Clearing the air: unraveling past and guiding future research in atmospheric chemosynthesis

SUMMARY

Atmospheric chemosynthesis is a recently proposed form of chemoautotrophic microbial primary production. The proposed process relies on the oxidation of trace concentrations of hydrogen (≤530 ppbv), carbon monoxide (≤90 ppbv), and methane (≤1,870 ppbv) gases using high-affinity enzymes. Atmospheric hydrogen and carbon monoxide oxidation have been primarily linked to microbial growth in desert surface soils scarce in liquid water and organic nutrients, and low in photosynthetic communities. It is well established that the oxidation of trace hydrogen and carbon monoxide gases widely supports the persistence of microbial communities in a diminished metabolic state, with the former potentially providing a reliable source of metabolic water. Microbial atmospheric methane oxidation also occurs in oligotrophic desert soils and is widespread throughout copiotrophic environments, with established links to microbial growth. Despite these findings, the direct link between trace gas oxidation and carbon fixation remains disputable. Here, we review the supporting evidence, outlining major gaps in our understanding of this phenomenon, and propose approaches to validate atmospheric chemosynthesis as a primary production process. We also explore the implications of this minimalistic survival strategy in terms of nutrient cycling, climate change, aerobiology, and astrobiology.

Atmospheric Carbon and Transport - America (ACT-America) Data Sets: Description, Management, and Delivery

The ACT-America project is a NASA Earth Venture Suborbital-2 mission designed to study the transport and fluxes of greenhouse gases. The open and freely available ACT-America data sets provide airborne in situ measurements of atmospheric carbon dioxide, methane, trace gases, aerosols, clouds, and meteorological properties, airborne remote sensing measurements of aerosol backscatter, atmospheric boundary layer height and columnar content of atmospheric carbon dioxide, tower-based measurements, and modeled atmospheric mole fractions and regional carbon fluxes of greenhouse gases over the Central and Eastern United States. We conducted 121 research flights during five campaigns in four seasons during 2016-2019 over three regions of the US (Mid-Atlantic, Midwest and South) using two NASA research aircraft (B-200 and C-130). We performed three flight patterns (fair weather, frontal crossings, and OCO-2 underflights) and collected more than 1,140 h of airborne measurements via level-leg flights in the atmospheric boundary layer, lower, and upper free troposphere and vertical profiles spanning these altitudes. We also merged various airborne in situ measurements onto a common standard sampling interval, which brings coherence to the data, creates geolocated data products, and makes it much easier for the users to perform holistic analysis of the ACT-America data products. Here, we report on detailed information of data sets collected, the workflow for data sets including storage and processing of the quality controlled and quality assured harmonized observations, and their archival and formatting for users. Finally, we provide some important information on the dissemination of data products including metadata and highlights of applications of ACT-America data sets.

Ozone chemistry and dynamics at a tropical coastal site impacted by the COVID-19 lockdown

The nationwide lockdown in India to curb the spread of Coronavirus disease 2019 (COVID-19) led to colossal reduction in anthropogenic emissions. Here, we investigated the impact of lockdown on surface ozone (O₃) and nitrogen dioxide (NO₂) over a tropical coastal station – Thumba, Thiruvananthapuram (8.5°N, 76.9°E). Daytime as well as night-time NO₂ showed reduction by 0.8 (40%) and 2.3 (35%) ppbv, respectively during the lockdown period of 25–30 March 2020 as compared with the same period of previous 3 years. Unlike many urban locations, daytime surface O₃ is found to be dramatically reduced by 15 ppbv (36%) with O₃ production rate being lower by a factor of 3 during the lockdown. Interestingly, a feature of O₃-hump during the onset of land breeze typically observed during 1997–1998 has reappeared with magnitude of 5–10 ppbv. A photochemical box model, capturing this feature, revealed that significant O₃ sustained till onset of land breeze over the land due to weaker titration with NO_x during lockdown. It is suggested that the transport of this O₃ rich air with onset of land breeze led to the observed hump. Our measurements unravel a remarkable impact of the COVID-19 lockdown on the chemistry and dynamics of O₃ over this tropical coastal environment.

