User:Alandmanson/soil microbiology

Soil microorganisms and conventional agriculture
Dr Kristine Nichols (8:25): "All of our soils that are under chemical conventional agriculture are almost completely devoid of microorganisms."

Bünemann et al. (2006) summarised the current understanding of how mineral fertilisers, organic amendments, microbial inoculants, and pesticides affect soil organisms. They found that:
 * Mineral fertilisers have limited direct effects, but they do have important secondary effects:
 * Their application can increase crop productivity, residue return, and soil organic matter and thus enhance soil biological activity
 * N fertilisation can result in soil acidification, which often has negative effects on soil organisms.
 * Organic amendments such as manure, compost and biosolids provide a direct source of C for soil organisms as well as an indirect C source via increased plant growth and plant residue returns.
 * Non-target effects of microbial inoculants appear to be small and transient.
 * Few significant effects of herbicides on soil organisms have been documented.
 * Negative effects of insecticides and fungicides are more common. Long-term use of Cu fungicides can result in persistent, toxic effects.
 * Organic waste products such as municipal composts and biosolids can also lead to the accumulation of elements that are toxic to soil organisms.

Bünemann, E.K., Schwenke, G.D. and Van Zwieten, L., 2006. Impact of agricultural inputs on soil organisms—a review. Soil Research, 44(4), pp.379-406.

Soil microbiology and pH
Contrast research done on microbiology and pH on one hand, and work research done on microbiology and Mn?

Biodiversity and manganese oxides - the presence of manganese oxides allows oxidation of SOM without poisoning by acidity in anaerobic conditions?? See |Central_Metabolism_(Flooded_soils)

Other interesting interactions?
Can microbial activity (especially filamentous microbes) transport acidity and/or alkalinity to counteract or accentuate spatial variability in soil pH - eg black truffle may need free lime in their habitat because they generate extreme acidity when fruiting?

Effects of wetting and drying extend the range of soil pH that a particular microbe must tolerate to survive.

Elevated CO2
Sun, Y., Wang, C., Yang, J., Liao, J., Chen, H.Y. and Ruan, H., 2021. Elevated CO2 shifts soil microbial communities from K‐ to r‐strategists.DOI PDF

Effects of pH
Aciego Pietri, J.A. and Brookes, P.C., 2008. Relationships between soil pH and microbial properties in a UK arable soil. Soil Biology and Biochemistry, 40(7), pp.1856-1861. DOI

Bickel, S., Chen, X., Papritz, A. and Or, D., 2019. A hierarchy of environmental covariates control the global biogeography of soil bacterial richness. Scientific reports, 9(1), pp.1-10. Abstract Soil bacterial communities are central to ecosystem functioning and services, yet spatial variations in their composition and diversity across biomes and climatic regions remain largely unknown. We employ multivariate general additive modeling of recent global soil bacterial datasets to elucidate dependencies of bacterial richness on key soil and climatic attributes. Although results support the well-known association between bacterial richness and soil pH, a hierarchy of novel covariates offers surprising new insights. Defining climatic soil water content explains both, the extent and connectivity of aqueous micro-habitats for bacterial diversity and soil pH, thus providing a better causal attribution. Results show that globally rare and abundant soil bacterial phylotypes exhibit different levels of dependency on environmental attributes. Surprisingly, the strong sensitivity of rare bacteria to certain environmental conditions improves their predictability relative to more abundant phylotypes that are often indifferent to variations in environmental drivers.

