Bacterial utilization of formic and acetic acid in rainwater

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.

Thermodynamic and optical properties of HCOOH(H2O)n and HCOOH(NH3)(H2O)(n-1) clusters at various temperatures and pressures: a computational study

Density functional theory has been used to compute the gas-phase geometries, binding energies, ZPE-corrected binding energies, BSSE-corrected binding energies, binding enthalpies, and binding free energies of HCOOH(H₂O)_n and HCOOH(NH₃)(H₂O)_(n-1) clusters with n = 1-8, 10, 12, 14, 16, 18, and 20. Enthalpies and free energies are calculated for a range of atmospherically relevant temperatures (T) and pressures (P) (from T = 298.15 K, P = 1013.25 hPa to T = 216.65 K, P = 226.32 hPa). The optical properties of those clusters have been studied at the CAM-B3LYP/aug-cc-pVDZ level of theory.

Metabolically active bacteria detected with click chemistry in low organic matter rainwater

Rain contains encapsulated bacteria that can be transported over vast distances during relatively short periods of time. However, the ecological significance of bacteria in "precontact" rainwater-rainwater prior to contact with non-atmospheric surfaces-remains relatively undefined given the methodological challenges of studying low-abundance microbes in a natural assemblage. Here, we implement single-cell "click" chemistry in a novel application to detect the protein synthesis of bacteria in precontact rainwater samples as a measure of metabolic activity. Using epifluorescence microscopy, we find approximately 103-104 bacteria cells mL-1 with up to 7.2% of the observed cells actively synthesizing protein. Additionally, our measurement of less than 30 μM total organic carbon in the samples show that some rainwater bacteria can metabolize substrates in very low organic matter conditions, comparable to extremophiles in the deep ocean. Overall, our results raise new questions for the field of rainwater microbiology and may help inform efforts to develop quantitative microbial risk assessments for the appropriate use of harvested rainwater.

Different characteristics of microbial diversity and special functional microbes in rainwater and topsoil before and after 2019 new coronavirus epidemic in Inner Mongolia Grassland

Grassland ecosystems are vital terrestrial ecosystems. As areas sensitive to climate change, they are critical for assessing the effects of global climate change. In China, grasslands account for over 40% of the land area. There is currently limited information on microbial diversity evolution in different grassland areas, particularly microorganisms with ice nucleation activity (INA) and their potential resources with potential influence to regulate regional precipitation and climate. We used Illumina MiSeq to sequence the 16S rRNA V3-V4 hypervariable region and performed a simple droplet freezing experiment to determine the variation in the grassland microbial community species composition and community structure. Rainwater and topsoil samples from the Hulunbuir Grassland in Inner Mongolia collected over three years were characterized. The dominant bacterial genus in the rainwater was Massilia, and the dominant fungus was Cladosporium. Additionally, the dominant bacteria in the soil were Sphingomonas, and the dominant fungus was Gibberella. There were differences in the microbial communities before and after the coronavirus disease epidemic. Pathogenic microorganisms exhibited inconsistent responses to environmental changes. The low relative abundance of known high-INA microorganisms and the higher freezing temperature indicated that unknown high-efficiency biological ice nucleating particles may be present. We found significant differences in species diversity and richness between the rainwater and soil populations in grassland areas by analyzing the sample community structures. Our research results revealed the species composition and structure of the microbiota in grassland ecosystems in China, indicating that environmental media and human activities may affect the microbiota in the grassland area and indicating underlying microorganisms with high INA.

