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Ferruginous (Fe-rich, SO4-poor) conditions are generally restricted to freshwater sediments on Earth today, but were likely widespread during the Archean and Proterozoic Eons. Lake Towuti, Indonesia, is a large ferruginous lake that likely hosts geochemical processes analogous to those that operated in the ferruginous Archean ocean. The metabolic potential of microbial communities and related biogeochemical cycling under such conditions remain largely unknown. We combined geochemical measurements (pore water chemistry, sulfate reduction rates) with metagenomics to link metabolic potential with geochemical processes in the upper 50 cm of sediment. Microbial diversity and quantities of genes for dissimilatory sulfate reduction (dsrAB) and methanogenesis (mcrA) decrease with increasing depth, as do rates of potential sulfate reduction. The presence of taxa affiliated with known iron- and sulfate-reducers implies potential use of ferric iron and sulfate as electron acceptors. Pore-water concentrations of acetate imply active production through fermentation. Fermentation likely provides substrates for respiration with iron and sulfate as electron donors and for methanogens that were detected throughout the core. The presence of ANME-1 16S and mcrA genes suggests potential for anaerobic methane oxidation. Overall our data suggest that microbial community metabolism in anoxic ferruginous sediments support coupled Fe, S and C biogeochemical cycling.
Lake Towuti is a tectonic basin, surrounded by ultramafic rocks. Lateritic soils form through weathering and deliver abundant iron (oxy)hydroxides but very little sulfate to the lake and its sediment. To characterize the sediment biogeochemistry, we collected cores at three sites with increasing water depth and decreasing bottom water oxygen concentrations. Microbial cell densities were highest at the shallow site a feature we attribute to the availability of labile organic matter (OM) and the higher abundance of electron acceptors due to oxic bottom water conditions. At the two other sites, OM degradation and reduction processes below the oxycline led to partial electron acceptor depletion. Genetic information preserved in the sediment as extracellular DNA (eDNA) provided information on aerobic and anaerobic heterotrophs related to Nitrospirae. Chloroflexi, and Therrnoplasmatales. These taxa apparently played a significant role in the degradation of sinking OM. However, eDNA concentrations rapidly decreased with core depth. Despite very low sulfate concentrations, sulfate-reducing bacteria were present and viable in sediments at all three sites, as confirmed by measurement of potential sulfate reduction rates. Microbial community fingerprinting supported the presence of taxa related to Deltaproteobacteria and Firmicutes with demonstrated capacity for iron and sulfate reduction. Concomitantly, sequences of Ruminococcaceae, Clostridiales, and Methanornicrobiales indicated potential for fermentative hydrogen and methane production. Such first insights into ferruginous sediments showed that microbial populations perform successive metabolisms related to sulfur, iron, and methane. In theory, iron reduction could reoxidize reduced sulfur compounds and desorb OM from iron minerals to allow remineralization to methane. Overall, we found that biogeochemical processes in the sediments can be linked to redox differences in the bottom waters of the three sites, like oxidant concentrations and the supply of labile OM. At the scale of the lacustrine record, our geomicrobiological study should provide a means to link the extant subsurface biosphere to past environments.
Sulfate reduction is the quantitatively most important process to degrade organic matter in anoxic marine sediment and has been studied intensively in a variety of settings. Guaymas Basin, a young marginal ocean basin, offers the unique opportunity to study sulfate reduction in an environment characterized by organic-rich sediment, high sedimentation rates, and high geothermal gradients (100-958 degrees C km(-1)). We measured sulfate reduction rates (SRR) in samples taken during the International Ocean Discovery Program (IODP) Expedition 385 using incubation experiments with radiolabeled (SO42-)-S-35 carried out at in situ pressure and temperature. The highest SRR (387 nmol cm(-3) d(-1)) was recorded in near-surface sediments from Site U1548C, which had the steepest geothermal gradient (958 degrees C km(-1)). At this site, SRR were generally over an order of magnitude higher than at similar depths at other sites (e.g., 387-157 nmol cm(-3) d(-1) at 1.9 mbsf from Site U1548C vs. 46-1.0 nmol cm(-3) d(-1) at 2.1 mbsf from Site U1552B). Site U1546D is characterized by a sill intrusion, but it had already reached thermal equilibrium and SRR were in the same range as nearby Site U1545C, which is minimally affected by sills. The wide temperature range observed at each drill site suggests major shifts in microbial community composition with very different temperature optima but awaits confirmation by molecular biological analyses. At the transition between the mesophilic and thermophilic range around 40 degrees C-60 degrees C, sulfate-reducing activity appears to be decreased, particularly in more oligotrophic settings, but shows a slight recovery at higher temperatures.
