Hilairy E. Hartnett

Influence of oxygen exposure time on organic carbon preservation in continental margin sediments

Today, over 90% of all organic carbon burial in the ocean occurs in continental margin sediments. This burial is intrinsically linked to the cycling of biogeochemically important elements (such as N, P, S, Fe and Mn) and, on geological timescales, largely controls the oxygen content of the atmosphere. Currently there is a volatile debate over which processes govern sedimentary organic carbon preservation. In spite of numerous studies demonstrating empirical relationships between organic carbon burial and such factors as primary productivity, the flux of organic carbon through the water column, sedimentation rate,, organic carbon degradation rate, and bottom-water oxygen concentration,, the mechanisms directly controlling sedimentary organic carbon preservation remain unclear. Furthermore, as organic carbon burial is the process that, along with pyrite burial, balances O2 concentrations in the atmosphere, it is desirable that any mechanism proposed to control organic carbon preservation include a feedback buffering atmospheric oxygen concentrations over geological time. Here we compare analyses of sediments underlying two regions of the eastern North Pacific Ocean, one which has oxygen-depleted bottom waters and one with typical oxygen distributions. Organic carbon burial efficiency is strongly correlated with the length of time accumulating particles are exposed to molecular oxygen in sediment pore waters. Oxygen exposure time effectively incorporates other proposed environmental variables, and may exert a direct control on sedimentary organic carbon preservation and atmospheric oxygen concentrations.

Role of a strong oxygen-deficient zone in the preservation and degradation of organic matter: A carbon budget for the continental margins of northwest Mexico and Washington State

Rates of organic carbon oxidation in marine sediments were determined for the continental margins of northwest Mexico and Washington State, with the goal of assessing the role of oxygen in the preservation of organic matter on a margin with a strong oxygen-deficient zone and on a typical western continental margin. Total carbon oxidation rates (including rates for individual electron acceptors: O2, NO3−, and SO4=) were determined at depths ranging from 100 to 3000 m on both margins. Carbon oxidation rates were generally higher on the Washington margin than on the Mexican margin. The relative importance of the different electron acceptors varied across the two margins and was related primarily to the availability of O2 and NO3− from the overlying water. The relative contribution of O2 consumption increased in deeper sediments (>2000 m) as aerobic processes began to dominate the total carbon oxidation rate. Denitrification rates were highest in Washington sediments; however, denitrification represented a larger fraction of the total carbon oxidation rate in the Mexican sediments (∼40% for Mexico vs. ∼30% for Washington). Sulfate reduction accounted for as much as 79% of the total carbon oxidation rate in shallow sediments and less than 20% in deep sediments on both margins. The offshore trends in carbon oxidation rate appeared to be related to the organic carbon input rate. Pore-water O2 and NO3− penetration depths were shallowest in nearshore stations and increased offshore. Regeneration ratios of C:N:P reveal “non-Redfield” behavior on both margins. Carbon budgets for the two margins demonstrate that off Mexico, a much greater percentage of the organic matter produced in the surface ocean reached the sediments (>15% vs. <8% for Mexico and Washington, respectively). On the Mexican margin, ∼8% of the primary production escaped oxidation in the surface sediments to be permanently buried, as compared with only ∼1.2% of the primary production on the Washington margin. This suggests that oxygen-deficient conditions on Mexican margin are linked to enhanced carbon preservation.

