Soil bacterial community composition altered by increased nutrient availability in Arctic tundra soils

Koyama, Akihiro; Wallenstein, Matthew D.; Simpson, Robert G.; Moore, John C.

doi:10.3389/fmicb.2014.00516

Cited by 169 publications

(136 citation statements)

References 97 publications

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“…Bacterial community shifts may be resulting in potentially altered substrate use preference by decomposers, as well as different genetic functional activity. This is supported by other studies from Arctic soil and permafrost ecosystems that provide evidence of altered microbial community composition and rapid functional response to temperature manipulations, thawing soils, or fertilization treatments (Deslippe et al, 2012;Koyama et al, 2014;Mackelprang et al, 2011). For example, Actinobacteria abundance was found to increase in response to both increased temperature (Deslippe et al, 2012) and in freshly thawed permafrost soils (Mackelprang et al, 2011), similar to the response we observed in the Deep zone (Fig.…”

Section: Bacterial Community Shiftssupporting

confidence: 77%

“…Mackelprang et al (2011) also reported varying shifts in a wide array of functional genes in response to permafrost thaw. In addition, Koyama et al (2014) documented a decrease in the oligotrophic Acidobacteria phylum in response to fertilizer soil inputs which they attributed to be a direct result of competition with copiotrophic α-, β-, and γ -Proteobacteria which increased in abundance with fertilizer treatment. While oligotrophic organisms such as Acidobacteria are adapted to survive in low nutrient environments, they are often outcompeted in more fertile soils by generalist copiotrophs (such as Proteobacteria), which are better equipped to harvest available nutrients.…”

Section: Bacterial Community Shiftsmentioning

confidence: 99%

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Soil bacterial community and functional shifts in response to altered snowpack in moist acidic tundra of northern Alaska

Ricketts

Poretsky

Welker

et al. 2016

SOIL

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Abstract. Soil microbial communities play a central role in the cycling of carbon (C) in Arctic tundra ecosystems, which contain a large portion of the global C pool. Climate change predictions for Arctic regions include increased temperature and precipitation (i.e. more snow), resulting in increased winter soil insulation, increased soil temperature and moisture, and shifting plant community composition. We utilized an 18-year snow fence study site designed to examine the effects of increased winter precipitation on Arctic tundra soil bacterial communities within the context of expected ecosystem response to climate change. Soil was collected from three preestablished treatment zones representing varying degrees of snow accumulation, where deep snow ∼ 100 % and intermediate snow ∼ 50 % increased snowpack relative to the control, and low snow ∼ 25 % decreased snowpack relative to the control. Soil physical properties (temperature, moisture, active layer thaw depth) were measured, and samples were analysed for C concentration, nitrogen (N) concentration, and pH. Soil microbial community DNA was extracted and the 16S rRNA gene was sequenced to reveal phylogenetic community differences between samples and determine how soil bacterial communities might respond (structurally and functionally) to changes in winter precipitation and soil chemistry. We analysed relative abundance changes of the six most abundant phyla (ranging from 82 to 96 % of total detected phyla per sample) and found four (Acidobacteria, Actinobacteria, Verrucomicrobia, and Chloroflexi) responded to deepened snow. All six phyla correlated with at least one of the soil chemical properties (% C, % N, C : N, pH); however, a single predictor was not identified, suggesting that each bacterial phylum responds differently to soil characteristics. Overall, bacterial community structure (beta diversity) was found to be associated with snow accumulation treatment and all soil chemical properties. Bacterial functional potential was inferred using ancestral state reconstruction to approximate functional gene abundance, revealing a decreased abundance of genes required for soil organic matter (SOM) decomposition in the organic layers of the deep snow accumulation zones. These results suggest that predicted climate change scenarios may result in altered soil bacterial community structure and function, and indicate a reduction in decomposition potential, alleviated temperature limitations on extracellular enzymatic efficiency, or both. The fate of stored C in Arctic soils ultimately depends on the balance between these mechanisms.

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Section: Bacterial Community Shiftssupporting

confidence: 77%

Section: Bacterial Community Shiftsmentioning

confidence: 99%

Soil bacterial community and functional shifts in response to altered snowpack in moist acidic tundra of northern Alaska

Ricketts

Poretsky

Welker

et al. 2016

SOIL

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“…Our results stand in contrast to negative relationships between bacterial diversity and N additions reported from previous studies conducted at individual sites (19,43). This finding points to the importance of local context and highlights the pitfalls associated with extrapolating results obtained from individual sites to other ecosystems or soil types.…”

Section: Resultscontrasting

confidence: 56%

Consistent responses of soil microbial communities to elevated nutrient inputs in grasslands across the globe

