. Soil biodiversity and biomass are essential drivers of ecosystem functions. However, unlike plant communities, little is known about how the diversity and biomass of soil microbial communities are interlinked across globally distributed biomes, and how variations in this relationship influence ecosystem function. To fill this knowledge gap, we conducted a field survey across global biomes, with contrasting vegetation and climate types. We show that soil carbon (C) content is associated to the microbial diversity–biomass relationship and ratio in soils across global biomes. This ratio provides an integrative index to identify those locations on Earth wherein diversity is much higher compared with biomass and vice versa. The soil microbial diversity-to-biomass ratio peaks in arid environments with low C content, and is very low in C-rich cold environments. Our study further advances that the reductions in soil C content associated with land use intensification and climate change could cause dramatic shifts in the microbial diversity-biomass ratio, with potential consequences for broad soil processes.

scholarly journals Interannual and Spatial Variability of Cyanotoxins in the Prespa Lake Area, Greece

Water ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 357
Author(s):  
Valentini Maliaka ◽  
Miquel Lürling ◽  
Christian Fritz ◽  
Yvon J.M. Verstijnen ◽  
Elisabeth J. Faassen ◽  
...  
Keyword(s):  
Water Quality ◽  
Spatial Variability ◽  
Spatial Heterogeneity ◽  
Dry Weight ◽  
Ecosystem Functions ◽  
Lake Area ◽  
Total Chlorophyll ◽  
Tissue Samples ◽  
Cyanobacteria Blooms ◽  
Prespa Lake

The Prespa Lakes area in Greece—comprised partly of lake Great and lake Lesser Prespa and the Vromolimni pond—has a global importance for biodiversity. Although the waters show regular cyanobacteria blooms, assessments of water quality threats are limited. Samples collected in 2012 revealed scattered and low microcystin (MC) concentrations in Great Prespa (<0.2 μg MC L−1) whereas considerable spatial heterogeneity in both total chlorophyll (2.4–93 µg L−1) and MC concentrations (0.04–52.4 µg MC L−1) was detected in Lesser Prespa. In 2013, there was far less spatial variability of MC concentrations in Lesser Prespa (0.4–1.53 µg L−1), however in 2014, increased concentrations were detected near the lakeshore (25–861 µg MC L−1). In Vromolimni pond the MC concentrations were on average 26.6 (±6.4) µg MC L−1 in 2012, 2.1 (±0.3) µg MC L−1 in 2013 and 12.7 (±12.5) µg MC L−1 in 2014. In 2013, no anatoxins, saxitoxins, nor cylindrospermopsins were detected in Lesser Prespa and Vromolimni waters. Tissue samples from carps, an otter and Dalmatian Pelicans contained 0.4–1.9 µg MC g−1 dry weight. These results indicate that cyanotoxins could be a threat to the ecosystem functions of particularly Lesser Prespa and Vromolimni.

scholarly journals Disentangling Responses of the Subsurface Microbiome to Wetland Status and Implications for Indicating Ecosystem Functions

2021 ◽  
Vol 9 (2) ◽  
pp. 211
Author(s):  
Jie Gao ◽  
Miao Liu ◽  
Sixue Shi ◽  
Ying Liu ◽  
Yu Duan ◽  
...  
Keyword(s):  
Microbial Community ◽  
High Throughput Sequencing ◽  
Carbon Fixation ◽  
Microbial Community Composition ◽  
Ecosystem Functions ◽  
Microbial Composition ◽  
Wetland Ecosystems ◽  
Soil Microbial ◽  
Geochemical Properties ◽  
Microbial Groups

In this study, we analyzed microbial community composition and the functional capacities of degraded sites and restored/natural sites in two typical wetlands of Northeast China—the Phragmites marsh and the Carex marsh, respectively. The degradation of these wetlands, caused by grazing or land drainage for irrigation, alters microbial community components and functional structures, in addition to changing the aboveground vegetation and soil geochemical properties. Bacterial and fungal diversity at the degraded sites were significantly lower than those at restored/natural sites, indicating that soil microbial groups were sensitive to disturbances in wetland ecosystems. Further, a combined analysis using high-throughput sequencing and GeoChip arrays showed that the abundance of carbon fixation and degradation, and ~95% genes involved in nitrogen cycling were increased in abundance at grazed Phragmites sites, likely due to the stimulating impact of urine and dung deposition. In contrast, the abundance of genes involved in methane cycling was significantly increased in restored wetlands. Particularly, we found that microbial composition and activity gradually shifts according to the hierarchical marsh sites. Altogether, this study demonstrated that microbial communities as a whole could respond to wetland changes and revealed the functional potential of microbes in regulating biogeochemical cycles.

