Australia: The Land Where Time Began

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Soil Microbiomes – Atmospheric Chemosynthesis Widespread Across the Poles Associated With Limitation of Moisture, Carbon and Nitrogen

In oligotrophic cold desert soil microbiomes are extraordinarily diverse. Oligotrophic sites that have low levels of phototrophic primary producers are increasingly being reported, and this has led researchers to question their sources of carbon and energy. Recently the gap has been filled by a novel process of microbial fixation termed atmospheric chemosynthesis that has been shown to support primary production at 2 deserts in East Antarctica. Energy that has been liberated by 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) that is designated IE. In this study Ray et al., propose that the genetic determinants of the process; RuBisC0 type IE (rbcL 1E) and high affinity group 1h-[NiFe]-hydrogenase (hhyL) are widespread across cold desert soils and that process is associated with environments that are dry and poor in nutrients. They used quantitative PCR (qPCR) to quantify these genes in 122 soil microbiomes across the 3 poles; spanning the Tibetan Plateau, 10 Antarctic and 3 high Artic sites. Both genes were found to be ubiquitous, as they were present at variable abundances in all 122 soils that were examined (rbcL 1E, 6.25 x 10³-1.66 x 10⁹ copies/ g soil; hhyL, 6.84 x 10³ – 5.07 x 10⁸ copies/g soil). It was revealed by random forest and correlation analysis for the Antarctic and the high Arctic sites against 26 measured soil physicochemical parameters, that the rbcL 1E and hhyL genes were associated with lower soil moisture, carbon and nitrogen content. Ray et al. highlight the global potential of microbiomes in desert soils to be supported by this new minimalistic mode of carbon fixation, especially throughout dry oligotrophic environments, which encompass more than 35% of the surface of the Earth, though further studies are required to quantify the rates of trace gas carbon fixation and the organisms that are involved.

Introduction

Dry oligotrophic environments comprise more than 35% of the surface of the Earth (Mares & History, 1999). Dry areas are expected to expand to cover up to 56% of the surface of the Earth by the end of the 21st century as a result of global warming (Cherlet et al., 2018). Microbiomes of polar soil are diverse and abundant, and drive important ecological processes (Yergeau et al., 2006; Cowan et al., 2014; Kleinteich et al., 2017), in spite of their exposure to frequent cycles of freeze-thaw, intense UV radiation, and limited availability of carbon, nitrogen and moisture (Wynn-Williams, 1990; Yergeau et al., 2006; Margesin & Miteva, 2011; Pearce et al., 2012; Cowan et al., 2014). Actinobacteria, Proteobacteria and Bacteriodetes often dominate the microbiomes of such cold desert soils (Tindall, 2004; Carey et al., 2010; Bottos et al., 2014; Tytgatet et al., 2014; Zhang et al., 2020), with high numbers of phototrophic primary producers, in particular Cyanobacteria and algae (Friedman, 1982; Elster, 2002; Namsaraev et al., 2010; Jansson & Tas, 2014). In ice free deserts, however, these phototrophs are often restricted to lithic niches that protect them from intense UV radiation and desiccation (Walker & Pace, 2007; Pointing et al., 2009; Wierzchos et al., 2012; Cowan et al., 2014; McKay et al., 2016; Goordial et al., 2017). Oligotrophic deserts that comprise little to no detectable photoautotrophs have a worldwide distribution, which leads researchers to question what carbon and energy sources support the microbial communities functioning in these harsh ecosystems (Warren-Rhodes et al., 2006; Albertsen et al., 2013; Ferrari et al.,2015; Ji et al., 2015; Tebo et al., 2015; Zhang et al., 2020).

A novel form of autotrophy that is not dependent on light, termed atmospheric chemosynthesis was discovered (Ji et al., 2017) in soils across 2 deserts that were oligotrophic in East Antarctica; the arid Robinson Ridge (average organic carbon 0.17%, moisture 4.4%) in the Windmill Islands and the hyper-arid Adams Flat (average organic carbon 0.09%, moisture 0.42%) in the Vestfold Hills region. H₂ oxidising bacteria at these sites were proposed to employ high affinity 1H-[NiFe] hydrogenases that scavenge and oxidise Hydrogen gas that has diffused into subsurface soils from the atmosphere. It was proposed that the energy liberated  from this oxidation process would support maintenance of the cell as well as the fixation of carbon via the Calvin-Benson-Bassham (CBB) cycle, and that it was linked to a novel chemotrophic form of ribulose-1,5 bisphosphate carboxylase/oxygenase (RuBisCO), type IE (Grostern & Alvarez-Cohen, 2013; Tebo et al., 2015; Ji et al., 2017). RuBisCO type IE (rbcL1E), is phylogenetically distinct from the photoautotrophic RuBisCO types IA and IB, as well as being notably distinct from the other chemoautotrophic RuBisCO red-types IC and ID, diverging from these clades prior their own separation (Park et al., 2009; Tebo et al., 2015). The broader ecological role and significance of this novel RuBisCO has not yet been determined, in spite of this discovery.

