The effect of stream microbial inoculation on in-stream carbon processing

2020 ◽  
Author(s):  
Jakob Schelker ◽  
Florian Caillon ◽  
Katharina Besemer ◽  
Peter Peduzzi ◽  
Astrid Harjung
Keyword(s):  
Microbial Community ◽  
Community Dynamics ◽  
Soil Microbes ◽  
Microbial Community Composition ◽  
Microbial Life ◽  
Soil Microbial ◽  
Microbial Inoculation ◽  
Microbial Community Dynamics ◽  
Small Streams ◽  
Carbon Processing

<p>Hydrological events mobilize chemically diverse dissolved organic matter (DOM) from soils to streams. Further, such events can also cause an influx of soil microbial life into fluvial systems. Here we present results from the HYDRO-DIVERSITY project, which aims to investigate the dynamic transfer of DOM and microbial life from catchment soils to streams, as well as their downstream fate. We studied the microbial community composition and DOM quality using 16S Illumina sequencing and fluorescence and absorbance spectroscopy. Data from small streams showed strong changes in DOM composition and in the microbial community delivered from soils during hydrological events. Moreover, we performed a flume experiment, in which soil microbial inoculation and the processing of DOM across different biofilm ages were evaluated. As such, biofilm age did not directly affect the establishment of soil microbes in the stream ecosystem. However, in-stream processing of soil DOM appeared to be affected by the inoculation event. This poses the fundamental question, if the processing of DOM in streams and rivers depends on the transient presence of specific soil microbes in stream ecosystems. Overall our results show that soils provide a dynamic and relevant influx of microbes and DOM to first order streams and that this dynamic influx likely affects microbial community dynamics of downstream fluvial networks as well as in-stream DOM processing. </p>

scholarly journals Microbial Community Dynamics Associated with Rhizosphere Carbon Flow

2003 ◽  
Vol 69 (11) ◽  
pp. 6793-6800 ◽  
Author(s):  
Jessica L. Butler ◽  
Mark A. Williams ◽  
Peter J. Bottomley ◽  
David D. Myrold
Keyword(s):  
Microbial Community ◽  
Growth Stage ◽  
Shoot Growth ◽  
Community Dynamics ◽  
Lolium Multiflorum ◽  
Microbial Community Composition ◽  
Gram Positive ◽  
Soil Microbial ◽  
Microbial Community Dynamics ◽  
Period 2

ABSTRACT Root-deposited photosynthate (rhizodeposition) is an important source of readily available carbon (C) for microbes in the vicinity of growing roots. Plant nutrient availability is controlled, to a large extent, by the cycling of this and other organic materials through the soil microbial community. Currently, our understanding of microbial community dynamics associated with rhizodeposition is limited. We used a 13C pulse-chase labeling procedure to examine the incorporation of rhizodeposition into individual phospholipid fatty acids (PLFAs) in the bulk and rhizosphere soils of greenhouse-grown annual ryegrass (Lolium multiflorum Lam. var. Gulf). Labeling took place during a growth stage in transition between active root growth and rapid shoot growth on one set of plants (labeling period 1) and 9 days later during the rapid shoot growth stage on another set of plants (labeling period 2). Temporal differences in microbial community composition were more apparent than spatial differences, with a greater relative abundance of PLFAs from gram-positive organisms (i15:0 and a15:0) in the second labeling period. Although more abundant, gram-positive organisms appeared to be less actively utilizing rhizodeposited C in labeling period 2 than in labeling period 1. Gram-negative bacteria associated with the 16:1ω5 PLFA were more active in utilizing 13C-labeled rhizodeposits in the second labeling period than in the first labeling period. In both labeling periods, however, the fungal PLFA 18:2ω6,9 was the most highly labeled. These results demonstrate the effectiveness of using 13C labeling and PLFA analysis to examine the microbial dynamics associated with rhizosphere C cycling by focusing on the members actively involved.

scholarly journals Soil microbial community dynamics and assembly under long-term land use change

2017 ◽  
Vol 93 (10) ◽  
Author(s):  
Dennis Goss-Souza ◽  
Lucas William Mendes ◽  
Clovis Daniel Borges ◽  
Dilmar Baretta ◽  
Siu Mui Tsai ◽  
...  
Keyword(s):  
Land Use ◽  
Microbial Community ◽  
Land Use Change ◽  
Soil Microbial Community ◽  
Community Dynamics ◽  
Soil Microbial ◽  
Microbial Community Dynamics

scholarly journals Visualizing Microbial Community Dynamics via a Controllable Soil Environment

mSystems ◽  
2020 ◽  
Vol 5 (1) ◽  
Author(s):  
Arunima Bhattacharjee ◽  
Dusan Velickovic ◽  
Thomas W. Wietsma ◽  
Sheryl L. Bell ◽  
Janet K. Jansson ◽  
...  
Keyword(s):  
Soil Moisture ◽  
Microbial Community ◽  
Microbial Communities ◽  
Community Dynamics ◽  
Soil Microbial Communities ◽  
Soil Microbiome ◽  
Soil Core ◽  
Soil Microbial ◽  
Functional Relationships ◽  
Microbial Community Dynamics