Clarholm, M. and Skyllberg, U., 2013. Translocation of metals by trees and fungi regulates pH, soil organic matter turnover and nitrogen availability in acidic forest soils. Soil Biology and Biochemistry, 63, pp.142-153. DOI

Delgado‐Baquerizo, M., Reith, F., Dennis, P.G., Hamonts, K., Powell, J.R., Young, A., Singh, B.K. and Bissett, A., 2018. Ecological drivers of soil microbial diversity and soil biological networks in the Southern Hemisphere. Ecology, 99(3), pp.583-596. PDF

Delgado-Baquerizo, M., Oliverio, A.M., Brewer, T.E., Benavent-González, A., Eldridge, D.J., Bardgett, R.D., Maestre, F.T., Singh, B.K. and Fierer, N., 2018. A global atlas of the dominant bacteria found in soil. Science, 359(6373), pp.320-325.

De Vries, F.T., Manning, P., Tallowin, J.R., Mortimer, S.R., Pilgrim, E.S., Harrison, K.A., Hobbs, P.J., Quirk, H., Shipley, B., Cornelissen, J.H., Kattge, J., and Bardgett, R. D. 2012. Abiotic drivers and plant traits explain landscape‐scale patterns in soil microbial communities. Ecology letters, 15(11), pp.1230-1239.

Fan, K., Weisenhorn, P., Gilbert, J.A., Shi, Y., Bai, Y. and Chu, H., 2018. Soil pH correlates with the co-occurrence and assemblage process of diazotrophic communities in rhizosphere and bulk soils of wheat fields. Soil Biology and Biochemistry, 121, pp.185-192. DOI

Fierer, N. and Jackson, R.B., 2006. The diversity and biogeography of soil bacterial communities. Proceedings of the National Academy of Sciences, 103(3), pp.626-631. DOI PDF Abstract For centuries, biologists have studied patterns of plant and animal diversity at continental scales. Until recently, similar studies were impossible for microorganisms, arguably the most diverse and abundant group of organisms on Earth. Here, we present a continental-scale description of soil bacterial communities and the environmental factors influencing their biodiversity. We collected 98 soil samples from across North and South America and used a ribosomal DNA-fingerprinting method to compare bacterial community composition and diversity quantitatively across sites. Bacterial diversity was unrelated to site temperature, latitude, and other variables that typically predict plant and animal diversity, and community composition was largely independent of geographic distance. The diversity and richness of soil bacterial communities differed by ecosystem type, and these differences could largely be explained by soil pH (r2 = 0.70 and r2 = 0.58, respectively; P < 0.0001 in both cases). Bacterial diversity was highest in neutral soils and lower in acidic soils, with soils from the Peruvian Amazon the most acidic and least diverse in our study. Our results suggest that microbial biogeography is controlled primarily by edaphic variables and differs fundamentally from the biogeography of “macro” organisms.

Jones, D.L., Cooledge, E.C., Hoyle, F.C., Griffiths, R.I. and Murphy, D.V., 2019. pH and exchangeable aluminum are major regulators of microbial energy flow and carbon use efficiency in soil microbial communities. Soil Biology and Biochemistry, 138, p.107584. DOI PDF Abstract The microbial partitioning of organic carbon (C) into either anabolic (i.e. growth) or catabolic (i.e. respiration) metabolic pathways represents a key process regulating the amount of added C that is retained in soil. The factors regulating C use efficiency (CUE) in agricultural soils, however, remain poorly understood. The aim of this study was to investigate substrate CUE from a wide range of soils (n = 970) and geographical area (200,000 km2) to determine which soil properties most influenced C retention within the microbial community. Using a 14C-labeling approach, we showed that the average CUE across all soils was 0.65 ± 0.003, but that the variation in CUE was relatively high within the sample population (CV 14.9%). Of the major properties measured in our soils, we found that pH and exchangeable aluminum (Al) were highly correlated with CUE. We identified a critical pH transition point at which CUE declined (pH 5.5). This coincided exactly with the point at which Al3+ started to become soluble. In contrast, other soil factors [e.g. total C and nitrogen (N), dissolved organic C (DOC), clay content, available calcium, phosphorus (P) and sulfur (S), total base cations] showed little or no relationship with CUE. We also found no evidence to suggest that nutrient stoichiometry (C:N, C:P and C:S ratios) influenced CUE in these soils. Based on current evidence, we postulate that the decline in microbial CUE at low pH and high Al reflects a greater channeling of C into energy intensive metabolic pathways involved in overcoming H+/Al3+ stress (e.g. cell repair and detoxification). The response may also be associated with shifts in microbial community structure, which are known to be tightly associated with soil pH. We conclude that maintaining agricultural soils above pH 5.5 maximizes microbial energy efficiency.

