Mary K. Firestone

University of California, Berkeley

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Jennifer Pett‐Ridge

University of California, Merced

Erin Nuccio

Lawrence Livermore National Laboratory

Donald J. Herman

University of California, Berkeley

Steven J. Blazewicz

Lawrence Livermore National Laboratory

Jizhong Zhou

University of Oklahoma

Eoin Brodie

Lawrence Berkeley National Laboratory

Shuijin Hu

North Carolina State University

Ella T. Sieradzki

University of California, Berkeley

Daliang Ning

University of Oklahoma

Mengting Yuan

University of Hawaii System

Cooperative Institutions

University of California, Berkeley

Lawrence Berkeley National Laboratory

University of Oklahoma

Zhejiang University

Lawrence Livermore National Laboratory

Chinese Academy of Sciences

University of California System

Pacific Northwest National Laboratory

Oak Ridge National Laboratory

University of California, Davis

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Cumulative Effects of Simulated Acid Rain on Soil Chemical and Microbial Characteristics and Conifer Seedling Growth

Soil Science Society of America Journal (1987)

J. G. McColl Mary K. Firestone

Abstract Effects of simulated acid rain treatments of HNO 3 and H 2 SO 4 , in the mole ratio of 3:1 and pH 5.6, 4.5, 4.0, and 3.0, were tested on seedlings of Douglas‐fir ( Pseudotsuga menzesii [Mirb.] Franco), sugar pine ( Pinus lambertiana Dougl.), and ponderosa pine ( Pinus ponderosa Laws) growing in A‐horizon samples of two forest soils. Two wet periods of 34 and 27 weeks duration, separated by a dry period of 18 weeks, simulated climatic conditions common in the Sierra Nevada, California. Representative results are presented for soil supporting Douglas‐fir, plus results of growth and shoot‐N for all three species. Effects differed between soils but were usually increased from one wet period to the next, and markedly decreased with soil depth. Effects commonly appeared in the pH 3.0 treatment only. Little or no effects were noted for seedling growth, visual symptoms of foliar damage, N concentration in shoots, or for the general soil microbial assays of CO 2 evolution and microbial biomass. There were notable decreases in exchangeable cations and soil pH, and increases in soil Al, Mn, Fe, and Zn. Effects on N transformations in soil were inconsistent, but in the pH 3.0 treatment there were some significant increases in mineralizable N and denitrification potential, and decreases in nitrification potential. Similar results were obtained for N transformations in one of the same forest soils supporting ponderosa pine in an earlier experiment of only 12 weeks duration, but at greater acidity of pH 2.0.

Dry weight

10.2136/sssaj1987.03615995005100030040x

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Citations (14)

Taxon-specific microbial growth and mortality patterns reveal distinct temporal population responses to rewetting in a California grassland soil

The ISME Journal (2020)

Steven J. Blazewicz Bruce A. Hungate Benjamin J. Koch Erin Nuccio Ember M. Morrissey

Biogeochemical Cycle

Biogeochemistry

10.1038/s41396-020-0617-3

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Citations (103)

Rhizosphere priming of soil organic matter by bacterial groups in a grassland soil

Soil Biology and Biochemistry (2010)

Jeffrey A. Bird Donald J. Herman Mary K. Firestone

Growing season

Bulk soil

10.1016/j.soilbio.2010.08.010

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Citations (231)

Responses of soil bacterial and fungal communities to extreme desiccation and rewetting

The ISME Journal (2013)

Romain L. Barnard Catherine A. Osborne Mary K. Firestone

Acidobacteria

Soil microbiology

10.1038/ismej.2013.104

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Citations (836)

Methodological variability in microbial community level physiological profiles

Soil Science Society of America Journal (2002)

Teri C. Balser James W. Kirchner Mary K. Firestone

We performed two experiments to assess the methodological variability of microbial community‐level physiological profiles (CLPP, using the BiOLOG assay) in soil from a California annual grassland ecosystem. In a study to assess the impact of sample preparation, we found that bacteria adhered to soil surfaces are numerically dominant and have CLPPs indistinguishable from that of intact soil. Studies that allow soil particles to settle prior to dilution or plating may not accurately reflect the substrate utilization pattern of whole soil. In a hierarchical ANOVA, we found that nearly all of the methodological variability in the CLPP assay comes from soil replicates rather than plate replicates. Many laboratories replicate at the level of the CLPP plate. Our results indicate that to best represent a given soil sample, it is important to replicate soil subsamples, rather than CLPP plates.

