Meeting Minutes for October 13, 2016

Raw DICOM image files of CT-scanned termite mound Tp

Multiple energy sources and metabolic strategies sustain microbial diversity in Antarctic desert soils

Numerous diverse microorganisms reside in the cold desert soils of continental Antarctica, though we lack a holistic understanding of the metabolic processes that sustain them. Here, we profile the composition, capabilities, and activities of the microbial communities in 16 physicochemically diverse mountainous and glacial soils. We assembled 451 metagenome-assembled genomes from 18 microbial phyla and inferred through Bayesian divergence analysis that the dominant lineages present are likely native to Antarctica. In support of earlier findings, metagenomic analysis revealed that the most abundant and prevalent microorganisms are metabolically versatile aerobes that use atmospheric hydrogen to support aerobic respiration and sometimes carbon fixation. Surprisingly, however, hydrogen oxidation in this region was catalyzed primarily by a phylogenetically and structurally distinct enzyme, the group 1l [NiFe]-hydrogenase, encoded by nine bacterial phyla. Through gas chromatography, we provide evidence that both Antarctic soil communities and an axenic Bacteroidota isolate (Hymenobacter roseosalivarius) oxidize atmospheric hydrogen using this enzyme. Based on ex situ rates at environmentally representative temperatures, hydrogen oxidation is theoretically sufficient for soil communities to meet energy requirements and, through metabolic water production, sustain hydration. Diverse carbon monoxide oxidizers and abundant methanotrophs were also active in the soils. We also recovered genomes of microorganisms capable of oxidizing edaphic inorganic nitrogen, sulfur, and iron compounds and harvesting solar energy via microbial rhodopsins and conventional photosystems. Obligately symbiotic bacteria, including Patescibacteria, Chlamydiae, and predatory Bdellovibrionota, were also present. We conclude that microbial diversity in Antarctic soils reflects the coexistence of metabolically flexible mixotrophs with metabolically constrained specialists.DATA AVAILABILTY: All amplicon sequencing data, raw metagenomes, metagenomic assemblies, and metagenome-assembled genomes were deposited to the National Center for Biotechnology Information (NCBI) Sequence Read Archive under the BioProject accession no. PRJNA630822. All other study data are included in the article and/or supporting information.An Australian Research Council Discovery Early Career Researcher Award (ARC DECRA) Fellowship, an Australian Antarctic Division grant, a South African National Antarctic Program grant, a National Health & Medical Research Council Emerging Leadership 2 (NHMRC EL2) Fellowship, an Australian Government Research Training Stipend Scholarship, a Monash International Tuition Scholarship, a Monash Postgraduate Publications Award, a South African National Antarctic Programme (SANAP) postdoctoral grant.https://www.pnas.orghj2022BiochemistryGeneticsMicrobiology and Plant Patholog

Technical Note: Disturbance of soil structure can lead to release of entrapped methane in glacier forefield soils

Investigations of sources and sinks of atmospheric CH4 are needed to understand the global CH4 cycle and climate-change mitigation options. Glaciated environments might play a critical role due to potential feedbacks with global glacial meltdown. In an emerging glacier forefield, an ecological shift occurs from an anoxic, potentially methanogenic subglacial sediment to an oxic proglacial soil, in which soil-microbial consumption of atmospheric CH4 is initiated. The development of this change in CH4 turnover can be quantified by soil-gas profile analysis. We found evidence for CH4 entrapped in glacier forefield soils when comparing two methods for the collection of soil-gas samples: a modified steel rod (SR) designed for one-time sampling and rapid screening (samples collected ∼1 min after hammering the SR into the soil), and a novel multilevel sampler (MLS) for repetitive sampling through a previously installed access tube (samples collected weeks after access-tube installation). In glacier forefields on siliceous bedrock, sub-atmospheric CH4 concentrations were observed with both methods. Conversely, elevated soil-CH4 concentrations were observed in calcareous glacier forefields, but only in samples collected with the SR, while MLS samples all showed sub-atmospheric CH4 concentrations. Time-series of SR soil-gas sampling (additional samples collected 2, 3, 5, and 7 min after hammering) confirmed the transient nature of the elevated soil-CH4 concentrations, which were decreasing from ∼100 μL L−1 towards background levels within minutes. This hints towards the existence of entrapped CH4 in calcareous glacier forefield soil that can be released when sampling soil-gas with the SR. Laboratory experiments with miniature soil cores collected from two glacier forefields confirmed CH4 entrapment in these soils. Treatment by sonication and acidification resulted in a massive release of CH4 from calcareous cores (on average 0.3–1.8 μg CH4 (g d.w.)−1) (d.w. – dry weight); release from siliceous cores was 1–2 orders of magnitude lower (0.02–0.03 μg CH4 (g d.w.)−1). Clearly, some form of CH4 entrapment exists in calcareous glacier forefield soils, and to a much lesser extent in siliceous glacier forefield soils. Its nature and origin remain unclear and will be subject of future investigations.ISSN:1726-4170ISSN:1726-417

