Type II Aerobic Methane Oxidizing Bacteria (AMOB) Drive Methane Oxidation in Pulsed Wetlands as Indicated by 13C-Phospholipid Fatty Acid Composition

Methane (CH4) is a potent greenhouse gas and management strategies have been proposed to limit CH4 emissions from freshwater wetlands. The methanotrophic bacteria can intercept much of the CH4 produced by methanogenic archaea and thus management protocols for wetlands could conceivably include manipulations not only to limit the production of CH4 by methanogens, but also to enhance the consumption of CH4 by benthic or planktonic methanotrophs. The hydrological characteristic of a wetland is a major determinant of the CH4 emission rates. A major consideration for CH4 production is whether a wetland is static or flowing (wetlands connected to rivers and streams). Very little is known about the effects of hydrologic pulsing on wetland carbon dynamics and especially CH4 oxidation. Furthermore, although it has been established that methanotrophs are very active at the oxic sediment water interface of wetlands, little is known about the ecology of methanotrophs in the “pulsing fringe”. Stable isotope
probing (SIP) of biomarker Phospholipid Fatty Acids provide a means to connect CH4 oxidation to specific methanotrophs and track the shifts in community structure. Three landscape treatments were: 1) upland aerobic soil, 2) the intermediately flooded zone, and 3) the permanently flooded site with two landscape level replicates in a freshwater pulsing experimental wetlands at the Olentangy River Wetland (ORW) Research Park, The Ohio State University, Columbus. Two soil depths (organic horizon, 0-8 cm that includes the oxidized layer in flooded sites and 8-16 cm depth of surface mineral layer) were sampled at each site four times/year over a two-year period (early spring, mid summer, early fall and mid winter). Immediately after sampling the samples are stored at -20° C and transported under dry ice to the Soil Microbial Ecology Lab, SENR, the Ohio State University, Columbus for analysis. Samples were taken back to the lab to determine potential CH4 oxidation and 13C-PLFA analyses after extraction and analysis on GC-C-IRMS.The PF sites had significantly higher (p<0.05) Potential Methane Oxidation (PMO) than the IF sites. PMO rates at 0-8 cm depth of soil were significantly higher than those at depth of 8-16 cm (p<0.05). PMO in Winter was also significantly higher than in Summer (p< 0.01). PLFA profiling of methanotrophs showed that the Type type II methanotrophs and I methanotrophs were more pronounced in winter that was highly correlated by the seasonal dynamics of PMO. Concentrations of the Type II methanotroph PLFA biomarker (18:ω8c, 18:ω9c and 18:ω7c) were significantly higher (p<0.05) than the Type I PLFA biomarkers (16:ω5c).The highest potential to oxidize the substrate-available methane in the Permanently Flooded site is entirely attributed to the
methanotrophic population (as reflected by the relative abundance of the signature PLFAs). Even if with very low 13C incorporation, the PLFA profile in the Intermittently Flooded site is dominated by the Type II methanotrophs

Spatial distribution of prokaryotic communities in hypersaline soils

Increasing salinization in wetland systems is a major threat to ecosystem services carried out by microbial communities. Thus, it is paramount to understand how salinity drives both microbial community structures and their diversity. Here we evaluated the structure and diversity of the prokaryotic communities from a range of highly saline soils (EC1:5 from 5.96 to 61.02 dS/m) from the Odiel Saltmarshes and determined their association with salinity and other soil physicochemical features by analyzing 16S rRNA gene amplicon data through minimum entropy decomposition (MED). We found that these soils harbored unique communities mainly composed of halophilic and halotolerant taxa from the phyla Euryarchaeota, Proteobacteria, Balneolaeota, Bacteroidetes and Rhodothermaeota. In the studied soils, several site-specific properties were correlated with community structure and individual abundances of particular sequence variants. Salinity had a secondary role in shaping prokaryotic communities in these highly saline samples since the dominant organisms residing in them were already well-adapted to a wide range of salinities. We also compared ESV-based results with OTU-clustering derived ones, showing that, in this dataset, no major differences in ecological outcomes were obtained by the employment of one or the other method.España, Ministerio de Economía, Industria y Competitividad CGL2013-46941-P and CGL2017-83385-PJunta de Andalucía BIO-21

Indexing Permafrost Soil Organic Matter Degradation Using High-Resolution Mass Spectrometry