Soil Microbiomes With the Genetic Capacity for Atmospheric Chemosynthesis Are Widespread Across the Poles and Are Associated With Moisture, Carbon, and Nitrogen Limitation

Soil microbiomes within oligotrophic cold deserts are extraordinarily diverse. Increasingly, oligotrophic sites with low levels of phototrophic primary producers are reported, leading researchers to question their carbon and energy sources. A novel microbial carbon fixation process termed atmospheric chemosynthesis recently filled this gap as it was shown to be supporting primary production at two Eastern Antarctic deserts. Atmospheric chemosynthesis uses energy liberated from the oxidation of atmospheric hydrogen to drive the Calvin-Benson-Bassham (CBB) cycle through a new chemotrophic form of ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), designated IE. Here, we propose that the genetic determinants of this process; RuBisCO type IE (rbcL1E) and high affinity group 1h-[NiFe]-hydrogenase (hhyL) are widespread across cold desert soils and that this process is linked to dry and nutrient-poor environments. We used quantitative PCR (qPCR) to quantify these genes in 122 soil microbiomes across the three poles; spanning the Tibetan Plateau, 10 Antarctic and three high Arctic sites. Both genes were ubiquitous, being present at variable abundances in all 122 soils examined (rbcL1E, 6.25 × 10³–1.66 × 10⁹ copies/g soil; hhyL, 6.84 × 10³–5.07 × 10⁸ copies/g soil). For the Antarctic and Arctic sites, random forest and correlation analysis against 26 measured soil physicochemical parameters revealed that rbcL1E and hhyL genes were associated with lower soil moisture, carbon and nitrogen content. While further studies are required to quantify the rates of trace gas carbon fixation and the organisms involved, we highlight the global potential of desert soil microbiomes to be supported by this new minimalistic mode of carbon fixation, particularly throughout dry oligotrophic environments, which encompass more than 35% of the Earth’s surface.

A Gaseous Milieu: Extending the Boundaries of the Rhizosphere

Plant root activities shape microbial community functioning in the soil, making the rhizosphere the epicenter of soil biogeochemical processes. With this opinion article, we argue to rethink the rhizosphere boundaries: as gases can diffuse several centimeters away from the roots into the soil, the portion of soil influenced by root activities is larger than the strictly root-adhering soil. Indeed, gases are key drivers of biogeochemical processes due to their roles as energy sources or communication molecules, which has the potential to modify microbial community structure and functioning. In order to get a more holistic perspective on this key environment, we advocate for interdisciplinarity in rhizosphere research by combining knowledge of soluble compounds with gas dynamics.

Lakes as nitrous oxide sources in the boreal landscape

Estimates of regional and global freshwater N2 O emissions have remained inaccurate due to scarce data and complexity of the multiple processes driving N2 O fluxes the focus predominantly being on summer time measurements from emission hot spots, agricultural streams. Here, we present four-season data of N2 O concentrations in the water columns of randomly selected boreal lakes covering a large variation in latitude, lake type, area, depth, water chemistry, and land use cover. Nitrate was the key driver for N2 O dynamics, explaining as much as 78% of the variation of the seasonal mean N2 O concentrations across all lakes. Nitrate concentrations varied among seasons being highest in winter and lowest in summer. Of the surface water samples, 71% were oversaturated with N2 O relative to the atmosphere. Largest oversaturation was measured in winter and lowest in summer stressing the importance to include full year N2 O measurements in annual emission estimates. Including winter data resulted in fourfold annual N2 O emission estimates compared to summer only measurements. Nutrient-rich calcareous and large humic lakes had the highest annual N2 O emissions. Our emission estimates for Finnish and boreal lakes are 0.6 and 29 Gg N2 O-N/year, respectively. The global warming potential of N2 O from lakes cannot be neglected in the boreal landscape, being 35% of that of diffusive CH4 emission in Finnish lakes.

