Several ways one goal—methanogenesis from unconventional substrates

Methane is the second most important greenhouse gas on earth. It is produced by methanogenic archaea, which play an important role in the global carbon cycle. Three main methanogenesis pathways are known: in the hydrogenotrophic pathway H2 and carbon dioxide are used for methane production, whereas in the methylotrophic pathway small methylated carbon compounds like methanol and methylated amines are used. In the aceticlastic pathway, acetate is disproportionated to methane and carbon dioxide. However, next to these conventional substrates, further methanogenic substrates and pathways have been discovered. Several phylogenetically distinct methanogenic lineages (Methanosphaera, Methanimicrococcus, Methanomassiliicoccus, Methanonatronarchaeum) have evolved hydrogen-dependent methylotrophic methanogenesis without the ability to perform either hydrogenotrophic or methylotrophic methanogenesis. Genome analysis of the deep branching Methanonatronarchaeum revealed an interesting membrane-bound hydrogenase complex affiliated with the hardly described class 4 g of multisubunit hydrogenases possibly providing reducing equivalents for anabolism. Furthermore, methylated sulfur compounds such as methanethiol, dimethyl sulfide, and methylmercaptopropionate were described to be converted into adapted methylotrophic methanogenesis pathways of Methanosarcinales strains. Moreover, recently it has been shown that the methanogen Methermicoccus shengliensis can use methoxylated aromatic compounds in methanogenesis. Also, tertiary amines like choline (N,N,N-trimethylethanolamine) or betaine (N,N,N-trimethylglycine) have been described as substrates for methane production in Methanococcoides and Methanolobus strains. This review article will provide in-depth information on genome-guided metabolic reconstructions, physiology, and biochemistry of these unusual methanogenesis pathways. Key points • Newly discovered methanogenic substrates and pathways are reviewed for the first time. • The review provides an in-depth analysis of unusual methanogenesis pathways. • The hydrogenase complex of the deep branching Methanonatronarchaeum is analyzed.

Phytoplankton and dimethylsulfide dynamics at two contrasting Arctic ice edges

Arctic sea ice is retreating and thinning and its rate of decline has steepened in the last decades. While phytoplankton blooms are known to seasonally propagate along the ice edge as it recedes from spring to summer, the substitution of thick multiyear ice (MYI) with thinner, ponded first-year ice (FYI) represents an unequal exchange when considering the roles sea ice plays in the ecology and climate of the Arctic. Consequences of this shifting sea ice on the phenology of phytoplankton and the associated cycling of the climate-relevant gas dimethylsulfide (DMS) and its precursor dimethylsulfoniopropionate (DMSP) remain ill constrained. In July–August 2014, two contrasting ice edges in the Canadian High Arctic were explored: a FYI-dominated ice edge in Barrow Strait and a MYI-dominated ice edge in Nares Strait. Our results reveal two distinct planktonic systems and associated DMS dynamics in connection to these diverging ice types. The surface waters exiting the ponded FYI in Barrow Strait were characterized by moderate chlorophyll a (Chl a, <2.1 µg L−1) as well as high DMSP (115 nmol L−1) and DMS (12 nmol L−1), suggesting that a bloom had already started to develop under the markedly melt-pond-covered (ca. 40 %) FYI. Heightened DMS concentrations at the FYI edge were strongly related to ice-associated seeding of DMS in surface waters and haline-driven stratification linked to ice melt (Spearman's rank correlation between DMS and salinity, rs=-0.91, p<0.001, n=20). However, surface waters exiting the MYI edge at the head of Nares Strait were characterized by low concentrations of Chl a (<0.5 µg L−1), DMSP (<16 nmol L−1), and DMS (<0.4 nmol L−1), despite the nutrient-replete conditions characterizing the surface waters. The increase in autotrophic biomass and methylated sulfur compounds took place several kilometers (ca. 100 km) away from the MYI edge, suggesting the requisite for ice-free, light-sufficient conditions for a phytoplankton bloom to fully develop and for sulfur compound dynamics to follow and expand. In light of the ongoing and projected climate-driven changes to Arctic sea ice, results from this study suggest that the early onset of autotrophic blooms under thinner, melt-pond-covered ice may have vast implications for the timing and magnitude of DMS pulses in the Arctic.