scholarly journals Dynamic Microbial Network Structure and Assembly Process in Rhizosphere and Bulk Soils Along a Coniferous Plantation Chronosequence

2021 ◽  
Author(s):  
Ying Wang ◽  
Liguo Dong ◽  
Min Zhang ◽  
Xiaoxiong Bai ◽  
Jiawen Zhang ◽  
...  
Keyword(s):  
Total Phosphorus ◽  
Fungal Community ◽  
Soil Microbial Communities ◽  
Dispersal Limitation ◽  
Soil Samples ◽  
Pinus Tabulaeformis ◽  
Bulk Soil ◽  
Microbial Composition ◽  
Soil Microbial ◽  
Plantation Development

Abstract Aims: During plantation development, microbial composition and diversity are critical for the establishment of plant diversity and multiple ecosystem functions. Here we aimed to evaluate the impacts of chronosequence and soil compartment on the bacterial and fungal community compositions, species co-occurrence, and assembly processes in forest ecosystem.Methods: Soils were collected in rhizosphere and bulk soils along a Pinus tabulaeformis plantation chronosequence (15, 30 and 60 years old). The bacterial and fungal communities were determined using amplicon sequencing.Results: The effect of stand age on the soil properties and microbial community structures was stronger than the effect of the soil compartment. In all soil samples, the dominant bacterial phyla were Proteobacteria, Acidobacteria, Actinobacteria, and Chloroflexi. Basidiomycota, Ascomycota, and Mortierellomycota were the dominant fungal phyla. Higher turnover rates of soil microbial communities were observed in rhizosphere soil than in bulk soil. Dispersal limitation governed the bacterial and fungal community assembly in all soil samples, and the fungal community was more susceptible to dispersal limitation. The bacterial and fungal keystone species compositions in the rhizosphere had significant positive correlations with the soil total phosphorus and nitrite nitrogen and total nitrogen and total phosphorus, respectively, indicating their importance in soil nitrogen and phosphorus cycling. The complexity of bacterial networks increased along the chronosequence. Fungal network complexity did not show a clear age-related trend but increased from bulk soil to the rhizosphere.Conclusions: During Pinus tabulaeformis plantation development, soil microbial assembly was less environmentally constrained due to an increase in resource availability.

scholarly journals Soil Microbial Biogeography in a Changing World: Recent Advances and Future Perspectives

mSystems ◽  
2020 ◽  
Vol 5 (2) ◽  
Author(s):  
Haiyan Chu ◽  
Gui-Feng Gao ◽  
Yuying Ma ◽  
Kunkun Fan ◽  
Manuel Delgado-Baquerizo
Keyword(s):  
Microbial Communities ◽  
Soil Microbial Communities ◽  
Well Being ◽  
Ecosystem Functions ◽  
Soil Microbial ◽  
Microbial Biogeography ◽  
Recent Advances ◽  
Technological Advances ◽  
Global Change Scenarios ◽  
Changing World

ABSTRACT Soil microbial communities are fundamental to maintaining key soil processes associated with litter decomposition, nutrient cycling, and plant productivity and are thus integral to human well-being. Recent technological advances have exponentially increased our knowledge concerning the global ecological distributions of microbial communities across space and time and have provided evidence for their contribution to ecosystem functions. However, major knowledge gaps in soil biogeography remain to be addressed over the coming years as technology and research questions continue to evolve. In this minireview, we state recent advances and future directions in the study of soil microbial biogeography and discuss the need for a clearer concept of microbial species, projections of soil microbial distributions toward future global change scenarios, and the importance of embracing culture and isolation approaches to determine microbial functional profiles. This knowledge will be critical to better predict ecosystem functions in a changing world.

Structure and function of alpine and arctic soil microbial communities

2005 ◽  
Vol 156 (7) ◽  
pp. 775-784 ◽  
Author(s):  
Diana R. Nemergut ◽  
Elizabeth K. Costello ◽  
Allen F. Meyer ◽  
Monte Y. Pescador ◽  
Michael N. Weintraub ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Soil Microbial Communities ◽  
Structure And Function ◽  
Soil Microbial ◽  
Arctic Soil ◽  
And Function
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