Ocean Aerobiology

Ocean aerobiology is defined here as the study of biological particles of marine origin, including living organisms, present in the atmosphere and their role in ecological, biogeochemical, and climate processes. Hundreds of trillions of microorganisms are exchanged between ocean and atmosphere daily. Within a few days, tropospheric transport potentially disperses microorganisms over continents and between oceans. There is a need to better identify and quantify marine aerobiota, characterize the time spans and distances of marine microorganisms’ atmospheric transport, and determine whether microorganisms acclimate to atmospheric conditions and remain viable, or even grow. Exploring the atmosphere as a microbial habitat is fundamental for understanding the consequences of dispersal and will expand our knowledge of biodiversity, biogeography, and ecosystem connectivity across different marine environments. Marine organic matter is chemically transformed in the atmosphere, including remineralization back to CO₂. The magnitude of these transformations is insignificant in the context of the annual marine carbon cycle, but may be a significant sink for marine recalcitrant organic matter over long (∼10⁴ years) timescales. In addition, organic matter in sea spray aerosol plays a significant role in the Earth’s radiative budget by scattering solar radiation, and indirectly by affecting cloud properties. Marine organic matter is generally a poor source of cloud condensation nuclei (CCN), but a significant source of ice nucleating particles (INPs), affecting the formation of mixed-phase and ice clouds. This review will show that marine biogenic aerosol plays an impactful, but poorly constrained, role in marine ecosystems, biogeochemical processes, and the Earth’s climate system. Further work is needed to characterize the connectivity and feedbacks between the atmosphere and ocean ecosystems in order to integrate this complexity into Earth System models, facilitating future climate and biogeochemical predictions.

Rainwater-driven microbial fuel cells for power generation in remote areas

The possibility of using rainwater as a sustainable anolyte in an air-cathode microbial fuel cell (MFC) is investigated in this study. The results indicate that the proposed MFC can work within a wide temperature range (from 0 to 30°C) and under aerobic or anaerobic conditions. However, the rainwater season has a distinct impact. Under anaerobic conditions, the summer rainwater achieves a promised open circuit potential (OCP) of 553 ± 2 mV without addition of nutrients at the ambient temperature, while addition of nutrients leads to an increase in the cell voltage to 763 ± 3 and 588 ± 2 mV at 30°C and ambient temperature, respectively. The maximum OCP for the winter rainwater (492 ± 1.5 mV) is obtained when the reactor is exposed to the air (aerobic conditions) at ambient temperature. Furthermore, the winter rainwater MFC generates a maximum power output of 7 ± 0.1 mWm-2 at a corresponding current density value of 44 ± 0.7 mAm-2 at 30°C. While, at the ambient temperature, the maximum output power is obtained with the summer rainwater (7.2 ± 0.1 mWm-2 at 26 ± 0.5 mAm-2). Moreover, investigation of the bacterial diversity indicates that Lactobacillus spp. is the dominant electroactive genus in the summer rainwater, while in the winter rainwater, Staphylococcus spp. is the main electroactive bacteria. The cyclic voltammetry analysis confirms that the electrons are delivered directly from the bacterial biofilm to the anode surface and without mediators. Overall, this study opens a new avenue for using a novel sustainable type of MFC derived from rainwater.

Chitosan: A review of sources and preparation methods

Chitosan, derived from chitin, has many desirable biomedical attributes. This review aims to explore different sources of chitin and methods of chitosan production with industrial consideration. This article first discussed different sources of chitin for industrial scale production, with considerations given to both their environmental impacts and commercialization potential. Secondly, this article reviews the two categories of chitosan preparation - chemical methods and biological methods - based on existing publications which used lobster by-products as a feedstock source. The mechanisms of the chemical methods are firstly summarized, and then the different chemical agents and reaction parameters used are discussed. Next, both enzymatic and fermentation-based approaches are reviewed under biological methods and compared with chemical methodologies, with lactic fermentation methods as the major focus. This article concludes that lobster cephalothorax could be an ideal source for chitosan preparation on an industrial scale; and chemical methods involve simpler processing overall, while producing chitosan with stronger bioactivities because of the lower molecular weight (MW) and higher degree of deacetylation (DD) achieved by the products. Moreover, due to biological methods inevitably necessitating further chemical processing, an approach involving some unconventional chemical methods has been regarded as a more suitable strategy for industrial scale chitosan production.