Uncovering the Metabolic Strategies of the Dormant Microbial Majority: towards Integrative Approaches

A grand challenge in microbiology is to understand how the dormant majority lives. In natural environments, most microorganisms are not growing and instead exist in a spectrum of dormant states. Despite this, most research on microbial metabolism continues to be growth-centric, and many overlook the fact that dormant cells require energy for maintenance. In this perspective, we discuss our research program to uncover the metabolic strategies that support microbial survival. We present two major principles underlying these studies. The first is the recent realization that microbial survival depends on previously unrecognized metabolic flexibility. The second is that new discoveries in this area depend on more sophisticated integration of approaches at the molecular, cellular, and ecosystem levels. These principles are illustrated with examples from the literature, including our own work demonstrating that bacteria can live on air, and areas for future methodological and theoretical development are highlighted.

Widespread soil bacterium that oxidizes atmospheric methane

The global atmospheric level of methane (CH₄), the second most important greenhouse gas, is currently increasing by ∼10 million tons per year. Microbial oxidation in unsaturated soils is the only known biological process that removes CH₄ from the atmosphere, but so far, bacteria that can grow on atmospheric CH₄ have eluded all cultivation efforts. In this study, we have isolated a pure culture of a bacterium, strain MG08 that grows on air at atmospheric concentrations of CH₄ [1.86 parts per million volume (p.p.m.v.)]. This organism, named Methylocapsa gorgona, is globally distributed in soils and closely related to uncultured members of the upland soil cluster α. CH₄ oxidation experiments and ¹³C-single cell isotope analyses demonstrated that it oxidizes atmospheric CH₄ aerobically and assimilates carbon from both CH₄ and CO₂ Its estimated specific affinity for CH₄ (a⁰ _s) is the highest for any cultivated methanotroph. However, growth on ambient air was also confirmed for Methylocapsa acidiphila and Methylocapsa aurea, close relatives with a lower specific affinity for CH₄, suggesting that the ability to utilize atmospheric CH₄ for growth is more widespread than previously believed. The closed genome of M. gorgona MG08 encodes a single particulate methane monooxygenase, the serine cycle for assimilation of carbon from CH₄ and CO₂, and CO₂ fixation via the recently postulated reductive glycine pathway. It also fixes dinitrogen and expresses the genes for a high-affinity hydrogenase and carbon monoxide dehydrogenase, suggesting that atmospheric CH₄ oxidizers harvest additional energy from oxidation of the atmospheric trace gases carbon monoxide (0.2 p.p.m.v.) and hydrogen (0.5 p.p.m.v.).

Comparative Adsorption of Acetone on Water and Ice Surfaces

Small organic molecules on ice and water surfaces are ubiquitous in nature and play a crucial role in many environmentally relevant processes. Herein, we combine surface‐specific vibrational spectroscopy and a controllable flow cell apparatus to investigate the molecular adsorption of acetone onto the basal plane of single‐crystalline hexagonal ice with a large surface area. By comparing the adsorption of acetone on the ice/air and the water/air interface, we observed two different types of acetone adsorption, as apparent from the different responses of both the free O−H and the hydrogen‐bonded network vibrations for ice and liquid water. Adsorption on ice occurs preferentially through interactions with the free OH group, while the interaction of acetone with the surface of liquid water appears less specific.

Particulate Matter and Gaseous Pollutions in Three Metropolises along the Chinese Yangtze River: Situation and Implications