Leff

Jones

Prober

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

1,051

702

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Soil microorganisms are critical to ecosystem functioning and the maintenance of soil fertility. However, despite global increases in the inputs of nitrogen (N) and phosphorus (P) to ecosystems due to human activities, we lack a predictive understanding of how microbial communities respond to elevated nutrient inputs across environmental gradients. Here we used high-throughput sequencing of marker genes to elucidate the responses of soil fungal, archaeal, and bacterial communities using an N and P addition experiment replicated at 25 globally distributed grassland sites. We also sequenced metagenomes from a subset of the sites to determine how the functional attributes of bacterial communities change in response to elevated nutrients. Despite strong compositional differences across sites, microbial communities shifted in a consistent manner with N or P additions, and the magnitude of these shifts was related to the magnitude of plant community responses to nutrient inputs. Mycorrhizal fungi and methanogenic archaea decreased in relative abundance with nutrient additions, as did the relative abundances of oligotrophic bacterial taxa. The metagenomic data provided additional evidence for this shift in bacterial life history strategies because nutrient additions decreased the average genome sizes of the bacterial community members and elicited changes in the relative abundances of representative functional genes. Our results suggest that elevated N and P inputs lead to predictable shifts in the taxonomic and functional traits of soil microbial communities, including increases in the relative abundances of fastergrowing, copiotrophic bacterial taxa, with these shifts likely to impact belowground ecosystems worldwide.soil bacteria | soil fungi | shotgun metagenomics | soil ecology | fertilization

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“…Interestingly, cold adapted Burkholderia species have also been recovered from coastal regions of the Ross Sea in Antarctica [27]. Copiotrophic a-and b-Proteobacteria were more responsive to shifts in nutrient status in Arctic soils than other taxa [28], supporting their proposed role as keystone taxa. Whether similar microbial community structural changes might be expected in oligotrophic Antarctic desert soils remains uncertain.…”

Section: Microbial Diversity In Cold Environmentsmentioning

confidence: 91%

Microbial diversity and functional capacity in polar soils

Makhalanyane

Goethem

Cowan

2016

Current Opinion in Biotechnology

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Global change is disproportionately affecting cold environments (polar and high elevation regions), with potentially negative impacts on microbial diversity and functional processes. In most cold environments the combination of low temperatures, and physical stressors, such as katabatic wind episodes and limited water availability result in biotic systems, which are in trophic terms very simple and primarily driven by microbial communities. Metagenomic approaches have provided key insights on microbial communities in these systems and how they may adapt to stressors and contribute towards mediating crucial biogeochemical cycles. Here we review, the current knowledge regarding edaphic-based microbial diversity and functional processes in Antarctica, and the Artic. Such insights are crucial and help to establish a baseline for understanding the impact of climate change on Polar Regions. AddressCentre for Microbial Ecology and Genomics, Department of Genetics, University of Pretoria, Pretoria 0028, South Africa Corresponding author: Cowan, Don Arthur (don.cowan@up.ac.za) IntroductionThe Congress of Parties (COP) 21 meeting in Paris (November 2015) highlighted the urgency of global climate change, and the critical need to reduce global average temperatures through curbing greenhouse gas emissions [1]. Nowhere are the effects of global change more apparent than in cold environments (polar and alpine regions), which are subject to accelerated rates of warming compared to other ecosystems [2 ,3]. Climatic models have predicted that temperatures in high latitude regions of the Northern Hemisphere are likely to increase by between 0.38C and 4.88C before the end of the twenty first century [4]. There is also evidence that regions in the Southern Hemisphere have experienced the fastest warming globally, with average increases of as much as 2.48C in the last fifty years [5].A major consequence of climate change in cold environments is the thawing of submerged and surface ice, which alters the hydrology of the systems and may have adverse effects on microbial processes [6 ]. In cold environments, microorganisms (bacteria, archaea and fungi) are major constituents of the total biomass, and are estimated to mediate the cycling of key biogeochemical elements such as nitrogen and carbon, with potentially important implications for the productivity of these systems [7]. Although the precise contribution of microbial processes to global change processes are not well known, there are efforts to incorporate biological processes into Earth systems models with the realization that they may be crucial in regulating soil organic matter (SOM) [8 ]. For instance, permafrost (defined as ground which remains frozen for at least two years) in cold environments stores roughly 1600 Pg of carbon, which if released would significantly contribute towards increasing global CO 2 levels [9]. The current contribution of microbial communities to constraining carbon losses in permafrost and the influence on CO 2 levels remains virtually unknown. In ...

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Soil bacterial community composition altered by increased nutrient availability in Arctic tundra soils

Cited by 169 publications

References 97 publications

Soil bacterial community and functional shifts in response to altered snowpack in moist acidic tundra of northern Alaska

Soil bacterial community and functional shifts in response to altered snowpack in moist acidic tundra of northern Alaska

Consistent responses of soil microbial communities to elevated nutrient inputs in grasslands across the globe

Microbial diversity and functional capacity in polar soils

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