Lauber, C.L., Hamady, M., Knight, R. and Fierer, N., 2009. Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Applied and environmental microbiology, 75(15), pp.5111-5120. Abstract Soils harbor enormously diverse bacterial populations, and soil bacterial communities can vary greatly in composition across space. However, our understanding of the specific changes in soil bacterial community structure that occur across larger spatial scales is limited because most previous work has focused on either surveying a relatively small number of soils in detail or analyzing a larger number of soils with techniques that provide little detail about the phylogenetic structure of the bacterial communities. Here we used a bar-coded pyrosequencing technique to characterize bacterial communities in 88 soils from across North and South America, obtaining an average of 1,501 sequences per soil. We found that overall bacterial community composition, as measured by pairwise UniFrac distances, was significantly correlated with differences in soil pH (r2 0.79), largely driven by changes in the relative abundances of Acidobacteria, Actinobacteria, and Bacteroidetes across the range of soil pHs. In addition, soil pH explains a significant portion of the variability associated with observed changes in the phylogenetic structure within each dominant lineage. The overall phylogenetic diversity of the bacterial communities was also correlated with soil pH (R2 0.50), with peak diversity in soils with near-neutral pHs. Together, these results suggest that the structure of soil bacterial communities is predictable, to some degree, across larger spatial scales, and the effect of soil pH on bacterial community composition is evident at even relatively coarse levels of taxonomic resolution.

Malik, A.A., Puissant, J., Buckeridge, K.M., Goodall, T., Jehmlich, N., Chowdhury, S., Gweon, H.S., Peyton, J.M., Mason, K.E., van Agtmaal, M. and Blaud, A., 2018. Land use driven change in soil pH affects microbial carbon cycling processes. Nature communications, 9(1), pp.1-10. DOI PDF Abstract Soil microorganisms act as gatekeepers for soil–atmosphere carbon exchange by balancing the accumulation and release of soil organic matter. However, poor understanding of the mechanisms responsible hinders the development of effective land management strategies to enhance soil carbon storage. Here we empirically test the link between microbial ecophysiological traits and topsoil carbon content across geographically distributed soils and land use contrasts. We discovered distinct pH controls on microbial mechanisms of carbon accumulation. Land use intensification in low-pH soils that increased the pH above a threshold (~6.2) leads to carbon loss through increased decomposition, following alleviation of acid retardation of microbial growth. However, loss of carbon with intensification in near-neutral pH soils was linked to decreased microbial biomass and reduced growth efficiency that was, in turn, related to trade-offs with stress alleviation and resource acquisition. Thus, less-intensive management practices in near-neutral pH soils have more potential for carbon storage through increased microbial growth efficiency, whereas in acidic soils, microbial growth is a bigger constraint on decomposition rates. Discussion We established landscape-scale empirical links between key microbial ecophysiological traits and soil C concentration supporting the central role of microorganisms in belowground carbon cycling. Results show that an efficient microbial physiology with a greater proportion of substrate allocated to biosynthesis manifests in the increased ability of such communities to store C in near-neutral pH soils. Trade-offs in microbial physiological traits determine the proportion of microbial organic C investment into biosynthesis. Growth and biosynthesis decline in scenarios of stress and resource limitation when cellular investment is far higher in traits focussed on stress tolerance and resource acquisition. We discern two distinct mechanisms of soil carbon accumulation across a pH threshold of 6.2 for these soils: at higher pH (>6.2), an efficient substrate metabolism leads to increased SOC accumulation; and in acidic wet environments (pH < 6.2), abiotic factors limit microbial growth and decomposition causing accumulation of SOC. This evidence supports the use of soil pH as an integrated proxy of land use change, parent material and climate39 to determine the site-specific effects of land management strategies on SOC accumulation. The mechanisms highlight the significance of microbial ecophysiological controls on soil organic matter accumulation in high pH soils. Here, less-intensive land management practices have greater potential for soil carbon storage through increased microbial growth efficiency that causes greater channeling of substrates into biomass synthesis. Intensification in low pH soils leads to alleviation of acid-related retardation of microbial growth and organic matter degradation, leading to large losses of carbon through microbial decomposition. In these systems, preserving equivalent amounts of organic C would involve managing the abiotic C-accumulating factors, like acidity and wetness, whilst enhancing plant production. We thus highlight the importance of including physiological attributes of soil microorganisms in designing restorative land management strategies aimed at mitigating losses of soil C by intensive agricultural practices.

