Soil carbon transformation and sequestration have received significant interest in recent years due to a growing need for quantitating its role in mitigating climate change. Even though our understanding of the nature of soil organic matter has recently been substantially revised, fundamental uncertainty remains about the quantitative importance of microbial necromass as part of persistent organic matter. Addressing this uncertainty has been hampered by the absence of quantitative assessments whether microbial matter makes up the majority of the persistent carbon in soil. Direct quantitation of microbial necromass in soil is very challenging because of an overlapping molecular signature with nonmicrobial organic carbon. Here, we use a comprehensive analysis of existing biomarker amino sugar data published between 1996 and 2018, combined with novel appropriation using an ecological systems approach, elemental carbon-nitrogen stoichiometry, and biomarker scaling, to demonstrate a suit of strategies for quantitating the contribution of microbe-derived carbon to the topsoil organic carbon reservoir in global temperate agricultural, grassland, and forest ecosystems. We show that microbial necromass can make up more than half of soil organic carbon. Hence, we suggest that next-generation field management requires promoting microbial biomass formation and necromass preservation to maintain healthy soils, ecosystems, and climate. Our analyses have important implications for improving current climate and carbon models, and helping develop management practices and policies.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/gcb.14781

Quantitative assessment of microbial necromass contribution to soil organic matter.

The impact of climate change and anthropogenic activities on alpine grassland over the Qinghai-Tibet Plateau

Summary
Boreal forest soils store a major proportion of the global terrestrial carbon (C) and below-ground inputs contribute as much as above-ground plant litter to the total C stored in the soil. A better understanding of the dynamics and drivers of root-associated fungal communities is essential to predict long-term soil C storage and climate feedbacks in northern ecosystems.
We used 454-pyrosequencing to identify fungal communities across fine-scaled soil profiles in a 5000 yr fire-driven boreal forest chronosequence, with the aim of pinpointing shifts in fungal community composition that may underlie variation in below-ground C sequestration.
In early successional-stage forests, higher abundance of cord-forming ectomycorrhizal fungi (such as Cortinarius and Suillus species) was linked to rapid turnover of mycelial biomass and necromass, efficient nitrogen (N) mobilization and low C sequestration. In late successional-stage forests, cord formers declined, while ericoid mycorrhizal ascomycetes continued to dominate, potentially facilitating long-term humus build-up through production of melanized hyphae that resist decomposition.
Our results suggest that cord-forming ectomycorrhizal fungi and ericoid mycorrhizal fungi play opposing roles in below-ground C storage. We postulate that, by affecting turnover and decomposition of fungal tissues, mycorrhizal fungal identity and growth form are critical determinants of C and N sequestration in boreal forests.

https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/nph.13208

Carbon sequestration is related to mycorrhizal fungal community shifts during long-term succession in boreal forests.

Globally, forests represent highly productive ecosystems that act as carbon sinks where soil organic matter is formed from residuals after biomass decomposition as well as from rhizodeposited carbon. Forests exhibit a high level of spatial heterogeneity and the importance of trees, the dominant primary producers, for their structure and functioning. Fungi, bacteria and archaea inhabit various forest habitats: foliage, the wood of living trees, the bark surface, ground vegetation, roots and the rhizosphere, litter, soil, deadwood, rock surfaces, invertebrates, wetlands or the atmosphere, each of which has its own specific features, such as nutrient availability or temporal dynamicy and specific drivers that affect microbial abundance, the level of dominance of bacteria or fungi as well as the composition of their communities. However, several microorganisms, and in particular fungi, inhabit or even connect multiple habitats, and most ecosystem processes affect multiple habitats. Forests are dynamic on a broad temporal scale with processes ranging from short-term events over seasonal ecosystem dynamics to long-term stand development after disturbances such as fires or insect outbreaks. The understanding of these processes can be only achieved by the exploration of the complex 'ecosystem microbiome' and its functioning using focused, integrative microbiological and ecological research performed across multiple habitats.

Forest microbiome: diversity, complexity and dynamics

The ecology of forest soils is an important field of research due to the role of forests as carbon sinks. Consequently, a significant amount of information has been accumulated concerning their ecology, especially for temperate and boreal forests. Although most studies have focused on fungi, forest soil bacteria also play important roles in this environment. In forest soils, bacteria inhabit multiple habitats with specific properties, including bulk soil, rhizosphere, litter, and deadwood habitats, where their communities are shaped by nutrient availability and biotic interactions. Bacteria contribute to a range of essential soil processes involved in the cycling of carbon, nitrogen, and phosphorus. They take part in the decomposition of dead plant biomass and are highly important for the decomposition of dead fungal mycelia. In rhizospheres of forest trees, bacteria interact with plant roots and mycorrhizal fungi as commensalists or mycorrhiza helpers. Bacteria also mediate multiple critical steps in the nitrogen cycle, including N fixation. Bacterial communities in forest soils respond to the effects of global change, such as climate warming, increased levels of carbon dioxide, or anthropogenic nitrogen deposition. This response, however, often reflects the specificities of each studied forest ecosystem, and it is still impossible to fully incorporate bacteria into predictive models. The understanding of bacterial ecology in forest soils has advanced dramatically in recent years, but it is still incomplete. The exact extent of the contribution of bacteria to forest ecosystem processes will be recognized only in the future, when the activities of all soil community members are studied simultaneously.