In this study Ray et al. proposed that terrestrial microbiomes that inhabit oligotrophic deserts throughout the world may have the genetic capacity to support cell growth by atmospheric chemosynthesis, particularly in environments where photoautotrophs are limited. They used quantitative PCR (qPCR) to target the rbcL1E and the 1h-NiFe-hydrogenase large subunit (hhyL) genes to survey 122 desert soils that spanned the Tibetan Plateau and 13 Antarctic and high Arctic sites. They analysed the taxonomic composition of each soil using amplicon sequencing. They also aimed to identify the abiotic parameters that are associated with the genetic capacity for atmospheric chemosynthesis within each region, by correlating the relative abundances of rbcL1E and hhyL against 26 measured soil physicochemical parameters. Their hypothesis was that atmospheric chemoautotrophy is associated with low levels of moisture and limitation of nutrients in cold desert soils, under the general exclusion of autotrophs.

Site description

Sampling was conducted across 14 cold desert sites that spanned Antarctica (the Windmill Islands and the Vestfold Hills) the high Arctic and the Tibetan Plateau. The Windmill Islands is a region that is located in Wilkes Land, East Antarctica, which is ice-free (Gasparon et al., 2007). The region, which is centred at 110^o30’E and 66^o22’S, covers an area of 75 km² (Goodwin, 1993), is at an elevation of below 100 m, and includes 5 major peninsulas and multiple rocky islands (Sisiliano et al., 2014; Bissett et al., 2016). In this study 5 sites from the Windmill Islands were sampled;

Mitchell Peninsula (MP; 66^o31’S, 110^o59’E.

Robinson Ridge (BP; 66^o22’S, 110^o35’E),

Browning Peninsula (BP; 66^o27’S, 110^o32’E),

Herring Island (HI; 66^o24’S, 110^o39’E), and

Casey Station (CST; 66^oS16’S, 110^o31’E).

Soil samples were also obtained from 5 sites near Davis station: (68^o35’S, 77^o58’E), the most southerly research station in East Antarctica;

Old Wallow (OW; 68^o36’S, 77^o57’E),

Heidemann Valley (HV; 68^o35’S, 78^o0’E,

Adams Flat (AF; 68^o33’S, 78^o1’E),

Rookery Lake (RL; 68^o30’S, 78^o7’E), and

The Ridge (TR; 68^o54’S, 78^o07’E).

These sites are located in the low-lying Vestfold Hills region of East Antarctica, a region that consists of many deep-sea inlets and lakes (Zhang et al., 2020). Previously, soils from the High Arctic were collected from a Canadian site,

Alexandra Fjord Highlands (AFH (78^o51’N, 75^o54’W), and 2 Norwegian sites;

Spitsbergen Slijeringa (SS; 78^o14’N, 15^o30’W) and

Spitsbergen Vestpynten (VP; 78^o14’N, 15^o20’W).

Specimens were also collected from the cold, high altitude Qinghai Plateau in Western China (TP; 32^o27’N, 80^o4’E), which was previously referred to as Earth’s 3^rd pole (Gao et al., 2018).

It is only recently that oxidation of atmospheric hydrogen has been identified as an energetic driver of microbial autotrophic CO₂ fixation through the CBB cycle (Ji et al., 2017). Atmospheric chemosynthesis has been overlooked as a niche process that had global significance that was not known until now. In this study Ray et al. confirm that the genetic determinants of this new form of chemoautotrophy (rbcL1E and hhyL) are abundant and widespread throughout soil microbiomes of polar regions that are geographically distinct throughout Antarctica, the High Arctic and the Tibetan Plateau. The hypothesis, that the minimalistic fixation of carbon strategy may be considered to be a phenomenon that occurs globally, and to be an important survival adaptation that is widespread in oligotrophic desert soil ecosystems.

The role of high affinity hydrogenases (hyyL) in fulfilling the energy requirements of soil bacteria that are dormant is well established (Constant et al., 2008, 2010, 2011; Berney & Cook, 2010; Berney et al., 2014; Greenberg et al., 2015; Islam et al., 2019; Piché-Choquette, & Constant, 2019), though the role of oxidation of hydrogen in contributing to primary production has only recently been discovered. H₂-oxidisers can reversibly lower their metabolic activity in periods of extreme environmental stress and, thereby, their energy requirements (Lennon & Jones, 2011). The aerobic oxidation of atmospheric hydrogen, under these conditions, provides bacteria with a ubiquitous and reliable energy source (Morita, 1999; Smith-Downey et al., 2008; Constant et al., 2011). According to Ray et al., the process is widespread, with hhyL being reported at high levels of 10⁶ to 10⁸ of genetic copies/g of soil in both oligotrophic and copiotrophic ecosystems (Constant et al., 2011). Greater expression of hhyL and hydrogen oxidising activity have, however, been linked to environments that have a lower content of carbon (King, 2003; Greening et al., 2004). The presence of high numbers of hhyL genes (4.18 x 10⁸ to 10.39 x 10⁷ copies/g of soil have been revealed in this study in cold desert soils across the 3 poles, many of which contained extremely low levels of carbon and nitrogen. It was noted by Ray et al. that though the qPCR primer are widely implemented (Constant et al., 2010, 2011; Meredith et al., 2014; Khdhiri et al., 2014; Khdhiri et al., 2015; Piché-Choquette et al., 2016), the discovery of high-affinity hydrogenases beyond group 1 h (D. Cowan, personal communication; Greening et al., 2014; Islam et al., 2020) suggests that the high affinity hydrogenase gene abundances that are quantified in this study are underestimations.