The situation of criteria atmospheric pollutants, including particulate matter and trace gases (SO₂, NO₂, CO and O₃), over three metropolises (Chongqing, Wuhan, and Nanjing), representing the upstream, midstream and downstream portions of the Yangtze River Basin from September 2015 to August 2016 were analyzed. The maximum annual mean PM2.5 and PM10 concentrations were 61.3 and 102.7 μg/m³ in Wuhan, while highest annual average gaseous pollutions occurred in Nanjing, with 49.6 and 22.9 ppb for 8 h O₃ and NO₂, respectively. Compared to a few years ago, SO₂ and CO mass concentrations have dropped to well below the qualification standards, and the O₃ and NO₂ concentrations basically meet the requirements though occasionally is still high. In contrary, about 13%, 25%, 22% for PM2.5, and 4%, 17%, 15% for PM10 exceed the Chinese Ambient Air Quality Standard (CAAQS) Grade II. Particulate matter, especially PM2.5, is the most frequent major pollutant to poor air quality with 73%, 64% and 88% accounting for substandard days. Mean PM2.5 concentrations on PM2.5 episode days are 2⁻3 times greater than non-episode days. On the basis of calculation of PM2.5/PM10 and PM2.5/CO ratios, the enhanced particulate matter pollution on episode days is closely related to secondary aerosol production. Except for O₃, the remaining five pollutants exhibit analogous seasonal patterns, with the highest magnitude in winter and lowest in summer. The results of back trajectories show that air pollution displays synergistic effects on local emissions and long range transport. O₃ commonly demonstrated negative correlations with other pollutants, especially during winter, while moderate to strong positive correlation between particulate matter and NO₂, SO₂, CO were seen. Compared to pollutant substandard ratios over three megacities in eastern China (Beijing, Shanghai, and Guangzhou), the situation in our studied second-tier cities are also severe. The results in this paper provide basic knowledge for pollution status of three cities along Chinese Yangtze River and are conductive to mitigating future negative air quality levels.

Characteristics of Fine Particles in an Urban Atmosphere-Relationships with Meteorological Parameters and Trace Gases

Atmospheric fine particles (diameter < 1 μm) attract a growing global health concern and have increased in urban areas that have a strong link to nucleation, traffic emissions, and industrial emissions. To reveal the characteristics of fine particles in an industrial city of a developing country, two-year measurements of particle number size distribution (15.1 nm–661 nm), meteorological parameters, and trace gases were made in the city of Wuhan located in central China from June 2012 to May 2014. The annual average particle number concentrations in the nucleation mode (15.1 nm–30 nm), Aitken mode (30 nm–100 nm), and accumulation mode (100 nm–661 nm) reached 4923 cm⁻³, 12193 cm⁻³ and 4801 cm⁻³, respectively. Based on Pearson coefficients between particle number concentrations and meteorological parameters, precipitation and temperature both had significantly negative relationships with particle number concentrations, whereas atmospheric pressure was positively correlated with the particle number concentrations. The diurnal variation of number concentration in nucleation mode particles correlated closely with photochemical processes in all four seasons. At the same time, distinct growth of particles from nucleation mode to Aitken mode was only found in spring, summer, and autumn. The two peaks of Aitken mode and accumulation mode particles in morning and evening corresponded obviously to traffic exhaust emissions peaks. A phenomenon of “repeated, short-lived” nucleation events have been created to explain the durability of high particle concentrations, which was instigated by exogenous pollutants, during winter in a case analysis of Wuhan. Measurements of hourly trace gases and segmental meteorological factors were applied as proxies for complex chemical reactions and dense industrial activities. The results of this study offer reasonable estimations of particle impacts and provide references for emissions control strategies in industrial cities of developing countries.

[Observation Analysis on the Characteristics of Meteorological Elements and Pollutants During a Continuous Fog and Haze Episode in Spring in Jiaxing City]

A continuous fog and haze episode occurred on 17-20 May, 2015 in Jiaxing. Trace gases (O₃, CO, SO₂ and NO₂), PM₁₀, PM_2.5, aerosol number concentration in the range of 10 nm-10 μm, meteorological elements, and radiosonde data from the 17st to the 22st of May were used to analyze the formation mechanism and pollutant characteristics during this episode. The results showed that subtropical high pressure lifted northward, a field pressure was dominant over Jiaxing leading to a weak ground wind speed, and a strong inversion layer occurred, this supplied moisture, power and thermal conditions for the occurrence and maintenance of the event. The episode included one precipitation process and two fog processes (rainy fog and radiation-advection fog). During the fog and haze process, the concentrations of NO₂, CO, PM₁₀ and PM_2.5 were high and the levels of SO₂ and O₃ were low. Strong precipitation had greater scavenge effects on PM₁₀, PM_2.5 and SO₂, while weak precipitation aggravated the pollution degree. The PM concentrations increased continuously during the rainy fog process, while it decreased firstly and then increased during the radiation-advection fog process. The spectral distributions of aerosol number concentration were unimodal and differed significantly under different types of weather conditions. The peaks of number concentration were located at 20-30 nm, 100 nm, 30-60 nm, 120 nm, 90 nm under clean, precipitation, fog and haze, rainy fog, radiation-advection fog conditions, respectively. The spectra of surface area concentration were trimodal under clean, precipitation, fog and haze, rainy fog conditions, and had four peaks under radiation-advection fog condition.