Airborne microorganisms exacerbate the formation of atmospheric ammonium and sulfate

Haze pollution is inseparable from the transformation of air pollutants especially the ammonium and sulfate. Chemical and physical processes play important roles in this transformation. However, the role of microbial processes has rarely been studied. In this report, we applied the cultivation-independent metagenomic approach to study airborne microorganisms, investigating the potential microbial-catalyzed transformation of ammonium and sulfate in PM_2.5 samples. Functional genes predict that airborne microorganisms have the potential to catalyze ammonium formation but not ammonium oxidation since no ammoxidation genes were identified. We also found that the frequency of sulfate-forming genes was 1.56 times of those for sulfate-reducing genes. It was speculated that microbial metabolisms in the atmosphere could contribute to the accumulation of ammonium and sulfate. With the increase of PM_2.5 concentration, the frequency of functional genes and the relative abundance of genera which involved in nitrogen and sulfur metabolisms increased. That suggested air pollution was conducive to the microbial-mediated formation of ammonium and sulfate. Overall, our results provided evidence for the possible role of microbial processes in the air pollutant transformation and brought a new perspective for studying the formation of secondary air pollutants.

Metatranscriptomic exploration of microbial functioning in clouds

Clouds constitute the uppermost layer of the biosphere. They host diverse communities whose functioning remains obscure, although biological activity potentially participates to atmospheric chemical and physical processes. In order to gain information on the metabolic functioning of microbial communities in clouds, we conducted coordinated metagenomics/metatranscriptomics profiling of cloud water microbial communities. Samples were collected from a high altitude atmospheric station in France and examined for biological content after untargeted amplification of nucleic acids. Living microorganisms, essentially bacteria, maintained transcriptional and translational activities and expressed many known complementary physiological responses intended to fight oxidants, osmotic variations and cold. These included activities of oxidant detoxification and regulation, synthesis of osmoprotectants/cryoprotectants, modifications of membranes, iron uptake. Consistently these energy-demanding processes were fueled by central metabolic routes involved in oxidative stress response and redox homeostasis management, such as pentose phosphate and glyoxylate pathways. Elevated binding and transmembrane ion transports demonstrated important interactions between cells and their cloud droplet chemical environments. In addition, polysaccharides, potentially beneficial for survival like exopolysaccharides, biosurfactants and adhesins, were synthesized. Our results support a biological influence on cloud physical and chemical processes, acting notably on the oxidant capacity, iron speciation and availability, amino-acids distribution and carbon and nitrogen fates.

Aerobic respiration of mineral-bound organic carbon in a soil

Associations with minerals can potentially augment soil organic carbon (SOC) stability by reducing the bioavailability and degradation of SOC. However, few studies have directly measured aerobic respiration of mineral-bound SOC. In this study, we investigated the microbial aerobic respiration and bioavailability of ferrihydrite-sorbed glucose (Fh-GLU) and ferrihydrite-sorbed formic acid (Fh-FA) by adding ¹³C-labeled compounds to a soil. During an 11-day incubation, 30.2% of free, non-Fh-sorbed glucose (GLU) and 61.8% of free formic acid (FA) were respired, whereas 4.2% and 27.9% of Fh-GLU and Fh-FA were respired, respectively. Our results demonstrated that Fh-bound GLU/FA had lower bioavailability compared to free organic compounds. Associations with Fh led to greater inhibition in the bioavailability of GLU than that for FA. The priming effects of added compounds on the respiration of native SOC were decreased by their association with Fh. Our results demonstrated that the bioavailability and priming effect of organic compounds depend on their interactions with minerals.