Tropical Lake Sentani in the Indonesian Province Papua consists of four separate basins and is surrounded by a catchment with a very diverse geology. We characterized the surface sediment (upper 5 cm) of the lake's four sub-basins based on multivariate statistical analyses (principal component analysis, hierarchical clustering) of major element compositions obtained by X-ray fluorescence scanning. Three types of sediment are identified based on distinct compositional differences between rivers, shallow/proximal and deep/distal lake sediments. The different sediment types are mainly characterized by the correlation of elements associated with redox processes (S, Mn, Fe), carbonates (Ca), and detrital input (Ti, Al, Si, K) derived by river discharge. The relatively coarse-grained river sediments mainly derive form the mafic catchment geology and contribution of the limestone catchment geology is only limited. Correlation of redox sensitive and detrital elements are used to reveal oxidation conditions, and indicate oxic conditions in river samples and reducing conditions for lake sediments. Organic carbon (TOC) generally correlates with redox sensitive elements, although a correlation between TOC and individual elements change strongly between the three sediment types. Pyrite is the quantitatively dominant reduced sulfur mineral, monosulfides only reach appreciable concentrations in samples from rivers draining mafic and ultramafic catchments. Our study shows large spatial heterogeneity within the lake's sub-basins that is mainly caused by catchment geology and topography, river runoff as well as the bathymetry and the depth of the oxycline. We show that knowledge about lateral heterogeneity is crucial for understanding the geochemical and sedimentological variations recorded by these sediments. The highly variable conditions make Lake Sentani a natural laboratory, with its different sub-basins representing different depositional environments under identical tropical climate conditions.
The effects of climate and topography on soil physico-chemical and microbial parameters were studied along an extensive latitudinal climate gradient in the Coastal Cordillera of Chile (26 degrees-38 degrees S). The study sites encompass arid (Pan de Azucar), semiarid (Santa Gracia), mediterranean (La Campana) and humid (Nahuelbuta) climates and vegetation, ranging from arid desert, dominated by biological soil crusts (biocrusts), semiarid shrubland and mediterranean sclerophyllous forest, where biocrusts are present but do have a seasonal pattern to temperate-mixed forest, where biocrusts only occur as an early pioneering development stage after disturbance. All soils originate from granitic parent materials and show very strong differences in pedogenesis intensity and soil depth. Most of the investigated physical, chemical and microbiological soil properties showed distinct trends along the climate gradient. Further, abrupt changes between the arid northernmost study site and the other semi-arid to humid sites can be shown, which indicate non-linearity and thresholds along the climate gradient. Clay and total organic carbon contents (TOC) as well as Ah horizons and solum depths increased from arid to humid climates, whereas bulk density (BD), pH values and base saturation (BS) decreased. These properties demonstrate the accumulation of organic matter, clay formation and element leaching as key-pedogenic processes with increasing humidity. However, the soils in the northern arid climate do not follow this overall latitudinal trend, because texture and BD are largely controlled by aeolian input of dust and sea salts spray followed by the formation of secondary evaporate minerals. Total soil DNA concentrations and TOC increased from arid to humid sites, while areal coverage by biocrusts exhibited an opposite trend. Relative bacterial and archaeal abundances were lower in the arid site, but for the other sites the local variability exceeds the variability along the climate gradient. Differences in soil properties between topographic positions were most pronounced at the study sites with the mediterranean and humid climate, whereas microbial abundances were independent on topography across all study sites. In general, the regional climate is the strongest controlling factor for pedogenesis and microbial parameters in soils developed from the same parent material. Topographic position along individual slopes of limited length augmented this effect only under humid conditions, where water erosion likely relocated particles and elements downward. The change from alkaline to neutral soil pH between the arid and the semi-arid site coincided with qualitative differences in soil formation as well as microbial habitats. This also reflects non-linear relationships of pedogenic and microbial processes in soils depending on climate with a sharp threshold between arid and semi-arid conditions. Therefore, the soils on the transition between arid and semi-arid conditions are especially sensitive and may be well used as indicators of long and medium-term climate changes. Concluding, the unique latitudinal precipitation gradient in the Coastal Cordillera of Chile is predestined to investigate the effects of the main soil forming factor - climate - on pedogenic processes.
