Lithogenic hydrogen supports microbial primary production in subglacial and proglacial environments

Surprising concentrations of hydrogen and non-geological methane and carbon dioxide in the soil

Due to its potential use as a carbon-free energy resource with minimal environmental and climate impacts, natural hydrogen (H2) produced by subsurface geochemical processes is today the target of intensive research. In H2 exploration practices, bacteria are thought to swiftly consume H2 and, therefore, small near-surface concentrations of H2, even orders of 102 ppmv in soils, are considered a signal of active migration of geological gas, potentially revealing underground resources. Here, we document an extraordinary case of a widespread occurrence of H2 (up to 1 vol%), together with elevated concentrations of CH4 and CO2 (up to 51 and 27 vol%, respectively), in aerated meadow soils along Italian Alps valleys. Based on current literature, this finding would be classified as a discovery of pervasive and massive geological H2 seepage. Nevertheless, an ensemble of gas geochemical and soil microbiological analyses, including bulk and clumped CH4 isotopes, radiocarbon of CH4 and CO2, and DNA and mcrA gene quantitative polymerase chain reaction analyses, revealed that H2 was only coupled to modern microbial gas. The H2-CO2-CH4-H2S association, wet soil proximity, and the absence of other geogenic gases in soils and springs suggest that H2 derives from near-surface fermentation, rather than geological degassing. H2 concentrations up to 1 vol% in soils are not conclusive evidence of deep gas seepage. This study provides a new reference for the potential of microbial H2, CH4 and CO2 in soils, to be considered in H2 exploration guidelines and soil carbon and greenhouse-gas cycle research.

Wood-Ljungdahl pathway encoding anaerobes facilitate low-cost primary production in hypersaline sediments at Great Salt Lake, Utah

Little is known of primary production in dark hypersaline ecosystems despite the prevalence of such environments on Earth today and throughout its geologic history. Here, we generated and analyzed metagenome-assembled genomes (MAGs) organized as operational taxonomic units (OTUs) from three depth intervals along a 30-cm sediment core from the north arm of Great Salt Lake, Utah. The sediments and associated porewaters were saturated with NaCl, exhibited redox gradients with depth, and harbored nitrogen-depleted organic carbon. Metabolic predictions of MAGs representing 36 total OTUs recovered from the core indicated that communities transitioned from aerobic and heterotrophic at the surface to anaerobic and autotrophic at depth. Dark CO2 fixation was detected in sediments and the primary mode of autotrophy was predicted to be via the Wood-Ljungdahl pathway. This included novel hydrogenotrophic acetogens affiliated with the bacterial class Candidatus Bipolaricaulia. Minor populations were dependent on the Calvin cycle and the reverse tricarboxylic acid cycle, including in a novel Thermoplasmatota MAG. These results are interpreted to reflect the favorability of and selectability for populations that operate the lowest energy requiring CO2-fixation pathway known, the Wood-Ljungdahl pathway, in anoxic and hypersaline conditions that together impart a higher energy demand on cells.

Rhodoferax lithotrophicus sp. nov., a neutrophilic iron-oxidizing and -reducing bacterium isolated from iron-rich freshwater sediments

A neutrophilic iron-oxidizing and -reducing bacterium, strain MIZ03T, was previously isolated from a wetland in Ibaraki, Japan. Here, we report the detailed characteristics of this strain. It was motile with a single polar flagellum, and Gram-stain-negative. It could grow not only chemolithoautotrophically but also chemoorganotrophically by aerobic respiration and fermentation. Major cellular fatty acids were C16 : 1  ω7c/C16 : 1  ω6c, and C16 : 0. Phylogenetic analyses indicated that strain MIZ03T belonged to the genus Rhodoferax. This strain was closely related to Rhodoferax ferrireducens with 98.5 % of 16S rRNA gene sequence similarity. Based on its phenotypic and genomic based characteristics, we conclude that strain MIZ03T represents a new species in the genus Rhodoferax. We propose the name Rhodoferax lithotrophicus sp. nov. to accommodate this strain. The type strain is MIZ03T (=JCM 34246T=DSM 113266T). We also propose the name Rhodoferax koreensis sp. nov., of which the type strain is DCY110T (=KCTC 52288T=JCM 31441T), for the effectively, but not yet validly, published name 'Rhodoferax koreense'.

Rapid Consumption of Dihydrogen Injected into a Shallow Aquifer by Ecophysiologically Different Microbes

The envisaged future dihydrogen (H2) economy requires a H2 gas grid as well as large deep underground stores. However, the consequences of an unintended spread of H2 through leaky pipes, wells, or subterranean gas migrations on groundwater resources and their ecosystems are poorly understood. Therefore, we emulated a short-term leakage incident by injecting gaseous H2 into a shallow aquifer at the TestUM test site and monitored the subsequent biogeochemical processes in the groundwater system. At elevated H2 concentrations, an increase in acetate concentrations and a decrease in microbial α-diversity with a concomitant change in microbial β-diversity were observed. Additionally, microbial H2 oxidation was indicated by temporally higher abundances of taxa known for aerobic or anaerobic H2 oxidation. After H2 concentrations diminished below the detection limit, α- and β-diversity approached baseline values. In summary, the emulated H2 leakage resulted in a temporally limited change of the groundwater microbiome and associated geochemical conditions due to the intermediate growth of H2 consumers. The results confirm the general assumption that H2, being an excellent energy and electron source for many microorganisms, is quickly microbiologically consumed in the environment after a leakage.