Rousk, J., Bååth, E., Brookes, P.C., Lauber, C.L., Lozupone, C., Caporaso, J.G., Knight, R. and Fierer, N., 2010. Soil bacterial and fungal communities across a pH gradient in an arable soil. The ISME journal, 4(10), pp.1340-1351. DOI PDF

Rousk, J., Brookes, P.C. and Bååth, E., 2011. Fungal and bacterial growth responses to N fertilization and pH in the 150-year ‘Park Grass’ UK grassland experiment. FEMS Microbiology Ecology, 76(1), pp.89-99. DOI PDF

Sun, Y., Wang, C., Yang, J., Liao, J., Chen, H.Y. and Ruan, H., 2021. Elevated CO2 shifts soil microbial communities from K‐to r‐strategists.DOI PDF

Zhalnina, K., Dias, R., de Quadros, P.D., Davis-Richardson, A., Camargo, F.A., Clark, I.M., McGrath, S.P., Hirsch, P.R. and Triplett, E.W., 2015. Soil pH determines microbial diversity and composition in the park grass experiment. Microbial ecology, 69(2), pp.395-406. DOI PDF

Manganese, microbes and pH
Bohu, T., Akob, D.M., Abratis, M., Lazar, C.S. and Küsel, K., 2016. Biological low-pH Mn (II) oxidation in a manganese deposit influenced by metal-rich groundwater. Applied and environmental microbiology, 82(10), pp.3009-3021. DOI PDF Quote: "We postulate here that because of the physicochemical characteristics of mineral structure (e.g., low crystallinity, large amorphous area, and high negative surface charge) ... Mn oxides may form microenvironments to shelter a niche-specific microbial community. While the Mn mineral deposit was oligotrophic, diverse nitrogen cycling related Mn(II)-oxidizing microorganisms occurred indigenously, suggesting the redox of Mn firmly coupled with the nitrogen cycle at acidic pH."

Sparrow, L.A. and Uren, N.C., 1987. Oxidation and reduction of Mn in acidic soils: effect of temperature and soil pH. Soil Biology and Biochemistry, 19(2), pp.143-148. DOI

Temperature sensitivity of SOM decomposition
Does soil pH affect temperature sensitivity of SOM decomposition?

Li, H., Yang, S., Semenov, M.V., Yao, F., Ye, J., Bu, R., Ma, R., Lin, J., Kurganova, I., Wang, X. and Deng, Y., 2021. Temperature sensitivity of SOM decomposition is linked with a K‐selected microbial community. Global Change Biology, 27(12), pp.2763-2779.

=Notes on soil microbiology Feb 2024= Some interesting microbe-related soil fertility and plant nutrition questions.


