Stability of a rhizosphere microbial community exposed to natural and manipulated environmental variability

Lovell, Carolyn

doi:10.1016/s0168-6496(01)00177-5

Cited by 10 publications

(16 citation statements)

References 17 publications

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“…It, however, should be noted that the effect of PLFAs derived from living rice roots could not be completely excluded. Although PLFA composition of rice roots was unavailable, the measurement of sea grass roots showed that plant roots contained mainly PLFAs 16:0, 18:2ω6c, 18:3ω3 and 18:1ω9 (over 90% of total PLFAs in the case of Spartina alterniflora ) [33]. Assuming rice roots contained similar PLFA composition, total and 13 C PLFAs, especially those of 16:0 and 18:1ω9 might be overestimated due to possible incomplete separation of living roots from soil.…”

Section: Resultsmentioning

confidence: 99%

Linking microbial community dynamics to rhizosphere carbon flow in a wetland rice soil

Murase

Watanabe

et al. 2004

FEMS Microbiology Ecology

104

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Wetland ecosystems are important reservoirs of biodiversity and significantly contribute to emissions of the greenhouse gases CO 2 , N 2 O, and CH 4. High an-thropogenic nitrogen (N) inputs from agriculture and fossil fuel combustion have been recognized as a severe threat to biodiversity and ecosystem functioning, such as control of greenhouse gas emissions. Therefore, it is important to understand how increased N input into pristine wetlands affects the composition and activity of microorganisms, especially in interaction with dominant wetland plants. In a series of incubations analyzed over 90 days, we disentangled the effects of N fertilization on the microbial community in bulk soil and the rhizosphere of Juncus acutiflorus, a common and abundant graminoid wetland plant. We observed an increase in greenhouse gas emissions when N is increased in incubations with J. acutiflorus, changing the system from a greenhouse gas sink to a source. Using 16S rRNA gene amplicon sequencing, we determined that the bacterial orders Opitutales, subgroup 6 Acido-bacteria, and Sphingobacteriales significantly responded to high N availability. Based on metagenomic data, we hypothesize that these groups are contributing to the increased greenhouse gas emissions. These results indicated that increased N input leads to shifts in microbial activity within the rhizosphere, altering N cycling dynamics. Our study provides a framework for connecting environmental conditions of wetland bulk and rhizosphere soil to the structure and metabolic output of microbial communities. IMPORTANCE Microorganisms living within the rhizospheres of wetland plants significantly contribute to greenhouse gas emissions. Understanding how microbes produce these gases under conditions that have been imposed by human activities (i.e., nitrogen pollution) is important to the development of future management strategies. Our results illustrate that within the rhizosphere of the wetland plant Juncus acutiflorus, physiological differences associated with nitrogen availability can influence microbial activity linked to greenhouse gas production. By pairing taxonomic information and environmental conditions like nitrogen availability with functional outputs of a system such as greenhouse gas fluxes, we present a framework to link certain taxa to both nitrogen load and greenhouse gas production. We view this type of combined information as essential in moving forward in our understanding of complex systems such as rhi-zosphere microbial communities.

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Section: Resultsmentioning

confidence: 99%

Linking microbial community dynamics to rhizosphere carbon flow in a wetland rice soil

Murase

Watanabe

et al. 2004

FEMS Microbiology Ecology

104

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“…The increasing discharges of agricultural fertilizers into coastal ecosystems have been shown to cause a progressive transition of creek-edge and bay-edge marshes into mudflats and wider creeks worldwide (MacGarvin, 2001 ; Tiner et al, 2006 ; Deegan et al, 2012 ). Thus, to prevent such ecological distress, it is crucial to examine the capacity of salt marshes to cycle N and to deal with exogenous N influxes (e.g., Lovell et al, 2001 ; Bowen et al, 2011 ; Peng et al, 2013 ). In spite of the urgency, the current knowledge of how microbial N cycling populations are ecologically assembled in salt marshes is still rudimentary.…”

Section: Discussionmentioning

confidence: 99%

“…For instance, whereas the ammonia-oxidizing bacteria (AOB) were found to respond to N fertilization, ammonia-oxidizing archaea (AOA) remained unaffected (Peng et al, 2013 ). Moreover, no significant effect was found on the nitrogen-fixing and denitrifying bacterial communities when exposed to added N (Piceno and Lovell, 2000 ; Lovell et al, 2001 ; Bowen et al, 2011 ). Of particular importance, and lacking in these studies, is a thorough understanding of the distribution and drivers of N cycling communities in a naturally developing salt marsh ecosystem.…”