The global co-occurrence of hhyL and rbcL1E has not been known, in spite of the widespread, abundant distribution of hhyL. It is indicated by the high and widespread co-occurrence of hhyL and rbcL1E across all the 122 soils that were analysed in this study that the energy that is liberated by oxidation of atmospheric hydrogen may be directed towards the growth of bacterial cells and primary production more pervasively than has been anticipated. Trace gas chemosynthetic bacteria have been indicted in previous studies to belong to the phyla Actinobacteria, C. eremiobacterota and C. dormibacterota phyla (Park et al., 2009; Ji et al., 2017). The rbcL1E has also been detected within Chloroflexota, Firmicutes and Verrucomicrobiota (Tebo et al., 2015. These taxa dominated soil communities from across the 3 poles in this study, and together they accounted for 76.2% of the composition of the microbial community. In cold nutrient-starved deserts, therefore, trace gas chemoautotrophs appear to have a selective advantage for survival.

Atmospheric chemosynthesis and photosynthesis have been proposed to both contribute to microbial primary production in oligotrophic environments, and contributions are likely to vary along the aridity gradient (Ji et al., 2017; Bay et al., 2018). Variability in photo and chemoautotrophic potential were indeed observed in this study with abundance of rbcL1E being particularly low in the high Arctic (10%), Casey station 4.8% and Browning Peninsula (9%) soils. Greater photosynthetic potential was contained in these sites as a result of higher abundances of Cyanobacteria (5.7 - 8.6%; Kleinteich et al., 2017; Pudasaini et al., 2017; Zhang et al., 2020). The abundances of the rbcL1E gene were also more variable than the hhyL gene, which reflects the more widespread role of the high affinity hydrogenases in supplying maintenance energy to dormant microbial communities (Berne & Cook, 2010; Constant et al., 2010, 2011; Berney et al., 2014; Greening et al., 2015) as well as for reproduction.

That atmospheric chemosynthesis occurs increasingly within drier, more nutrient starved soils has been proposed (Ji et al., 2017; Bay et al., 2018), resulting partly from the exclusions of phototrophic microorganisms under limitation of moisture (Warren-Rhodes et al., 2006; McKay, 2016). It was found by Ray et al. that the genetic capacity for atmospheric chemosynthesis was associated with soils that were increasingly drier and more nutrient-limited (Ji et al., 2017; Bay et al., 2018). It was revealed by random forest and Pearson correlations that rbcL1E and hhyL, relative to 16S rRNA, increased significantly across Antarctic and high Arctic soils that were increasingly moisture limited and TC. The relative abundance of rbcL1E, additionally, also increased significantly in soils that were limited in NO₃^-. A significant positive correlation with bioavailable substances that are used widely by geothermal chemoautotrophic bacteria such as NO₂^- and PO₄^- was not formed by either genetic determinant. The current understanding that rbcL1E catalysed primary production is not driven by geochemical energy sources is supported by this lack of data. As a result, within environments where soil nutrients are limited atmospheric chemosynthesis may occur. A potential metabolic significance that requires further investigation is suggested by positive correlations that have been detected between rbcL1E and multiple trace oxides measured by X-Ray fluorescence analysis MnO, MgO, CaO, and Na₂O.

Additional studies are recommended to be conducted in order to focus upon the isolation and characterisation of trace gas chemosynthetic bacteria. Additionally, metagenomics and biochemical studies, which includes hydrogenation oxidation and ¹⁴CO₂ assimilation assays should be performed on a broader range of environments where atmospheric chemosynthesis is likely to occur. Ray et al. suggest that sites should be targeted where organic carbon, water, and photoautotrophs are limited and the utilisation of gases by microbial communities is well documented (King, 2003; Lynch et al., 2012, 2014). This includes volcanic deposits and additional cold and hot deserts, such as the McMurdo Dry Valleys (Babalola et al., 2009; Van Goethem et al., 2016), Namib (van der Walt et al., 2016; Gunnigle et al., 2017), Thar (Rao et al., 2016), and Atacama (Lynch et al., 2014; Schulze-Makuch et al., 2018). Finally, this study highlights the genetic potential of microbial communities that live in cold oligotrophic deserts around the globe to conduct atmospheric chemosynthesis and their propensity for survival in regions with highly limited water and availability of nutrients.

Ray, A. E., et al. (2020). "Soil Microbiomes With the Genetic Capacity for Atmospheric Chemosynthesis Are Widespread Across the Poles and Are Associated With Moisture, Carbon, and Nitrogen Limitation." Frontiers in Microbiology 11(1936).