Impact of sea level change on coastal soil organic matter, priming effects and prokaryotic community assembly

2019 ◽  
Vol 95 (10) ◽  
Author(s):  
Thomas Dinter ◽  
Simone Geihser ◽  
Matthias Gube ◽  
Rolf Daniel ◽  
Yakov Kuzyakov
Keyword(s):  
Organic Matter ◽  
Salt Marsh ◽  
Soil Organic Matter ◽  
Salt Marshes ◽  
Extracellular Enzymes ◽  
Rrna Gene ◽  
Co2 Efflux ◽  
Prokaryotic Community ◽  
Priming Effects ◽  
Niche Adaptation

ABSTRACT Salt marshes are coastal areas storing high amounts of soil organic matter (SOM) while simultaneously being prone to tidal changes. Here, SOM-decomposition and accompanied priming effects (PE), which describe interactions between labile and old SOM, were studied under controlled flooding conditions. Soil samples from two Wadden Sea salt marsh zones, pioneer (Pio), flooded two times/day, and lower salt marsh (Low), flooded ∼eight times/month, were measured for 56 days concerning CO2-efflux and prokaryotic community shifts during three different inundation-treatments: total-drained (Drained), all-time-flooded (Waterlogged) or temporal-flooding (Tidal). Priming was induced by 14C-glucose addition. CO2-efflux from soil followed Low>Pio and Tidal>Drained>Waterlogged, likely due to O2-depletion and moisture maintenance, two key factors governed by tidal inundation with regard to SOM mineralisation. PEs in both zones were positive (Drained) or absent (Waterlogged, Tidal), presumably as a result of prokaryotes switching from production of extracellular enzymes to direct incorporation of labile C. A doubled amount of prokaryotic biomass in Low compared to Pio probably induced higher chances of cometabolic effects and higher PE. 16S-rRNA-gene-amplicon-based analysis revealed differences in bacterial and archaeal community composition between both zones, revealing temporal niche adaptation with flooding treatment. Strongest alterations were found in Drained, likely due to inundation-mediated changes in C-binding capacities.

scholarly journals Mechanistic strategies of microbial communities regulating lignocellulose deconstruction in a UK salt marsh

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Daniel R. Leadbeater ◽  
Nicola C. Oates ◽  
Joseph P. Bennett ◽  
Yi Li ◽  
Adam A. Dowle ◽  
...  
Keyword(s):  
Salt Marsh ◽  
Salt Marshes ◽  
Molecular Mechanisms ◽  
Surface Sediments ◽  
Gene Profiling ◽  
Oxidative Enzymes ◽  
Lignocellulose Degradation ◽  
Rrna Gene ◽  
Enzymatic Mechanisms

Abstract Background Salt marshes are major natural repositories of sequestered organic carbon with high burial rates of organic matter, produced by highly productive native flora. Accumulated carbon predominantly exists as lignocellulose which is metabolised by communities of functionally diverse microbes. However, the organisms that orchestrate this process and the enzymatic mechanisms employed that regulate the accumulation, composition and permanence of this carbon stock are not yet known. We applied meta-exo-proteome proteomics and 16S rRNA gene profiling to study lignocellulose decomposition in situ within the surface level sediments of a natural established UK salt marsh. Results Our studies revealed a community dominated by Gammaproteobacteria, Bacteroidetes and Deltaproteobacteria that drive lignocellulose degradation in the salt marsh. We identify 42 families of lignocellulolytic bacteria of which the most active secretors of carbohydrate-active enzymes were observed to be Prolixibacteracea, Flavobacteriaceae, Cellvibrionaceae, Saccharospirillaceae, Alteromonadaceae, Vibrionaceae and Cytophagaceae. These families secreted lignocellulose-active glycoside hydrolase (GH) family enzymes GH3, GH5, GH6, GH9, GH10, GH11, GH13 and GH43 that were associated with degrading Spartina biomass. While fungi were present, we did not detect a lignocellulolytic contribution from fungi which are major contributors to terrestrial lignocellulose deconstruction. Oxidative enzymes such as laccases, peroxidases and lytic polysaccharide monooxygenases that are important for lignocellulose degradation in the terrestrial environment were present but not abundant, while a notable abundance of putative esterases (such as carbohydrate esterase family 1) associated with decoupling lignin from polysaccharides in lignocellulose was observed. Conclusions Here, we identify a diverse cohort of previously undefined bacteria that drive lignocellulose degradation in the surface sediments of the salt marsh environment and describe the enzymatic mechanisms they employ to facilitate this process. Our results increase the understanding of the microbial and molecular mechanisms that underpin carbon sequestration from lignocellulose within salt marsh surface sediments in situ and provide insights into the potential enzymatic mechanisms regulating the enrichment of polyphenolics in salt marsh sediments.