Applicability of LIVE/DEAD BacLight stain with glutaraldehyde fixation for the measurement of bacterial abundance and viability in rainwater

Rainwater contains substantial bacteria and rain is an efficient pathway for the dissemination of bacteria from the atmosphere to land and water surfaces. However, quantitative information on rainwater bacteria is very limited due to the lack of a reliable method. In this study, the epifluorescence microscopy enumeration with the LIVE/DEAD BacLight Bacterial Viability Kit stain was verified to quantify the abundance of viable and non-viable bacterial cells in rainwater, with the 4',6-diamidino-2-phenylindole (DAPI) stain for the reference of total cell counts. Results showed that the total counts of bacterial cells by LIVE/DEAD BacLight staining were consistent with those by DAPI staining, and the average detection efficiency was (109±29)%. The ratio of cell count with glutaraldehyde fixation to that without fixation was (106±5)% on average. The bacterial concentration in negative control was usually an order of magnitude lower than that in rainwater samples. However, in case of small precipitation, the abundance in negative control could be more than that in rainwater samples. These results indicate that the enumeration with LIVE/DEAD BacLight bacterial viability assay coupled with glutaraldehyde fixation and careful negative control investigation is an approach applicable to the measurement of the concentration and viability of bacterial cells in rainwater.

Biotransformation of various saccharides and production of exopolymeric substances by cloud-borne Bacillus sp. 3B6

The ability of Bacillus sp. 3B6, a bacterial strain isolated from cloudwaters, to biotransform saccharides present in the atmosphere was evaluated using in situ 1D and 2D NMR spectroscopy. Bacillus is one of the genera most frequently described in the air and in atmospheric waters. Sugars present in these environments have a biogenic origin; they include alditols, monosaccharides, disaccharides, oligosaccharides, and polysaccharides. Bacillus sp. 3B6 was able to efficiently metabolize sugars, which could thus provide sources of energy for this bacterium and allow it to live and to be metabolically active in warm clouds. In addition, a number of these saccharides (L-arabitol, D-fructose, sucrose, D-glucose, cellotetraose, cellulose, and starch) were transformed to EPSs (exopolymeric substances). We have clearly identified the structure of two EPSs as 1,6-α-galactan and partially acetylated polyethylene glycol. 1,6-α-Galactan is a newly described polymer. The production of EPSs might protect this bacterium under hostile cloud environment conditions, including low nutrient availability, cold temperature and freeze-thaw processes, UV and radical exposure, and evaporation-condensation processes and thus desiccation and osmolarity changes. EPSs could also have a potential role in atmospheric processes because they can be considered as secondary organic aerosols and efficient cloud condensation nuclei.

Hailstones: a window into the microbial and chemical inventory of a storm cloud

Storm clouds frequently form in the summer period in temperate climate zones. Studies on these inaccessible and short-lived atmospheric habitats have been scarce. We report here on the first comprehensive biogeochemical investigation of a storm cloud using hailstones as a natural stochastic sampling tool. A detailed molecular analysis of the dissolved organic matter in individual hailstones via ultra-high resolution mass spectrometry revealed the molecular formulae of almost 3000 different compounds. Only a small fraction of these compounds were rapidly biodegradable carbohydrates and lipids, suitable for microbial consumption during the lifetime of cloud droplets. However, as the cloud environment was characterized by a low bacterial density (Me = 1973 cells/ml) as well as high concentrations of both dissolved organic carbon (Me = 179 µM) and total dissolved nitrogen (Me = 30 µM), already trace amounts of easily degradable organic compounds suffice to support bacterial growth. The molecular fingerprints revealed a mainly soil origin of dissolved organic matter and a minor contribution of plant-surface compounds. In contrast, both the total and the cultivable bacterial community were skewed by bacterial groups (γ-Proteobacteria, Sphingobacteriales and Methylobacterium) that indicated the dominance of plant-surface bacteria. The enrichment of plant-associated bacterial groups points at a selection process of microbial genera in the course of cloud formation, which could affect the long-distance transport and spatial distribution of bacteria on Earth. Based on our results we hypothesize that plant-associated bacteria were more likely than soil bacteria (i) to survive the airborne state due to adaptations to life in the phyllosphere, which in many respects matches the demands encountered in the atmosphere and (ii) to grow on the suitable fraction of dissolved organic matter in clouds due to their ecological strategy. We conclude that storm clouds are among the most extreme habitats on Earth, where microbial life exists.

