Biology subjects

Pold, G.

Publications and source records attributed to Pold, G..

5 recordsLinked to original sources

bioRxiv2025

Distribution of alternative routes for completing denitrification in microbial genomes and metagenomes of global biomes

Diverse microorgani sms can execute one or more steps in denitrification, during which nitrate or nitrite is successively reduced into nitric oxide, nitrous oxide, and ultimately dinitrogen. Many of the best-characterized denitrifiers are "complete" denitrifiers capable of executing all steps in the pathway, but whether they dominate in natural communities and what metabolic traits and environmental factors drive the global distribution of complete vs. partial denitrifiers remains to be determined. To address this, we conducted a comparative analysis of denitrification genes in 61,293 genomes, 3,991 metagenomes covering all major biomes, and 413 terrestrial and aquatic metatranscriptomes. We show that partial denitrifiers outnumber complete denitrifiers and the potential to initiate denitrification is more common than the potential to terminate it, both among genomes and at the community level across most biomes, particularly in nutrient rich environments. These patterns were also reflected in the metatranscriptomes. Our results further indicate that complete denitrifiers are more likely to be fast-growing organisms, favoring organic acid over sugar metabolism, and encoding the ability to oxidize and reduce a broader range of organic and inorganic compounds compared to partial denitrifiers. This suggests complete denitrifiers are metabolically flexible opportunists. Together, our results indicate an environmental footprint on the presence of denitrification genes which favors the genomic potential for partial over complete denitrification in most biomes and highlight that completion of the denitrification pathway is a community effort.

microbiology↗

bioRxiv2023

Phyloecology of nrfA-ammonifiers and their relative importance with denitrifiers in global terrestrial biomes

Nitrate ammonification is important for soil nitrogen retention. However, the ecology of nitrate ammonifiers and their prevalence compared with denitrifiers, being competitors for nitrate, are overlooked. Here, we screened more than 1 million genomes for nrfA, encoding the nitrite reductase in nitrate ammonification. Nearly 50% of the nitrate ammonifier assemblies carry at least one denitrification gene and, contrary to the current paradigm, have higher potential for nitrous oxide production than reduction. We then used a phylogeny-based approach to recruit nrfA and denitrification nitrite reductase gene fragments in 1,861 metagenomes covering the major terrestrial biomes. Denitrification genes dominated, except in tundra, and random forest modelling teased apart the influence of the soil C/N on nitrate ammonifier vs denitrifier abundances, showing an effect of nitrate rather than carbon content. This study demonstrates the multiple roles nitrate ammonifiers play in nitrogen cycling and the factors ultimately controlling the fate of nitrate in soil.

microbiology↗

bioRxiv2022

Distribution and environmental drivers of fungal denitrifiers in global soils

The microbial process denitrification is the primary source of the greenhouse gas nitrous oxide (N2O) from terrestrial ecosystems. Fungal denitrifiers, unlike many bacteria, lack the N2O reductase and are potential sources of N2O. Still, their diversity, distribution, and environmental determinants in terrestrial ecosystems remain unresolved. We used a phylogenetically informed approach to screen 1 980 soil and rhizosphere metagenomes representing 608 globally distributed sampling sites for the denitrification marker gene nirK, coding for nitrite reductase. We show that fungal denitrifiers are sparse, yet cosmopolitan and dominated by saprotrophs and opportunistic plant pathogens. Few showed biome-specific distribution patterns. However, members of the Fusarium oxysporum species complex, known to produce substantial amounts of N2O, were proportionally more abundant and diverse in the rhizosphere than in other biomes. Fungal denitrifiers were most frequently detected in croplands but were most abundant in forest soils. The overall low abundance of fungal relative to bacterial and archaeal denitrifiers suggests that their role in denitrification and contribution to soil N2O emissions may be less important than previously suggested. Nevertheless, in relative terms, they could play a role in soils characterized by high carbon to nitrogen ratio and low pH, especially in tundra and boreal and temperate coniferous forests. Our results further indicate that plant-pathogen interactions may favor fungal denitrifiers. Thus, increasing global warming with predicted proliferation of pathogens and the fact that many of the fungi with nirK detected in the metagenomes are stress-tolerant cosmopolitans suggest that fungal denitrifier abundance may increase in terrestrial ecosystems.

microbiology↗

bioRxiv2022

Substrate availability and not thermal-acclimation controls microbial temperature sensitivity response to long term warming

Microbes are responsible for cycling carbon (C) through soils, and the predictions of how soil C stocks change with warming are highly sensitive to the assumptions made about the mechanisms controlling the microbial physiology response to climate warming. Two mechanisms, microbial thermal-acclimation and changes in the quantity and quality of substrates available for microbial metabolism have been suggested to explain the long-term warming impact on microbial physiology. Yet studies disentangling these two mechanisms are lacking. To resolve the drivers of changes in microbial physiology in response to long-term warming, we sampled soils from 13- and 28-year old soil warming experiments in different seasons. We performed short-term laboratory incubations across a range of temperatures to measure the relationship between temperature sensitivity of physiology (growth, respiration, carbon use efficiency and extracellular enzyme activity) and the chemical composition of soil organic matter. We observed apparent thermal acclimation in microbial processes important for C cycling, but only when warming had exacerbated the seasonally-induced, already small soil organic matter pools. Irrespective of warming, greater quantity and quality of soil carbon enhanced the extracellular enzymatic pool and its temperature sensitivity. We suggest that fresh litter input into the system seasonally cancels apparent thermal acclimation of C-cycling processes. Our findings reveal that long-term warming has indirectly affected microbial physiology via reduced C availability in this system, implying that earth system models including these negative feedbacks may be best suited to describe long-term warming impact in soils.

microbiology↗

bioRxiv2019

Heavy and wet: evaluating the validity and implications of assumptions made when measuring growth efficiency using 18O water

1How microbes allocate carbon to growth vs. respiration plays a central role in determining the ability of soil to retain carbon. This carbon use efficiency (CUE) is increasingly measured using the 18O-H2O method, in which heavy oxygen incorporated into DNA is used to estimate growth. Here we evaluated the validity of some of the assumptions of this method using a literature search, and then tested how violating them affected estimates of the growth component of carbon use efficiency in soil. We found that the 18O method is consistently sensitive to assumptions made about oxygen sources to DNA, but that the effect of other assumptions depends on the microbial community present. We provide an example for how the tools developed here may be used with observed CUE values, and demonstrate that the original conclusions drawn from the data remain robust in the face of methodological bias. Our results lay the foundation for a better understanding of the consequences to the 18O method underlying assumptions. Future studies can use the approach developed here to identify how different incubation conditions and/or treatments might bias its CUE estimates and how trustworthy their results are. Further wet-lab work dissecting the assumptions of the 18O method in soil will help justify the scenarios under which it is reasonable to trust its results.

microbiology↗