ALBERT

Description: Microbial mats, due to stratification of the redox zones, have a potential to include a complete N cycle, however an attempt to evaluate a complete N cycle in these ecosystems has not been yet made. In this study, occurrence and rates of major N cycle processes were evaluated in intact microbial mats from Elkhorn Slough, Monterey Bay, CA, USA, and Baja California Sur, Mexico under oxic and anoxic conditions using 15N-labeling techniques. All of the major N transformation pathways, with the exception of anammox, were detected in both microbial mats. Nitrification rates were found to be low at both sites for both seasons investigated. The highest rates of ammonium assimilation were measured in Elkhorn Slough mats in April and corresponded to high in situ ammonium concentration in the overlying water. Baja mats featured higher ammonification than ammonium assimilation rates and this, along with their higher affinity for nitrate compared to ammonium and low dissimilatory nitrate reduction to ammonium rates, characterized their differences from Elkhorn Slough mats. Nitrogen fixation rates in Elkhorn Slough microbial mats were found to be low implying that other processes such as recycling and assimilation from water are main sources of N for these mats at the times sampled. Denitrification in all of the mats was incomplete with nitrous oxide as end product and not dinitrogen. Our findings highlight N cycling features not previously quantified in microbial mats and indicate a need of further investigations in these microbial ecosystems.

Description: Globally, large-scale land drainage has severely deteriorated the functioning and services of peatlands, making restoration plans of the utmost importance. Rewetting is essential for the restoration of drained peatlands, but the level of success including greenhouse gas (GHG) mitigation largely depends on the soil microbiome interactions under the prevailing biogeochemical conditions. Here, we investigated the effects of inundation of drained iron (Fe) -rich peat topsoils on nutrient release, surface water quality, GHG production and consumption, and on the composition and activity of the microbial community. The effect of the addition of different potential electron acceptors on methane (CH4) production and consumption were studied in incubation experiments. In response to inundation, porewater concentrations of Fe, total inorganic carbon, ammonium, and phosphorus increased. CH4 emissions increased in the control (i.e. without any additions) and Fe(III) oxide amended incubations upon inundation. This could be explained by the increase in the relative abundance of methanogens even though Fe(III) was previously hypothesized to lower methanogenic activity. In contrast, nitrite, nitrate, and sulfate-rich incubations inhibited methanogenesis. The prolonged exposure to nitrogen oxides stimulated denitrification with nitrous oxide (N2O) as the main gaseous product, together with an increase in the relative abundance of denitrifying microorganisms. Our results demonstrate that insights into the changes in microbial communities in relation to soil geochemistry explain differences in responses observed in different peat soils observed upon inundation. The increase in emissions of the potent GHGs CH4 and N2O from Fe-rich peat topsoils are a major adverse effect in the early stage of inundation.

Description: The Bothnian Sea is an oligotrophic brackish basin characterized by low salinity and high concentrations of reactive iron, methane, and ammonium in its sediments, enabling the activity and interactions of many microbial guilds. Here, we studied the microbial network in these sediments by analyzing geochemical and microbial community depth profiles at one offshore and two near coastal sites. Analysis of 16S rRNA gene amplicons revealed a distinct depth stratification of both archaeal and bacterial taxa. The microbial communities at the two near coastal sites were more similar to each other than the offshore site, which is likely due to differences in the quality and rate of organic matter degradation. The abundance of methanotrophic archaea of the ANME‐2a clade was shown to be related to the presence of methane and varied with sediment iron content. Metagenomic sequencing of sediment‐derived DNA from below the sulfate–methane transition zone revealed a broad potential for respiratory sulfur metabolism via partially reduced sulfur species. The potential for nitrogen cycling was dominated by reductive processes via a truncated denitrification pathway encoded exclusively by bacterial lineages. Gene‐centric fermentative metabolism analysis indicated a potential importance for acetate, formate, alcohol, and hydrogen metabolism. Methanogenic/‐trophic pathways were dominated by Methanosaetaceae, Methanosarcinaceae, Methanomassiliicoccaceae, Methanoregulaceae, and ANME‐2 archaea. Our results indicated flexible metabolic capabilities of core microbial community taxa, which could adapt to changing redox conditions, and with a spatial and depth distribution that is likely governed by the quality and input of available organic substrates and, for ANME‐2, of iron oxides.

Description: Microbial methane oxidation is a major biofilter preventing larger emissions of this powerful greenhouse gas from marine coastal areas into the atmosphere. In these zones, various electron acceptors such as sulfate, metal oxides, nitrate, or oxygen can be used. However, the key microbial players and mechanisms of methane oxidation are poorly understood. In this study, we inoculated a bioreactor with methane‐ and iron‐rich sediments from the Bothnian Sea to investigate microbial methane and iron cycling under low oxygen concentrations. Using metagenomics, we investigated shifts in microbial community composition after approximately 2.5 years of bioreactor operation. Marker genes for methane and iron cycling, as well as respiratory and fermentative metabolism, were identified and used to infer putative microbial metabolism. Metagenome‐assembled genomes representing novel Verrucomicrobia, Bacteroidetes, and Krumholzibacteria were recovered and revealed a potential for methane oxidation, organic matter degradation, and iron cycling, respectively. This work brings new hypotheses on the identity and metabolic versatility of microorganisms that may be members of such functional guilds in coastal marine sediments and highlights that microorganisms potentially composing the methane biofilter in these sediments may be more diverse than previously appreciated.