Methane production by three widespread marine phytoplankton species: release rates, precursor compounds, and potential relevance for the environment

Methane (CH4) production within the oceanic mixed layer is a widespread phenomenon, but the underlying mechanisms are still under debate. Marine algae might contribute to the observed CH4 oversaturation in oxic waters, but so far direct evidence for CH4 production by marine algae has only been provided for the coccolithophore Emiliania huxleyi. In the present study we investigated, next to E. huxleyi, other widespread haptophytes, i.e., Phaeocystis globosa and Chrysochromulina sp. We performed CH4 production and stable carbon isotope measurements and provide unambiguous evidence that all three investigated marine algae are involved in the production of CH4 under oxic conditions. Rates ranged from 1.9±0.6 to 3.1±0.4 µg of CH4 per gram of POC (particulate organic carbon) per day, with Chrysochromulina sp. and E. huxleyi showing the lowest and highest rates, respectively. Cellular CH4 production rates ranged from 16.8±6.5 (P. globosa) to 62.3±6.4 ag CH4 cell−1 d−1 (E. huxleyi; ag = 10−18 g). In cultures that were treated with 13C-labeled hydrogen carbonate, δ13CH4 values increased with incubation time, resulting from the conversion of 13C–hydrogen carbonate to 13CH4. The addition of 13C-labeled dimethyl sulfide, dimethyl sulfoxide, and methionine sulfoxide – known algal metabolites that are ubiquitous in marine surface layers – resulted in the occurrence of 13C-enriched CH4 in cultures of E. huxleyi, clearly indicating that methylated sulfur compounds are also precursors of CH4. By comparing the algal CH4 production rates from our laboratory experiments with results previously reported in two field studies of the Pacific Ocean and the Baltic Sea, we might conclude that algae-mediated CH4 release is contributing to CH4 oversaturation in oxic waters. Therefore, we propose that haptophyte mediated CH4 production could be a common and important process in marine surface waters.

Lanthanide-Dependent Methylotrophs of the Family Beijerinckiaceae: Physiological and Genomic Insights

ABSTRACT Methylotrophic bacteria use methanol and related C1 compounds as carbon and energy sources. Methanol dehydrogenases are essential for methanol oxidation, while lanthanides are important cofactors of many pyrroloquinoline quinone-dependent methanol dehydrogenases and related alcohol dehydrogenases. We describe here the physiological and genomic characterization of newly isolated Beijerinckiaceae bacteria that rely on lanthanides for methanol oxidation. A broad physiological diversity was indicated by the ability to metabolize a wide range of multicarbon substrates, including various sugars, and organic acids, as well as diverse C1 substrates such as methylated amines and methylated sulfur compounds. Methanol oxidation was possible only in the presence of low-mass lanthanides (La, Ce, and Nd) at submicromolar concentrations (>100 nM). In a comparison with other Beijerinckiaceae, genomic and transcriptomic analyses revealed the usage of a glutathione- and tetrahydrofolate-dependent pathway for formaldehyde oxidation and channeling methyl groups into the serine cycle for carbon assimilation. Besides a single xoxF gene, we identified two additional genes for lanthanide-dependent alcohol dehydrogenases, including one coding for an ExaF-type alcohol dehydrogenase, which was so far not known in Beijerinckiaceae. Homologs for most of the gene products of the recently postulated gene cluster linked to lanthanide utilization and transport could be detected, but for now it remains unanswered how lanthanides are sensed and taken up by our strains. Studying physiological responses to lanthanides under nonmethylotrophic conditions in these isolates as well as other organisms is necessary to gain a more complete understanding of lanthanide-dependent metabolism as a whole. IMPORTANCE We supplemented knowledge of the broad metabolic diversity of the Beijerinckiaceae by characterizing new members of this family that rely on lanthanides for methanol oxidation and that possess additional lanthanide-dependent enzymes. Considering that lanthanides are critical resources for many modern applications and that recovering them is expensive and puts a heavy burden on the environment, lanthanide-dependent metabolism in microorganisms is an exploding field of research. Further research into how isolated Beijerinckiaceae and other microbes utilize lanthanides is needed to increase our understanding of lanthanide-dependent metabolism. The diversity and widespread occurrence of lanthanide-dependent enzymes make it likely that lanthanide utilization varies in different taxonomic groups and is dependent on the habitat of the microbes.