Glacial Water: A Dynamic Microbial Medium

Microbial communities and nutrient dynamics in glaciers and ice sheets continuously change as the hydrological conditions within and on the ice change. Glaciers and ice sheets can be considered bioreactors as microbiomes transform nutrients that enter these icy systems and alter the meltwater chemistry. Global warming is increasing meltwater discharge, affecting nutrient and cell export, and altering proglacial systems. In this review, we integrate the current understanding of glacial hydrology, microbial activity, and nutrient and carbon dynamics to highlight their interdependence and variability on daily and seasonal time scales, as well as their impact on proglacial environments.

Relationships between fluid mixing, biodiversity, and chemosynthetic primary productivity in Yellowstone hot springs

The factors that influence biodiversity and productivity of hydrothermal ecosystems are not well understood. Here we investigate the relationship between fluid mixing, biodiversity, and chemosynthetic primary productivity in three co-localized hot springs (RSW, RSN, and RSE) in Yellowstone National Park that have different geochemistry. All three springs are sourced by reduced hydrothermal fluid, but RSE and RSN receive input of vapour phase gas and oxidized groundwaters, with input of both being substantially higher in RSN. Metagenomic sequencing revealed that communities in RSN were more biodiverse than those of RSE and RSW in all dimensions evaluated. Microcosm activity assays indicate that rates of dissolved inorganic carbon (DIC) uptake were also higher in RSN than in RSE and RSW. Together, these results suggest that increased mixing of reduced volcanic fluid with oxidized fluids generates additional niche space capable of supporting increasingly biodiverse communities that are more productive. These results provide insight into the factors that generate and maintain chemosynthetic biodiversity in hydrothermal systems and that influence the distribution, abundance, and diversity of microbial life in communities supported by chemosynthesis. These factors may also extend to other ecosystems not supported by photosynthesis, including the vast subterranean biosphere and biospheres beneath ice sheets and glaciers.

Iron Minerals Influence the Assembly of Microbial Communities in a Basaltic Glacial Catchment

The influence of mineralogy on the assembly of microbial communities in glacial environments has been difficult to assess due to complications in isolating mineralogy from other variables. Here we assess the abundance and composition of microbial communities that colonized defined minerals incubated for 12 months in two meltwater streams (N and S) emanating from Kaldalónsjökull (Kal), a basalt-hosted glacier in Iceland. The two streams shared similar meltwater geochemistry as well as bedrock and proglacial sediment elemental compositions. Yet genomic DNA and PCR-amplifiable 16S rRNA genes were detected only in Kal S. The amount of recoverable DNA was highest for hematite incubated in Kal S and the composition of 16S rRNA genes recovered from Kal S sediments was most like those recovered from hematite and magnetite, an effect driven largely by similarities in the relative abundance of the putative hydrogenotrophic iron reducer Rhodoferax. We suggest this is attributable to comminution and weathering reactions involving exposed iron silicate minerals that generate and release hydrogen and Fe(III) that can be coupled to support microbial metabolism in Kaldalónsjökull, and possibly other basaltic habitats. The low abundance of cells in Kal N could be due to low availability of Fe(III) or another substrate.

Microbial Community Structure and Metabolic Potential at the Initial Stage of Soil Development of the Glacial Forefields in Svalbard

Microbial communities have been identified as the primary inhabitants of Arctic forefields. However, the metabolic potential of microbial communities in these newly exposed soils remains underexplored due to limited access. Here, we sampled the very edge of the glacial forefield in Svalbard and performed the 16S rRNA genes and metagenomic analysis to illustrate the ecosystem characteristics. Burkholderiales and Micrococcales were the dominant bacterial groups at the initial stage of soil development of glacial forefields. 214 metagenome-assembled genomes were recovered from glacier forefield microbiome datasets, including only 2 belonging to archaea. Analysis of these metagenome-assembled genomes revealed that 41% of assembled genomes had the genetic potential to use nitrate and nitrite as electron acceptors. Metabolic pathway reconstruction for these microbes suggested versatility for sulfide and thiosulfate oxidation, H₂ and CO utilization, and CO₂ fixation. Our results indicate the importance of anaerobic processes in elemental cycling in the glacial forefields. Besides, a range of genes related to adaption to low temperature and other stresses were detected, which revealed the presence of diverse mechanisms of adaption to the extreme environment of Svalbard. This research provides ecological insight into the initial stage of the soil developed during the retreating of glaciers.