The microbial diversity of a storm cloud as assessed by hailstones

Being an extreme environment, the atmosphere may act as a selective barrier for bacterial dispersal, where only most robust organisms survive. By remaining viable during atmospheric transport, these cells affect the patterns of microbial distribution and modify the chemical composition of the atmosphere. The species evenness and richness, and the community composition of a storm cloud were studied applying cultivation-dependent and cultivation-independent techniques to a collection of hailstones. In toto 231 OTUs were identified, and the total species richness was estimated to be about 1800 OTUs. The diversity indices - species richness and evenness - suggest a functionally stable community, capable of resisting environmental stress. A broad substrate spectrum of the isolates with epiphytic origin (genus Methylobacterium) implied opportunistic ecologic strategy with high growth rates and fast growth responses. These may grow in situ despite their short residence times in cloud droplets. In addition, epiphytic isolates utilized many atmospheric organic compounds, including a variety of carboxylic acids. In summary, the highly diverse bacterial community, within which the opportunistic bacteria may be particularly important in terms of atmospheric chemistry, is likely to remain functional under stressful conditions. Overall our study adds important details to the growing evidence of active microbial life in clouds.

Characteristics and distribution of low molecular weight organic acids in the sediment porewaters in Bosten Lake, China

The composition and vertical profiles of low molecular-weight organic acids (LMWOAs) and the contribution of them to dissolved organic matter (DOM) in sediment porewaters in Bosten Lake, Xinjiang, China were investigated. The results showed that total concentration of LMWOAs was up to 94.5 micromol/L and their proportion in DOM was 5.6%, suggesting that LMWOAs were important chemical components in DOM in lake sediment porewaters. Among the seven LMWOAs, pyruvic and acetic acid had the highest concentrations with 26.30 and 8.31 micromol/L, accounting for 51.4% and 14.92% of LMWOAs, respectively. Trifluoroacetic and sorbic acid had the lowest concentrations, indicating that the compositions of LMWOAs in relative reducing environments were largely different from those reported in glacier, atmosphere and soils. The concentrations of lactic, acetic, formic, sorbic and oxalic acid decreased with increasing depth, probably relating to stronger microbial activities in the initial stage of early diagenesis. Trifluoroacetic acid was mainly anthropogenic with its concentration, showing a diffusive trend from the surface to bottom sediments. The concentrations of lactic acid and nitrate generally showed a consistent profile. The increasing concentration of pyruvic acid in the vertical profile was just opposite to that of sulfate, revealing a significant negative relationship between them. Oxalic acid remained constant except for an obvious peak at 6 cm depth. The results indicated the diversities in sources and behaviors for various LMWOAs during early diagenesis in sediments.

Microorganisms in the atmosphere over Antarctica

Antarctic microbial biodiversity is the result of a balance between evolution, extinction and colonization, and so it is not possible to gain a full understanding of the microbial biodiversity of a location, its biogeography, stability or evolutionary relationships without some understanding of the input of new biodiversity from the aerial environment. In addition, it is important to know whether the microorganisms already present are transient or resident - this is particularly true for the Antarctic environment, as selective pressures for survival in the air are similar to those that make microorganisms suitable for Antarctic colonization. The source of potential airborne colonists is widespread, as they may originate from plant surfaces, animals, water surfaces or soils and even from bacteria replicating within the clouds. On a global scale, transport of air masses from the well-mixed boundary layer to high-altitude sites has frequently been observed, particularly in the warm season, and these air masses contain microorganisms. Indeed, it has become evident that much of the microbial life within remote environments is transported by air currents. In this review, we examine the behaviour of microorganisms in the Antarctic aerial environment and the extent to which these microorganisms might influence Antarctic microbial biodiversity.