A Comprehensive Census of Microbial Diversity in Hot Springs of Tengchong, Yunnan Province China Using 16S rRNA Gene Pyrosequencing

The Rehai and Ruidian geothermal fields, located in Tengchong County, Yunnan Province, China, host a variety of geochemically distinct hot springs. In this study, we report a comprehensive, cultivation-independent census of microbial communities in 37 samples collected from these geothermal fields, encompassing sites ranging in temperature from 55.1 to 93.6°C, in pH from 2.5 to 9.4, and in mineralogy from silicates in Rehai to carbonates in Ruidian. Richness was low in all samples, with 21–123 species-level OTUs detected. The bacterial phylum Aquificae or archaeal phylum Crenarchaeota were dominant in Rehai samples, yet the dominant taxa within those phyla depended on temperature, pH, and geochemistry. Rehai springs with low pH (2.5–2.6), high temperature (85.1–89.1°C), and high sulfur contents favored the crenarchaeal order Sulfolobales, whereas those with low pH (2.6–4.8) and cooler temperature (55.1–64.5°C) favored the Aquificae genus Hydrogenobaculum. Rehai springs with neutral-alkaline pH (7.2–9.4) and high temperature (>80°C) with high concentrations of silica and salt ions (Na, K, and Cl) favored the Aquificae genus Hydrogenobacter and crenarchaeal orders Desulfurococcales and Thermoproteales. Desulfurococcales and Thermoproteales became predominant in springs with pH much higher than the optimum and even the maximum pH known for these orders. Ruidian water samples harbored a single Aquificae genus Hydrogenobacter, whereas microbial communities in Ruidian sediment samples were more diverse at the phylum level and distinctly different from those in Rehai and Ruidian water samples, with a higher abundance of uncultivated lineages, close relatives of the ammonia-oxidizing archaeon “Candidatus Nitrosocaldus yellowstonii”, and candidate division O1aA90 and OP1. These differences between Ruidian sediments and Rehai samples were likely caused by temperature, pH, and sediment mineralogy. The results of this study significantly expand the current understanding of the microbiology in Tengchong hot springs and provide a basis for comparison with other geothermal systems around the world.

Twelve testable hypotheses on the geobiology of weathering

Critical Zone (CZ) research investigates the chemical, physical, and biological processes that modulate the Earths surface. Here, we advance 12 hypotheses that must be tested to improve our understanding of the CZ: (1) Solar-to-chemical conversion of energy by plants regulates flows of carbon, water, and nutrients through plant-microbe soil networks, thereby controlling the location and extent of biological weathering. (2) Biological stoichiometry drives changes in mineral stoichiometry and distribution through weathering. (3) On landscapes experiencing little erosion, biology drives weathering during initial succession, whereas weathering drives biology over the long term. (4) In eroding landscapes, weathering-front advance at depth is coupled to surface denudation via biotic processes. (5) Biology shapes the topography of the Critical Zone. (6) The impact of climate forcing on denudation rates in natural systems can be predicted from models incorporating biogeochemical reaction rates and geomorphological transport laws. (7) Rising global temperatures will increase carbon losses from the Critical Zone. (8) Rising atmospheric P(CO2) will increase rates and extents of mineral weathering in soils. (9) Riverine solute fluxes will respond to changes in climate primarily due to changes in water fluxes and secondarily through changes in biologically mediated weathering. (10) Land use change will impact Critical Zone processes and exports more than climate change. (11) In many severely altered settings, restoration of hydrological processes is possible in decades or less, whereas restoration of biodiversity and biogeochemical processes requires longer timescales. (12) Biogeochemical properties impart thresholds or tipping points beyond which rapid and irreversible losses of ecosystem health, function, and services can occur.

Effect of biological soil crusts on soil elemental concentrations: implications for biogeochemistry and as traceable biosignatures of ancient life on land