From north to south, denudation rates from cosmogenic nuclides are similar to 10 t km(-2) yr(-1) at the arid Pan de Aziicar site, similar to 20 t km(2) yr(-1) at the semi-arid site of Santa Gracia, -60 t km(-2) yr(-1) at the Mediterranean climate site of La Campana, and similar to 30 t km(-2) yr(-1) at the humid site of Nahuelbuta. A and B horizons increase in thickness and elemental depletion or enrichment increases from north (similar to 26 degrees S) to south (similar to 38 degrees S) in these horizons. Differences in the degree of chemical weathering, quantified by the chemical depletion fraction (CDF), are significant only between the arid and sparsely vegetated site and the other three sites. Differences in the CDF between the sites, and elemental depletion within the sites are sometimes smaller than the variations induced by the bedrock heterogeneity. Microbial abundances (bacteria and archaea) in saprolite substantially increase from the arid to the semi-arid sites. With this study, we provide a comprehensive dataset characterizing the Critical Zone geochemistry in the Chilean Coastal Cordillera. This dataset confirms climatic controls on weathering and denudation rates and provides prerequisites to quantify the role of biota in future studies.
Microbial community composition and abundance after millennia of submarine permafrost warming
(2019)
Warming of the Arctic led to an increase in permafrost temperatures by about 0.3 degrees C during the last decade. Permafrost warming is associated with increasing sediment water content, permeability, and diffusivity and could in the long term alter microbial community composition and abundance even before permafrost thaws. We studied the long-term effect (up to 2500 years) of submarine permafrost warming on microbial communities along an onshore-offshore transect on the Siberian Arctic Shelf displaying a natural temperature gradient of more than 10 degrees C. We analysed the in situ development of bacterial abundance and community composition through total cell counts (TCCs), quantitative PCR of bacterial gene abundance, and amplicon sequencing and correlated the microbial community data with temperature, pore water chemistry, and sediment physicochemical parameters. On timescales of centuries, permafrost warming coincided with an overall decreasing microbial abundance, whereas millennia after warming microbial abundance was similar to cold onshore permafrost. In addition, the dissolved organic carbon content of all cores was lowest in submarine permafrost after millennial-scale warming. Based on correlation analysis, TCC, unlike bacterial gene abundance, showed a significant rank-based negative correlation with increasing temperature, while bacterial gene copy numbers showed a strong negative correlation with salinity. Bacterial community composition correlated only weakly with temperature but strongly with the pore water stable isotopes delta O-18 and delta D, as well as with depth. The bacterial community showed substantial spatial variation and an overall dominance of Actinobacteria, Chloroflexi, Firmicutes, Gemmatimonadetes, and Proteobacteria, which are amongst the microbial taxa that were also found to be active in other frozen permafrost environments. We suggest that, millennia after permafrost warming by over 10 degrees C, microbial community composition and abundance show some indications for proliferation but mainly reflect the sedimentation history and paleoenvironment and not a direct effect through warming.