Resistance and resilience of the forest soil microbiome to logging-associated compaction

Soil compaction is a major disturbance associated with logging, but we lack a fundamental understanding of how this affects the soil microbiome. We assessed the structural resistance and resilience of the microbiome using a high-throughput pyrosequencing approach in differently compacted soils at two forest sites and correlated these findings with changes in soil physical properties and functions. Alterations in soil porosity after compaction strongly limited the air and water conductivity. Compaction significantly reduced abundance, increased diversity, and persistently altered the structure of the microbiota. Fungi were less resistant and resilient than bacteria; clayey soils were less resistant and resilient than sandy soils. The strongest effects were observed in soils with unfavorable moisture conditions, where air and water conductivities dropped well below 10% of their initial value. Maximum impact was observed around 6-12 months after compaction, and microbial communities showed resilience in lightly but not in severely compacted soils 4 years post disturbance. Bacteria capable of anaerobic respiration, including sulfate, sulfur, and metal reducers of the Proteobacteria and Firmicutes, were significantly associated with compacted soils. Compaction detrimentally affected ectomycorrhizal species, whereas saprobic and parasitic fungi proportionally increased in compacted soils. Structural shifts in the microbiota were accompanied by significant changes in soil processes, resulting in reduced carbon dioxide, and increased methane and nitrous oxide emissions from compacted soils. This study demonstrates that physical soil disturbance during logging induces profound and long-lasting changes in the soil microbiome and associated soil functions, raising awareness regarding sustainable management of economically driven logging operations

Photosynthesis in poor nutrient soils, in compacted soils, and under drought

Plants require the uptake of nutrients (in most cases via roots) and their incorporation into plant organs for growth. In non-woody species, 83% of fresh weight is water, 7% is carbon, 5% is oxygen, with the remaining 5% including hydrogen and such nutrients. In natural ecosystems, availability of nutrients in soils is heterogeneous, and many species often adapt their growth to the amount of nutrients that roots can take up by exploring the available soil volume. In agricultural areas, the lack of some nutrients is frequent. In both cases, plants must also face periods of drought and soil compaction. These environmental stresses are therefore not uncommon in natural ecosystems and crops, and the stressed plants often experience a decrease in photosynthetic CO2 fixation. In this chapter, we review changes observed in photosynthesis in response to nutrient deficiencies, soil compaction, and drought. The current knowledge on photosynthesis in carnivorous plants, as a special case of plant species growing in nutrient poor soils, is also included. Pigment limitations (chlorosis and/or necrosis), stomatal limitations, ultrastructural effects and mesophyll conductance limitations, photochemistry (primary reactions), carboxylation and Calvin-cycle reactions, and carbohydrate metabolism and transport will be discussed. With regard to nutrients, we have focused on the most common nutrition-related stresses in plants, the deficiencies of macro- (nitrogen, phosphorous, and potassium) and micronutrients (iron, manganese, copper, and zinc). Other nutrient deficiencies (or toxicities, both in the cases of essential nutrient excess or heavy metals) are not reviewed here. For other nutrient deficiencies and toxicities, and the role of the above-mentioned, and other nutrients (such as calcium and magnesium) in gas exchange, and as intracellular signal transducers, enzyme activators, and structure and function stabilizers of biological membranes, readers are referred to papers published elsewhere (Marschner H, Mineral nutrition of higher plants. Academic, London, 1995; Cakmak I, Kirkby EA, Physiol Plant 133:692–704, 2008; Morales F, Warren CR, Photosynthetic responses to nutrient deprivation and toxicities. In: Flexas J, Loreto F, Medrano H (eds) Terrestrial photosynthesis in a changing environment: a molecular, physiological and ecological approach. Cambridge University Press, Cambridge, pp 312–330, 2012; Hochmal AK, Schulze S, Trompelt K, Hippler M, Biochim Biophys Acta 1847:993–1003, 2015).This study was supported by the Spanish Ministry of Economy and Competitiveness (MINECO; projects AGL2012-31988, AGL2013-42175-R, AGL2016-75226-R, and AGL2016-79868-R, co-financed with FEDER), the Aragón Government (Group A03), grant LO1204 (Sustainable development of research in the Centre of the Region Haná) from the National Program of Sustainability I, and by the Czech Science Foundation Agency (project 16-07366Y). FM wishes to thank JC Martínez for his help with some periodic bibliographic searches.Peer reviewe