scholarly journals Predicting decadal trends and transient responses of radiocarbon storage and fluxes in a temperate forest soil

2012 ◽  
Vol 9 (8) ◽  
pp. 3013-3028 ◽  
Author(s):  
C. A. Sierra ◽  
S. E. Trumbore ◽  
E. A. Davidson ◽  
S. D. Frey ◽  
K. E. Savage ◽  
...  
Keyword(s):  
Organic Matter ◽  
Soil Organic Matter ◽  
Soil Carbon ◽  
Empirical Model ◽  
Temperate Forest ◽  
Global Environmental Change ◽  
Carbon Dynamics ◽  
Co2 Efflux ◽  
Soil C ◽  
Soil Carbon Dynamics

Abstract. Representing the response of soil carbon dynamics to global environmental change requires the incorporation of multiple tools in the development of predictive models. An important tool to construct and test models is the incorporation of bomb radiocarbon in soil organic matter during the past decades. In this manuscript, we combined radiocarbon data and a previously developed empirical model to explore decade-scale soil carbon dynamics in a temperate forest ecosystem at the Harvard Forest, Massachusetts, USA. We evaluated the contribution of different soil C fractions to both total soil CO2 efflux and microbially respired C. We tested the performance of the model based on measurable soil organic matter fractions against a decade of radiocarbon measurements. The model was then challenged with radiocarbon measurements from a warming and N addition experiment to test multiple hypotheses about the different response of soil C fractions to the experimental manipulations. Our results showed that the empirical model satisfactorily predicts the trends of radiocarbon in litter, density fractions, and respired CO2 observed over a decade in the soils not subjected to manipulation. However, the model, modified with prescribed relationships for temperature and decomposition rates, predicted most but not all the observations from the field experiment where soil temperatures and nitrogen levels were increased, suggesting that a larger degree of complexity and mechanistic relations need to be added to the model to predict short-term responses and transient dynamics.

scholarly journals Respiration of 13C-Labeled Substrates Added to Soil in the Field and Subsequent 16S rRNA Gene Analysis of 13C-Labeled Soil DNA

2003 ◽  
Vol 69 (3) ◽  
pp. 1614-1622 ◽  
Author(s):  
P. Padmanabhan ◽  
S. Padmanabhan ◽  
C. DeRito ◽  
A. Gray ◽  
D. Gannon ◽  
...  
Keyword(s):  
Organic Matter ◽  
Soil Organic Matter ◽  
16S Rrna ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Gas Chromatography Mass Spectrometry ◽  
Rrna Gene ◽  
Labeled Compounds ◽  
Field Soil ◽  
Soil Dna

ABSTRACT Our goal was to develop a field soil biodegradation assay using 13C-labeled compounds and identify the active microorganisms by analyzing 16S rRNA genes in soil-derived 13C-labeled DNA. Our biodegradation approach sought to minimize microbiological artifacts caused by physical and/or nutritional disturbance of soil associated with sampling and laboratory incubation. The new field-based assay involved the release of 13C-labeled compounds (glucose, phenol, caffeine, and naphthalene) to soil plots, installation of open-bottom glass chambers that covered the soil, and analysis of samples of headspace gases for 13CO2 respiration by gas chromatography/mass spectrometry (GC/MS). We verified that the GC/MS procedure was capable of assessing respiration of the four substrates added (50 ppm) to 5 g of soil in sealed laboratory incubations. Next, we determined background levels of 13CO2 emitted from naturally occurring soil organic matter to chambers inserted into our field soil test plots. We found that the conservative tracer, SF6, that was injected into the headspace rapidly diffused out of the soil chamber and thus would be of little value for computing the efficiency of retaining respired 13CO2. Field respiration assays using all four compounds were completed. Background respiration from soil organic matter interfered with the documentation of in situ respiration of the slowly metabolized (caffeine) and sparingly soluble (naphthalene) compounds. Nonetheless, transient peaks of 13CO2 released in excess of background were found in glucose- and phenol-treated soil within 8 h. Cesium-chloride separation of 13C-labeled soil DNA was followed by PCR amplification and sequencing of 16S rRNA genes from microbial populations involved with 13C-substrate metabolism. A total of 29 full sequences revealed that active populations included relatives of Arthrobacter, Pseudomonas, Acinetobacter, Massilia, Flavobacterium, and Pedobacter spp. for glucose; Pseudomonas, Pantoea, Acinetobacter, Enterobacter, Stenotrophomonas, and Alcaligenes spp. for phenol; Pseudomonas, Acinetobacter, and Variovorax spp. for naphthalene; and Acinetobacter, Enterobacter, Stenotrophomonas, and Pantoea spp. for caffeine.