Biological soil crusts (BSCs) are topsoil biosedimentary structures built by photosynthetic microbes commonly found today on arid soils. They play a role in soil stabilization and the fertility of arid lands, and are considered modern analogues of ancient terrestrial microbial communities. We determined the concentrations of four biogenic and 21 other elements, mostly metals, in surface soils that hosted BSCs, in the soils underneath those crusts, and in proximate but non-crusted surface soils. The samples were from six sites in the Colorado Plateau highlands and the Sonoran Desert lowlands. In spite of the variability in climate and geologic setting, we found statistically significant overall trends of enrichment in biogenic elements and depletion in non-biogenic elements when BSCs were compared with non-crusted soils. The differences between crusted and non-crusted soils were statistically significant at approximately 95% confidence for C, N (enrichments) and for Ca, Cr, Mn, Cu, Zn, As, and Zr (depletions). These trends are best explained by the activity of microbes. As expected, no differences in the concentrations of C, N, P, and S were detected between the soils underneath the crusts and the non-crusted soils, but the former showed depletion of non-biogenic elements, indicating that the leaching effect of crust microbes extends downward in the soil. These patterns speak to the need for a sustained input of allochthonous material, possibly dust, to maintain BSC fertility. These elemental patterns can be considered a biosignature that may be preserved in the rock record and might help identify ancient microbial communities on land.

Korarchaeota Diversity, Biogeography, and Abundance in Yellowstone and Great Basin Hot Springs and Ecological Niche Modeling Based on Machine Learning

Over 100 hot spring sediment samples were collected from 28 sites in 12 areas/regions, while recording as many coincident geochemical properties as feasible (>60 analytes). PCR was used to screen samples for Korarchaeota 16S rRNA genes. Over 500 Korarchaeota 16S rRNA genes were screened by RFLP analysis and 90 were sequenced, resulting in identification of novel Korarchaeota phylotypes and exclusive geographical variants. Korarchaeota diversity was low, as in other terrestrial geothermal systems, suggesting a marine origin for Korarchaeota with subsequent niche-invasion into terrestrial systems. Korarchaeota endemism is consistent with endemism of other terrestrial thermophiles and supports the existence of dispersal barriers. Korarchaeota were found predominantly in >55°C springs at pH 4.7–8.5 at concentrations up to 6.6×106 16S rRNA gene copies g−1 wet sediment. In Yellowstone National Park (YNP), Korarchaeota were most abundant in springs with a pH range of 5.7 to 7.0. High sulfate concentrations suggest these fluids are influenced by contributions from hydrothermal vapors that may be neutralized to some extent by mixing with water from deep geothermal sources or meteoric water. In the Great Basin (GB), Korarchaeota were most abundant at spring sources of pH<7.2 with high particulate C content and high alkalinity, which are likely to be buffered by the carbonic acid system. It is therefore likely that at least two different geological mechanisms in YNP and GB springs create the neutral to mildly acidic pH that is optimal for Korarchaeota. A classification support vector machine (C-SVM) trained on single analytes, two analyte combinations, or vectors from non-metric multidimensional scaling models was able to predict springs as Korarchaeota-optimal or sub-optimal habitats with accuracies up to 95%. To our knowledge, this is the most extensive analysis of the geochemical habitat of any high-level microbial taxon and the first application of a C-SVM to microbial ecology.

High-resolution nitrogen gas profiles in sediment porewaters using a new membrane probe for membrane-inlet mass spectrometry

A probe inlet for membrane-inlet mass spectrometry (MIMS) was developed to measure dissolved nitrogen and argon gas in sediment porewaters. This technique represents a significant improvement in the measurement of dissolved gas ratios in sediment cores and in small volume samples (<5 ml). The probe is stable, inexpensive and has relatively fast equilibration times (f4–5 min) for dissolved N2/Ar ratio analyses. The membrane probe is mounted at the end of a stainless steel capillary (0.75 mm OD) connecteddirectlytotheinletsystemofaquadrupolemassspectrometer.Themembraneisf1mm0.5mmresultinginprofiles thathaveadepthresolution of <2mm.Nitrogen/argonratiosmeasuredwiththeprobeinlethaveaprecision of <0.2%.Porewater N2/Ar ratios measured in cores collected from Raritan Bay, NJ, indicated that N2 was in equilibrium with the atmosphere in overlying waters and that nitrogen was up to 8% supersaturated by a depth of 1 cm. The increase in N2 is consistent with nitrogen production from denitrification of f2 mmol N2 m 2 day 1 . High-resolution nitrate profiles also provide evidence for