The distribution of methylated sulfur compounds, DMS and DMSP, in Canadian subarctic and Arctic marine waters during summer 2015

We present seawater concentrations of dimethyl sulfide (DMS) and dimethylsulfoniopropionate (DMSP) measured across a transect from the Labrador Sea to the Canadian Arctic Archipelago during summer 2015. Using an automated ship-board gas chromatography system and a membrane-inlet mass spectrometer, we measured a wide range of DMS (∼ 1 to 18 nM) and DMSP (∼ 1 to 150 nM) concentrations. The highest DMS and DMSP concentrations occurred in a localized region of Baffin Bay, where surface waters were characterized by high chlorophyll a (chl a) fluorescence, indicative of elevated phytoplankton biomass. Across the full sampling transect, there were only weak relationships between DMS(P), chl a fluorescence and other measured variables, including positive relationships between DMSP : chl a ratios and several taxonomic marker pigments, and elevated DMS(P) concentrations in partially ice-covered areas. Our high spatial resolution measurements allowed us to examine DMS variability over small scales (< 1 km), documenting strong DMS concentration gradients across surface hydrographic frontal features. Our new observations fill in an important observational gap in the Arctic Ocean and provide additional information on sea–air DMS fluxes from this ocean region. In addition, this study constitutes a significant contribution to the existing Arctic DMS(P) dataset and provides a baseline for future measurements in the region.

The distribution of methylated sulfur compounds, DMS and DMSP, in Canadian Subarctic and Arctic marine waters during summer, 2015

We present seawater concentrations of dimethylsulfide (DMS), and dimethylsulfoniopropionate (DMSP) measured across a transect from the Labrador Sea to the Canadian Arctic Archipelago, during summer 2015. Using an automated ship-board gas chromatography system, and a membrane-inlet mass spectrometer, we measured a range of DMS (~ 1 nM to 18 nM) and DMSP concentrations (~ 1 nM to 150 nM) that was consistent with previous observations in the Arctic Ocean. The highest DMS and DMSP concentrations occurred in a localized region of Baffin Bay, where surface waters were characterized by high chlorophyll a (chl a) fluorescence, indicative of elevated phytoplankton biomass. Across the full sampling transect, there were only weak relationships between DMS/P, chl a fluorescence and other measured variables, including positive relationships between DMSP : chl a ratios and several taxonomic marker pigments, and elevated DMS/P concentrations in partially ice-covered areas. Our high spatial resolution measurements allowed us to examine DMS variability over small scales (

Genetic Basis for Metabolism of Methylated Sulfur Compounds in Methanosarcina Species

ABSTRACTMethanosarcina acetivoransuses a variety of methylated sulfur compounds as carbon and energy sources. Previous studies implicated themtsD,mtsF, andmtsHgenes in catabolism of dimethylsulfide, but the genes required for use of other methylsulfides have yet to be established. Here, we show that a four-gene locus, designatedmtpCAP-msrH, is specifically required for growth on methylmercaptopropionate (MMPA). ThemtpC,mtpA, andmtpPgenes encode a putative corrinoid protein, a coenzyme M (CoM) methyltransferase, and amajorfacilitatorsuperfamily (MFS) transporter, respectively, whilemsrHencodes a putative transcriptional regulator. Mutants lackingmtpCormtpAdisplay a severe growth defect in MMPA medium but are unimpaired during growth on other substrates. ThemtpCAPgenes comprise a transcriptional unit that is highly and specifically upregulated during growth on MMPA, whereasmsrHis monocistronic and constitutively expressed. Mutants lackingmsrHfail to transcribemtpCAPand grow poorly in MMPA medium, consistent with the assignment of its product as a transcriptional activator. ThemtpCAP-msrHlocus is conserved in numerous marine methanogens, including eightMethanosarcinaspecies that we showed are capable of growth on MMPA. Mutants lacking themtsD,mtsF, andmtsHgenes display a 30% reduction in growth yield when grown on MMPA, suggesting that these genes play an auxiliary role in MMPA catabolism. A quadruple ΔmtpCAPΔmtsDΔmtsFΔmtsHmutant strain was incapable of growth on MMPA. Reanalysis ofmtsD,mtsF, andmtsHmutants suggests that the preferred substrate for MtsD is dimethylsulfide, while the preferred substrate for MtsF is methanethiol.IMPORTANCEMethylated sulfur compounds play pivotal roles in the global sulfur and carbon cycles and contribute to global temperature homeostasis. Although the degradation of these molecules by aerobic bacteria has been well studied, relatively little is known regarding their fate in anaerobic ecosystems. In this study, we identify the genetic basis for metabolism of methylmercaptopropionate, dimethylsulfide, and methanethiol by strictly anaerobic methanogens of the genusMethanosarcina. These data will aid the development of predictive sulfur cycle models and enable molecular ecological approaches for the study of methylated sulfur metabolism in anaerobic ecosystems.