 * Soil pH has important effects on microbial community composition and function. Our soils are more acid than the well-reseached temperate soils of Europe and N America; I think there are great opportunities to explore microbial ecology in naturally acid soils (soil pH<5.5). Soil pH can be seen as a master variable, but what are the mechanisms and processes that directly affect microbes? And how does soil spacial and temporal variability affect microbial function? How do changes in soil solution pH with fluctuations in soil moisture, ionic strength and root proximity (without acid or base addition) affect microbes?
 * Fierer, N. and Jackson, R.B., 2006. The diversity and biogeography of soil bacterial communities. Proceedings of the National Academy of Sciences, 103(3), pp.626-631
 * Rasmussen, C., Heckman, K., Wieder, W.R., Keiluweit, M., Lawrence, C.R., Berhe, A.A., Blankinship, J.C., Crow, S.E., Druhan, J.L., Hicks Pries, C.E. and Marin-Spiotta, E., 2018. Beyond clay: towards an improved set of variables for predicting soil organic matter content. Biogeochemistry, 137, pp.297-306.
 * Sumner, M.E. and Yamada, T., 2002. Farming with acidity. Communications in Soil Science and Plant Analysis, 33(15-18), pp.2467-2496.


 * A recent paper (Dai et al., 2023) suggested that many of the pH effects on microbes are related to micronutrient availability. This is likely to include both deficiency and toxicity of nutrients and toxicity of non-nutrient elements such as aluminium. I am particularly interested in Al and Mn toxicity in acid soils. Molybdenum deficiency is critical for N fixation in many acid soils, but Mo availability in soil is very difficult to measure (as is B deficiency). Zinc deficiency is widespread in highly weathered acid soils. Copper deficiency is an issue in some soils.
 * Dai, Z., Guo, X., Lin, J., Wang, X., He, D., Zeng, R., Meng, J., Luo, J., Delgado-Baquerizo, M., Moreno-Jiménez, E. and Brookes, P.C., 2023. Metallic micronutrients are associated with the structure and function of the soil microbiome. Nature Communications, 14(1), p.8456.
 * Nitrogen fixation: Can free-living N-fixing microbes function in acid soils? Are some reliant on Mn within a particular pH range?
 * Smercina, D.N., Evans, S.E., Friesen, M.L. and Tiemann, L.K., 2019. To fix or not to fix: controls on free-living nitrogen fixation in the rhizosphere. Applied and Environmental Microbiology, 85(6), pp.e02546-18.


 * Nitrogen cycle beyond N fixation: Microbial effects on soil N can be really interesting. Plant roots interact with microbes in many ways, and these are worth exploring: Bracken seems to promote nitrification, whereas many of our grasses inhibit nitrification. Roots exude organic acids that release "bound" soil organic matter, making it more available for microbial mineralization.
 * Griffiths, R.P. and Filan, T., 2007. Effects of bracken fern invasions on harvested site soils in Pacific Northwest (USA) coniferous forests. Northwest Science, 81(3), pp.191-198.
 * Bardon, C., Misery, B., Piola, F., Poly, F. and Le Roux, X., 2018. Control of soil N cycle processes by Pteridium aquilinum and Erica cinerea in heathlands along a pH gradient. Ecosphere, 9(9), p.e02426.
 * Subbarao, G.V., Yoshihashi, T., Worthington, M., Nakahara, K., Ando, Y., Sahrawat, K.L., Rao, I.M., Lata, J.C., Kishii, M. and Braun, H.J., 2015. Suppression of soil nitrification by plants. Plant Science, 233, pp.155-164.
 * Clarholm, M., Skyllberg, U. and Rosling, A., 2015. Organic acid induced release of nutrients from metal-stabilized soil organic matter–the unbutton model. Soil Biology and Biochemistry, 84, pp.168-176.
 * Keiluweit, M., Bougoure, J.J., Nico, P.S., Pett-Ridge, J., Weber, P.K. and Kleber, M., 2015. Mineral protection of soil carbon counteracted by root exudates. Nature Climate Change, 5(6), pp.588-595.