Composition and flux of explosive gas release at LUSI mud volcano (East Java, Indonesia)

The LUSI mud volcano has been erupting since May 2006 in the densely populated Sidoarjo regency (East Java, Indonesia), forcing the evacuation of 40,000 people and destroying industry, farmland, and over 10,000 homes. Mud extrusion rates of 180,000 m(3) d(-1) were measured in the first few months of the eruption, decreasing to a loosely documented 4000 m for methane and approximately 600 m for carbon dioxide; however, the mass fractions of these gases are insufficient to explain the observed dynamics. Rather, the primary driver of the cyclic bubble-bursting activity is decompressional boiling of water, which initiates a few tens of meters below the surface, setting up slug flow in the upper conduit. Our measured gas flux and conceptual model lead to a corresponding upper-bound estimate for the mud-water mass flux of 10(5) m(3) d(-1).

Exoplanet Biosignatures: A Review of Remotely Detectable Signs of Life

Abstract In the coming years and decades, advanced space- and ground-based observatories will allow an unprecedented opportunity to probe the atmospheres and surfaces of potentially habitable exoplanets for signatures of life. Life on Earth, through its gaseous products and reflectance and scattering properties, has left its fingerprint on the spectrum of our planet. Aided by the universality of the laws of physics and chemistry, we turn to Earths biosphere, both in the present and through geologic time, for analog signatures that will aid in the search for life elsewhere. Considering the insights gained from modern and ancient Earth, and the broader array of hypothetical exoplanet possibilities, we have compiled a comprehensive overview of our current understanding of potential exoplanet biosignatures, including gaseous, surface, and temporal biosignatures. We additionally survey biogenic spectral features that are well known in the specialist literature but have not yet been robustly vetted in the context of exoplanet biosignatures. We briefly review advances in assessing biosignature plausibility, including novel methods for determining chemical disequilibrium from remotely obtainable data and assessment tools for determining the minimum biomass required to maintain short-lived biogenic gases as atmospheric signatures. We focus particularly on advances made since the seminal review by Des Marais et al. The purpose of this work is not to propose new biosignature strategies, a goal left to companion articles in this series, but to review the current literature, draw meaningful connections between seemingly disparate areas, and clear the way for a path forward. Key Words: Exoplanets—Biosignatures—Habitability markers—Photosynthesis—Planetary surfaces—Atmospheres—Spectroscopy—Cryptic biospheres—False positives. Astrobiology 18, 663–708.

Evidence for high‐temperature in situ nifH transcription in an alkaline hot spring of Lower Geyser Basin, Yellowstone National Park

Genes encoding nitrogenase (nifH) were amplified from sediment and photosynthetic mat samples collected in the outflow channel of Mound Spring, an alkaline thermal feature in Yellowstone National Park. Results indicate the genetic capacity for nitrogen fixation over the entire range of temperatures sampled (57.2°C to 80.2°C). Amplification of environmental nifH transcripts revealed in situ expression of nifH genes at temperatures up to 72.7°C. However, we were unable to amplify transcripts of nifH at the higher-temperature locations (> 72.7°C). These results indicate that microbes at the highest temperature sites contain the genetic capacity to fix nitrogen, yet either do not express nifH or do so only transiently. Field measurements of nitrate and ammonium show fixed nitrogen limitation as temperature decreases along the outflow channel, suggesting nifH expression in response to the downstream decrease in bioavailable nitrogen. Nitrogen stable isotope values of Mound Spring sediment communities further support geochemical and genetic data. DNA and cDNA nifH amplicons form several unique phylogenetic clades, some of which appear to represent novel nifH sequences in both photosynthetic and chemosynthetic microbial communities. This is the first report of in situ nifH expression in strictly chemosynthetic zones of terrestrial (non-marine) hydrothermal systems, and sets a new upper temperature limit (72.7°C) for nitrogen fixation in alkaline, terrestrial hydrothermal environments.