Winter climate change effects on soil C and N cycles in urban grasslands

Despite growing recognition of the role that cities have in global biogeochemical cycles, urban systems are among the least understood of all ecosystems. Urban grasslands are expanding rapidly along with urbanization, which is expected to increase at unprecedented rates in upcoming decades. The large and increasing area of urban grasslands and their impact on water and air quality justify the need for a better understanding of their biogeochemical cycles. There is also great uncertainty about the effect that climate change, especially changes in winter snow cover, will have on nutrient cycles in urban grasslands. We aimed to evaluate how reduced snow accumulation directly affects winter soil frost dynamics, and indirectly greenhouse gas fluxes and the processing of carbon (C) and nitrogen (N) during the subsequent growing season in northern urban grasslands. Both artificial and natural snow reduction increased winter soil frost, affecting winter microbial C and N processing, accelerating C and N cycles and increasing soil : atmosphere greenhouse gas exchange during the subsequent growing season. With lower snow accumulations that are predicted with climate change, we found decreases in N retention in these ecosystems, and increases in N2 O and CO2 flux to the atmosphere, significantly increasing the global warming potential of urban grasslands. Our results suggest that the environmental impacts of these rapidly expanding ecosystems are likely to increase as climate change brings milder winters and more extensive soil frost.

Characterization of wet and dry deposition in the downwind of industrial sources in a dry tropical area

An atmospheric deposition study was conducted in the downwind of Shaktinagar Thermal Power Plant (STPP), Renusagar Thermal Power Plant (RTPP), and Anpara Thermal Power Plant (ATPP), at Singrauli region, Uttar Pradesh (UP), India to characterize dry and wet deposition in relation to different pollution loading. During the study period, dry and wet depositions and levels of gaseous pollutants (SO2 and NO2) were estimated across the sites. Dry deposition was collected on a monthly basis and wet deposition on an event basis. Depositions were analyzed for pH, nitrate (NO3-), ammonium (NH4+), and sulphate (SO4(2-)) contents. Dry deposition rate both collected as clearfall and throughfall varied between 0.15 to 2.28 and 0.33 to 3.48 g m(-2) day(-1), respectively, at control and maximally polluted sites. The pH of dry deposition varied from 5.81 to 6.89 during winter and 6.09 to 7.02 during summer across the sites. During the rainy season, the mean pH of clear wet deposition varied from 6.56 to 7.04 and throughfall varied from 6.81 to 7.22. The concentrations of NO2 and SO2 pollutants were highest during the winter season. Mean SO2 concentrations varied from 18 to 75 g m(-3) at control and differently polluted sites during the winter season. The variation in NO2 concentrations did not show a pattern similar to that of SO2. The highest NO2 concentration during the winter season was 50 g m(-3), observed near RTPP. NO2 concentration did not show much variation among different sites, suggesting that the sources of NO2 emission are evenly distributed along the sites. The concentrations of NH4+, NO3-, and SO4(2-) ions in dry deposition were found to be higher in summer as compared to the winter season. In dry deposition (clearfall) the concentrations of NH4+, NO3-, and SO4(2-) varied from 0.13 to 1.0, 0.81 to 1.95, and 0.82 to 3.27 mg l(-1), respectively, during winter. In wet deposition (clearfall), the above varied from 0.14 to 0.74, 0.81 to 1.82, and 0.67 to 2.70 mg l(-1), respectively. The study clearly showed that both dry and wet depositions varied between the sites and season, suggesting significant impact of industrial activities in modifying the atmospheric input. The nonacidic deposition suggests that there is no threat of acidification of the receiving ecosystem at present.