Replicate

Soil test

Dilution

Soil bacteria

Soil microbiology

10.2136/sssaj2002.5190

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Citations (34)

Soil microbial community response to corrinoids is shaped by a natural reservoir of vitamin B12

The ISME Journal (2024)

Zachary F. Hallberg Alexa M. Nicolas Zoila I. Alvarez-Aponte Kenny C. Mok Ella T. Sieradzki

Abstract Soil microbial communities perform critical ecosystem services through the collective metabolic activities of numerous individual organisms. Most microbes use corrinoids, a structurally diverse family of cofactors related to vitamin B12. Corrinoid structure influences the growth of individual microbes, yet how these growth responses scale to the community level remains unknown. Analysis of metagenome-assembled genomes suggests that corrinoids are supplied to the community by members of the archaeal and bacterial phyla Thermoproteota, Actinobacteria, and Proteobacteria. Corrinoids were found largely adhered to the soil matrix in a grassland soil, at levels exceeding those required by cultured bacteria. Enrichment cultures and soil microcosms seeded with different corrinoids showed distinct shifts in bacterial community composition, supporting the hypothesis that corrinoid structure can shape communities. Environmental context influenced both community- and taxon-specific responses to specific corrinoids. These results implicate corrinoids as key determinants of soil microbiome structure and suggest that environmental micronutrient reservoirs promote community stability.

Corrinoid

Microcosm

10.1093/ismejo/wrae094

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Citations (5)

The Influence of Nitrate, Nitrite, and Oxygen on the Composition of the Gaseous Products of Denitrification in Soil

Soil Science Society of America Journal (1979)

Mary K. Firestone M. S. Smith R. B. Firestone James M. Tiedje

Abstract [ 18 N]‐N 2 O produced by denitrification of 18 NO ‐ 3 in soil slurries readily exchanged with nonlabeled pools of added N 2 O. This supports the role of N 2 O as a free, obligate intermediate of denitrification in soils. The observation that N 2 O diffuses freely from the site of active denitrification in soils means that any factor which produces a change in the relative rate of N 2 O reduction compared to the rate of N 2 O production can alter the proportion of N 2 O and N 2 resulting. Increased concentration of NO 3 ‐ and NO 2 ‐ resulted in increased production of N 2 O relative to N 2 as the product of denitrification. The influence of NO 2 ‐ was much stronger than that of NO 3 ‐ , with low concentrations of NO 2 ‐ causing N 2 O to become a significant product of denitrification. This suggests that NO 2 ‐ , not NO 3 ‐ , may be the influential species. Additions of small quantities of O 2 (0.02 atm) caused a large decrease in denitrification activity and resulted in a significant increase in the N 2 O/N 2 ratio.

Nitrous oxide

10.2136/sssaj1979.03615995004300060016x

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Citations (217)

Large losses of ammonium-nitrogen from a rice ecosystem under elevated CO ₂

Science Advances (2020)

Chenchao Xu Kaihang Zhang Wanying Zhu Jing Xiao Chen Zhu

Inputs of nitrogen into terrestrial ecosystems, mainly via the use of ammonium-based fertilizers in agroecosystems, are enormous, but the fate of this nitrogen under elevated atmospheric carbon dioxide (CO

Nitrogen Cycle

10.1126/sciadv.abb7433

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Citations (40)

Evaluation of accelerated H⁺applications in predicting soil chemical and microbial changes due to acid rain

Communications in Soil Science and Plant Analysis (1982)

K. Killham Mary K. Firestone

Abstract A comparison was made between three acidified, simulated rain treatments which have been used to assess the impact of acid rain on soil chemical and microbial processes. There were significant differences in effects on chemical and microbial characteristics of soil exposed to the three treatments due to differences in the rate of H+ ion application, even though the total quantity of protons supplied was the same in each case. An input of 30 cm of simulated rain of pH 3.0 over 6 months increased microbial activity and caused only slight changes in soil pH and soil nitrogen status. Treatments in which the rate of H+ input was accelerated by increasing solution volume, or acidity, inhibited microbial activity and caused soil chemical changes in excess of those produced by the more gradual yet equivalent H+ loading. We conclude that the effects of short‐term, accelerated acid treatments cannot be used to realistically forecast long‐term impacts of acid rain. The results of such experiments may be useful in identifying processes or parameters for studies of longer duration.

Acid rain

10.1080/00103628209367328

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Citations (7)

Disentangling direct from indirect relationships in association networks

Proceedings of the National Academy of Sciences (2022)

Naijia Xiao Aifen Zhou Megan L. Kempher Benjamin Yamin Zhou Zhou Jason Shi

Significance Networks are fundamental units for studying complex systems, but reconstructing networks from large-scale experimental data is very challenging in systems biology and microbial ecology, primarily due to the difficulty in unraveling direct and indirect interactions. By tackling several mathematical challenges, this study provides a conceptual framework for disentangling direct and indirect relationships in association networks. The application of iDIRECT (Inference of Direct and Indirect Relationships with Effective Copula-based Transitivity) to synthetic, gene expression, and microbial community data demonstrates that it is a powerful, robust, and reliable tool for network inference. The framework developed here will greatly enhance our capability to discern network interactions in various complex systems and allow scientists to address research questions that could not be approached previously.

Benchmark (surveying)

10.1073/pnas.2109995119

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Citations (116)