ABSTRACT Understanding the basic biology that underpins soil microbiome interactions is required to predict the metaphenomic response to environmental shifts. A significant knowledge gap remains in how such changes affect microbial community dynamics and their metabolic landscape at microbially relevant spatial scales. Using a custom-built SoilBox system, here we demonstrated changes in microbial community growth and composition in different soil environments (14%, 24%, and 34% soil moisture), contingent upon access to reservoirs of nutrient sources. The SoilBox emulates the probing depth of a common soil core and enables determination of both the spatial organization of the microbial communities and their metabolites, as shown by confocal microscopy in combination with mass spectrometry imaging (MSI). Using chitin as a nutrient source, we used the SoilBox system to observe increased adhesion of microbial biomass on chitin islands resulting in degradation of chitin into N-acetylglucosamine (NAG) and chitobiose. With matrix-assisted laser desorption/ionization (MALDI)-MSI, we also observed several phospholipid families that are functional biomarkers for microbial growth on the chitin islands. Fungal hyphal networks bridging different chitin islands over distances of 27 mm were observed only in the 14% soil moisture regime, indicating that such bridges may act as nutrient highways under drought conditions. In total, these results illustrate a system that can provide unprecedented spatial information about interactions within soil microbial communities as a function of changing environments. We anticipate that this platform will be invaluable in spatially probing specific intra- and interkingdom functional relationships of microbiomes within soil. IMPORTANCE Microbial communities are key components of the soil ecosystem. Recent advances in metagenomics and other omics capabilities have expanded our ability to characterize the composition and function of the soil microbiome. However, characterizing the spatial metabolic and morphological diversity of microbial communities remains a challenge due to the dynamic and complex nature of soil microenvironments. The SoilBox system, demonstrated in this work, simulates an ∼12-cm soil depth, similar to a typical soil core, and provides a platform that facilitates imaging the molecular and topographical landscape of soil microbial communities as a function of environmental gradients. Moreover, the nondestructive harvesting of soil microbial communities for the imaging experiments can enable simultaneous multiomics analysis throughout the depth of the SoilBox. Our results show that by correlating molecular and optical imaging data obtained using the SoilBox platform, deeper insights into the nature of specific soil microbial interactions can be achieved.

scholarly journals Microbial community dynamics in the forefield of glaciers

2014 ◽  
Vol 281 (1795) ◽  
pp. 20140882 ◽  
Author(s):  
James A. Bradley ◽  
Joy S. Singarayer ◽  
Alexandre M. Anesio
Keyword(s):  
Microbial Community ◽  
Large Scale ◽  
Community Dynamics ◽  
Microbial Community Composition ◽  
Future Research ◽  
Nutrient Pools ◽  
Microbial Community Dynamics ◽  
Ice Retreat ◽  
External Sources ◽  
Bacteria And Fungi

Retreating ice fronts (as a result of a warming climate) expose large expanses of deglaciated forefield, which become colonized by microbes and plants. There has been increasing interest in characterizing the biogeochemical development of these ecosystems using a chronosequence approach. Prior to the establishment of plants, microbes use autochthonously produced and allochthonously delivered nutrients for growth. The microbial community composition is largely made up of heterotrophic microbes (both bacteria and fungi), autotrophic microbes and nitrogen-fixing diazotrophs. Microbial activity is thought to be responsible for the initial build-up of labile nutrient pools, facilitating the growth of higher order plant life in developed soils. However, it is unclear to what extent these ecosystems rely on external sources of nutrients such as ancient carbon pools and periodic nitrogen deposition. Furthermore, the seasonal variation of chronosequence dynamics and the effect of winter are largely unexplored. Modelling this ecosystem will provide a quantitative evaluation of the key processes and could guide the focus of future research. Year-round datasets combined with novel metagenomic techniques will help answer some of the pressing questions in this relatively new but rapidly expanding field, which is of growing interest in the context of future large-scale ice retreat.

scholarly journals Citrate and malonate increase microbial activity and alter microbial community composition in uncontaminated and diesel-contaminated soil microcosms

SOIL ◽  
2016 ◽  
Vol 2 (3) ◽  
pp. 487-498 ◽  
Author(s):  
Belinda C. Martin ◽  
Suman J. George ◽  
Charles A. Price ◽  
Esmaeil Shahsavari ◽  
Andrew S. Ball ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Activity ◽  
Community Dynamics ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Plant Root ◽  
Root Exudation ◽  
Microbial Community Composition ◽  
Gas Chromatography Mass Spectrometry ◽  
Potential Implication ◽  
Microbial Community Dynamics

Abstract. Petroleum hydrocarbons (PHCs) are among the most prevalent sources of environmental contamination. It has been hypothesized that plant root exudation of low molecular weight organic acid anions (carboxylates) may aid degradation of PHCs by stimulating heterotrophic microbial activity. To test their potential implication for bioremediation, we applied two commonly exuded carboxylates (citrate and malonate) to uncontaminated and diesel-contaminated microcosms (10 000 mg kg−1; aged 40 days) and determined their impact on the microbial community and PHC degradation. Every 48 h for 18 days, soil received 5 µmol g−1 of (i) citrate, (ii) malonate, (iii) citrate + malonate or (iv) water. Microbial activity was measured daily as the flux of CO2. After 18 days, changes in the microbial community were assessed by a community-level physiological profile (CLPP) and 16S rRNA bacterial community profiles determined by denaturing gradient gel electrophoresis (DGGE). Saturated PHCs remaining in the soil were assessed by gas chromatography–mass spectrometry (GC-MS). Cumulative soil respiration increased 4- to 6-fold with the addition of carboxylates, while diesel contamination resulted in a small, but similar, increase across all carboxylate treatments. The addition of carboxylates resulted in distinct changes to the microbial community in both contaminated and uncontaminated soils but only a small increase in the biodegradation of saturated PHCs as measured by the n-C17 : pristane biomarker. We conclude that while the addition of citrate and malonate had little direct effect on the biodegradation of saturated hydrocarbons present in diesel, their effect on the microbial community leads us to suggest further studies using a variety of soils and organic acids, and linked to in situ studies of plants, to investigate the role of carboxylates in microbial community dynamics.

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