scholarly journals Predicting decadal trends and transient responses of radiocarbon storage and fluxes in a temperate forest soil

2012 ◽  
Vol 9 (2) ◽  
pp. 2197-2232 ◽  
Author(s):  
C. A. Sierra ◽  
S. E. Trumbore ◽  
E. A. Davidson ◽  
S. D. Frey ◽  
K. E. Savage ◽  
...  
Keyword(s):  
Organic Matter ◽  
Soil Organic Matter ◽  
Soil Carbon ◽  
Empirical Model ◽  
Temperate Forest ◽  
Global Environmental Change ◽  
Carbon Dynamics ◽  
Co2 Efflux ◽  
Soil C ◽  
Soil Carbon Dynamics

Abstract. Representing the response of soil carbon dynamics to global environmental change requires the incorporation of multiple tools in the development of predictive models. An important tool to construct and test models is the incorporation of bomb radiocarbon in soil organic matter during the past decades. In this manuscript, we combined radiocarbon data and a previously developed empirical model to explore decade-scale soil carbon dynamics in a temperate forest ecosystem at the Harvard Forest, Massachusetts, USA. We evaluated the contribution of different soil C fractions to both total soil CO2 efflux and microbially-respired C. We tested the performance of the model based on measurable soil organic matter fractions against a decade of radiocarbon measurements. The model was then challenged with radiocarbon measurements from a warming and N addition experiment to test multiple hypotheses about the different response of soil C fractions to the experimental manipulations. Our results showed that the empirical model satisfactorily predicts the trends of radiocarbon in litter, density fractions, and respired CO2 observed over a decade in the soils not subjected to manipulation. However, the model, modified with prescribed relationships for temperature and decomposition rates, predicted most but not all the observations from the field experiment where soil temperatures and nitrogen levels were increased, suggesting that a larger degree of complexity and mechanistic relations need to be added to the model to predict short-term responses and transient dynamics.

Characterization of organic matter decomposition in the Venice Lagoon using the Tea Bag Index

2021 ◽  
Author(s):  
Alice Puppin ◽  
Marcella Roner ◽  
Alvise Finotello ◽  
Massimiliano Ghinassi ◽  
Laura Tommasini ◽  
...  
Keyword(s):  
Organic Matter ◽  
Salt Marsh ◽  
Sea Level ◽  
Salt Marshes ◽  
Litter Quality ◽  
Venice Lagoon ◽  
Organic Matter Decomposition ◽  
Tea Bag Index ◽  
Decomposition Processes ◽  
Surface Accretion

<p>Salt-marsh evolution importantly depends on complex feedbacks between hydrodynamic, morphological, and biological processes. These crucial ecogeomorphic structures support a diverse range of ecosystem services, including coastal protection and biodiversity increase. In addition, they are among the most carbon‐rich ecosystems on Earth, as their high primary production coupled with rapid surface accretion results into the ability to sequester atmospheric carbon at high rates. However, salt-marsh future is at risk today, due to the effects of climate changes and local anthropogenic disturbances, in particular sea-level rise and reduced fluvial sediment delivery to the coasts. The organic matter captured and stored by salt marshes results from the balance between inputs and outputs and may contribute to marsh surface accretion, which determines their ability to keep pace with sea-level rise. Therefore, a better understanding of the processes regulating organic matter dynamics on salt marshes is a critical step to elucidate their carbon sink potential and to address salt-marsh management and conservation issues. Toward this goal, we analysed organic matter decomposition processes within salt-marsh ecosystems by burying 712 commercially available tea bags within different marshes in the Venice Lagoon (Italy), following the Tea Bag Index protocol. The process provides the values of two key parameters: the decomposition rate (k) and litter stabilisation factor (S). Based on standardized litter bag experiments, the Tea Bag Index focuses on the effects of abiotic conditions, neglecting litter-quality influences. The mean values of the decomposition metrics from our analyses are in general consistent with previous results and indicate a quite fast decomposition of the organic matter with a remaining mass of about 34% of the initial labile mass after 90 days. We next explore the possible dependence of k and S on environmental drivers. Temperature showed the most significant relationship with decomposition processes, suggesting an organic-matter decay acceleration with warming temperature, in line with previous literature. Moreover, the statistical analysis indicated some significant trends of the decomposition rate also with surface elevation and distance from the marsh edge. This suggests that, at the marsh scale, higher and probably less frequently flooded sites are exposed to faster decomposition, likely due to greater oxygen availability enhancing microbial respiration. In conclusion, the organic matter decay we observed is rapid enough to consume all the labile material before it can be buried and stabilized, hence increased global temperatures may not have a significant effect in increasing organic matter decomposition in coastal marshes. Therefore, we argue that, at least in the short term, the remaining mass of the organic matter contributing to carbon sequestration and marsh accretion, strongly depends on the initial litter quality, recalcitrant or labile, which may differ considerably between different species and plant parts and may be affected by climate change effects.</p>