Section: Introductionmentioning

confidence: 99%

Reconstructing the Genetic Potential of the Microbially-Mediated Nitrogen Cycle in a Salt Marsh Ecosystem

et al. 2016

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Coastal ecosystems are considered buffer zones for the discharge of land-derived nutrients without accounting for potential negative side effects. Hence, there is an urgent need to better understand the ecological assembly and dynamics of the microorganisms that are involved in nitrogen (N) cycling in such systems. Here, we employed two complementary methodological approaches (i.e., shotgun metagenomics and quantitative PCR) to examine the distribution and abundance of selected microbial genes involved in N transformations. We used soil samples collected along a well-established pristine salt marsh soil chronosequence that spans over a century of ecosystem development at the island of Schiermonnikoog, The Netherlands. Across the examined soil successional stages, the structure of the populations of genes involved in N cycling processes was strongly related to (shifts in the) soil nitrogen levels (i.e., NO3−, NH4+), salinity and pH (explaining 73.8% of the total variation, R2 = 0.71). Quantification of the genes used as proxies for N fixation, nitrification and denitrification revealed clear successional signatures that corroborated the taxonomic assignments obtained by metagenomics. Notably, we found strong evidence for niche partitioning, as revealed by the abundance and distribution of marker genes for nitrification (ammonia-oxidizing bacteria and archaea) and denitrification (nitrite reductase nirK, nirS and nitrous oxide reductase nosZ clades I and II). This was supported by a distinct correlation between these genes and soil physico-chemical properties, such as soil physical structure, pH, salinity, organic matter, total N, NO3−, NH4+ and SO42−, across four seasonal samplings. Overall, this study sheds light on the successional trajectories of microbial N cycle genes along a naturally developing salt marsh ecosystem. The data obtained serve as a foundation to guide the formulation of ecological models that aim to effectively monitor and manage pristine and impacted salt marsh areas. Such models should account for the ecology as well as the historical contingency of N cycling communities.

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“…The diazotroph assemblages associated with salt marsh plant rhizospheres are somewhat stable. Only minor changes in the assemblages were observed when long and short-term fertilization and above ground biomass removal experiments were performed [ 29 , 30 , 31 , 79 ]. The drastic difference in the diazotroph assemblages in 2005 and 2006 as observed in DGGE band determination and deemed significant by PCA cluster analysis, indicate that the moderate drought event that occurred in 2004 directly affected these assemblages.…”

Section: Discussionmentioning

confidence: 99%

Responses of Salt Marsh Plant Rhizosphere Diazotroph Assemblages to Drought

2018

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Drought has many consequences in the tidally dominated Spartina sp. salt marshes of the southeastern US; including major dieback events, changes in sediment chemistry and obvious changes in the landscape. These coastal systems tend to be highly productive, yet many salt marshes are also nitrogen limited and depend on plant associated diazotrophs as their source of ‘new’ nitrogen. A 4-year study was conducted to investigate the structure and composition of the rhizosphere diazotroph assemblages associated with 5 distinct plant zones in one such salt marsh. A period of greatly restricted tidal inundation and precipitation, as well as two periods of drought (June–July 2004, and May 2007) occurred during the study. DGGE of nifH PCR amplicons from rhizosphere samples, Principal Components Analysis of the resulting banding patterns, and unconstrained ordination analysis of taxonomic data and environmental parameters were conducted. Diazotroph assemblages were organized into 5 distinct groups (R2 = 0.41, p value < 0.001) whose presence varied with the environmental conditions of the marsh. Diazotroph assemblage group detection differed during and after the drought event, indicating that persistent diazotrophs maintained populations that provided reduced supplies of new nitrogen for vegetation during the periods of drought.

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Stability of a rhizosphere microbial community exposed to natural and manipulated environmental variability

Cited by 10 publications

References 17 publications

Linking microbial community dynamics to rhizosphere carbon flow in a wetland rice soil

Linking microbial community dynamics to rhizosphere carbon flow in a wetland rice soil

Reconstructing the Genetic Potential of the Microbially-Mediated Nitrogen Cycle in a Salt Marsh Ecosystem

Responses of Salt Marsh Plant Rhizosphere Diazotroph Assemblages to Drought

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