<div><p>Microbial degradation of soil organic matter (SOM) is a key process for terrestrial carbon cycling, although the molecular details of these transformations remain unclear. This study reports the application of ultrahigh resolution mass spectrometry to profile the molecular composition of SOM and its degradation during a simulated warming experiment. A soil sample, collected near Barrow, Alaska, USA, was subjected to a 40-day incubation under anoxic conditions and analyzed before and after the incubation to determine changes of SOM composition. A CHO index based on molecular C, H, and O data was utilized to codify SOM components according to their observed degradation potentials. Compounds with a CHO index score between –1 and 0 in a water-soluble fraction (WSF) demonstrated high degradation potential, with a highest shift of CHO index occurred in the N-containing group of compounds, while similar stoichiometries in a base-soluble fraction (BSF) did not. Additionally, compared with the classical H:C vs O:C van Krevelen diagram, CHO index allowed for direct visualization of the distribution of heteroatoms such as N in the identified SOM compounds. We demonstrate that CHO index is useful not only in characterizing arctic SOM at the molecular level but also enabling quantitative description of SOM degradation, thereby facilitating incorporation of the high resolution MS datasets to future mechanistic models of SOM degradation and prediction of greenhouse gas emissions.</p></div

Molecular distribution of extracted SOM compounds from a 40-day soil warming incubation experiment.

<p>(a) Box-and-whisker plots of the mass distribution of SOM compounds, including the base-soluble fraction (BSF) at day 0 (BSF0) and day 40 (BSF40) and the water-soluble fraction (WSF) at day 0 (WSF0) and day 40 (WSF40). <b>(b and c)</b> van Krevelen diagram along with CHO index showing the molecular distribution of WSF SOM compounds before (b) and after (c) incubation. <b>(d)</b> Percentages of molecular formulae identified with CHO index values between -2 and 2 before and after soil incubation and are normalized to the total number of formulae displayed in (b) and (c). Compound classes are labeled above colored bars as follows: (A) lipids, (B) unsaturated hydrocarbons, (C) peptides, (D) aminosugars, (E) carbohydrates, (F) lignin, (G) condensed hydrocarbons, (H) tannins.</p

Heatmaps for CHO index as a function of molecular mass of extracted SOM compounds before and after the soil warming experiment.

<p>The color bar represents the relative abundance of compounds identified in each of the SOM extract: <b>(a)</b> WSF0, <b>(b)</b> WSF40, <b>(c)</b> BSF0, and <b>(d)</b> BSF40. A positive correlation between CHO index and mass can be observed for mass > 600 Da.</p

Number weighted (Mean _#) and magnitude-weighted mean (Mean _w) properties for SOM extracts from a simulated soil warming experiment.

<p>The CHO index was calculated as (2×[<i>O</i>]–[<i>H</i>])/[<i>C</i>].</p

Potential carbon emissions dominated by carbon dioxide from thawed permafrost soils

© 2016 Macmillan Publishers Limited, part of Springer Nature. Increasing temperatures in northern high latitudes are causing permafrost to thaw, making large amounts of previously frozen organic matter vulnerable to microbial decomposition. Permafrost thaw also creates a fragmented landscape of drier and wetter soil conditions that determine the amount and form (carbon dioxide (CO2), or methane (CH 4)) of carbon (C) released to the atmosphere. The rate and form of C release control the magnitude of the permafrost C feedback, so their relative contribution with a warming climate remains unclear. We quantified the effect of increasing temperature and changes from aerobic to anaerobic soil conditions using 25 soil incubation studies from the permafrost zone. Here we show, using two separate meta-analyses, that a 10 °C increase in incubation temperature increased C release by a factor of 2.0 (95% confidence interval (CI), 1.8 to 2.2). Under aerobic incubation conditions, soils released 3.4 (95% CI, 2.2 to 5.2) times more C than under anaerobic conditions. Even when accounting for the higher heat trapping capacity of CH 4, soils released 2.3 (95% CI, 1.5 to 3.4) times more C under aerobic conditions. These results imply that permafrost ecosystems thawing under aerobic conditions and releasing CO2 will strengthen the permafrost C feedback more than waterlogged systems releasing CO2 and CH 4 for a given amount of C

Temporal Dynamics of In-Field Bioreactor Populations Reflect the Groundwater System and Respond Predictably to Perturbation

Temporal variability complicates testing the influences of environmental variability on microbial community structure and thus function. An in-field bioreactor system was developed to assess oxic versus anoxic manipulations on <i>in situ</i> groundwater communities. Each sample was sequenced (16S SSU rRNA genes, average 10,000 reads), and biogeochemical parameters are monitored by quantifying 53 metals, 12 organic acids, 14 anions, and 3 sugars. Changes in dissolved oxygen (DO), pH, and other variables were similar across bioreactors. Sequencing revealed a complex community that fluctuated in-step with the groundwater community and responded to DO. This also directly influenced the pH, and so the biotic impacts of DO and pH shifts are correlated. A null model demonstrated that bioreactor communities were driven in part not only by experimental conditions but also by stochastic variability and did not accurately capture alterations in diversity during perturbations. We identified two groups of abundant OTUs important to this system; one was abundant in high DO and pH and contained heterotrophs and oxidizers of iron, nitrite, and ammonium, whereas the other was abundant in low DO with the capability to reduce nitrate. In-field bioreactors are a powerful tool for capturing natural microbial community responses to alterations in geochemical factors beyond the bulk phase