Description: In this work we used controlled microcosms to study the effect of temperature and pH on brGDGTs in lake water. We collected surface water from Kennedy Lake, Tucson, AZ, a shallow eutrophic artificial reservoir previously described by Martínez-Sosa & Tierney (2019). From the collected samples we set up a series of microcosms, consisting of 1L glass flasks filled with lake water, and manipulated single environmental factors including temperature and pH. For our temperature incubations, we selected four conditions (9C, 18C, 27C and 35C) and incubated 3 1L flasks under each condition for two periods of time (4 or 6 weeks). For the pH incubations, we used commercially available freshwater aquarium non-phosphate buffers (Proprietary composition, Seachem, Madison, GA, USA) to manipulate the pH of the microcosms. For these experiments we targeted four pH conditions (4, 5, 6 and 7), and included two control samples: one where we added enough buffer to maintain the initial pH (Control + Buffer), and another to which we added no buffer (Control - Buffer). GDGTs were analyzed on an Agilent 1260 Infinity HPLC coupled to an Agilent 6120 single quadrupole mass spectrometer using two BEH HILIC silica columns (2.1 x 150 mm, 1.7 um; Waters) and the methodology of Hopmans et al. (2016). We calculated peak areas using the MATLAB package software ORIGAmI (Fleming et al. 2016) and estimated the concentration of brGDGTs by comparing the obtained peaks with a C46 internal standard (Huguet et al. 2006) normalized to the volume of each sample.

Description: For the past decade, observations of carbonyl sulfide (OCS or COS) have been investigated as a proxy for carbon uptake by plants. OCS is destroyed by enzymes that interact with CO2 during photosynthesis, namely carbonic anhydrase (CA) and RuBisCO, where CA is the more important one. The majority of sources of OCS to the atmosphere are geographically separated from this large plant sink, whereas the sources and sinks of CO2 are co-located in ecosystems. The drawdown of OCS can therefore be related to the uptake of CO2 without the added complication of co-located emissions comparable in magnitude. Here we review the state of our understanding of the global OCS cycle and its applications to ecosystem carbon cycle science. OCS uptake is correlated well to plant carbon uptake, especially at the regional scale. OCS can be used in conjunction with other independent measures of ecosystem function, like solar-induced fluorescence and carbon and water isotope studies. More work needs to be done to generate global coverage for OCS observations and to link this powerful atmospheric tracer to systems where fundamental questions concerning the carbon and water cycle remain.

Description: Metagenomes encode an enormous diversity of proteins, reflecting a multiplicity of functions and activities1,2. Exploration of this vast sequence space has been limited to a comparative analysis against reference microbial genomes and protein families derived from those genomes. Here, to examine the scale of yet untapped functional diversity beyond what is currently possible through the lens of reference genomes, we develop a computational approach to generate reference-free protein families from the sequence space in metagenomes. We analyse 26,931 metagenomes and identify 1.17 billion protein sequences longer than 35 amino acids with no similarity to any sequences from 102,491 reference genomes or the Pfam database3. Using massively parallel graph-based clustering, we group these proteins into 106,198 novel sequence clusters with more than 100 members, doubling the number of protein families obtained from the reference genomes clustered using the same approach. We annotate these families on the basis of their taxonomic, habitat, geographical and gene neighbourhood distributions and, where sufficient sequence diversity is available, predict protein three-dimensional models, revealing novel structures. Overall, our results uncover an enormously diverse functional space, highlighting the importance of further exploring the microbial functional dark matter.

Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Atmospheric Measurement Techniques 7 (2014): 2787-2805, doi:10.5194/amt-7-2787-2014.

