Leake, J. R. | bioRxiv Science

bioRxiv2024

The role of carbonic anhydrase in rock weathering and pH regulation by the soil bacterium Burkholderia thailandensis E264

Enhanced rock weathering (ERW) is increasingly recognized as a way to sequester atmospheric carbon dioxide (CO2) to slow global warming, but its effectiveness needs to be optimized. Carbonic anhydrase (CA), an enzyme capable of accelerating rock weathering both in vitro and in soil, offers a valuable target due to its ability to convert CO2 into carbonic acid. This conversion promotes rock dissolution, enabling immediate CO2 absorption through cation release and charge-balance mechanisms. Studies have shown that bacteria grown in axenic, rock-amended media increase CA gene expression, but the influence of bacterial CA on rock dissolution rates remains unclear. To investigate this, we used a reverse genetics approach with the phosphate-solubilizing bacterium Burkholderia thailandensis E264. We examined three CA-inactivated mutants alongside the wildtype, growing them in minimal media with basalt rock dust (0-10% w/v) at an initial pH of 6.0. After 7 days, we measured weathering potential through elemental concentrations, pH, and dissolved inorganic carbon. In 1% basalt medium, inactivation of the CA1 gene (BTH_I1052) significantly reduced base cation weathering by 41% compared to the wildtype, whereas inactivation of CA2 (BTH_I0345) and CA3 (BTH_I1199) had no significant effect. In the highly buffered, 10% basalt medium, CA1 had a minor role in weathering, and both CA2 and CA3 had no effect. These findings suggest that CA genes in B. thailandensis operate differently and that CA1s effect is pH-dependent. Surprisingly, CA1 was localized intracellularly, raising questions about how intracellular CAs might influence mineral dissolution, potentially through acidity export or abiontic enzyme activity after cell lysis. ImportanceWhile purified carbonic anhydrase (CA) protein has been shown to increase mineral dissolution rates in mineral-amended media in vitro, it remains unclear if the bacterial CA gene directly drives this process. This study used CA-inactivated mutants of the soil bacterium Burkholderia thailandensis in basalt-amended liquid media and found that only one of the three CA genes influenced mineral dissolution rates. This finding supports prior evidence that bacterial CAs may contribute to mineral dissolution in soils. Importantly, it also showed that not all CA genes in a bacterium may activate under the same conditions, which could impact how soil bacterial CAs are leveraged to enhance weathering. Furthermore, cellular localisation predictions indicated that all three CA genes in B. thailandensis are cytosolic, challenging the common focus on extracellular CAs and suggesting that CA proteins may influence the external environment without needing to be actively exported from the cell.

microbiology↗

bioRxiv2023

Environmental DNA is more effective than soil-pit hand sorting in evaluating earthworm biodiversity responses to more regenerative agricultural management

Regenerating soil biodiversity is vital to help reverse declines in the health of agricultural soils caused by intensification, and to support sustainable food production and agro-ecosystem services. Earthworms are key functional components of soil biodiversity, with different ecotypes and species delivering specific beneficial soil functions. However, conventional monitoring by hand-sorting from soil pits is highly labour intensive, can reliably identify only adults to species, and may under-record anecics (deep-burrowing ecotypes). Here, we compare soil environmental DNA (eDNA) metabarcoding using two different primer sets and next-generation sequencing, with hand-sorting from standard soil-pits. The experiment comprised four conventionally managed arable fields into which strips of grass-clover ley had been introduced three years earlier. Earthworm population responses had been recorded by hand-sorting for the first two years and our goal was to assess these in the third year and to compare them both by hand and with the use of eDNA. The eDNA method found the same 8 species as hand-sorting, but had greater power for detecting anecic earthworms and quantifying local species richness. Earthworm abundance increased by over 55% into the third year of the leys, surpassing abundances in adjacent permanent grasslands, helping to explain the observed soil health regeneration. Both overall relative abundances and site occupancy proportions of earthworm eDNA were found to have potential as proxies for abundance, and the performance of each of these measures and the implications for further work are discussed. We demonstrate that eDNA can overcome some of the significant barriers and limitations to monitoring earthworm diversity and recommend its wider use both to better understand the earthworm population benefits of different soil management practices, and to guide agricultural policy and practice decisions affecting soil health.

ecology↗