Forest Soil Bacteria: Diversity, Involvement in Ecosystem Processes, and Response to Global Change

There is growing evidence of the importance of extramatrical mycelium (EMM) of mycorrhizal fungi in carbon (C) cycling in ecosystems. However, our understanding has until recently been mainly based on laboratory experiments, and knowledge of such basic parameters as variations in mycelial production, standing biomass and turnover as well as the regulatory mechanisms behind such variations in forest soils is limited. Presently, the production of EMM by ectomycorrhizal (EM) fungi has been estimated at similar to 140 different forest sites to be up to several hundreds of kg per ha per year, but the published data are biased towards Picea abies in Scandinavia. Little is known about the standing biomass and turnover of EMM in other systems, and its influence on the C stored or lost from soils. Here, focussing on ectomycorrhizas, we discuss the factors that regulate the production and turnover of EMM and its role in soil C dynamics, identifying important gaps in this knowledge. C availability seems to be the key factor determining EMM production and possibly its standing biomass in forests but direct effects of mineral nutrient availability on the EMM can be important. There is great uncertainty about the rate of turnover of EMM. There is increasing evidence that residues of EM fungi play a major role in the formation of stable N and C in SOM, which highlights the need to include mycorrhizal effects in models of global soil C stores.

/pdf/the-production-and-turnover-of-extramatrical-mycelium-of-52l9aeds2p.pdf

The production and turnover of extramatrical mycelium of ectomycorrhizal fungi in forest soils: role in carbon cycling

Partitioning of soil respiration is a challenging task when resolving the C cycling in forest ecosystems. Our aim was to partition the respiration of newly grown extramatrical ectomycorrhizal mycelium (ECM) and fine roots (and their associated microorganisms) in a young Norway spruce forest. Ingrowth mesh bags of 16 cm diameter and 12 cm height were placed in the upper soil and left for 12–16 months in 2010 and 2011. The 2 mm mesh size allowed the ingrowth of ECM and fine roots whereas a 45 μm mesh size allowed only the ingrowth of ECM. The mesh bags were filled with either homogenized EA horizon soil, pure quartz sand (QS) or crushed granite (CG, only 2011), each with five replicates. Controls without any ingrowth were established for each substrate by solid plastic tubes (2010) and by 1 μm mesh bags (2011). Fluxes of CO2 from the mesh bags and controls were measured biweekly during the growing season by the closed chamber method. The contribution of ECM to soil respiration was largest in the QS treatments, reaching cumulatively 1.2 and 2.2 Mg C ha−1 6 months−1 in 2010 and 2011, respectively. For EA and CG treatments, the cumulative respiration from ECM was larger than from controls, however the differences being not statistically significant. The respiration of newly grown fine roots in QS amounted to 1.0 Mg C ha−1 in 2010, but could not be identified in 2011 since fluxes from 2 mm and 45 μm mesh bags were similar. The correlation of total root length in single QS mesh bags to CO2 fluxes was poor. The contribution of fine root respiration was also not detectable in the EA and CG treatment. No correlation was found between the autumnal biomass of newly grown ECM and its cumulative respiration. Our results suggest a substantial contribution of newly grown ECM to soil respiration. Respiration of ECM might be larger than respiration of fine roots.

Contribution of newly grown extramatrical ectomycorrhizal mycelium and fine roots to soil respiration in a young Norway spruce site

The partitioning of below ground carbon inputs into roots and extramatrical ectomycorrhizal mycelium (ECM) is crucial for the C cycle in forest soils. Here we studied simultaneously the newly grown biomass of ECM and fine roots in a young Norway spruce stand. Ingrowth mesh bags of 16 cm diameter and 12 cm height were placed in the upper soil and left for 12 to 16 months. The 2 mm mesh size allowed the ingrowth of fungal hyphae and roots whereas a 45 μm mesh size allowed only the ingrowth of hyphae. The mesh bags were filled with either EA horizon soil, pure quartz sand or crushed granite. Controls without any ingrowth were established for each substrate by solid tubes (2010) and by 1 μm mesh bags (2011). The fungal biomass in the substrates was estimated by the PLFA 18:2ω6,9 and ECM biomass was calculated as difference between fungal biomass in mesh bags and controls. The maximum ECM biomass was 438 kg ha−1 in October 2010 in 2 mm mesh bags with EA substrate, and the minimum was close to zero in 2011 in 45 μm mesh bags with quartz sand. The high P content of the crushed granite did not influence the ECM biomass. Fine root biomass reached a maximum of 2,343 kg ha−1 in October 2010 in mesh bags with quartz sand after 16 months exposure. In quartz sand and crushed granite, ECM biomass correlated positively with fine root biomass and the number of root tips, and negatively with specific root length. The ratio of ECM biomass/fine root biomass in October ranged from 0.1 to 0.3 in quartz sand and crushed granite, but from 0.7 to 1.8 in the EA substrate. The results for the EA substrate suggest a large C flux to ECM under field conditions.

Biomass of extramatrical ectomycorrhizal mycelium and fine roots in a young Norway spruce stand — a study using ingrowth bags with different substrates

Jonny Neumann

Papers

The production and turnover of extramatrical mycelium of ectomycorrhizal fungi in forest soils: role in carbon cycling

Contribution of newly grown extramatrical ectomycorrhizal mycelium and fine roots to soil respiration in a young Norway spruce site

Biomass of extramatrical ectomycorrhizal mycelium and fine roots in a young Norway spruce stand — a study using ingrowth bags with different substrates