Genomic and metabolic adaptations of biofilms to ecological windows of opportunity in glacier-fed streams

In glacier-fed streams, ecological windows of opportunity allow complex microbial biofilms to develop and transiently form the basis of the food web, thereby controlling key ecosystem processes. Using metagenome-assembled genomes, we unravel strategies that allow biofilms to seize this opportunity in an ecosystem otherwise characterized by harsh environmental conditions. We observe a diverse microbiome spanning the entire tree of life including a rich virome. Various co-existing energy acquisition pathways point to diverse niches and the exploitation of available resources, likely fostering the establishment of complex biofilms during windows of opportunity. The wide occurrence of rhodopsins, besides chlorophyll, highlights the role of solar energy capture in these biofilms while internal carbon and nutrient cycling between photoautotrophs and heterotrophs may help overcome constraints imposed by oligotrophy in these habitats. Mechanisms potentially protecting bacteria against low temperatures and high UV-radiation are also revealed and the selective pressure of this environment is further highlighted by a phylogenomic analysis differentiating important components of the glacier-fed stream microbiome from other ecosystems. Our findings reveal key genomic underpinnings of adaptive traits contributing to the success of complex biofilms to exploit environmental opportunities in glacier-fed streams, which are now rapidly changing owing to global warming.

A Single Bacterium Capable of Oxidation and Reduction of Iron at Circumneutral pH

Fe(II)-oxidizing microorganisms and Fe(III)-reducing microorganisms, which drive the biogeochemical Fe cycle on the Earth's surface, are phylogenetically and ecologically diverse. However, no single organism capable of aerobic Fe(II) oxidation and anaerobic Fe(III) reduction at circumneutral pH have been reported so far. Here, we report a novel neutrophilic Fe(II)-oxidizing Rhodoferax bacterium, strain MIZ03, isolated from an iron-rich wetland in Japan. Our cultivation experiments demonstrate that MIZ03 represents a much more versatile metabolism for energy acquisition than previously recognized in the genus Rhodoferax. MIZ03 can grow chemolithoautotrophically at circumneutral pH by oxidation of Fe(II), H2, or thiosulfate as the sole electron donor under (micro)aerobic conditions (i.e., using O2 as the sole electron acceptor). In addition, it can reduce Fe(III) or nitrate under anaerobic conditions. Thus, this is the first report demonstrating the presence of a single bacterium capable of both Fe(II) oxidation and Fe(III) reduction at circumneutral pH. The observed physiology was consistent with its 4.9-Mbp complete genome encoding key genes for iron oxidation/reduction (foxEY and mtrABC), for nitrate reduction (narGHI), for thiosulfate oxidation (soxABCDXYZ), and for carbon fixation via the Calvin cycle. Our metagenomic survey suggests that there are more Rhodoferax members capable of Fe(II) oxidation and Fe(III) reduction. Such bifunctional Rhodoferax may have an ecological advantage in suboxic/anoxic environments at circumneutral pH by recycling of Fe as the electron donor and acceptor. IMPORTANCE The biogeochemical cycle of iron (Fe) via reactions of oxidation, reduction, precipitation, and dissolution is involved in the cycle of other ecologically relevant elements, such as C, N, P, S, As, Co, Ni, and Pb. The Fe cycle on the Earth's surface is driven by a variety of Fe(II)-oxidizing microorganisms and Fe(III)-reducing microorganisms. Here, we discovered a novel bacterium, Rhodoferax sp. strain MIZ03, capable of both Fe(II) oxidation and Fe(III) reduction at circumneutral pH, and we report its physiological characteristics and complete genome sequence. The unexpected capability of this bacterium provides novel insights into the Fe cycle in the environment. Moreover, this bacterium will help to better understand the molecular mechanisms of microbial Fe redox cycling as a model organism.

Active microbial ecosystem in glacier basal ice fuelled by iron and silicate comminution-derived hydrogen

The basal zone of glaciers is characterized by physicochemical properties that are distinct from firnified ice due to strong interactions with underlying substrate and bedrock. Basal ice (BI) ecology and the roles that the microbiota play in biogeochemical cycling, weathering, and proglacial soil formation remain poorly described. We report on basal ice geochemistry, bacterial diversity (16S rRNA gene phylogeny), and inferred ecological roles at three temperate Icelandic glaciers. We sampled three physically distinct basal ice facies (stratified, dispersed, and debris bands) and found facies dependent on biological similarities and differences; basal ice character is therefore an important sampling consideration in future studies. Based on a high abundance of silicates and Fe-containing minerals and, compared to earlier BI literature, total C was detected that could sustain the basal ice ecosystem. It was hypothesized that C-fixing chemolithotrophic bacteria, especially Fe-oxidisers and hydrogenotrophs, mutualistically support associated heterotrophic communities. Basal ice-derived rRNA gene sequences corresponding to genera known to harbor hydrogenotrophic methanogens suggest that silicate comminution-derived hydrogen can also be utilized for methanogenesis. PICRUSt-predicted metabolism suggests that methane metabolism and C-fixation pathways could be highly relevant in BI, indicating the importance of these metabolic routes. The nutrients and microbial communities release from melting basal ice may play an important role in promoting pioneering communities establishment and soil development in deglaciating forelands.