scholarly journals Effects of selected groundwater chemical traits on a salt marsh community

2011 ◽  
Vol 70 (1) ◽  
pp. 41-51 ◽  
Author(s):  
Mahmut Kilinç ◽  
Hamdi Kutbay ◽  
Erkan Yalçin ◽  
Ali Bilgin ◽  
Kenan Avci ◽  
...  
Keyword(s):  
Organic Matter ◽  
Salt Marsh ◽  
Soil Organic Matter ◽  
Water Depth ◽  
Positive Impact ◽  
Exchangeable Sodium ◽  
Ammophila Arenaria ◽  
Marsh Vegetation ◽  
Marsh Community ◽  
Chemical Traits

Effects of selected groundwater chemical traits on a salt marsh communityElectrical conductivity, exchangeable sodium ratio and water depth have negative impacts, whereas soil organic matter concentration has a positive impact on Black Sea salt marsh vegetation. The most saline soils were characterized bySalicornia prostratavegetation and associated with exchangeable sodium ratio.Alhagi pseudalhagiandTamarix smrynensispopulations were associated with water depth, whileJuncus littoralis, Ammophila arenariaandE. paraliaswere associated with soil organic matter.Euphorbia paralias, Ammophila arenariaandIris orientaliswere associated with acidity.

scholarly journals Tillage-induced short-term soil organic matter turnover and respiration

SOIL ◽  
2016 ◽  
Vol 2 (3) ◽  
pp. 475-486 ◽  
Author(s):  
Sebastian Rainer Fiedler ◽  
Peter Leinweber ◽  
Gerald Jurasinski ◽  
Kai-Uwe Eckhardt ◽  
Stephan Glatzel
Keyword(s):  
Organic Matter ◽  
Soil Organic Matter ◽  
Anaerobic Fermentation ◽  
Inhibitory Effect ◽  
Hot Water ◽  
Co2 Efflux ◽  
Short Term ◽  
Soil Organic Matter Turnover ◽  
Ionisation Mass Spectrometry ◽  
Carbon Compounds

Abstract. Tillage induces decomposition and mineralisation of soil organic matter (SOM) by the disruption of macroaggregates and may increase soil CO2 efflux by respiration, but these processes are not well understood at the molecular level. We sampled three treatments (mineral fertiliser: MF; biogas digestate: BD; unfertilised control: CL) of a Stagnic Luvisol a few hours before and directly after tillage as well as 4 days later from a harvested maize field in northern Germany and investigated these samples by means of pyrolysis-field ionisation mass spectrometry (Py-FIMS) and hot-water extraction. Before tillage, the Py-FIMS mass spectra revealed differences in relative ion intensities of MF and CL compared to BD most likely attributable to the cattle manure used for the biogas feedstock and to relative enrichments during anaerobic fermentation. After tillage, the CO2 effluxes were increased in all treatments, but this increase was less pronounced in BD. We explain this by restricted availability of readily biodegradable carbon compounds and possibly an inhibitory effect of sterols from digestates. Significant changes in SOM composition were observed following tillage. In particular, lignin decomposition and increased proportions of N-containing compounds were detected in BD. In MF, lipid proportions increased at the expense of ammonia, ammonium, carbohydrates and peptides, indicating enhanced microbial activity. SOM composition in CL was unaffected by tillage. Our analyses provide strong evidence for significant short-term SOM changes due to tillage in fertilised soils.

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