Description: Our understanding of biosphere–atmosphere exchange has been considerably enhanced by eddy covariance measurements. However, there remain many trace gases, such as molecular hydrogen (H2), that lack suitable analytical methods to measure their fluxes by eddy covariance. In such cases, flux-gradient methods can be used to calculate ecosystem-scale fluxes from vertical concentration gradients. The budget of atmospheric H2 is poorly constrained by the limited available observations, and thus the ability to quantify and characterize the sources and sinks of H2 by flux-gradient methods in various ecosystems is important. We developed an approach to make nonintrusive, automated measurements of ecosystem-scale H2 fluxes both above and below the forest canopy at the Harvard Forest in Petersham, Massachusetts, for over a year. We used three flux-gradient methods to calculate the fluxes: two similarity methods that do not rely on a micrometeorological determination of the eddy diffusivity, K, based on (1) trace gases or (2) sensible heat, and one flux-gradient method that (3) parameterizes K. We quantitatively assessed the flux-gradient methods using CO2 and H2O by comparison to their simultaneous independent flux measurements via eddy covariance and soil chambers. All three flux-gradient methods performed well in certain locations, seasons, and times of day, and the best methods were trace gas similarity for above the canopy and K parameterization below it. Sensible heat similarity required several independent measurements, and the results were more variable, in part because those data were only available in the winter, when heat fluxes and temperature gradients were small and difficult to measure. Biases were often observed between flux-gradient methods and the independent flux measurements, and there was at least a 26% difference in nocturnal eddy-derived net ecosystem exchange (NEE) and chamber measurements. H2 fluxes calculated in a summer period agreed within their uncertainty and pointed to soil uptake as the main driver of H2 exchange at Harvard Forest, with H2 deposition velocities ranging from 0.04 to 0.10 cm s−1.

Description: L. K. Meredith was supported through the following funding sources: NSF Graduate Research Fellowship, multiple grants from NASA to MIT for the Advanced Global Atmospheric Gases Experiment (AGAGE), MIT Center for Global Change Science, MIT Joint Program on the Science and Policy of Global Change, MIT Martin Family Society of Fellows for Sustainability, MIT Ally of Nature Research Fund, MIT William Otis Crosby Lectureship, and MIT Warren Klein Fund. Operation of the EMS flux tower was supported by the Office of Science (BER), US Dept. of Energy (DE-SC0004985), and is a component of the Harvard Forest LTER, supported by National Science Foundation.

Description: Author Posting. © The Author(s), 2013. This is the author's version of the work. It is posted here by permission of Society for Applied Microbiology for personal use, not for redistribution. The definitive version was published in Environmental Microbiology Reports 6 (2014): 226-238, doi:10.1111/1758-2229.12116.

Description: Microbe-mediated soil uptake is the largest and most uncertain variable in the budget of atmospheric hydrogen (H2). The diversity and ecophysiological role of soil microorganisms that can consume low atmospheric abundances of H2 with high-affinity [NiFe]-hydrogenases is unknown. We expanded the library of atmospheric H2-consuming strains to include four soil Harvard Forest Isolate (HFI) Streptomyces spp., Streptomyces cattleya, and Rhodococcus equi by assaying for high-affinity hydrogenase (hhyL) genes and quantifying H2 uptake rates. We find that aerial structures (hyphae and spores) are important for Streptomyces H2 consumption; uptake was not observed in Streptomyces griseoflavus Tu4000 (deficient in aerial structures) and was reduced by physical disruption of Streptomyces sp. HFI8 aerial structures. H2 consumption depended on the life cycle stage in developmentally distinct actinobacteria: Streptomyces sp. HFI8 (sporulating) and R. equi (non-sporulating, non-filamentous). Strain HFI8 took up H2 only after forming aerial hyphae and sporulating, while R. equi only consumed H2 in the late exponential and stationary phase. These observations suggest that conditions favoring H2 uptake by actinobacteria are associated with energy and nutrient limitation. Thus, H2 may be an important energy source for soil microorganisms inhabiting systems in which nutrients are frequently limited.

Description: L.K.M. was supported by from the following funding sources: NSF Graduate Research Fellowship, multiple grants from NASA to MIT for the Advanced Global Atmospheric Gases Experiment (AGAGE), MIT Center for Global Change Science, MIT Joint Program on the Science and Policy of Global Change, MIT Martin Family Society of Fellows for Sustainability, MIT Ally of Nature Research Fund, MIT William Otis Crosby Lectureship, and MIT Warren Klein Fund. D. R. was funded through MIT Undergraduate Research Opportunities Program (UROP) with support from the Lord Foundation and Jordan J. Baruch Fund (1947) and was supported by the Harvard Forest REU Program.