Activity and diversity of methane-oxidizing bacteria in glacier forefields on siliceous and calcareous bedrock

The global methane (CH4) cycle is largely driven by methanogenic archaea and methane-oxidizing bacteria (MOB), but little is known about their activity and diversity in pioneer ecosystems. We conducted a field survey in forefields of 13 receding Swiss glaciers on both siliceous and calcareous bedrock to investigate and quantify CH4 turnover based on soil-gas CH4 concentration profiles, and to characterize the MOB community by sequencing and terminal restriction fragment length polymorphism (T-RFLP) analysis of pmoA. Methane turnover was fundamentally different in the two bedrock categories. Of the 36 CH4 concentration profiles from siliceous locations, 11 showed atmospheric CH4 consumption at concentrations of ~1–2 μL L−1 with soil-atmosphere CH4 fluxes of –0.14 to –1.1 mg m−2 d−1. Another 11 profiles showed no apparent activity, while the remaining 14 exhibited slightly increased CH4 concentrations of ~2–10 μL L−1 , most likely due to microsite methanogenesis. In contrast, all profiles from calcareous sites suggested a substantial, yet unknown CH4 source below our sampling zone, with soil-gas CH4 concentrations reaching up to 1400 μL L−1. Remarkably, most soils oxidized ~90 % of the deep-soil CH4, resulting in soil-atmosphere fluxes of 0.12 to 31 mg m−2 d−1. MOB showed limited diversity in both siliceous and calcareous forefields: all identified pmoA sequences formed only 5 operational taxonomic units (OTUs) at the species level and, with one exception, could be assigned to either Methylocystis or the as-yet-uncultivated Upland Soil Cluster γ (USCγ). The latter dominated T-RFLP patterns of all siliceous and most calcareous samples, while Methylocystis dominated in 4 calcareous samples. Members of Upland Soil Cluster α (USCα) were not detected. Apparently, USCγ adapted best to the oligotrophic cold climate conditions at the investigated pioneer sites.ISSN:1726-4170ISSN:1726-417

High Temporal and Spatial Variability of Atmospheric-Methane Oxidation in Alpine Glacier Forefield Soils

ISSN:0099-2240ISSN:1098-533

DICOM images termite mound Ms6

Raw DICOM image files of CT-scanned termite mound Ms

Data from: Technical note: rapid image-based field methods improve the quantification of termite mound structures and greenhouse-gas fluxes

Termite mounds (TMs) mediate biogeochemical processes with global relevance, such as turnover of the important greenhouse gas methane (CH4). However, the complex internal and external morphology of TMs impede an accurate quantitative description. Here we present two novel field methods, photogrammetry (PG) and cross-section image analysis, to quantify TM external and internal mound structure of 29 TMs of three termite species. Photogrammetry was used to measure epigeal volume (VE), surface area (AE) and mound basal area (AB) by reconstructing 3D models from digital photographs, and compared against a water-displacement method and the conventional approach of approximating TMs by simple geometric shapes. To describe TM internal structure, we introduce TM macro- and micro-porosity (θM and θµ), the volume fractions of macroscopic chambers, and microscopic pores in the wall material, respectively. Macro-porosity was estimated using image analysis of single TM cross-sections, and compared against full x-ray tomography (CT) scans of 17 TMs. For these TMs we present complete pore fractions to assess species-specific differences in internal structure. The PG method yielded VE nearly identical to a water-displacement method, while approximation of TMs by simple geometric shapes led to errors of 4–200 %. Likewise, using PG substantially improved the accuracy of CH4 emission estimates by 10–50 %. Comprehensive CT scanning revealed that investigated TMs have species-specific ranges of θM and θµ, but similar total porosity. Image analysis of single TM cross-sections produced good estimates of θM for species with thick walls and evenly distributed chambers. The new image-based methods allow rapid and accurate quantitative characterisation of TMs to answer ecological, physiological and biogeochemical questions. The PG method should be applied when measuring greenhouse-gas emissions from TMs to avoid large errors from inadequate shape approximations

DICOM images termite mound Mn1

Raw DICOM image files of CT-scanned termite mound Mn

Transitions (2016-04)

Raw DICOM image files of CT-scanned termite mound Ms