Changing chemical composition of precipitation in Wilmington, North Carolina, U.S.A.: implications for the Continental U.S.A

The H+(aq) concentration in Wilmington, NC, precipitation has decreased by approximately 50% during the preceding two decades, similar to trends seen nationwide. The decrease in acidity is important because solution pH plays a key role in atmospheric reactions, and because the change is so large. This study presents the first long-range study of dissolved organic carbon (DOC) levels in precipitation which demonstrates that DOC concentrations have decreased by approximately half in Wilmington, NC, precipitation. The concentrations of H+(aq) and DOC are highly correlated primarily because small organic acids contribute to both DOC and H+(aq) in precipitation. Ammonium ion concentrations in precipitation have increased due to increased agricultural activities, and this also affects precipitation pH. The reduction of SO2 emissions in 1995 imposed by the Clean Air Act Amendment, better control of emissions of volatile organic compounds, and the increase in ammonia emissions all contribute to the decreasing H+(aq) in precipitation nationwide. These compositional changes in precipitation have many environmental implications, such as decreased acid deposition to lakes, changing speciation for trace metals in precipitation, increased ammonium deposition to coastal waters, and decreased DOC transport to the open ocean.

The prospect of alien life in exotic forms on other worlds

The nature of life on Earth provides a singular example of carbon-based, water-borne, photosynthesis-driven biology. Within our understanding of chemistry and the physical laws governing the universe, however, lies the possibility that alien life could be based on different chemistries, solvents, and energy sources from the one example provided by Terran biology. In this paper, we review some of these possibilities. Silanes may be used as functional analogs to carbon molecules in environments very different from Earth; solvents other than water may be compatible for life-supporting processes, especially in cold environments, and a variety of energy sources may be utilized, some of which have no Terran analog. We provide a detailed discussion of two possible habitats for alien life which are generally not considered as such: the lower cloud level of the Venusian atmosphere and Titan's surface environment.

Venus, Mars, and the ices on Mercury and the moon: astrobiological implications and proposed mission designs

Venus and Mars likely had liquid water bodies on their surface early in the Solar System history. The surfaces of Venus and Mars are presently not a suitable habitat for life, but reservoirs of liquid water remain in the atmosphere of Venus and the subsurface of Mars, and with it also the possibility of microbial life. Microbial organisms may have adapted to live in these ecological niches by the evolutionary force of directional selection. Missions to our neighboring planets should therefore be planned to explore these potentially life-containing refuges and return samples for analysis. Sample return missions should also include ice samples from Mercury and the Moon, which may contain information about the biogenic material that catalyzed the early evolution of life on Earth (or elsewhere). To obtain such information, science-driven exploration is necessary through varying degrees of mission operation autonomy. A hierarchical mission design is envisioned that includes spaceborne (orbital), atmosphere (airborne), surface (mobile such as rover and stationary such as lander or sensor), and subsurface (e.g., ground-penetrating radar, drilling, etc.) agents working in concert to allow for sufficient mission safety and redundancy, to perform extensive and challenging reconnaissance, and to lead to a thorough search for evidence of life and habitability.

Atmospheric acidification in the Asian region

Atmospheric acidification in the Asian region is discussed from the perspectives of currently available regional measurements, and the knowledge now available from several decades of acidic deposition research in the northern mid-latitudes. The main conclusions emerge: (1) that there is insufficient information currently available to enable a quantitative assessment of the present state or future potential for atmospheric acidification across the whole region; and (2) that within the limitations imposed by (1) the possibility of future acidification in certain areas cannot be ruled out if economic development and energy use on a per capita basis evolve to the levels of the major industrial countries. These two conclusions point to the need for systematic, multidisciplinary studies covering the whole region. The studies should assess quantitatively the current levels of acidic and alkaline emissions (both natural and anthropogenic) to the atmosphere, identify the relevant chemical transformations and transport/deposition pathways in the regional atmosphere, and assess the susceptibility of regional plants, soils and groundwaters to acidification.