Biology subjects

Reji, L.

Publications and source records attributed to Reji, L..

4 recordsLinked to original sources

bioRxiv2025

Moisture Controls on Hydrogen Oxidizing Bacteria: Implications for the Global Soil Hydrogen Sink

Assessing the impact of increasing anthropogenic H2 emissions on Earths radiative balance depends on understanding the soil microbial H2 sink--the largest and the most uncertain term in the global H2 budget. A primary control regulating the soil sink is soil moisture, with a relationship that remains poorly constrained. Here, we assess the sensitivity of microbial H2 oxidation to soil moisture in laboratory experiments with three temperate soils--silty loam, sandy loam, and loamy sand. Using genome-resolved metagenomics, we link H2 oxidation dynamics in these soils to specific microbial taxa adapted to withstand desiccation that have differential contributions to H2 uptake along the moisture gradient. The experiments reveal a notably low moisture threshold for H2 oxidizer activity, at water potentials between -70 and -100 MPa across all soil types, including in an arid sandy soil. These measurements, which represent some of the lowest water potentials reported for soil microbial activity, point to atmospheric H2 as a vital resource for microbial survival under stressful conditions. Through global simulations, we further show that the low moisture threshold for microbial activation increases the contribution of arid and semi-arid regions for soil H2 uptake by 4-7pp, while decreasing the contribution of temperate and continental regions (-7pp), even when assuming a linear scaling between uptake potential and soil organic carbon, as suggested by our experiments. Our results highlight the importance of H2 uptake under extreme hydrological conditions, particularly the roles of desertification, dryland expansion, and H2-oxidizer ecophysiology in modulating long-term changes in H2 uptake.

microbiology↗

bioRxiv2024

Distinct Microbiomes Underlie Divergent Responses of Methane Emissions from Diverse Wetland soils to Oxygen Shifts

Hydrological shifts in wetlands, a globally important methane (CH4) source, are critical constraints on CH4 emissions and carbon-climate feedbacks. A limited understanding of how hydrologically driven oxygen (O2) variability affects microbial CH4 cycling in diverse wetlands makes wetland CH4 emissions uncertain. Transient O2 exposure significantly stimulated anoxic CH4 production in incubations of Sphagnum peat from a temperate bog by enriching for polyphenol oxidizers and polysaccharide degraders, enhancing substrate flow toward methanogenesis under subsequent anoxic conditions. To assess whether shifts in soil microbiome structure and function operate similarly across wetland types, here we examined the sensitivity of different wetland soils to transient oxygenation. In slurry incubations of Sphagnum peat from a minerotrophic fen, and sediments from a freshwater marsh and saltmarsh, we examined temporal shifts in microbiomes coupled with geochemical characterization of slurries and incubation headspaces. Oxygenation did not affect microbiome structure and anoxic CH4 production in mineral-rich fen-origin peat and freshwater marsh soils. Key taxa linked to O2-stimulated CH4 production in the bog-origin peat were notably rare in the fen-origin peat, supporting microbiome structure as a primary determinant of wetland response to O2 shifts. In contrast to freshwater wetland experiments, saltmarsh geochemistry--particularly pH--and microbiome structure were persistently and significantly altered post-oxygenation, albeit with no significant impact on greenhouse gas emissions. These divergent responses suggest wetlands may be differentially resilient to O2 fluctuations. With climate change driving greater O2 variability in wetlands, our results inform mechanisms of wetland resiliency and highlight microbiome structure as a potential resiliency biomarker.

microbiology↗

bioRxiv2023

A Genomic View of Environmental and Life History Controls on Microbial Nitrogen Acquisition Strategies

Microorganisms have evolved diverse strategies to acquire the vital element nitrogen (N) from the environment. Ecological and physiological controls on the distribution of these strategies among microbes remain unclear. Here we examine the distribution of 10 major N-acquisition strategies in taxonomically and metabolically diverse microbial genomes, including those from the Genomic Catalog of Earths Microbiomes dataset. We utilize a marker gene-based approach to assess relationships between N acquisition strategy prevalence and microbial life history strategies. Our results underscore energetic costs of assimilation as a broad control on strategy distribution. The most prevalent strategies are the uptake of ammonium and simple amino acids, while biological nitrogen fixation is the least common. Deviations from this energy-based framework include the higher-than-expected prevalence of the assimilatory pathway for chitin, a large organic polymer. Notably, oxygen-respiring chemoorganotrophic and phototrophic microbes possess [~]2-fold higher numbers of total strategies compared to anaerobic microbes. Environmental controls on N acquisition are evidenced by the enrichment of inorganic N assimilation strategies among free-living taxa compared to host-associated taxa. Physiological constrains such as pathway incompatibility add further complexity to N-acquisition strategy distributions. Finally, we discuss the necessity for microbially-relevant environmental metadata for improving mechanistic and prediction-oriented analyses of genomic data.

microbiology↗

bioRxiv2019

Aerobic heterotrophy and RuBisCO-mediated CO2 metabolism in marine Thaumarchaeota

Thaumarchaeota constitute an abundant and ubiquitous phylum of Archaea that play critical roles in the global nitrogen and carbon cycles. Most well-characterized members of the phylum are chemolithoautotrophic ammonia-oxidizing archaea (AOA), which comprise up to 5 and 20 % of the total single-celled life in soil and marine systems, respectively. Using two high-quality metagenome-assembled genomes (MAGs), here we describe a divergent marine thaumarchaeal clade that is devoid of the ammonia-oxidation machinery and the AOA-specific carbon-fixation pathway. Phylogenomic analyses placed these genomes within the uncultivated and largely understudied marine pSL12-like thaumarchaeal clade. The predominant mode of nutrient acquisition appears to be aerobic heterotrophy, evidenced by the presence of respiratory complexes and various organic carbon degradation pathways. Unexpectedly, both genomes encoded a form III RuBisCO. Genomic composition of the MAGs is consistent with the role of RuBisCO in nucleotide salvage, as has been proposed previously for archaea harboring the form III variant. Metabolic reconstructions revealed a complete nonoxidative pentose phosphate pathway (PPP) and gluconeogenesis, which can cyclize the RuBisCO-mediated carbon metabolic pathway. We conclude that these genomes represent a hitherto unrecognized evolutionary link between predominantly anaerobic basal thaumarchaeal lineages and mesophilic marine AOA, with important implications for diversification within the phylum Thaumarchaeota.

microbiology↗